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Wang Q, Yang JH, Chen X, Zhang YJ, Zhu XY, Li XF, Su J, Churangui CRG, Yang B, Lu GP, Xu Y. [Metagenomic next-generation sequencing-based retrospective investigation of the drug resistance sites of Mycoplasma pneumoniae in children]. Zhonghua Er Ke Za Zhi 2024; 62:457-461. [PMID: 38623014 DOI: 10.3760/cma.j.cn112140-20240105-00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Objective: To analyze the drug-resistant gene loci of Mycoplasma pneumoniae (MP) using metagenomic next-generation sequencing (mNGS). Methods: From November 2022 to October 2023, 697 clinical samples (including sputum, alveolar lavage fluid and blood) of 686 children with Mycoplasma pneumoniae positive detected by mNGS were retrospectively analyzed. Samples were divided into intensive care unit (ICU) group and non-ICU group, Chi-square test was used to compare groups, and Mann-Kendall trend test was used to analyze the change trend of the detection rate of drug resistance gene loci over time. Results: Of the 697 samples, 164 were from the ICU group and 533 were from the non-ICU group. The detection rate of Mycoplasma pneumoniae resistance gene was 44.3% (309/697), and all detected drug-resistant gene loci of MP were A2063G. The detection rate of Mycoplasma pneumoniae in ICU group was 50.0% (82/164), and the detection rates of Mycoplasma pneumoniae resistance gene loci in sputum, alveolus lavage fluid and blood samples were 75.0% (18/24) and 48.4% (62/128), respectively. The detection rate in sputum was higher than alveolus lavage fluid samples (χ2=5.72,P=0.017). The detection rate of Mycoplasma pneumoniae in non-ICU group was 42.6% (227/533), the detection rate of Mycoplasma pneumoniae resistance gene loci in sputum and alveolar lavage fluid was 40.0% (16/40), 44.3% (201/454), and no detection rate in blood samples (0/12). There was no significant difference in the detection rate of alveolar lavage fluid and sputum (χ2=0.27, P=0.602). From November 2022 to October 2023, the detection rate of submitted samples showed an increasing trend month by month (overall: Z=3.99, ICU inspection group: Z=2.93, non-ICU group: Z=3.01, all P<0.01). Among the bacteria commonly detected with Mycoplasma pneumoniae, Streptococcus pneumoniae accounted for the highest proportion, the detection rate was 15.5% (108/697), and Epstein-Barr virus accounted for the highest proportion of 17.6% (123/697). Conclusions: From November 2022 to October 2023, the detection rate of Mycoplasma pneumoniae drug resistance gene loci showed an increasing trend. The detection rate of drug resistance gene loci in sputum samples of ICU group was higher than alveolus lavage fluid. No new drug resistance site were detected.
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Affiliation(s)
- Q Wang
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - J H Yang
- Vision Medicals Co., Ltd., Guangzhou, Guangzhou 510700, China
| | - X Chen
- Department of Neonatology, Pediatric Hospital Affiliated to Fudan University, Shanghai 201102, China
| | - Y J Zhang
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - X Y Zhu
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - X F Li
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - J Su
- Department of Critical Care Medicine, Henan Children's Hospital, Zhengzhou 450018, China
| | - C R G Churangui
- Department of Pediatrics, Chifeng City Hospital, Chifeng 024099, China
| | - B Yang
- Vision Medicals Co., Ltd., Guangzhou, Guangzhou 510700, China
| | - G P Lu
- Department of Critical Care Medicine, Pediatric Hospital Affiliated to Fudan University, Shanghai 201102, China
| | - Y Xu
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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2
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Liu J, Dai L, Wang Q, Li C, Liu Z, Gong T, Xu H, Jia Z, Sun W, Wang X, Lu M, Shang T, Zhao N, Cai J, Li Z, Chen H, Su J, Liu Z. Multimodal analysis of cfDNA methylomes for early detecting esophageal squamous cell carcinoma and precancerous lesions. Nat Commun 2024; 15:3700. [PMID: 38697989 PMCID: PMC11065998 DOI: 10.1038/s41467-024-47886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
Detecting early-stage esophageal squamous cell carcinoma (ESCC) and precancerous lesions is critical for improving survival. Here, we conduct whole-genome bisulfite sequencing (WGBS) on 460 cfDNA samples from patients with non-metastatic ESCC or precancerous lesions and matched healthy controls. We develop an expanded multimodal analysis (EMMA) framework to simultaneously identify cfDNA methylation, copy number variants (CNVs), and fragmentation markers in cfDNA WGBS data. cfDNA methylation markers are the earliest and most sensitive, detectable in 70% of ESCCs and 50% of precancerous lesions, and associated with molecular subtypes and tumor microenvironments. CNVs and fragmentation features show high specificity but are linked to late-stage disease. EMMA significantly improves detection rates, increasing AUCs from 0.90 to 0.99, and detects 87% of ESCCs and 62% of precancerous lesions with >95% specificity in validation cohorts. Our findings demonstrate the potential of multimodal analysis of cfDNA methylome for early detection and monitoring of molecular characteristics in ESCC.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lijun Dai
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qiang Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Chenghao Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhichao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Tongyang Gong
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Hengyi Xu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Ziqi Jia
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Wanyuan Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Minyi Lu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Tongxuan Shang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Ning Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Jiahui Cai
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Zhigang Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
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3
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Liu Y, Chen X, Ma Y, Song C, Ma J, Chen C, Su J, Ma L, Saiyin H. Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Mol Psychiatry 2024:10.1038/s41380-024-02562-0. [PMID: 38654124 DOI: 10.1038/s41380-024-02562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Pathogenic mutant huntingtin (mHTT) infiltrates the adult Huntington's disease (HD) brain and impairs fetal corticogenesis. However, most HD animal models rarely recapitulate neuroanatomical alterations in adult HD and developing brains. Thus, the human cortical organoid (hCO) is an alternative approach to decode mHTT pathogenesis precisely during human corticogenesis. Here, we replicated the altered corticogenesis in the HD fetal brain using HD patient-derived hCOs. Our HD-hCOs had pathological phenotypes, including deficient junctional complexes in the neural tubes, delayed postmitotic neuronal maturation, dysregulated fate specification of cortical neuron subtypes, and abnormalities in early HD subcortical projections during corticogenesis, revealing a causal link between impaired progenitor cells and chaotic cortical neuronal layering in the HD brain. We identified novel long, oriented, and enriched polyQ assemblies of HTTs that hold large flat Golgi stacks and scaffold clathrin+ vesicles in the neural tubes of hCOs. Flat Golgi stacks conjugated polyQ assemblies by ADP-ribosylation factor 1 (ARF1). Inhibiting ARF1 activation with Brefeldin A (BFA) disassociated polyQ assemblies from Golgi. PolyQ assembles with mHTT scaffolded fewer ARF1 and formed shorter polyQ assembles with fewer and shorter Golgi and clathrin vesicles in neural tubes of HD-hCOs compared with those in hCOs. Inhibiting the activation of ARF1 by BFA in healthy hCOs replicated impaired junctional complexes in the neural tubes. Together, endogenous polyQ assemblies with mHTT reduced the Golgi recruiting ARF1 in the neuroepithelium, impaired the Golgi structure and activities, and altered the corticogenesis in HD-hCO.
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Affiliation(s)
- Yang Liu
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinyu Chen
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yunlong Ma
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chenyun Song
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jixin Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cheng Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lixiang Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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Fan XK, Li MY, Qin Y, Shen C, Lu Y, Sun ZM, Yang J, Tao R, Zhou JY, Hang D, Su J. [Associations of onset age, diabetes duration and glycated hemoglobin level with ischemic stroke risk in type 2 diabetes patients: a prospective cohort study]. Zhonghua Liu Xing Bing Xue Za Zhi 2024; 45:498-505. [PMID: 38678344 DOI: 10.3760/cma.j.cn112338-20231009-00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Objective: To investigate the associations of onset age, diabetes duration, and glycated hemoglobin (HbA1c) levels with ischemic stroke risk in type 2 diabetes patients. Methods: The participants were from Comprehensive Research on the Prevention and Control of the Diabetes in Jiangsu Province. The study used data from baseline survey from December 2013 to January 2014 and follow-up until December 31, 2021. After excluding the participants who had been diagnosed with stroke at baseline survey and those with incomplete information on onset age, diabetes duration, and HbA1c level, a total of 17 576 type 2 diabetes patients were included. Cox proportional hazard model was used to calculate the hazard ratio (HR) and 95%CI of onset age, diabetes duration, and HbA1c level for ischemic stroke. Results: During the median follow-up time of 8.02 years, 2 622 ischemic stroke cases were registered. Multivariate Cox proportional risk regression model showed that a 5-year increase in type 2 diabetes onset age was significantly associated with a 5% decreased risk for ischemic stroke (HR=0.95, 95%CI: 0.92-0.99). A 5-year increase in diabetes duration was associated with a 5% increased risk for ischemic stroke (HR=1.05, 95%CI: 1.02-1.10). Higher HbA1c (per 1 standard deviation increase:HR=1.17, 95%CI: 1.13-1.21) was associated with an increased risk for ischemic stroke. Conclusion: The earlier onset age of diabetes, longer diabetes duration, and high levels of HbA1c are associated with an increased risk for ischemic stroke in type 2 diabetes patients.
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Affiliation(s)
- X K Fan
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - M Y Li
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Y Qin
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - C Shen
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Y Lu
- Suzhou Prefectural Center for Disease Control and Prevention, Suzhou 215003, China
| | - Z M Sun
- Huai'an Prefectural Center for Disease Control and Prevention, Huai'an 223001, China
| | - J Yang
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - R Tao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - J Y Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - D Hang
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - J Su
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Chen Z, Li C, Zhou Y, Li P, Cao G, Qiao Y, Yao Y, Su J. Histone 3 lysine 9 acetylation-specific reprogramming regulates esophageal squamous cell carcinoma progression and metastasis. Cancer Gene Ther 2024; 31:612-626. [PMID: 38291129 DOI: 10.1038/s41417-024-00738-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Dysregulation of histone acetylation is widely implicated in tumorigenesis, yet its specific roles in the progression and metastasis of esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we profiled the genome-wide landscapes of H3K9ac for paired adjacent normal (Nor), primary ESCC (EC) and metastatic lymph node (LNC) esophageal tissues from three ESCC patients. Compared to H3K27ac, we identified a distinct epigenetic reprogramming specific to H3K9ac in EC and LNC samples relative to Nor samples. This H3K9ac-related reprogramming contributed to the transcriptomic aberration of targeting genes, which were functionally associated with tumorigenesis and metastasis. Notably, genes with gained H3K9ac signals in both primary and metastatic lymph node samples (common-gained gene) were significantly enriched in oncogenes. Single-cell RNA-seq analysis further revealed that the corresponding top 15 common-gained genes preferred to be enriched in mesenchymal cells with high metastatic potential. Additionally, in vitro experiment demonstrated that the removal of H3K9ac from the common-gained gene MSI1 significantly downregulated its transcription, resulting in deficiencies in ESCC cell proliferation and migration. Together, our findings revealed the distinct characteristics of H3K9ac in esophageal squamous cell carcinogenesis and metastasis, and highlighted the potential therapeutic avenue for intervening ESCC through epigenetic modulation via H3K9ac.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China
| | - Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yue Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China
| | - Pengcheng Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China
| | - Guoquan Cao
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yunbo Qiao
- Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200125, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
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Li J, Zheng G, Jiang D, Deng C, Zhang Y, Ma Y, Su J. Mendelian randomization analysis reveals a causal effect of Streptococcus salivarius on diabetic retinopathy through regulating host fasting glucose. J Cell Mol Med 2024; 28:e18200. [PMID: 38506069 PMCID: PMC10951888 DOI: 10.1111/jcmm.18200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Diabetic retinopathy (DR) is one of leading causes of vision loss in adults with increasing prevalence worldwide. Increasing evidence has emphasized the importance of gut microbiome in the aetiology and development of DR. However, the causal relationship between gut microbes and DR remains largely unknown. To investigate the causal associations of DR with gut microbes and DR risk factors, we employed two-sample Mendelian Randomization (MR) analyses to estimate the causal effects of 207 gut microbes on DR outcomes. Inputs for MR included Genome-wide Association Study (GWAS) summary statistics of 207 taxa of gut microbes (the Dutch Microbiome Project) and 21 risk factors for DR. The GWAS summary statistics data of DR was from the FinnGen Research Project. Data analysis was performed in May 2023. We identified eight bacterial taxa that exhibited significant causal associations with DR (FDR < 0.05). Among them, genus Collinsella and species Collinsella aerofaciens were associated with increased risk of DR, while the species Bacteroides faecis, Burkholderiales bacterium_1_1_47, Ruminococcus torques, Streptococcus salivarius, genus Burkholderiales_noname and family Burkholderiales_noname showed protective effects against DR. Notably, we found that the causal effect of species Streptococcus salivarius on DR was mediated through the level of host fasting glucose, a well-established risk factor for DR. Our results reveal that specific gut microbes may be causally linked to DR via mediating host metabolic risk factors, highlighting potential novel therapeutic or preventive targets for DR.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Gongwei Zheng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Dingping Jiang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Chunyu Deng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Yaru Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Yunlong Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Jianzhong Su
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
- Oujiang LaboratoryZhejiang Lab for Regenerative Medicine, Vision and Brain HealthWenzhouChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouChina
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Yuan J, Li K, Peng H, Zhang Y, Yao Y, Qu J, Su J. Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline. STAR Protoc 2024; 5:102841. [PMID: 38236768 PMCID: PMC10827591 DOI: 10.1016/j.xpro.2024.102841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
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Yuan J, Li K, Peng H, Zhang Y, Yao Y, Qu J, Su J. Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline. STAR Protoc 2024; 5:102806. [PMID: 38175747 PMCID: PMC10793169 DOI: 10.1016/j.xpro.2023.102806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/20/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Whole-exome sequencing (WES) is a major approach to uncovering gene-disease associations and pinpointing effector genes. Here, we present a protocol for estimating genetic associations of rare and common variants in large-scale case-control WES studies using MAGICpipeline, an open-access analysis pipeline. We describe steps for assessing gene-based rare-variant association analyses by incorporating multiple variant pathogenic annotations and statistical techniques. We then detail procedures for identifying disease-related modules and hub genes using weighted correlation network analysis, a systems biology approach. For complete details on the use and execution of this protocol, please refer to Su et al. (2023).1.
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Affiliation(s)
- Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Kai Li
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
| | - Hui Peng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yue Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China.
