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Chen Z, Wang X, Jin Z, Li B, Jiang D, Wang Y, Jiang M, Zhang D, Yuan P, Zhao Y, Feng F, Lin Y, Jiang L, Wang C, Meng W, Ye W, Wang J, Qiu W, Liu H, Huang D, Hou Y, Wang X, Jiao Y, Ying J, Liu Z, Liu Y. Deep learning on tertiary lymphoid structures in hematoxylin-eosin predicts cancer prognosis and immunotherapy response. NPJ Precis Oncol 2024; 8:73. [PMID: 38519580 PMCID: PMC10959936 DOI: 10.1038/s41698-024-00579-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Tertiary lymphoid structures (TLSs) have been associated with favorable immunotherapy responses and prognosis in various cancers. Despite their significance, their quantification using multiplex immunohistochemistry (mIHC) staining of T and B lymphocytes remains labor-intensive, limiting its clinical utility. To address this challenge, we curated a dataset from matched mIHC and H&E whole-slide images (WSIs) and developed a deep learning model for automated segmentation of TLSs. The model achieved Dice coefficients of 0.91 on the internal test set and 0.866 on the external validation set, along with intersection over union (IoU) scores of 0.819 and 0.787, respectively. The TLS ratio, defined as the segmented TLS area over the total tissue area, correlated with B lymphocyte levels and the expression of CXCL13, a chemokine associated with TLS formation, in 6140 patients spanning 16 tumor types from The Cancer Genome Atlas (TCGA). The prognostic models for overall survival indicated that the inclusion of the TLS ratio with TNM staging significantly enhanced the models' discriminative ability, outperforming the traditional models that solely incorporated TNM staging, in 10 out of 15 TCGA tumor types. Furthermore, when applied to biopsied treatment-naïve tumor samples, higher TLS ratios predicted a positive immunotherapy response across multiple cohorts, including specific therapies for esophageal squamous cell carcinoma, non-small cell lung cancer, and stomach adenocarcinoma. In conclusion, our deep learning-based approach offers an automated and reproducible method for TLS segmentation and quantification, highlighting its potential in predicting immunotherapy response and informing cancer prognosis.
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Affiliation(s)
- Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xiaobing Wang
- 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, China
| | - Zelin Jin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Bosen Li
- Department of General Surgery/Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanqiu Wang
- Departments of Pathology, International Peace Maternity and Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengping Jiang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Dandan Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Pei Yuan
- 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, China
| | - Yahui 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, China
| | - Feiyue Feng
- Thoracic Surgery Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Lin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Liping Jiang
- 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, China
| | - Chenxi Wang
- 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, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Wang
- Departments of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenqing Qiu
- Shanghai Xuhui Central Hospital, Shanghai, China
| | - Houbao Liu
- Shanghai Xuhui Central Hospital, Shanghai, China
- Department of General Surgery/Biliary Tract Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan Huang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Institute of Pathology, Fudan University, Shanghai, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuefei Wang
- Department of General Surgery/Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China
| | - Yuchen Jiao
- 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, China.
| | - Jianming Ying
- 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, 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, China.
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.
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Qian Z, Liang J, Huang R, Song W, Ying J, Bi X, Zhao J, Shi Z, Liu W, Liu J, Li Z, Zhou J, Huang Z, Zhang Y, Zhao D, Wu J, Wang L, Chen X, Mao R, Zhou Y, Guo L, Hu H, Ge D, Li X, Luo Z, Yao J, Li T, Chen Q, Wang B, Wei Z, Chen K, Qu C, Cai J, Jiao Y, Bao L, Zhao H. HBV integrations reshaping genomic structures promote hepatocellular carcinoma. Gut 2024:gutjnl-2023-330414. [PMID: 38395437 DOI: 10.1136/gutjnl-2023-330414] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/01/2024] [Indexed: 02/25/2024]
Abstract
OBJECTIVE Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), mostly characterised by HBV integrations, is prevalent worldwide. Previous HBV studies mainly focused on a few hotspot integrations. However, the oncogenic role of the other HBV integrations remains unclear. This study aimed to elucidate HBV integration-induced tumourigenesis further. DESIGN Here, we illuminated the genomic structures encompassing HBV integrations in 124 HCCs across ages using whole genome sequencing and Nanopore long reads. We classified a repertoire of integration patterns featured by complex genomic rearrangement. We also conducted a clustered regularly interspaced short palindromic repeat (CRISPR)-based gain-of-function genetic screen in mouse hepatocytes. We individually activated each candidate gene in the mouse model to uncover HBV integration-mediated oncogenic aberration that elicits tumourigenesis in mice. RESULTS These HBV-mediated rearrangements are significantly enriched in a bridge-fusion-bridge pattern and interchromosomal translocations, and frequently led to a wide range of aberrations including driver copy number variations in chr 4q, 5p (TERT), 6q, 8p, 16q, 9p (CDKN2A/B), 17p (TP53) and 13q (RB1), and particularly, ultra-early amplifications in chr8q. Integrated HBV frequently contains complex structures correlated with the translocation distance. Paired breakpoints within each integration event usually exhibit different microhomology, likely mediated by different DNA repair mechanisms. HBV-mediated rearrangements significantly correlated with young age, higher HBV DNA level and TP53 mutations but were less prevalent in the patients subjected to prior antiviral therapies. Finally, we recapitulated the TONSL and TMEM65 amplification in chr8q led by HBV integration using CRISPR/Cas9 editing and demonstrated their tumourigenic potentials. CONCLUSION HBV integrations extensively reshape genomic structures and promote hepatocarcinogenesis (graphical abstract), which may occur early in a patient's life.
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Affiliation(s)
- Zhaoyang Qian
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Junbo Liang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, 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, China
| | - Xinyu Bi
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenyu Shi
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wenjie Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianmei Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyu Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianguo Zhou
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen Huang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yefan Zhang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongbing Zhao
- Department of Pancreatic and Gastric Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liming Wang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Mao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanchi Zhou
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, 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, China
| | - Hanjie Hu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dazhuang Ge
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingchen Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiwen Luo
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinjie Yao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tengyan Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qichen Chen
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingzhi Wang
- Department of Pathology, 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, China
| | - Zhewen Wei
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kun Chen
- Department of Immunology, 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, China
| | - Chunfeng Qu
- Department of Immunology, 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, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- 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, China
| | - Yuchen Jiao
- 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, China
| | - Li Bao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- 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, China
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Chang J, Liu M, Liu C, Zhou S, Jiao Y, Sun H, Ji Y. Effects of vitamins and polyunsaturated fatty acids on cognitive function in older adults with mild cognitive impairment: a meta-analysis of randomized controlled trials. Eur