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9
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Yang MS, Fan XK, Su J, Wan XL, Yu H, Lu Y, Hua YJ, Jin JR, Pei P, Yu CQ, Sun DJY, Lyu J, Tao R, Zhou JY. [A prospective study on association between sleep duration and the risk of chronic obstructive pulmonary disease in adults in Suzhou]. Zhonghua Liu Xing Bing Xue Za Zhi 2024; 45:331-338. [PMID: 38514308 DOI: 10.3760/cma.j.cn112338-20230918-00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Objective: To investigate the prospective association of sleep duration with the development of chronic obstructive pulmonary disease (COPD) in adults in Suzhou. Methods: The study used the data of 53 269 participants aged 30-79 years recruited in the baseline survey from 2004 to 2008 and the follow-up until December 31, 2017 of China Kadoorie Biobank (CKB) conducted in Wuzhong District, Suzhou. After excluding participants with airflow limitation, self-reported chronic bronchitis/emphysema/coronary heart disease history at the baseline survey and abnormal or incomplete data, a total of 45 336 participants were included in the final analysis. The association between daily sleep duration and the risk for developing COPD was analyzed by using a Cox proportional hazard regression model, and the hazard ratio (HR) values and their 95%CI were calculated. The analysis was stratified by age, gender and lifestyle factors, and cross-analysis was conducted according to smoking status and daily sleep duration. Results: The median follow-up time was 11.12 years, with a total of 515 COPD diagnoses in the follow-up. After adjusting for potential confounders, multifactorial Cox proportional hazard regression analysis showed that daily sleep duration ≥10 hours was associated with higher risk for developing COPD (HR=1.42, 95%CI: 1.03-1.97). The cross analysis showed that excessive daily sleep duration increased the risk for COPD in smokers (HR=2.49, 95%CI: 1.35-4.59, interaction P<0.001). Conclusion: Longer daily sleep duration (≥10 hours) might increase the risk for COPD in adults in Suzhou, especially in smokers.
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Affiliation(s)
- M S Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - X K Fan
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Su
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - X L Wan
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - H Yu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Y Lu
- Suzhou Prefectural Center for Disease Control and Prevention, Suzhou 215003, China
| | - Y J Hua
- Suzhou Prefectural Center for Disease Control and Prevention, Suzhou 215003, China
| | - J R Jin
- Wuzhong District Center for Disease Control and Prevention of Suzhou, Suzhou 215128, China
| | - P Pei
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China
| | - C Q Yu
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100191, China
| | - D J Y Sun
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100191, China
| | - J Lyu
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100191, China
| | - R Tao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - J Y Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China School of Public Health, Nanjing Medical University, Nanjing 211166, China
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10
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Lin X, Lei Y, Pan M, Hu C, Xie B, Wu W, Su J, Li Y, Tan Y, Wei X, Xue Z, Xu R, Di M, Deng H, Liu S, Yang X, Qu J, Chen W, Zhou X, Zhao F. Augmentation of scleral glycolysis promotes myopia through histone lactylation. Cell Metab 2024; 36:511-525.e7. [PMID: 38232735 DOI: 10.1016/j.cmet.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
Myopia is characterized of maladaptive increases in scleral fibroblast-to-myofibroblast transdifferentiation (FMT). Scleral hypoxia is a significant factor contributing to myopia, but how hypoxia induces myopia is poorly understood. Here, we showed that myopia in mice and guinea pigs was associated with hypoxia-induced increases in key glycolytic enzymes expression and lactate levels in the sclera. Promotion of scleral glycolysis or lactate production induced FMT and myopia; conversely, suppression of glycolysis or lactate production eliminated or inhibited FMT and myopia. Mechanistically, increasing scleral glycolysis-lactate levels promoted FMT and myopia via H3K18la, and this promoted Notch1 expression. Genetic analyses identified a significant enrichment of two genes encoding glycolytic enzymes, ENO2 and TPI1. Moreover, increasing sugar intake in guinea pigs not only induced myopia but also enhanced the response to myopia induction via the scleral glycolysis-lactate-histone lactylation pathway. Collectively, we suggest that scleral glycolysis contributes to myopia by promoting FMT via lactate-induced histone lactylation.
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Affiliation(s)
- Xiaolei Lin
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yi Lei
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Miaozhen Pan
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Changxi Hu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Bintao Xie
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Wenjing Wu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jianzhong Su
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325101, Zhejiang, China
| | - Yating Li
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yuhan Tan
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Xiaohuan Wei
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Zhengbo Xue
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Ruiyan Xu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Mengqi Di
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Hanyu Deng
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Shengcong Liu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Xingxing Yang
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jia Qu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; Research Unit of Myopia Basic Research and Clinical Prevention and Control, Chinese Academy of Medical Sciences (2019RU025), Wenzhou 325027, Zhejiang, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325101, Zhejiang, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China.
| | - Xiangtian Zhou
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; Research Unit of Myopia Basic Research and Clinical Prevention and Control, Chinese Academy of Medical Sciences (2019RU025), Wenzhou 325027, Zhejiang, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325101, Zhejiang, China.
| | - Fei Zhao
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325101, Zhejiang, China.
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Ma Y, Zhou Y, Jiang D, Dai W, Li J, Deng C, Chen C, Zheng G, Zhang Y, Qiu F, Sun H, Xing S, Han H, Qu J, Wu N, Yao Y, Su J. Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19. Cell Prolif 2024; 57:e13558. [PMID: 37807299 PMCID: PMC10905359 DOI: 10.1111/cpr.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023] Open
Abstract
Human organoids recapitulate the cell type diversity and function of their primary organs holding tremendous potentials for basic and translational research. Advances in single-cell RNA sequencing (scRNA-seq) technology and genome-wide association study (GWAS) have accelerated the biological and therapeutic interpretation of trait-relevant cell types or states. Here, we constructed a computational framework to integrate atlas-level organoid scRNA-seq data, GWAS summary statistics, expression quantitative trait loci, and gene-drug interaction data for distinguishing critical cell populations and drug targets relevant to coronavirus disease 2019 (COVID-19) severity. We found that 39 cell types across eight kinds of organoids were significantly associated with COVID-19 outcomes. Notably, subset of lung mesenchymal stem cells increased proximity with fibroblasts predisposed to repair COVID-19-damaged lung tissue. Brain endothelial cell subset exhibited significant associations with severe COVID-19, and this cell subset showed a notable increase in cell-to-cell interactions with other brain cell types, including microglia. We repurposed 33 druggable genes, including IFNAR2, TYK2, and VIPR2, and their interacting drugs for COVID-19 in a cell-type-specific manner. Overall, our results showcase that host genetic determinants have cellular-specific contribution to COVID-19 severity, and identification of cell type-specific drug targets may facilitate to develop effective therapeutics for treating severe COVID-19 and its complications.
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Affiliation(s)
- Yunlong Ma
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Yijun Zhou
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Dingping Jiang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jingjing Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Cheng Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Gongwei Zheng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Yaru Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Fei Qiu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haojun Sun
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Shilai Xing
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haijun Han
- School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Nan Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
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Chen C, An G, Yu X, Wang S, Lin P, Yuan J, Zhuang Y, Lu X, Bai Y, Zhang G, Su J, Qu J, Xu L, Wang H. Screening Mutations of the Monogenic Syndromic High Myopia by Whole Exome Sequencing From MAGIC Project. Invest Ophthalmol Vis Sci 2024; 65:9. [PMID: 38315492 PMCID: PMC10851780 DOI: 10.1167/iovs.65.2.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
Purpose This observational study aimed to identify mutations in monogenic syndromic high myopia (msHM) using data from reported samples (n = 9370) of the Myopia Associated Genetics and Intervention Consortium (MAGIC) project. Methods The targeted panel containing 298 msHM-related genes was constructed and screening of clinically actionable variants was performed based on whole exome sequencing. Capillary sequencing was used to verify the identified gene mutations in the probands and perform segregation analysis with their relatives. Results A total of 381 candidate variants in 84 genes and 85 eye diseases were found to contribute to msHM in 3.6% (335/9370) of patients with HM. Among them, the 22 genes with the most variations accounted for 62.7% of the diagnostic cases. In the genotype-phenotype association analysis, 60% (201/335) of suspected msHM cases were recalled and 25 patients (12.4%) received a definitive genetic diagnosis. Pathogenic variants were distributed in 18 msHM-related diseases, mainly involving retinal dystrophy genes (e.g. TRPM1, CACNA1F, and FZD4), connective tissue disease genes (e.g. FBN1 and COL2A1), corneal or lens development genes (HSF4, GJA8, and MIP), and other genes (TEK). The msHM gene mutation types were allocated to four categories: nonsense mutations (36%), missense mutations (36%), frameshift mutations (20%), and splice site mutations (8%). Conclusions This study highlights the importance of thorough molecular subtyping of msHM to provide appropriate genetic counselling and multispecialty care for children and adolescents with HM.
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Affiliation(s)
- Chong Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Gang An
- Institute of PSI Genomics Co., Ltd., Wenzhou, China
| | - Xiaoguang Yu
- Institute of PSI Genomics Co., Ltd., Wenzhou, China
| | - Siyu Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Peng Lin
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Youyuan Zhuang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Lu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yu Bai
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Guosi Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Liangde Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Hong Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
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13
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Yao Y, Yang J, Sun H, Kong H, Wang S, Xu K, Dai W, Jiang S, Bai Q, Xing S, Yuan J, Liu X, Lu F, Chen Z, Qu J, Su J. DeepGraFT: A novel semantic segmentation auxiliary ROI-based deep learning framework for effective fundus tessellation classification. Comput Biol Med 2024; 169:107881. [PMID: 38159401 DOI: 10.1016/j.compbiomed.2023.107881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Fundus tessellation (FT) is a prevalent clinical feature associated with myopia and has implications in the development of myopic maculopathy, which causes irreversible visual impairment. Accurate classification of FT in color fundus photo can help predict the disease progression and prognosis. However, the lack of precise detection and classification tools has created an unmet medical need, underscoring the importance of exploring the clinical utility of FT. Thus, to address this gap, we introduce an automatic FT grading system (called DeepGraFT) using classification-and-segmentation co-decision models by deep learning. ConvNeXt, utilizing transfer learning from pretrained ImageNet weights, was employed for the classification algorithm, aligning with a region of interest based on the ETDRS grading system to boost performance. A segmentation model was developed to detect FT exits, complementing the classification for improved grading accuracy. The training set of DeepGraFT was from our in-house cohort (MAGIC), and the validation sets consisted of the rest part of in-house cohort and an independent public cohort (UK Biobank). DeepGraFT demonstrated a high performance in the training stage and achieved an impressive accuracy in validation phase (in-house cohort: 86.85 %; public cohort: 81.50 %). Furthermore, our findings demonstrated that DeepGraFT surpasses machine learning-based classification models in FT classification, achieving a 5.57 % increase in accuracy. Ablation analysis revealed that the introduced modules significantly enhanced classification effectiveness and elevated accuracy from 79.85 % to 86.85 %. Further analysis using the results provided by DeepGraFT unveiled a significant negative association between FT and spherical equivalent (SE) in the UK Biobank cohort. In conclusion, DeepGraFT accentuates potential benefits of the deep learning model in automating the grading of FT and allows for potential utility as a clinical-decision support tool for predicting progression of pathological myopia.
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Affiliation(s)
- Yinghao Yao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jiaying Yang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Haojun Sun
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hengte Kong
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Sheng Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Ke Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Wei Dai
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Siyi Jiang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - QingShi Bai
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Shilai Xing
- Institute of PSI Genomics, Wenzhou Global Eye & Vision Innovation Center, Wenzhou, 325024, China
| | - Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Xinting Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhenhui Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Jia Qu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325011, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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Li DX, Fan W, Zhu L, Hu X, Li Y, Ma HX, Wang HF, Ye Y, Su J, Huang XY. [Monitoring and analysis on host animals of hemorrhagic fever with renal syndrome in Henan Province from 2019 to 2022]. Zhonghua Yu Fang Yi Xue Za Zhi 2024; 58:18-24. [PMID: 38228545 DOI: 10.3760/cma.j.cn112150-20230829-00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Objective: To investigate the distribution and hantavirus (HV) carrying state in host animals of hemorrhagic fever with renal syndrome (HFRS) in Henan Province from 2019 to 2022. Methods: Host animal monitoring was carried out at the monitoring sites of HFRS in Henan Province. The real-time fluorescence quantitative PCR was used to detect hantavirus in rat lungs. The types of hantavirus were analyzed. The positive samples were sequenced and then sequence homology and variation were analyzed. Results: A total of 1 308 rodents were captured from 2019 to 2022, 16 specimens of rat lungs tested positive for hantavirus nucleic acid. The positive rate of HV was 1.22% (16/1 308). According to type, the positive rate of HV in Apodius agrarius was the highest (68.75%, 11/16). According to distribution, the positive rate of HV in field samples was the highest (2.50%, 12/480), and the positive rate of HV in residential samples was 0.53% (4/759). The typing results of 16 positive samples showed that all viruses were hantavirus type Ⅰ (hantaan virus). The positive samples were sequenced and eight S gene fragments (GenBank number: OQ681444-OQ681451) and six M gene fragments (OQ681438-OQ681443) were obtained. The S and M gene fragments were similar to the Shaanxi 84FLi strain and Sichuan SN7 strain. Phylogenetic analysis of S and M gene fragments showed that they all belonged to the hantaan virus-H5 subtype. Amino acid sequence analysis revealed that, compared with the hantaan virus vaccine strain 84FLi, the 74th amino acid encoded by eight S fragments was replaced by aspartamide with serine. Tryptophan was replaced by glycine at the 14th position of Gn region in XC2022047, and isoleucine was replaced by alanine at the 359 position of XC2022022 and XC2022024. Conclusion: The hantavirus carried by host animals in Henan Province from 2019 to 2022 belongs to the type Ⅰ (hantaan virus), and Apodemus agrarius is still the dominant host animal of the hantaan virus. Compared with the vaccine strains, amino acid sites are replaced in the immune epitopes of the S and M gene fragments.
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Affiliation(s)
- D X Li
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - W Fan
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - L Zhu
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - X Hu
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - Y Li
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - H X Ma
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - H F Wang
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - Y Ye
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - J Su
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
| | - X Y Huang
- Infectious Disease Prevention and Control Institute, Center for Disease Control and Prevention of Henan Province, Zhengzhou 450016, China
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15
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Zhou Y, Zhang Y, Peng M, Zhang Y, Li C, Shu L, Hu Y, Su J, Xu J. scDMV: a zero-one inflated beta mixture model for DNA methylation variability with scBS-seq data. Bioinformatics 2024; 40:btad772. [PMID: 38141207 PMCID: PMC10786675 DOI: 10.1093/bioinformatics/btad772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/11/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
MOTIVATION The utilization of single-cell bisulfite sequencing (scBS-seq) methods allows for precise analysis of DNA methylation patterns at the individual cell level, enabling the identification of rare populations, revealing cell-specific epigenetic changes, and improving differential methylation analysis. Nonetheless, the presence of sparse data and an overabundance of zeros and ones, attributed to limited sequencing depth and coverage, frequently results in reduced precision accuracy during the process of differential methylation detection using scBS-seq. Consequently, there is a pressing demand for an innovative differential methylation analysis approach that effectively tackles these data characteristics and enhances recognition accuracy. RESULTS We propose a novel beta mixture approach called scDMV for analyzing methylation differences in single-cell bisulfite sequencing data, which effectively handles excess zeros and ones and accommodates low-input sequencing. Our extensive simulation studies demonstrate that the scDMV approach outperforms several alternative methods in terms of sensitivity, precision, and controlling the false positive rate. Moreover, in real data applications, we observe that scDMV exhibits higher precision and sensitivity in identifying differentially methylated regions, even with low-input samples. In addition, scDMV reveals important information for GO enrichment analysis with single-cell whole-genome sequencing data that are often overlooked by other methods. AVAILABILITY AND IMPLEMENTATION The scDMV method, along with a comprehensive tutorial, can be accessed as an R package on the following GitHub repository: https://github.com/PLX-m/scDMV.
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Affiliation(s)
- Yan Zhou
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Ying Zhang
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Minjiao Peng
- School of Mathematics and Statistics and KLAS, Northeast Normal University, Changchun, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lianjie Shu
- Faculty of Business Administration, University of Macau, Macau, China
| | - Yaohua Hu
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jinfeng Xu
- Department of Biostatistics, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
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16
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Justvig SP, Su J, Clark LM, Messina C, Sridhar S, Mintzer JP. Regional tissue oxygenation in asymptomatic neonates at high risk for neonatal abstinence syndrome and impact of non-pharmacologic interventions: A case report. J Neonatal Perinatal Med 2024; 17:137-145. [PMID: 38160367 DOI: 10.3233/npm-230099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
BACKGROUND Improving neonatal abstinence syndrome (NAS) management is an important concern, and objective measures of its physiologic impact remain elusive. We sought to determine whether near-infrared spectroscopy (NIRS)-derived tissue oxygenation (rSO2) and fractional tissue oxygen extraction (FTOE) demonstrated physiologically plausible changes correlating with standard NAS scoring. METHODS Thirty subjects (mean 39 weeks' GA and 3 127 g BW) underwent cerebral and peripheral muscle NIRS monitoring on Days of Life (DOL) Three, Five, and Seven. We examined correlations between NAS scores and FTOE and assessed the impact of non-pharmacologic swaddling and cuddling. RESULTS No statistically significant correlations between NAS scores and FTOE were observed; however, plausible trends were demonstrated between NAS scores and cerebral measurements. Buprenorphine-exposed babies (57%) showed significantly lower FTOE when swaddled (DOL7). CONCLUSIONS Tissue oxygenation monitoring demonstrates potential to provide objective, clinically relevant physiologic information on infants at risk for NAS. Further study is required to determine whether NIRS-derived measures could assist in individualizing NAS care.
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Affiliation(s)
- S P Justvig
- Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - J Su
- General Surgery, University of Hawaii, Honolulu, HI, USA
| | - L M Clark
- Pediatrics, Stony Brook Children's, Stony Brook, NY, USA
| | - C Messina
- Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - S Sridhar
- Pediatrics, Stony Brook Children's, Stony Brook, NY, USA
| | - J P Mintzer
- Neonatology, Mountainside Medical Center, Montclair, NJ, USA
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Visram A, De La Torre A, White D, Su J, Masih-Khan E, Chu M, Jimenez-Zepeda V, McCurdy A, LeBlanc R, Song K, Mian H, Louzada M, Sebag M, Bergstrom D, Stakiw J, Reiman A, Kotb R, Aslam M, Venner C, Kaedbey R, Gul E, Reece D. Real world data on outcomes of anti-CD38 antibody treated, including triple class refractory, patients with multiple myeloma: a multi-institutional report from the Canadian Myeloma Research Group (CMRG) Database. Blood Cancer J 2023; 13:181. [PMID: 38065967 PMCID: PMC10709576 DOI: 10.1038/s41408-023-00946-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/09/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Multiple myeloma (MM) remains incurable despite the availability of novel agents. This multi-center retrospective cohort study used the Canadian Myeloma Research Group Database to describe real-world outcomes of patients withanti-CD38 monoclonal antibody (mAb) refractory MM subsequently treated with standard of care (SoC) regimens. Patients with triple class refractory (TCR) disease (refractory to a proteasome inhibitor, immunomodulatory drug, and anti-CD38 mAb) were examined as a distinct cohort. Overall, 663 patients had disease progression on anti-CD38 mAb therapy, 466 received further treatment (346 with SoC regimens were included, 120 with investigational agents on clinical trial and were excluded). The median age at initiation of subsequent SoC therapy of 67.9 (range 39.6-89.6) years with a median of 3 prior lines (range 1-9). The median PFS and OS from the start of subsequent therapy was 4.6 (95% CI 4.1-5.6) months and 13.3 (95% CI 10.6-16.6) months, respectively. The median PFS and OS of patients with TCR disease (n = 199) was 4.4 (95% CI 3.6-5.3) months and 10.5 (95% CI 8.5-13.8) months. Our results reinforce that real-world patients with relapsed MM, particularly those with TCR disease, have dismal outcomes. There remains an urgent unmet need for the development of and access to effective therapeutics for these patients.
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Affiliation(s)
- A Visram
- Department of Medicine, The Ottawa Hospital, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - A De La Torre
- Division of Hematology, Dalhousie University and Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | - D White
- Division of Hematology, Dalhousie University and Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | - J Su
- Canadian Myeloma Research Group, Toronto, ON, Canada
| | - E Masih-Khan
- Canadian Myeloma Research Group, Toronto, ON, Canada
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - M Chu
- Department of Oncology, Cross Cancer Institute, Edmonton, Alberta, Edmonton, AB, Canada
| | - V Jimenez-Zepeda
- Tom Baker Cancer Center, Department of Hematology, University of Calgary, Calgary, AB, Canada
| | - A McCurdy
- Department of Medicine, The Ottawa Hospital, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - R LeBlanc
- Hôpital Maisonneuve-Rosemont, Université de Montréal, Montreal, QC, Canada
| | - K Song
- The Leukemia/Bone Marrow Transplant Program of BC, British Columbia Cancer Agency, Vancouver, Canada
| | - H Mian
- Juravinski Cancer Centre (Hamilton-CCO), Hamilton, ON, Canada
| | - M Louzada
- University of Western Ontario, London Health Sciences Centre, London, ON, Canada
| | - M Sebag
- Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - D Bergstrom
- Division of Hematology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - J Stakiw
- Saskatoon Cancer Centre, Saskatoon, SK, Canada
| | - A Reiman
- Oncology, Saint John Regional Hospital, Saint John, NB, Canada
| | - R Kotb
- Medical Oncology and Hematology, Cancer Care Manitoba, Winnipeg, MB, Canada
| | - M Aslam
- Allan Blair Cancer Center, Regina, SK, Canada
| | - C Venner
- BC Cancer - Vancouver Centre, Lymphoma and Myeloma Program, University of British Columbia, Vancouver, BC, Canada
| | - R Kaedbey
- Segal Cancer Centre, Jewish General Hospital, McGill University, Montreal, Montreal, QC, Canada
| | - E Gul
- Canadian Myeloma Research Group, Toronto, ON, Canada
| | - D Reece
- Canadian Myeloma Research Group, Toronto, ON, Canada.
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
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Zhang H, Zhou M, Zhou QL, Luo X, Zheng R, Su J, Xiong GW, Cheng Y, Li YT, Zhang PP, Zhang K, Dai M, Huang XK, Zhang YN, Shi ZH, Tao J, Zhou YQ, Feng PY, Chen ZG, Yang QT. [Preliminary insights into the practice of hypoallergenic home visiting program]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1957-1963. [PMID: 38186142 DOI: 10.3760/cma.j.cn112150-20230903-00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Allergic diseases affect about 40% of the world's population. Environmental factors are important in the occurrence and development of allergic diseases. Dust mites are one of the most important allergens in the indoor environment. The World Health Organization proposes the "four-in-one, combination of prevention and treatment" treatment principle for allergic diseases, in which environmental control to avoid or reduce allergens is the first choice for treatment. Modern people spend much more time at home (including sleeping) than outdoors, and the control of the home environment is particularly critical. This practice introduces the hypoallergenic home visit program, which including home environment assessment, environmental and behavioral intervention guidance, and common household hypoallergenic supplies and service guidance for the patient's home environment. The real-time semi-quantitative testing of dust mite allergens, qualitative assessments of other indoor allergens, record of patients' household items and lifestyle, and precise, individualized patient prevention and control education will be conducted. The hypoallergenic home visit program improves the doctors' diagnosis and treatment data dimension, and becomes a patient management tool for doctors outside the hospital. It also helps patients continue to scientifically avoid allergens and irritants in the environment, effectively build a hypoallergenic home environment, reduce exposure to allergens in the home environment, and achieve the goal of combining the prevention and treatment of allergic diseases.
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Affiliation(s)
- H Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - M Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Q L Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - X Luo
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - R Zheng
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - J Su
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - G W Xiong
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y Cheng
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y T Li
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - P P Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - K Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - M Dai
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - X K Huang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y N Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Z H Shi
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - J Tao
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y Q Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Respiratory and Intensive Care, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - P Y Feng
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Dermatology and Cosmetic Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Z G Chen
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Q T Yang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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Yu X, Yuan J, Chen ZJ, Li K, Yao Y, Xing S, Xue Z, Zhang Y, Peng H, An G, Yu X, Qu J, Su J. Whole-Exome Sequencing Among School-Aged Children With High Myopia. JAMA Netw Open 2023; 6:e2345821. [PMID: 38039006 PMCID: PMC10692858 DOI: 10.1001/jamanetworkopen.2023.45821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
Importance High myopia (HM) is one of the leading causes of visual impairment worldwide. Genetic factors are known to play an important role in the development of HM. Objective To identify risk variants in a large HM cohort and to examine the implications of genetic testing of schoolchildren with HM. Design, Setting, and Participants This cohort study retrospectively reviewed whole-exome sequencing (WES) results in 6215 schoolchildren with HM who underwent genetic testing between September 2019 and July 2020 in Wenzhou City, China. HM is defined as a spherical equivalent refraction (SER) of -6.00 diopters (D) or less. The study setting was a genetic testing laboratory and a multicenter school census. Data were analyzed from July 2021 to June 2022. Main Outcomes and Measures The frequency and distribution of positive germline variants, the percentage of individuals with HM in both eyes, and subsequent variant yield for common high myopia (CHM; -8.00 D ≤ SER ≤ -6.00 D), ultra myopia (UM; -10.00 D ≤ SER < -8.00 D), and extreme myopia (EM; SER < -10.00 D). Results Of the 6215 schoolchildren with HM, 3278 (52.74%) were male. Their mean (SD) age was 14.87 (2.02) years, including 355 students in primary school, 1970 in junior high school, and 3890 in senior high school. The mean (SD) SER was -7.51 (-1.36) D for the right eye and -7.46 (-1.34) D for the left eye. Among schoolchildren with HM, genetic testing yielded 271 potential pathogenic variants in 75 HM candidate genes in 964 diagnoses (15.52%). A total of 36 known variants were found in 490 HM participants (7.88%) and 235 protein-truncating variants (PTVs) in 506 participants (8.14%). Involved variant yield was significantly positively associated with SER (Cochran-Armitage test for trend Z = 2.5492; P = .01), which ranged from 7.66% in the CHM group, 8.70% in the UM group, to 11.90% in the EM group. We also found that primary school students with EM had the highest variant yield of PTVs (8 of 35 students [22.86%]), which was 1.77 and 4.78 times that of the UM and CHM, respectively. Conclusions and Relevance In this cohort study of WES for HM, several potential pathogenic variants were identified in a substantial number of schoolchildren with HM. The high variation frequency in younger students with EM can provide clues for genetic screening and clinical examinations of HM to promote long-term follow-up assessment.
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Affiliation(s)
- Xiangyi Yu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhen Ji Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
| | - Kai Li
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
| | - Shilai Xing
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of PSI Genomics, Wenzhou, China
| | - Zhengbo Xue
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yue Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hui Peng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Gang An
- Institute of PSI Genomics, Wenzhou, China
| | | | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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20
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Xu H, Jia Z, Liu F, Li J, Huang Y, Jiang Y, Pu P, Shang T, Tang P, Zhou Y, Yang Y, Su J, Liu J. Biomarkers and experimental models for cancer immunology investigation. MedComm (Beijing) 2023; 4:e437. [PMID: 38045830 PMCID: PMC10693314 DOI: 10.1002/mco2.437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
The rapid advancement of tumor immunotherapies poses challenges for the tools used in cancer immunology research, highlighting the need for highly effective biomarkers and reproducible experimental models. Current immunotherapy biomarkers encompass surface protein markers such as PD-L1, genetic features such as microsatellite instability, tumor-infiltrating lymphocytes, and biomarkers in liquid biopsy such as circulating tumor DNAs. Experimental models, ranging from 3D in vitro cultures (spheroids, submerged models, air-liquid interface models, organ-on-a-chips) to advanced 3D bioprinting techniques, have emerged as valuable platforms for cancer immunology investigations and immunotherapy biomarker research. By preserving native immune components or coculturing with exogenous immune cells, these models replicate the tumor microenvironment in vitro. Animal models like syngeneic models, genetically engineered models, and patient-derived xenografts provide opportunities to study in vivo tumor-immune interactions. Humanized animal models further enable the simulation of the human-specific tumor microenvironment. Here, we provide a comprehensive overview of the advantages, limitations, and prospects of different biomarkers and experimental models, specifically focusing on the role of biomarkers in predicting immunotherapy outcomes and the ability of experimental models to replicate the tumor microenvironment. By integrating cutting-edge biomarkers and experimental models, this review serves as a valuable resource for accessing the forefront of cancer immunology investigation.
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Affiliation(s)
- Hengyi Xu
- State Key Laboratory of Molecular OncologyNational Cancer Center /National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ziqi Jia
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Fengshuo Liu
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jiayi Li
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yansong Huang
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yiwen Jiang
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Pengming Pu
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tongxuan Shang
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Pengrui Tang
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yongxin Zhou
- Eight‐year MD ProgramSchool of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yufan Yang
- School of MedicineTsinghua UniversityBeijingChina
| | - Jianzhong Su
- Oujiang LaboratoryZhejiang Lab for Regenerative Medicine, Vision, and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center /National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Breast Surgical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Huang Y, Jiang L, Liu J, Xu Y, Mo F, Su J, Tao R. Investigating a Causal Relationship Between Diabetes Mellitus and Oropharyngeal Cancer: A Mendelian Randomization Study. Community Dent Health 2023; 40:212-220. [PMID: 37988677 DOI: 10.1922/cdh_00025huang09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/01/2023] [Indexed: 11/23/2023]
Abstract
OBJECTIVE Previous observational studies reported an association of diabetes mellitus (DM) with oropharyngeal cancer (OPC), however, the potential causality of the association between them remains unclear. METHODS To explore this causal relationship in individuals of European descent, a two-sample Mendelian randomization (MR) study was conducted. A genome-wide association study (GWAS) of DM was used to represent the exposure factor (T1DM: n = 24,840; T2DM: n = 215,654), and GWAS of OPC represented the outcome (n = 3,448). RESULTS Forty-one single nucleotide polymorphisms (SNPs) related to T1DM and fifty-four SNPs related to T2DM were identified as effective instrumental variables (IVs) in the two-sample MR analyses. In IVW estimates, neither T1DM nor T2DM significantly contributed to an increased risk of OPC [T1DM: OR 1.0322 (95% CI 0.9718, 1.0963), P = 0.3033; T2DM: OR 0.9998 (95% CI 0.9995, 1.0002), P = 0.2858]. Four other regression models produced similar results. MR-Egger regression results [Cochran's Q statistic was 47.1544 (P = 0.1466) in T1DM, and 35.5084 (P = 0.9512) in T2DM] suggested no horizontal pleiotropy between IVs and outcomes. CONCLUSION Our findings suggest little evidence to support the genetic role of diabetes mellitus in OPC development in the European population.
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Affiliation(s)
- Y Huang
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - L Jiang
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - J Liu
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - Y Xu
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - F Mo
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - J Su
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
| | - R Tao
- Department of Periodontics and Oral medicine, College of Stomatology, Guangxi Medical University, China
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Liu Z, Zhang Y, Ma N, Yang Y, Ma Y, Wang F, Wang Y, Wei J, Chen H, Tartarone A, Velotta JB, Dayyani F, Gabriel E, Wakefield CJ, Kidane B, Carbonelli C, Long L, Liu Z, Su J, Li Z. Progenitor-like exhausted SPRY1 +CD8 + T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma. Cancer Cell 2023; 41:1852-1870.e9. [PMID: 37832554 DOI: 10.1016/j.ccell.2023.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Neoadjuvant immune checkpoint blockade (ICB) demonstrates promise in operable esophageal squamous cell carcinoma (ESCC), but lacks available efficacy biomarkers. Here, we perform single-cell RNA-sequencing of tumors from patients with ESCC undergoing neoadjuvant ICB, revealing a subset of exhausted CD8+ T cells expressing SPRY1 (CD8+ Tex-SPRY1) that displays a progenitor exhausted T cell (Tpex) phenotype and correlates with complete response to ICB. We validate CD8+ Tex-SPRY1 cells as an ICB-specific predictor of improved response and survival using independent ICB-/non-ICB cohorts and demonstrate that expression of SPRY1 in CD8+ T cells enforces Tpex phenotype and enhances ICB efficacy. Additionally, CD8+ Tex-SPRY1 cells contribute to proinflammatory phenotype of macrophages and functional state of B cells, which thereby promotes antitumor immunity by enhancing CD8+ T cell effector functions. Overall, our findings unravel progenitor-like CD8+ Tex-SPRY1 cells' role in effective responses to ICB for ESCC and inform mechanistic biomarkers for future individualized immunotherapy.
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Affiliation(s)
- Zhichao Liu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Ning Ma
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China
| | - Yunlong Ma
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Feng Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jinzhi Wei
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Alfredo Tartarone
- Division of Medical Oncology, Department of Onco-Hematology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ) 85028, Italy
| | - Jeffrey B Velotta
- Department of Thoracic Surgery, Kaiser Permanente Oakland Medical Center, Kaiser Permanente Northern California, Oakland, CA 94611, USA
| | - Farshid Dayyani
- Chao Comprehensive Cancer Center, University of California Irvine, Orange, CA 92868, USA
| | - Emmanuel Gabriel
- Department of Surgery, Division of Surgical Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Connor J Wakefield
- Department of Internal Medicine, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA
| | - Biniam Kidane
- Section of Thoracic Surgery, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Cristiano Carbonelli
- Pneumology Unit, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo 71013, Italy
| | - Lingyun Long
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China.
| | - Zhigang Li
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai 200030, China.
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Yu X, Su J, Wang B, Wang YM. [A case of lung adenocarcinoma with markedly elevated amylase in airway secretions]. Zhonghua Jie He He Hu Xi Za Zhi 2023; 46:1124-1126. [PMID: 37914425 DOI: 10.3760/cma.j.cn112147-20230727-00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
A 45-year-old male patient was admitted to the hospital because of intermittent cough and expectoration for more than 1 year, worsened by dyspnea for 2 months, and was finally diagnosed with lung adenocarcinoma. The CT scan of the chest revealed lesions of diversity with fibrosis, mass and effusion, but his severe cough limited biopsy of the lesions. The difficult process of diagnosis was aided by the further analysis of the sputum, which showed significantly elevated amylase without any evidence of pancreatic disease. The cough was relieved by intravenous pumping octreotide acetate, and both CT-guided lung biopsy and transbronchial biopsy revealed the lung adenocarcinoma. The diagnostic process of this case provided a helpful diagnostic thinking and demonstrated the rare clinical features of lung adenocarcinoma.
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Affiliation(s)
- X Yu
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Center of Respiratory Medicine, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - J Su
- Department of Pulmonary and Critical Care Medicine, The second people's Hospital of Foshan, Foshan 528000, China
| | - B Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Y M Wang
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Center of Respiratory Medicine, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China Clinical Center for Pulmonary Infections, Capital Medical University, Beijing 100029, China
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24
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Gao GY, Cao LJ, Yu ZQ, Jiang M, Han Y, Bai X, Su J, Ruan CG. [Analysis of clinical phenotype and gene mutation characteristics of MYH9-related disorder]. Zhonghua Yi Xue Za Zhi 2023; 103:2964-2970. [PMID: 37752057 DOI: 10.3760/cma.j.cn112137-20230328-00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Objective: To investigate the clinical phenotype and gene mutation characteristics of MYH9-related disorder (MYH9-RD). Methods: The clinical data of 66 patients with MYH9-RD in the First Affiliated Hospital of Soochow University from January 2010 to December 2022 were retrospectively analyzed. According to the bleeding symptom, the patients were divided into bleeding and non-bleeding group, and according to the mutation sites, the patients were divided into non-muscle myosin heavy chain ⅡA head region (MD) and tail region (TD) mutation group. Statistical analysis was made to explore the clinical features in different groups such as platelet counts, bleeding, renal function, cataracts and hearing as well as MYH9 gene mutations. Results: A total of 66 MYH9-RD patients were included, with 28 males and 38 females, diagnosis age of 1-63(26±2) years. And 41% (27/66) of the patients had no family history. All patients presented with macrothrombocytopenia and normal platelet aggregation(10/10), 92% (54/59) of the patients had visible blue inclusion bodies in neutrophils, 30% (20/66) had bleeding symptoms, 45% (22/49) had proteinuria or glomerulonephropathy, 20% (8/41) had bilateral hearing impairment, and 10% (4/42) had bilateral cataracts. 18 mutation sites were identified in total, including 15 missense, 1 splicing and 2 termination mutations. Among them, p.Asp1424Asn, p.Arg1933* and p.Arg702His/Cys mutations were identified in 56% (29/52) of the patients, and p.Ser96Leu, Arg1165Cys and p.Glu1841Lys mutations were recurrent mutations, while p.Ala44Thr, p.Asp1447Ala and c.3838-2A>G mutations were novel mutations. The average platelet count of patients in bleeding group was (19±3)×109/L, which was significantly less than (36±3)×109/L in non-bleeding group (P<0.001). Compared with TD mutation group, patients of MD mutation group were presented with lower platelet count and higher risk of bleeding, as well as more severe clinical presentations including renal and hearing impairment and cataracts (all P<0.05). Conclusion: Mutations of p.Asp1424Asn, p.Arg1933* and p.Arg702His/Cys in MYH9 gene are hotspot mutations for MYH9-RD patients, Compared with TD mutation group, patients of MD mutation group were presented with lower platelet count and higher risk of bleeding, as well as more severe clinical presentations including renal and hearing impairment and cataracts.
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Affiliation(s)
- G Y Gao
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - L J Cao
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - Z Q Yu
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - M Jiang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - Y Han
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - X Bai
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - J Su
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
| | - C G Ruan
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, Suzhou 215006,China
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Liu K, Chen YJ, Su J, Fan XK, Yu H, Qin Y, Yang J, Zhu Z, Guan HY, Shen C, Pan EC, Lu Y, Zhou JY, Wu M. [Association of category of dietary intake and physical activity with the risk of mortality in patients with type 2 diabetes mellitus: a prospective cohort study]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1591-1598. [PMID: 37875446 DOI: 10.3760/cma.j.cn112338-20230328-00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Objective: To investigate the association between dietary intake and physical activity category and their combined effects on all-cause and cause-specific mortality risk in patients with type 2 diabetes mellitus (T2DM). Methods: Between December 2013 and December 2021, a prospective cohort study was conducted on 19 863 T2DM patients in Changshu City, Qingjiangpu District (formerly Qinghe District), and Huai'an District, included in the national basic health service management. Information on deaths and underlying causes of death was obtained from the Jiangsu Provincial CDC and Prevention Death Surveillance System. Cox proportional hazards models were used to estimate the intensity of associations between dietary intake, physical activity, and their combined effects with all-cause and cause-specific mortality in patients with T2DM. Results: As of December 31, 2021, the research subjects had been followed up for 150 283 person-years, with a median follow-up time of 8.15 years. During the follow-up period, 3 293 people died, including 1 124 deaths from cardiovascular disease (CVD) and 875 deaths from cancer. Cox regression analysis showed that compared with the population of 0-1 recommended food group, those having more than five recommended food groups had a 19% lower risk of all-cause mortality [hazard ratio (HR)=0.81, 95%CI: 0.70-0.94] and a 33% lower risk of all-cause mortality (HR=0.67, 95%CI: 0.52-0.87). Compared with the T2DM population in the physical activity Q1 group, the risk of all-cause mortality, CVD mortality, and cancer mortality among the physical activity Q4 group reduced by 50% (HR=0.50, 95%CI: 0.45-0.56), 50% (HR=0.50, 95%CI: 0.41-0.61), and 27% (HR=0.73, 95%CI: 0.60-0.88), respectively. The combined effect showed that compared with the population in the intake of food categories 0-2 and low physical activity groups, the risk of all-cause, CVD mortality, and cancer mortality in the intake of food categories 4-9 and high physical activity groups reduced by 55% (HR=0.45, 95%CI: 0.38-0.53), 56% (HR=0.44, 95%CI: 0.32-0.59), and 40% (HR=0.60, 95%CI: 0.44-0.82), respectively. Conclusion: Type of dietary intake, physical activity, and their combined effects are associated with a reduced mortality risk in patients with T2DM.
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Affiliation(s)
- K Liu
- School of Public Health, Southeast University, Nanjing 210009, China
| | - Y J Chen
- Department of Non-communicable Chronic Disease Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing 210003, China
| | - J Su
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - X K Fan
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - H Yu
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Y Qin
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Yang
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Z Zhu
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - H Y Guan
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - C Shen
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - E C Pan
- Department of Chronic Disease Prevention and Control, Huai'an City Center for Disease Control and Prevention, Huai'an 223001, China
| | - Y Lu
- Department of Chronic Disease Prevention and Control, Suzhou City Center for Disease Control and Prevention, Suzhou 215004, China
| | - J Y Zhou
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - M Wu
- School of Public Health, Southeast University, Nanjing 210009, China Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Hu RX, Su J. [Removal effect of disinfection factors in low concentration on Pseudomonas aeruginosa biofilm]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1620-1624. [PMID: 37859380 DOI: 10.3760/cma.j.cn112150-20221213-01199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Experimental model of Pseudomonas aeruginosa biofilm was established in vitro by using biofilm reactor. The aim of this study was evaluating the removal effect of two kinds of water flowing through bactericide resin on Pseudomonas aeruginosa biofilm, and exploring the effectiveness of continuous treatment with low concentration disinfection factor on dental unit waterlines. The experimental group selected 1-2 mg/L iodinated resin (IR) filtered water and bromined hydantoin resin (BHR) filtered water with the control group selecting the sterile distilled water. Biofilms were treated by using the immersion method for 3, 7, 10, 20, and 40 days. Total viable count (TVC) and laser confocal microscopy method (CLSM) were selected to evaluate the biofilm removal effect. The result of TVC showed that in group IR, the bacterial clearance after the treatment of 3, 7, 10, and 20 days was lower than 99.9% and unqualified. The bacterial clearance after the treatment of 40 days was 99.9%,which is qualified. In group BHR, it was lower than 99.9% and unqualified after the treatment of 3, 7, and 10 days. It was and 99.99%, 100.00% after the treatment of 20, 40 days, respectively. The result of CLSM showed that before treatment, Pseudomonas aeruginosa biofilm showed a sheet and mass distribution. The bacterial coverage was 19.24%±1.97%. The proportion of viable bacteria was 93.91%±1.39%, and the biofilm matrix coverage was 17.69%±1.11%. After 20 days of treatment, the biofilm was decreased in the IR group, with the biofilm bacterial coverage reducing to 6.77%±1.61%, the proportion of live bacteria reducing to 54.85%±5.65%, and the biofilm matrix coverage reducing to 2.41%±0.85%.There was significant difference from the pre-treatment and the control (F=359.996,P<0.001). No biofilm-like structure was found in the BHR group. After 40 days of treatment, there was still a small amount of biofilm matrix residue in the IR group, with no bacterial coverage observed. The biofilm matrix coverage was 0.67%±0.47% (F=1 021.373,P<0.001). No biofilm-like structure was found in the BHR group. In conclusion, the continuous application of BHR filter water has more advantages in killing microorganisms in biofilms, removing live and dead bacteria and biofilm matrix in biofilms. Treatment water containing corresponding low concentration disinfection factors can play an important role in the field of biofilm control in dental unit waterlines.
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Affiliation(s)
- R X Hu
- Periodontal Department,Beijing Stomatological Hospital Affiliated to Capital Medical University, Beijing 100050, China
| | - J Su
- Periodontal Department,Beijing Stomatological Hospital Affiliated to Capital Medical University, Beijing 100050, China
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Choi AR, D'Agostino R, Farris M, Abdulhaleem M, Wang Y, Smith M, Ruiz J, Lycan T, Petty W, Cramer CK, Tatter SB, Laxton A, White J, Su J, Whitlow CT, Xing F, Chan MD. Genomic Signature for Oligometastatic Disease in Non-Small Cell Lung Cancer Patients with Brain Metastases. Int J Radiat Oncol Biol Phys 2023; 117:S129. [PMID: 37784331 DOI: 10.1016/j.ijrobp.2023.06.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Biomarkers for oligometastatic disease remain elusive and few studies have attempted to correlate genomic data to the presence of true oligometastatic disease. MATERIALS/METHODS Patients with non-small cell lung cancer (NSCLC) and brain metastases were identified in our departmental database. Electronic medical records were used to identify patients for whom liquid biopsy-based comprehensive genomic profiling (Guardant Health) was available. Oligometastatic disease was defined as patients having ≤5 non-brain metastases without diffuse involvement of a single organ. Widespread disease was any spread beyond oligometastatic. Fisher's exact tests were used to identify mutations statistically associated (p<0.1) with either oligometastatic or widespread extracranial disease. A score of +1 was assigned for every mutation present associated with oligometastatic disease, and -1 was assigned for mutations associated with widespread disease. Scores were summed for each patient to create a risk score for the likelihood of oligometastatic disease, with scores subsequently correlated to the likelihood of having oligometastatic disease vs widespread disease. For oligometastatic patients, a competing risk analysis was done to assess for cumulative incidence of oligometastatic progression accounting for the potential competing risks of widespread progression of extracranial disease or death. Cox regression was used to determine the association between oligometastatic risk score and oligometastatic progression. RESULTS One hundred thirty patients met study criteria and were included in the analysis. 51 patients (39%) had oligometastatic disease. Genetic mutations included in the Guardant panel associated (p<0.1) with the presence of oligometastatic extracranial disease included ATM, JAK2, MAP2K2, and NTRK1; ARID1A and CCNE1 were associated with widespread disease. Patients with a positive, neutral and negative risk score for oligometastatic disease had a 78%, 41% and 11.5% likelihood of having oligometastatic disease, respectively (p<0.0001). Overall survival for patients with positive, neutral and negative risk scores for oligometastatic disease was 86% vs 82% vs 64% at 6 months (p = 0.2). The competing risk analysis found that the oligometastatic risk score was significantly associated with the likelihood of oligometastatic progression based on the Wald Chi-square test. Patients with positive, neutral and negative risk scores for oligometastatic disease had a cumulative incidence of oligometastatic progression of 77% vs 35% vs 33% at 6 months (p = 0.03 from competing risk model). CONCLUSION Elucidation of a genomic signature for oligometastatic disease derived from non-invasive liquid biopsy appears feasible for NSCLC patients. Patients with the oligometastatic signature exhibited higher rates of early oligometastatic progression. Validation of this signature could lead to a biomarker that has the potential to direct local therapies in oligometastatic patients.
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Affiliation(s)
- A R Choi
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - R D'Agostino
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC
| | - M Farris
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - M Abdulhaleem
- Department of HospitalMedicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Y Wang
- Department of Molecular and Cellular Bioscience, Wake Forest University School of Medicine, Winston-Salem, NC
| | - M Smith
- Department of Molecular and Cellular Bioscience, Wake Forest University School of Medicine, Winston-Salem, NC
| | - J Ruiz
- Department of Internal Medicine, Section of Hematology and Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - T Lycan
- Department of Internal Medicine, Section of Hematology and Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - W Petty
- Department of Internal Medicine, Section of Hematology and Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - C K Cramer
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - S B Tatter
- Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC
| | - A Laxton
- Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC
| | - J White
- Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC
| | - J Su
- Department of Diagnostic Radiology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - C T Whitlow
- Department of Diagnostic Radiology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - F Xing
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - M D Chan
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC
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Han F, Wang Q, Su J. Preface for special issue on nonlinear dynamics modeling and control for brain science and brain-like intelligence. Cogn Neurodyn 2023; 17:1117-1118. [PMID: 37786653 PMCID: PMC10542058 DOI: 10.1007/s11571-023-09959-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Affiliation(s)
- Fang Han
- College of Information Science and Technology, Donghua University, Shanghai, China
| | - Qingyun Wang
- Department of Dynamics and Control, Beihang University, Beijing, China
| | - Jianzhong Su
- Department of Mathematics, University of Texas at Arlington, Arlington, USA
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Salunkhe RR, O'Sullivan B, Huang SH, Su J, Xu W, Hosni A, Waldron J, Irish J, de Almeida J, Witterick I, Montero E, Gilbert RW, Razak AA, Zhang L, Brown D, Goldstein D, Gullane P, Tong L, Hahn E. Dawn of Staging for Head and Neck Soft Tissue Sarcoma: Validation of the Novel 8 th Edition AJCC T Classification and Proposed Stage Groupings. Int J Radiat Oncol Biol Phys 2023; 117:S149. [PMID: 37784378 DOI: 10.1016/j.ijrobp.2023.06.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) After decades of stagnation, the 8th edition TNM (TNM8) introduced a new T classification for head and neck (HN) soft tissue sarcomas (STS). New size cutoffs of 2 and 4 cm define T1-3, and a novel T4 category is defined by local invasion of adjoining structures. These size cutoffs had been chosen arbitrarily to advance data collection in this unique disease site since literature showed approximately 70% of HN STS did not reach the previous size threshold (5 cm) for the existing T1 category. The definition of the TNM8 T categories also align with mucosal HN cancers. No stage grouping for HN STS was defined since this new classification required more data collection to derive stage groups. This study aims to validate the TNM8 T classification and to propose stage groupings. MATERIALS/METHODS Clinical data of all adult (>16 years) HN STS patients treated from 1988 - 2019 with curative intent in our tertiary cancer center were retrieved from a prospective database, and supplemented with chart review. As per TNM8, cutaneous angiosarcoma, embryonal and alveolar rhabdomyosarcoma, Kaposi sarcoma, and dermatofibrosarcoma protuberans were excluded due to their different behavior. Multivariate analysis (MVA) identified prognostic factors for overall survival (OS). Adjusted hazard ratios (AHR) and recursive partitioning analysis (RPA) were used to derive stage groupings. Stage grouping performance for OS was assessed and also compared against the existing TNM8 groups for non-HN STS. RESULTS A total of 221 patients (N1: 2; M1: 2) were included. Of the 219 M0 patients, 63% were males; median tumor size was 3.0 cm (range: 0.3-14.0); the proportion of TNM8 T1-T4 were 35%, 34%, 26%, and 5%, respectively. Median follow up was 5.9 years. Five-year OS was 79%. MVA confirmed the prognostic value of T category (T4 HR 7.73, 95% CI 3.62-16.5) and grade (G2/3 vs G1 HR 3.7, 95% CI 1.82-7.53), in addition to age (HR 1.03, 95% CI 1.01-1.04) (all p<0.001) for OS. AHR model derived T1-3_Grade 1 as stage 1; T1-3_Grade 2/3 as stage II; and T4_any Grade or any T_N1 as stage III (Table 1); the corresponding 5-year OS was 93%, 73%, and 38%, respectively. Both patients with M1 died within 1.5 years after diagnosis and M1 disease was designated stage IV. The AHR-grouping outperformed the RPA and non-HN TNM8 stage grouping for hazard consistency, hazard discrimination, percent variance explained, hazard difference, and sample size balance. CONCLUSION The novel T4 category introduced in TNM8 is associated with a >7 fold increased risk of death. Grade continues to be a critical prognostic factor in HN STS. The TNM8 HN STS T classifications have been validated, and the proposed new stage groupings with TNM8 incorporating grade have excellent performance for OS.
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Affiliation(s)
- R R Salunkhe
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - B O'Sullivan
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - S H Huang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - J Su
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - W Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Irish
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J de Almeida
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - I Witterick
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - E Montero
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - R W Gilbert
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A A Razak
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - L Zhang
- Mount Sinai Hospital, Toronto, ON, Canada
| | - D Brown
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - D Goldstein
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - P Gullane
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Tong
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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Barcelona MVN, Huang SH, Su J, Tong L, Bratman SV, Cho J, Hahn E, Hope AJ, Hosni A, Kim J, McPartlin A, O'Sullivan B, Ringash JG, Siu LL, Spreafico A, Eng L, Yao CM, Xu W, Waldron J, Tsai CJ. Outcomes after Contemporary Definitive Radiotherapy Alone in Patients with TNM-7 Stage III/IV Head and Neck Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:e565-e566. [PMID: 37785730 DOI: 10.1016/j.ijrobp.2023.06.1889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study was undertaken to determine outcomes and prognostic factors of definitive intensity-modulated radiotherapy (IMRT) alone for patients with TNM-7 stage III/IV HNSCC who did not receive concurrent chemotherapy. MATERIALS/METHODS We evaluated TNM-7 stage III/IV HNSCC patients treated with definitive IMRT alone in our institution from 2004-2019. Patients were reclassified according to TNM-8 staging. Stage II HPV+ oropharyngeal cancers (OPC) were subdivided into T1-2N2 and T3N0-2 for analysis. The rationale for chemotherapy omission was obtained retrospectively from clinical documentation. Recurrence-free survival (RFS) and overall survival (OS) were estimated stratified by HPV status (determined by p16 staining, sometimes supplemented by HPV DNA testing). Multivariable analysis (MVA) identified prognostic factors for RFS and OS, taking into account stage and IMRT regimen. Age, performance status, and smoking were also examined for OS. RESULTS A total of 1083 patients were included (460 HPV+ and 623 HPV-). Reasons for omission of chemotherapy were: age >70 years or frailty (n = 551, 51%), cisplatin contraindication (n = 241, 22%), patient refusal (n = 106, 10%), and clinician's decision (n = 185, 17%). Median age was 67 years for HPV+ and 70 years for HPV- cohorts. IMRT mostly utilized altered fractionation regimens (n = 1016, 94%): moderately accelerated (Acc) (70 Gy/35 fractions [f]/6 weeks [w], 55%), hypofractionated (Hypo) (60 Gy/25f/5w, 14%), and hyperfractionated-accelerated (Hyper) (64 Gy/40f/4w, 25%). Median follow-up was 5 years. Five-year RFS and OS for HPV+ TNM-8 stage I/T1-2N2/T3N0-N2/III were 89%/86%/76%/52% and 83%/80%/64%/33% respectively (p<0.01). The same outcomes for HPV- TNM-8 stage III/IVA/IVB were 58%/52%/39% and 47%/27%/13%, respectively (p<0.01). MVA confirmed that HPV+ T3N0-2 subset within stage II and stage III (vs stage I) had lower RFS, and HPV- stage IVA and IVB (vs stage III) carried worse RFS and OS (Table). CONCLUSION Despite the retrospective nature and inherent selection bias, this large single institutional study shows that altered fractionated IMRT alone is an acceptable alternative for elderly, frail or cisplatin ineligible patients with HPV+ stage I/IIA (T1-2N2) OPC. Patients with HPV+ T3N0-2/stage III OPC and HPV- stage III/IV HNSCC have poor outcomes with IMRT alone and may benefit from alternative strategies.
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Affiliation(s)
- M V N Barcelona
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - S H Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Su
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Tong
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - S V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A McPartlin
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - B O'Sullivan
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J G Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L L Siu
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Spreafico
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Eng
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C M Yao
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - W Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C J Tsai
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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Shiau C, Cao J, Gregory M, Kim Y, He S, Reeves J, Wang S, Lester NA, Su J, Wang PL, Beechem J, Hong TS, Wo JY, Ting D, Hemberg M, Hwang WL. Intercellular Mechanisms of Therapeutic Resistance at the Tumor-Stromal Interface Using Ultra High-Plex Single-Cell Spatial Transcriptomics and Genetically-Engineered Tumoroids. Int J Radiat Oncol Biol Phys 2023; 117:S101-S102. [PMID: 37784270 DOI: 10.1016/j.ijrobp.2023.06.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) There is a major gap in knowledge regarding how intercellular interactions in the tumor microenvironment (TME) mediate therapeutic resistance. Achievement of this goal has been limited by a lack of (1) spatial context in dissociated single-cell methods; (2) single-cell resolution in spatial profiling approaches; (3) high quality data and yield with FFPE patient specimens; and (4) computational methods for ligand-receptor analyses that consider both gene expression and spatial coordinates. MATERIALS/METHODS We developed an innovative spatial biology paradigm that combines cutting-edge experimental and computational methods to enable high-resolution, spatially-guided discovery of critical mediators of therapeutic resistance. We applied this approach to dissect the single-cell spatial transcriptomic landscape of untreated vs. chemoradiotherapy-treated primary human pancreatic ductal adenocarcinoma (PDAC; n = 21) using ultra-high plex spatial molecular imaging (SMI) optimized for high-sensitivity, subcellular detection of up to 6000 gene transcripts in FFPE sections-an order of magnitude greater than contemporary methods. RESULTS We recovered over 1,000,000 high-quality single cells in situ representing more than 20 distinct cell types, including epithelial, immune, endothelial, endocrine, and diverse stromal cells. We developed an optimal transport-based computational method to infer cell-cell communication at the cancer-stromal interface. Treatment with chemoradiotherapy was associated with the largest increase in fibroblast-malignant interactions. Comparing the SMI data with orthogonal single-nucleus RNA-sequencing and digital spatial profiling data, we identified CLCF1-CNTFR as the fibroblast-malignant interaction most associated with resistance to chemoradiotherapy in PDAC. CLCF1 is a gp130-family cytokine that activates Jak-STAT signaling and acts as a potent neurotrophic factor. Notably, the CLCF1-CNTRF (fibroblast-malignant) interaction has prominent pro-oncogenic effects in lung adenocarcinoma and an engineered CNTFR decoy receptor with therapeutic potential has been developed. To functionally validate the role of the CLCF1-CNTFR (fibroblast-malignant) interaction in mediating resistance to cytotoxic therapy, we created CRISPR-engineered cancer-fibroblast tumoroids and modulated expression of this ligand-receptor pair. Pancreatic cancer cell viability in the presence of 5-fluorouracil was better maintained with increased CLCF1-CNTFR signaling. CONCLUSION In this study, we integrated ultra high-plex single-cell spatial transcriptomics, optimal transport ligand-receptor predictions, and genetically-engineered stromal tumoroids to identify and validate CLCF1-CNTFR as an important intercellular mechanism of resistance to chemoradiotherapy in PDAC-pioneering a paradigm for translating single-cell spatial biology to clinical oncology.
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Affiliation(s)
- C Shiau
- Massachusetts General Hospital, Boston, MA
| | - J Cao
- Brigham and Women's Hospital, Boston, MA
| | - M Gregory
- Nanostring Technologies, Seattle, WA
| | - Y Kim
- Nanostring Technologies, Seattle, WA
| | - S He
- Nanostring Technologies, Seattle, WA
| | - J Reeves
- Nanostring Technologies, Seattle, WA
| | - S Wang
- Columbia University, New York, NY
| | - N A Lester
- Massaschusetts General Hospital, Boston, MA
| | - J Su
- Massachusetts General Hospital, BOSTON, MA
| | - P L Wang
- Massaschusetts General Hospital, Boston, MA
| | - J Beechem
- Nanostring Technologies, Seattle, WA
| | - T S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - J Y Wo
- Newton-Wellesley Hospital, Newton, MA
| | - D Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - M Hemberg
- Brigham and Women's Hospital, Boston, MA
| | - W L Hwang
- Broad Institute of MIT and Harvard, Cambridge, MA
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Johnny C, Huang SH, Su J, Bratman S, Cho J, Hahn E, Hosni A, Hope A, Kim J, O'Sullivan B, Ringash JG, Waldron J, Spreafico A, Eng L, Goldstein D, Tong L, Xu W, McPartlin A. The Prognostic and Predictive Value of Pre-Treatment Total Lymphocyte Count in HPV+ Oropharyngeal Carcinoma Receiving Definitive (Chemo-) Radiation. Int J Radiat Oncol Biol Phys 2023; 117:e591-e592. [PMID: 37785789 DOI: 10.1016/j.ijrobp.2023.06.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Evidence of prognostic importance of pre-radiotherapy (RT) total lymphocyte counts (TLC) and interaction with addition of cisplatin (CRT) in HPV-positive oropharyngeal carcinoma (HPV+OPC) is conflicting. Recent data suggest patients with high TLC may not benefit from the addition of chemotherapy (Price et al, JCO 2022). We assess the prognostic and predictive value of TLC in a large single center HPV+OCP cohort. MATERIALS/METHODS All HPV+OPC patients treated at a single academic center with definitive RT/CRT between 2005-2018 were included. Pre-treatment TLC up to 6 weeks prior to RT start were considered. Multivariable analysis (MVA) was applied to assess the prognostic importance of TLC (continuous variable), adjusted for age, gender, performance status, TNM-8 stage, and smoking status in the CRT and RT subgroups. The actuarial rates of locoregional control (LRC), distant control (DC), and overall survival (OS) were calculated using Kaplan-Meier and competing risk methods, stratified by low vs high TLC (determined using Contal and O'Quigley method for optimal cutoff). RESULTS Among 1153 eligible patients, 707 (61%) were treated with CRT. Median age was 59.7 (range 22.7-92.2) years. 526 patients were (46%) TNM-8 stage I, 366 (32%) stage II and 261 (23%) stage III. Median TLC was 1.6 x 109/L (range 0.1-8.5). Median follow-up was 5.5 years. On MVA, TLC was prognostic for patients receiving CRT (OS [adjusted hazard ration (aHR) 0.55 (0.38-0.79), p = 0.002], DC [aHR 0.57 (0.37-0.88), p = 0.011], LRC [aHR 0.57 (0.36-0.89), p = 0.014]) but not RT (OS [aHR 1.04 (0.82-1.31), p = 0.74], LRC [aHR 1.26 (0.86-1.85), p = 0.23], DC [aHR 0.87 (0.64-1.19), p = 0.4)]. The optimal TLC cut-off for OS with CRT was 1.9 x 109/L. Low vs high TLC patients receiving CRT had significantly inferior 5-year DC (87% vs 93%, p = 0.017) and OS (84% vs 90%, p = 0.026). The benefit of higher TLC was most evident in stage II disease (table 1). CRT vs RT improved OS for stage II/III disease at high and low TLC. CONCLUSION Pre-treatment TLC is prognostic in a large cohort of HPV+OPC patients receiving CRT but not RT alone. Further investigation of the interaction of cisplatin and immune response during RT is warranted. The omission of chemotherapy based on TLC is not supported.
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Affiliation(s)
- C Johnny
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - S H Huang
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - J Su
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - S Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Center/University of Toronto, Toronto, ON, Canada
| | - J Cho
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hope
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - J Kim
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - B O'Sullivan
- CHUM (The University of Montreal Hospital Centre), Montreal, QC, Canada
| | - J G Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Spreafico
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Eng
- Department of Medical Oncology and Haematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - D Goldstein
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - L Tong
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - W Xu
- Department of Biostatistics, Princess Margaret Cancer Center/University of Toronto, Toronto, ON, Canada
| | - A McPartlin
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
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Zhao N, Zhang Z, Wang Q, Li L, Wei Z, Chen H, Zhou M, Liu Z, Su J. DNA damage repair profiling of esophageal squamous cell carcinoma uncovers clinically relevant molecular subtypes with distinct prognoses and therapeutic vulnerabilities. EBioMedicine 2023; 96:104801. [PMID: 37725855 PMCID: PMC10518355 DOI: 10.1016/j.ebiom.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/20/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND DNA damage repair (DDR) is a critical process that maintains genomic integrity and plays essential roles at both the cellular and organismic levels. Here, we aimed to characterize the DDR profiling of esophageal squamous cell carcinoma (ESCC), investigate the prognostic value of DDR-related features, and explore their potential for guiding personalized treatment strategies. METHODS We analyzed bulk and single-cell transcriptomics data from 377 ESCC cases from our institution and other publicly available cohorts to identify major DDR subtypes. The heterogeneity in cellular and functional properties, tumor microenvironment (TME) characteristics, and prognostic significance of these DDR subtypes were investigated using immunogenomic analysis and in vitro experiments. Additionally, we experimentally validated a combinatorial immunotherapy strategy using syngeneic mouse models of ESCC. FINDINGS DDR alteration profiling enabled us to identify two distinct DDR subtypes, DDRactive and DDRsilent, which exhibited independent prognostic values in locoregional ESCC but not in metastatic ESCC. The DDRsilent subtype was characterized by an inflamed but immune-suppressed microenvironment with relatively high immune cell infiltration, abnormal immune checkpoint expression, T-cell exhaustion, and enrichment of cancer-related pathways. Moreover, DDR subtyping indicates that BRCA1 and HFM1 are robust and independent prognostic factors in locoregional ESCC. Finally, we proposed and verified that the concomitant triggering of GITR or blockade of BTLA with PD-1 blockade or cisplatin chemotherapy represents effective combination strategies for high-risk locoregional ESCC tumors. INTERPRETATION Our discovery of DDR-based molecular subtypes will enhance our understanding of tumor heterogeneity and have significant clinical implications for the therapeutic and management strategies of locoregional ESCC. FUNDING This study was supported by the National Key R&D Program of China (2021YFC2501000, 2022YFC3401003), National Natural Science Foundation of China (82172882), the Beijing Natural Science Foundation (7212085), the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-018, 2021-I2M-1-067), the Fundamental Research Funds for the Central Universities (3332021091), and the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences (2019PT310027).
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Affiliation(s)
- Ning Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Zicheng Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, PR China
| | - Qiang Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Lin Li
- Department of Pathology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Zichao Wei
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China; Key Laboratory of Cancer and Microbiome, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China.
| | - Meng Zhou
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, PR China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China.
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, PR China.
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Hwang WL, Su J, Shiau C, Wang PL, Guo JA, Lester NA, Barth JL, Hoffman HI, Aguirre A, Hong TS, Wo JY, Ting D, Zheng L, Mino-Kenudson M, Jacks T. Molecular Mechanisms of Intratumoral Nerve Recruitment and Perineural Invasion Elucidated with Spatial Transcriptomics and CRISPR Activation. Int J Radiat Oncol Biol Phys 2023; 117:S21. [PMID: 37784453 DOI: 10.1016/j.ijrobp.2023.06.244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Perineural invasion (PNI) is an aggressive manifestation of tumor-nerve interactions associated with postoperative recurrence, metastasis, pain, and decreased survival. Hence, PNI is included in the staging criteria of several malignancies and often an indication for treatment intensification using adjuvant radiotherapy. However, the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown-hindering the development of new therapies targeting this key pathological process. Moreover, prior studies were limited by a lack of cell-type information, spatial context, and/or a fragmented focus on a small number of pathways. MATERIALS/METHODS Using pancreatic ductal adenocarcinoma (PDAC) as an exemplar given the exceptionally high frequency of PNI in this malignancy, we performed the first comprehensive, cell-type specific, and spatially resolved whole-transcriptome analysis of human PDAC to identify molecular mediators of tumor-nerve crosstalk and PNI. We constructed 12 custom tissue microarrays (TMAs) derived from matched malignant regions with and without tumor-nerve proximity (n = 288 cores). We performed whole-transcriptome digital spatial profiling (DSP) to independently determine mRNA abundance from the malignant, fibroblast, and nerve compartments through optical sectioning. RESULTS We mapped malignant subtypes we previously identified onto the spatial data and found strong (p<0.0001) positive nerve associations with the mesenchymal, basaloid, and neural-like progenitor subtypes and a negative nerve association with the classical subtype. Numerous genes expressed by malignant cells were enriched (e.g., MMP2, PLXND1, NRP1) or depleted (e.g., SEMA3B) in association with radial distance from nerves, including recapitulation of prior literature. To functionally explore these candidate mediators of tumor-nerve crosstalk, we derived genetically-engineered murine organoids (KrasLSL-G12D/+; Trp53FL/FL; Rosa26-dCas9-VPR) and transduced them with guide RNAs to overexpress subtype-specific transcription factors or candidate genes from the spatial analysis. We quantified (1) cancer cell invasion through extracellular matrix using cultured dorsal root ganglia (DRG) sensory neurons as the chemoattractant, and (2) the role of cancer-intrinsic signaling on nerve recruitment/outgrowth by applying conditioned media or exogenous proteins to cultured DRG sensory neurons and tracking their growth with live imaging. CONCLUSION Our results suggest that the mechanisms enabling cancer cells to recruit nerves into the tumor microenvironment are distinct from those facilitating perineural invasion. This study has transformed our understanding of how cancer cells and the peripheral nervous system collaborate to promote tumor growth, survival, and dissemination, and is now guiding prioritization of therapeutic strategies that synergize with adjuvant radiotherapy in the burgeoning field of cancer neuroscience.
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Affiliation(s)
- W L Hwang
- Harvard Medical School / Massachusetts General Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - J Su
- Massachusetts General Hospital, BOSTON, MA
| | - C Shiau
- Massachusetts General Hospital, Boston, MA
| | - P L Wang
- Massaschusetts General Hospital, Boston, MA
| | - J A Guo
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - N A Lester
- Massaschusetts General Hospital, Boston, MA
| | - J L Barth
- Massaschusetts General Hospital, Boston, MA
| | | | - A Aguirre
- Dana-Farber Cancer Institute, Boston, MA
| | - T S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - J Y Wo
- Newton-Wellesley Hospital, Newton, MA
| | - D Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - L Zheng
- Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - T Jacks
- Massachusetts Institute of Technology, Cambridge, MA
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Saha S, Huang SH, O'Sullivan B, Su J, Xu W, Hosni A, Waldron J, Irish J, de Almeida J, Witterick I, Monteiro E, Gilbert RW, Catton CN, Chung P, Brown D, Goldstein D, Razak AA, Gullane P, Hahn E. Outcomes of Head and Neck Cutaneous Angiosarcoma Treated in the IMRT Era. Int J Radiat Oncol Biol Phys 2023; 117:e620-e621. [PMID: 37785859 DOI: 10.1016/j.ijrobp.2023.06.2004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Clinical behavior, natural history, and varied presentations of cutaneous angiosarcomas of the head and neck region (HN), in conjunction with its rarity, have rendered standardization of treatment elusive. We aimed to assess outcomes and patterns of failure for patients treated with surgery and radiation (Sx+RT), and radiation alone (RT). MATERIALS/METHODS A retrospective review of all HN angiosarcoma patients amenable for upfront Sx or RT in our institution between 2004-2018 was completed. Generally, treatment included Sx when feasible, and RT for large or extensive/ill-defined tumors. Demographic, tumor characteristics, local (LC), regional (RC), distant control (DC), and overall survival (OS), as well as patterns (in-field, marginal, out-of-field) of local failure at 5-year were estimated. Univariate analysis (UVA) was conducted to assess association with outcomes. RESULTS A total of 33 patients were eligible (14 Sx+RT and 19 RT). Tumor locations were: scalp (16, 48%). face (n = 12, 36%), and overlapping (5, 15%). Lesion types were: nodular (n = 23, 70%), flat (n = 4, 12%) and mixed (n = 6, 18%). Tumor size was larger in the RT group (median: 10.00 vs 2.85 cm, p<0.01). RT and Sx+RT patients had otherwise similar baseline characteristics: median age 74.3; male 70%; and ECOG performance status ≤1 85%. RT dose fractionations ranged from 50-70 Gy in 25-35 fractions in the RT group and 50-66 Gy in 25-33 fractions in the Sx+RT group. Four (12%) patients received neoadjuvant chemotherapy. Median follow up was 5.5 years. Five-year LC, RC, DC, and OS for RT vs Sx+RT groups were 68% vs 85% (p = 0.28); 95% vs 86% (p = 0.89); 79% vs 86% (p = 0.39); and 45% vs 55% (p = 0.71), respectively. The in-field/marginal/out-of-field local failure rate at 5 years were 16% vs 7% (p = 0.46), 26% vs 15% (p = 0.41), and 13% vs 0% (p = 0.24) for the RT vs Sx+RT groups, respectively. UVA showed that scalp location and ulceration/bleeding were strong adverse features for OS. Bone invasion was significantly associated with lower DC (Table). Lesion type (nodular/flat/mixed), tumor size, and treatment type (Sx+RT vs RT), were not significantly associated with LC or pattern of local failure. CONCLUSION Scalp tumors, as compared to face, portended poorer prognosis, and ulceration/bleeding and bone invasion were associated with increased distant metastases. Sx+RT was the preferred treatment modality when possible and typically used for smaller and better defined tumors. RT was reserved for larger and extensive/ill-defined disease; despite this, in the IMRT era, RT achieves reasonable rates of control, markedly superior to historical series.
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Affiliation(s)
- S Saha
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - S H Huang
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - B O'Sullivan
- CHUM (The University of Montreal Hospital Centre), Montreal, QC, Canada
| | - J Su
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - W Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - J Irish
- Department of Otolaryngology - Head & Neck Surgery, University Health Network-University of Toronto, Toronto, ON, Canada
| | - J de Almeida
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - I Witterick
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - E Monteiro
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, ON, Canada
| | - R W Gilbert
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - C N Catton
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - P Chung
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - D Brown
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - D Goldstein
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - A A Razak
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - P Gullane
- Department of Otolaryngology-Head & Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - E Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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Tu W, Zheng C, Zheng Y, Feng Z, Lin H, Jiang Y, Chen W, Chen Y, Lee Y, Su J, Zheng W. The investigation of interaction and chaperon-like activity of α-synuclein as a protein in pathophysiology of Parkinson's disease upon direct interaction with tectorigenin. Int J Biol Macromol 2023; 249:125702. [PMID: 37414324 DOI: 10.1016/j.ijbiomac.2023.125702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Analyzing the therapeutic potential of a therapeutic biomolecule requires an understanding of how it may interact with proteins and modify their corresponding functions. α-Synuclein is a protein which is widely involved in the pathogenesis of Parkinson's disease (PD) and shows chaperon-like activity. We have selected tectorigenin, a most common methoxyisoflavone extracted from plants, among therapeutic bioactive molecules that are documented to have different therapeutic effects. Herein, we aimed to explore how tectorigenin interacts with α-synuclein in vitro by mimicking the physiological environment. Spectroscopic as well as theoretical studies including molecular docking simulation, were used to examine the effects of tectorigenin on the conformation and dynamics of α-synuclein. It was shown that tectorigenin is able to quench the protein emission spectra relied on a mixed static-dynamic quenching mechanism. Furthermore, it was displayed that tectorigenin binding to α-synuclein leads to microenvironmental changes in the tertiary structure of protein, however the protein's secondary structure was almost unchanged. It was also deduced that tectorigenin results in thermal stability of α-synuclein structure, evidenced by less perturbation of α-synuclein secondary structure following elevation of temperature in the presence of tectorigenin relative to that of free form. Molecular docking simulation demonstrated that non-covalent reactions, mainly hydrogen bonds, had a key role in the interaction and stabilization of α-synuclein in the presence of tectorigenin. Moreover, chaperon-like activity of α-synuclein was improved in the presence of tectorigenin against two model proteins, βL-crystallin and catalase. The findings showed that tectorigenin can lead to stabilization of α-synuclein, which may be used as a therapeutic agent in prevention of neurodegenerative diseases.
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Affiliation(s)
- Wenzhan Tu
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Cheng Zheng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yuyin Zheng
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Zhenhua Feng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Haiyan Lin
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yiwei Jiang
- Alberta Institute, Wenzhou Medical University, Wenzhou 325000, China
| | - WangChao Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yuhan Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Lee
- Second affiliation of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jianzhong Su
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.
| | - Wu Zheng
- Rehabilitation Medicine Center, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Integrative & Optimized Medicine Research Center, China-USA Institute for Acupuncture and Rehabilitation, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
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Ma Y, Deng C, Zhou Y, Zhang Y, Qiu F, Jiang D, Zheng G, Li J, Shuai J, Zhang Y, Yang J, Su J. Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data. Cell Genom 2023; 3:100383. [PMID: 37719150 PMCID: PMC10504677 DOI: 10.1016/j.xgen.2023.100383] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/26/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Advances in single-cell RNA sequencing (scRNA-seq) techniques have accelerated functional interpretation of disease-associated variants discovered from genome-wide association studies (GWASs). However, identification of trait-relevant cell populations is often impeded by inherent technical noise and high sparsity in scRNA-seq data. Here, we developed scPagwas, a computational approach that uncovers trait-relevant cellular context by integrating pathway activation transformation of scRNA-seq data and GWAS summary statistics. scPagwas effectively prioritizes trait-relevant genes, which facilitates identification of trait-relevant cell types/populations with high accuracy in extensive simulated and real datasets. Cellular-level association results identified a novel subpopulation of naive CD8+ T cells related to COVID-19 severity and oligodendrocyte progenitor cell and microglia subsets with critical pathways by which genetic variants influence Alzheimer's disease. Overall, our approach provides new insights for the discovery of trait-relevant cell types and improves the mechanistic understanding of disease variants from a pathway perspective.
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Affiliation(s)
- Yunlong Ma
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Yijun Zhou
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Fei Qiu
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Dingping Jiang
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Gongwei Zheng
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jingjing Li
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jianwei Shuai
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Yan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310012, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
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Shi X, Xue Z, Ye K, Yuan J, Zhang Y, Qu J, Su J. Roles of non-coding RNAs in eye development and diseases. Wiley Interdiscip Rev RNA 2023; 14:e1785. [PMID: 36849659 DOI: 10.1002/wrna.1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/17/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
The prevalence of ocular disorders is dramatically increasing worldwide, especially those that cause visual impairment and permanent loss of vision, including cataract, glaucoma, age-related macular degeneration, and diabetic retinopathy. Extensive evidence has shown that ncRNAs are key regulators in various biogenesis and biological functions, controlling gene expression related to histogenesis and cell differentiation in ocular tissues. Aberrant expression and function of ncRNA can lead to dysfunction of visual system and mediate progression of eye disorders. Here, we mainly offer an overview of the role of precise modulation of ncRNAs in eye development and function in patients with eye diseases. We also highlight the challenges and future perspectives in conducting ncRNA studies, focusing specifically on the role of ncRNAs that may hold expanded promise for their diagnostic and therapeutic applications in various eye diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Xinrui Shi
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhengbo Xue
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kaicheng Ye
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian Yuan
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Yan Zhang
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jia Qu
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
- Institute of PSI Genomics, Zhejiang, China
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Zhang J, Hou W, Zhao Q, Xiao S, Linghu H, Zhang L, Du J, Cui H, Yang X, Ling S, Su J, Kong Q. Deep annotation of long noncoding RNAs by assembling RNA-seq and small RNA-seq data. J Biol Chem 2023; 299:105130. [PMID: 37543366 PMCID: PMC10498003 DOI: 10.1016/j.jbc.2023.105130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators in various biological processes. However, due to their low expression, their systematic characterization is difficult to determine. Here, we performed transcript annotation by a newly developed computational pipeline, termed RNA-seq and small RNA-seq combined strategy (RSCS), in a wide variety of cellular contexts. Thousands of high-confidence potential novel transcripts were identified by the RSCS, and the reliability of the transcriptome was verified by analysis of transcript structure, base composition, and sequence complexity. Evidenced by the length comparison, the frequency of the core promoter and the polyadenylation signal motifs, and the locations of transcription start and end sites, the transcripts appear to be full length. Furthermore, taking advantage of our strategy, we identified a large number of endogenous retrovirus-associated lncRNAs, and a novel endogenous retrovirus-lncRNA that was functionally involved in control of Yap1 expression and essential for early embryogenesis was identified. In summary, the RSCS can generate a more complete and precise transcriptome, and our findings greatly expanded the transcriptome annotation for the mammalian community.
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Affiliation(s)
- Jiaming Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Songling Xiao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hongye Linghu
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lixin Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiawei Du
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hongdi Cui
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xu Yang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shukuan Ling
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Jianzhong Su
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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Wu W, Hu A, Xu H, Su J. LincRNA-EPS Alleviates Inflammation in TMJ Osteoarthritis by Binding to SRSF3. J Dent Res 2023; 102:1141-1151. [PMID: 37464762 DOI: 10.1177/00220345231180464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Temporomandibular joint osteoarthritis (TMJOA) is a common inflammatory disease that can cause pain, cartilage degradation, and subchondral bone loss. However, the key regulatory factors and new targets for the treatment of TMJOA have yet to be determined. Long noncoding RNAs (lncRNAs) have shown remarkable potential in regulating tissue homeostasis and disease development. The long intergenic RNA-erythroid prosurvival (lincRNA-EPS) is reported to be an effective inhibitor of inflammation, but its role in TMJOA is unexplored. Here, we found that lincRNA-EPS is downregulated and negatively correlated with inflammatory factors in the condyles of TMJOA mice. LincRNA-EPS knockout aggravated inflammation and tissue destruction after TMJOA modeling. The in vitro studies confirmed that loss of lincRNA-EPS facilitated inflammatory factor expression in condylar chondrocytes, while recovered expression of lincRNA-EPS showed anti-inflammatory effects. Mechanistically, RNA sequencing revealed that the inflammatory response pathway nuclear factor-kappa B (NF-κB) was mostly affected by lincRNA-EPS deficiency. Moreover, lincRNA-EPS was proved to effectively bind to serine/arginine-rich splicing factor 3 (SRSF3) and inhibit its function in pyruvate kinase isoform M2 (PKM2) formation, thus restraining the PKM2/NF-κB pathway and the expression of inflammatory factors. In addition, local injection of the lincRNA-EPS overexpression lentivirus significantly alleviated inflammation, cartilage degradation, and subchondral bone loss in TMJOA mice. Overall, lincRNA-EPS regulated the inflammatory process of condylar chondrocytes by binding to SRSF3 and showed translational application potential in the treatment of TMJOA.
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Affiliation(s)
- W Wu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - A Hu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - H Xu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - J Su
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
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Hou W, Zong M, Zhao Q, Yang X, Zhang J, Liu S, Li X, Chen L, Tang C, Wang X, Dong Z, Gao M, Su J, Kong Q. Network characterization linc1393 in the maintenance of pluripotency provides the principles for lncRNA targets prediction. iScience 2023; 26:107469. [PMID: 37588167 PMCID: PMC10425947 DOI: 10.1016/j.isci.2023.107469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/07/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. However, the functional mechanisms have not yet been fully explored. Characterizing the interactions of lncRNAs with chromatin is central to determining their functions but, due to precise and efficient approaches lacking, our understanding of their functional mechanisms has progressed slowly. In this study, we demonstrate that a nuclear lncRNA linc1393 maintains mouse ESC pluripotency by recruiting SET1A near its binding sites, to establish H3K4me3 status and activate the expression of specific pluripotency-related genes. Moreover, we characterized the principles of lncRNA-chromatin interaction and transcriptional regulation. Accordingly, we developed a computational framework based on the XGBoost model, LncTargeter, to predict the targets of a given lncRNA, and validated its reliability in various cellular contexts. Together, these findings elucidate the roles and mechanisms of lncRNA on pluripotency maintenance, and provide a promising tool for predicting the regulatory networks of lncRNAs.
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Affiliation(s)
- Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ming Zong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xu Yang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiaming Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shuanghui Liu
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuanwen Li
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijun Chen
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chun Tang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyu Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhixiong Dong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meiling Gao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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Wang R, Su J, Fan XK, Zhou JY, Yang J, Wu M, Du WC. [Epidemiological characteristics of falls in the elderly in Jiangsu from 2006 to 2021]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1209-1215. [PMID: 37661611 DOI: 10.3760/cma.j.cn112338-20221109-00955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Objective: To understand the epidemiological characteristics and influencing factors of elderly unintentional fall-related injuries (EUFI) in Jiangsu from 2006 to 2021 and provide a scientific basis for the prevention of falls in the elderly and the formulation of related policies. Methods: Data on EUFI was collected from the first diagnosed cases in the injury surveillance hospitals in Jiangsu from 2006 to 2021, and epidemiological characteristics of injuries were analyzed. logistic regression was performed to identify the risk factors for EUFI. Results: The number of EUFI increased from 2006 to 2021, ranked as the first cause of elderly unintentional injuries during these years. The proportion of EUFI among elderly unintentional injuries increased in the same period. The male-to-female ratio is 1∶1.4. Falls mainly occurred during 8:00-10:00 am (32.7%). The most common place where falls occurred was at home (63.6%). From 2006 to 2014, leisure activities (62.1%), housework/study (23.1%), and work (5.2%) were the top three activities when injuries occurred. During 2015-2021, leisure activities (41.7%), housework/study (22.6%) and walking (20.5%) were the top three activities when injuries occurred. The major fall-related injuries were fractures (39.9%), with the injured parts at low limbs (32.5%), of which most were mild injuries (60.3%), and the primary outcome was hospitalization after treatment (74.1%). logistic regression showed that the risk factors of EUFI were female, old age, immigrants, winter, public residence, housework/study, and leisure activities. Higher education, occupation of household and production and transportation equipment operators were protective factors (all P<0.05). Conclusions: Fall is the leading cause of unintentional injuries in the elderly in Jiangsu, especially the elderly female population. Corresponding measures should be taken to prevent and intervene in falls in the elderly in the community according to the distribution characteristics.
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Affiliation(s)
- R Wang
- School of Public Health, Southeast University, Nanjing 210009, China
| | - J Su
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - X K Fan
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Y Zhou
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Yang
- Department of Child and Adolescent Health Promotion, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - M Wu
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - W C Du
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Zhou M, Luo X, Zhou QL, Zhou WH, Zheng R, Zhang YN, Wu XF, Wu S, Su J, Xiong GW, Cheng Y, Li YT, Zhang PP, Zhang K, Dai M, Huang XK, Shi ZH, Tao J, Zhou YQ, Feng PY, Chen ZG, Yang QT. [Diagnosis and treatment procedures and health management for patients with hereditary angioedema]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1280-1285. [PMID: 37574324 DOI: 10.3760/cma.j.cn112150-20230509-00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
As a recognized rare and highly fatal disease, hereditary angioedema (HAE) is difficult to diagnose and characterized by recurrent edema involving the head, limbs, genitals and larynx, etc. Diagnosis of HAE is not difficult. However, low incidence and lack of clinical characteristics lead to difficulty of doctors on timely diagnosis and correct intervention for HAE patients. Therefore, it is crucial to improve the awareness of this disease and prevent its recurrence. for HAE patients. In view of absent cognition of doctors and the general public on HAE, patients often suffer from sudden death or become disabled due to laryngeal edema which cannot be treated in time. Thus, based on the Internet mobile terminal platform, the team set up an all-day rapid emergency response system which is provided for HAE patients by setting up "one-click help". The aim is to offer optimization on overall management of HAE and designed the intelligent follow-up management to provide timely assistance and specialized suggestion for patients with acute attacks.
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Affiliation(s)
- M Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - X Luo
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Q L Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - W H Zhou
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - R Zheng
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Y N Zhang
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - X F Wu
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - S Wu
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - J Su
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - G W Xiong
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y Cheng
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y T Li
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - P P Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - K Zhang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - M Dai
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - X K Huang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Z H Shi
- Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - J Tao
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Y Q Zhou
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Respiratory and Intensive Care, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - P Y Feng
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Dermatology and Cosmetic Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Z G Chen
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Q T Yang
- Department of Allergy, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China Department of Otolaryngology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
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Chen Z, Li C, Zhou Y, Yao Y, Liu J, Wu M, Su J. Liquid biopsies for cancer: From bench to clinic. MedComm (Beijing) 2023; 4:e329. [PMID: 37492785 PMCID: PMC10363811 DOI: 10.1002/mco2.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Over the past two decades, liquid biopsy has been increasingly used as a supplement, or even, a replacement to the traditional biopsy in clinical oncological practice, due to its noninvasive and early detectable properties. The detections can be based on a variety of features extracted from tumor‑derived entities, such as quantitative alterations, genetic changes, and epigenetic aberrations, and so on. So far, the clinical applications of cancer liquid biopsy mainly aimed at two aspects, prediction (early diagnosis, prognosis and recurrent evaluation, therapeutic response monitoring, etc.) and intervention. In spite of the rapid development and great contributions achieved, cancer liquid biopsy is still a field under investigation and deserves more clinical practice. To better open up future work, here we systematically reviewed and compared the latest progress of the most widely recognized circulating components, including circulating tumor cells, cell-free circulating DNA, noncoding RNA, and nucleosomes, from their discovery histories to clinical values. According to the features applied, we particularly divided the contents into two parts, beyond epigenetics and epigenetic-based. The latter was considered as the highlight along with a brief overview of the advances in both experimental and bioinformatic approaches, due to its unique advantages and relatively lack of documentation.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Chenghao Li
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
| | - Yue Zhou
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Yinghao Yao
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Min Wu
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
| | - Jianzhong Su
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
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Chen YJ, Qin Y, Yu H, Zhu Z, Shen C, Lu Y, Cheng TT, Zhang N, Gu SJ, Zhou JY, Wu M, Su J. [A prospective cohort study of long-term fasting blood glucose variability and risk of mortality in patients with type 2 diabetes]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1099-1105. [PMID: 37482713 DOI: 10.3760/cma.j.cn112338-20221226-01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Objective: To investigate the association between long-term fasting blood glucose (FPG) variability and all-cause mortality in patients with type 2 diabetes. Methods: A total of 7 174 type 2 diabetic patients included in National Basic Public Health Service Program in Changshu of Jiangsu Province were recruited as participants. Long-term glucose variability was assessed using standard deviation (SD), coefficient of variation (CV), average real variability (ARV), and variability independent of the mean (VIM) across FPG measurements at the more than three visits. Death information were mainly obtained from the death registry system in Jiangsu. Then Cox proportional hazards regression models were used to estimate the associations of four variability indicators and all-cause mortality's hazard ratios (HRs) and their 95%CIs. Results: Among 55 058.50 person-years of the follow-up, the mean follow-up time was 7.67 years, and 898 deaths occurred during the follow-up period. After adjustment, compared with T1 group, the Cox regression model showed that HRs of T3 group in SD, CV, ARV and VIM were 1.24 (95%CI: 1.03-1.49), 1.20 (95%CI: 1.01-1.43), 1.28 (95%CI: 1.07-1.55) and 1.20 (95%CI:1.01-1.41), respectively. HRs of per 1 SD higher SD, CV, ARV and VIM were 1.13 (95%CI: 1.06-1.21), 1.08 (95%CI: 1.01-1.15), 1.05 (95%CI: 1.00-1.12) and 1.09 (95%CI: 1.02-1.16) for all-cause mortality, respectively. In the stratified analysis, age, gender, hypoglycemic agent and insulin uses had no effect on the above associations (all P for interaction >0.05). Conclusion: Long-term FPG glycemic variability was positively associated with the risk of all-cause mortality in type 2 diabetes patients.
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Affiliation(s)
- Y J Chen
- Department of Non-communicable Chronic Disease Prevention, Nanjing Municipal Center for Disease Control and Prevention, Nanjing 210003, China
| | - Y Qin
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - H Yu
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Z Zhu
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - C Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Y Lu
- Department of Non-communicable Chronic Disease Prevention, Suzhou Prefectural Center for Disease Control and Prevention, Suzhou 215004, China
| | - T T Cheng
- Department of Infectious Disease Control Division, Suzhou National New & Hi-Tech Industrial Development Zone (Huqiu District) Center for Disease Control and Prevention, Suzhou 215163, China
| | - N Zhang
- Changshu County Center for Disease Control and Prevention, Changshu 215500, China
| | - S J Gu
- Department of Non-communicable Chronic Disease Prevention, Changshu County Center for Disease Control and Prevention, Changshu 215500, China
| | - J Y Zhou
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - M Wu
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Su
- Department of Non-communicable Chronic Disease Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Guo RP, Yang LY, Zhao JF, Su J. [Advance on cyclin D1 and CDK4 in cutaneous melanoma]. Zhonghua Bing Li Xue Za Zhi 2023; 52:767-770. [PMID: 37408419 DOI: 10.3760/cma.j.cn112151-20221230-01090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Affiliation(s)
- R P Guo
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Beijing 100191, China
| | - L Y Yang
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Beijing 100191, China
| | - J F Zhao
- Department of Pathology, Yan'an Branch of Peking University Third Hospital, Yan'an Traditional Chinese Medicine Hospital, Yan'an 716000,China
| | - J Su
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Beijing 100191, China Department of Pathology, Yan'an Branch of Peking University Third Hospital, Yan'an Traditional Chinese Medicine Hospital, Yan'an 716000,China
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Zhou M, Bao S, Gong T, Wang Q, Sun J, Li J, Lu M, Sun W, Su J, Chen H, Liu Z. The transcriptional landscape and diagnostic potential of long non-coding RNAs in esophageal squamous cell carcinoma. Nat Commun 2023; 14:3799. [PMID: 37365153 DOI: 10.1038/s41467-023-39530-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a deadly cancer with no clinically relevant biomarkers for early detection. Here, we comprehensively characterized the transcriptional landscape of long non-coding RNAs (lncRNAs) in paired tumor and normal tissue specimens from 93 ESCC patients, and identified six key malignancy-specific lncRNAs that were integrated into a Multi-LncRNA Malignancy Risk Probability model (MLMRPscore). The MLMRPscore performed robustly in distinguishing ESCC from normal controls in multiple in-house and external multicenter validation cohorts, including early-stage I/II cancer. In addition, five candidate lncRNAs were confirmed to have non-invasive diagnostic potential in our institute plasma cohort, showing superior or comparable diagnostic accuracy to current clinical serological markers. Overall, this study highlights the profound and robust dysregulation of lncRNAs in ESCC and demonstrates the potential of lncRNAs as non-invasive biomarkers for the early detection of ESCC.
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Affiliation(s)
- Meng Zhou
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Siqi Bao
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Tongyang Gong
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Qiang Wang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Jie Sun
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Jiaqi Li
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China
| | - Minyi Lu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Wanyuan Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China
| | - Jianzhong Su
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, 325027, Wenzhou, P. R. China.
| | - Hongyan Chen
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
- Key Laboratory of Cancer and Microbiome, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, P. R. China.
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Yang MS, Fan XK, Su J, Yu H, Lu Y, Hua YJ, Pei P, Lyu J, Tao R, Zhou JY, Wu M. [Incidence of chronic obstructive pulmonary disease and risk factors in the Suzhou cohort]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:868-876. [PMID: 37380406 DOI: 10.3760/cma.j.cn112338-20221202-01033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Objective: To understand the incidence of chronic obstructive pulmonary disease (COPD) in the Suzhou cohort, and explore the risk factors for the development of COPD in Suzhou, and provide a scientific basis for COPD prevention. Methods: This study was based on the China Kadoorie Biobank project in Wuzhong District, Suzhou. After excluding individuals with airflow obstruction and self-reported chronic bronchitis, emphysema, or pulmonary heart disease at baseline, 45 484 individuals were finally included in the analysis. Cox proportional risk models were used to analyze risk factors of COPD and calculate hazard ratios and 95% confidence interval (CI) in the Suzhou cohort. The effect modifications of smoking on the association between other risk factors and COPD were evaluated. Results: Complete follow-up was available through December 31, 2017. Participants were followed up for a median of 11.12 years, and 524 individuals were diagnosed with COPD during the follow-up period; the incidence was 105.54 per 100 000 person-years. Multivariate Cox proportional risk regression models showed that age (HR=3.78, 95%CI:3.32-4.30), former smoking (HR=2.00, 95%CI:1.24-3.22), current smoking (<10 cigarettes/day, HR=2.14, 95%CI:1.36-3.35;≥10 cigarettes/day, HR=2.69, 95%CI:1.60-4.54), history of respiratory disease (HR=2.08, 95%CI:1.33-3.26), daily sleep duration ≥10 hours (HR=1.41, 95%CI:1.02-1.95) were associated with increased risk of COPD. However, education level of primary school and above (primary or junior high school, HR=0.65, 95%CI:0.52-0.81; high school and above, HR=0.54, 95%CI:0.33-0.87), consuming fresh fruit daily (HR=0.59, 95%CI:0.42-0.83) and consuming spicy food weekly (HR=0.71, 95%CI:0.53-0.94) were associated with reduced risk of COPD. Conclusions: The incidence of COPD is low in Suzhou. Older age, smoking, history of respiratory disease, and long sleep duration were risk factors for the development of COPD in the Suzhou cohort.
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Affiliation(s)
- M S Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - X K Fan
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Su
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - H Yu
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Y Lu
- Department of Non-communicable Chronic Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou 215004, China
| | - Y J Hua
- Department of Non-communicable Chronic Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou 215004, China
| | - P Pei
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China
| | - J Lyu
- Peking University Center for Public Health and Epidemic Preparedness & Response, Beijing 100191, China Department of Epidemiology and Health Statistics, School of Public Health, Peking University, Beijing 100191, China
| | - R Tao
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - J Y Zhou
- Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - M Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China Department of Non-communicable Chronic Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Xing S, Jiang S, Wang S, Lin P, Sun H, Peng H, Yang J, Kong H, Wang S, Bai Q, Qiu R, Dai W, Yuan J, Ma Y, Yu X, Yao Y, Su J. Association of mitochondrial DNA variation with high myopia in a Han Chinese population. Mol Genet Genomics 2023:10.1007/s00438-023-02036-y. [PMID: 37277661 PMCID: PMC10363046 DOI: 10.1007/s00438-023-02036-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
High myopia (HM), which is characterized by oxidative stress, is one of the leading causes of visual impairment and blindness across the world. Family and population genetic studies have uncovered nuclear-genome variants in proteins functioned in the mitochondria. However, whether mitochondrial DNA mutations are involved in HM remains unexplored. Here, we performed the first large-scale whole-mitochondrial genome study in 9613 HM cases and 9606 control subjects of Han Chinese ancestry for identifying HM-associated mitochondrial variants. The single-variant association analysis identified nine novel genetic variants associated with HM reaching the entire mitochondrial wide significance level, including rs370378529 in ND2 with an odds ratio (OR) of 5.25. Interestingly, eight out of nine variants were predominantly located in related sub-haplogroups, i.e. m.5261G > A in B4b1c, m.12280A > G in G2a4, m.7912G > A in D4a3b, m.94G > A in D4e1, m.14857 T > C in D4e3, m.14280A > G in D5a2, m.16272A > G in G2a4, m.8718A > G in M71 and F1a3, indicating that the sub-haplogroup background can increase the susceptible risk for high myopia. The polygenic risk score analysis of the target and validation cohorts indicated a high accuracy for predicting HM with mtDNA variants (AUC = 0.641). Cumulatively, our findings highlight the critical roles of mitochondrial variants in untangling the genetic etiology of HM.
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Affiliation(s)
- Shilai Xing
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyi Jiang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Haojun Sun
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hui Peng
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jiaying Yang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengte Kong
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sheng Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingshi Bai
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ruowen Qiu
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Jian Yuan
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Yunlong Ma
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou, 325024, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
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50
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Wang W, Lin P, Wang S, Zhang G, Chen C, Lu X, Zhuang Y, Su J, Wang H, Xu L. In-depth mining of single-cell transcriptome reveals the key immune-regulated loops in age-related macular degeneration. Front Mol Neurosci 2023; 16:1173123. [PMID: 37273909 PMCID: PMC10235539 DOI: 10.3389/fnmol.2023.1173123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/20/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Age-related macular degeneration (AMD), an ever-increasing ocular disease, has become one of the leading causes of irreversible blindness. Recent advances in single-cell genomics are improving our understanding of the molecular mechanisms of AMD. However, the pathophysiology of this multifactorial disease is complicated and still an ongoing challenge. To better understand disease pathogenesis and identify effective targets, we conducted an in-depth analysis of the single-cell transcriptome of AMD. Methods The cell expression specificity of the gene (CESG) was selected as an index to identify the novel cell markers. A computational framework was designed to explore the cell-specific TF regulatory loops, containing the interaction of gene pattern signatures, transcription factors regulons, and differentially expressed genes. Results Three potential novel cell markers were DNASE1L3 for endothelial cells, ABCB5 for melanocytes, and SLC39A12 for RPE cells detected. We observed a notable change in the cell abundance and crosstalk of fibroblasts cells, melanocytes, schwann cells, and T/NK cells between AMD and controls, representing a complex cellular ecosystem in disease status. Finally, we identified six cell type related and three disease-associated ternary loops and elaborated on the robust association between key immune-pathway and AMD. Discussion In conclusion, this study facilitates the optimization of screening for AMD-related receptor ligand pathways and proposes to further improve the interpretability of disease associations from single-cell data. It illuminated that immune-related regulation paths could be used as potential diagnostic markers for AMD, and in the future, also as therapeutic targets, providing insights into AMD diagnosis and potential interventions.
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Affiliation(s)
- Wencan Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Peng Lin
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Siyu Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Guosi Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chong Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Lu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Youyuan Zhuang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of PSI Genomics Co., Ltd., Wenzhou, China
| | - Hong Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
| | - Liangde Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou, China
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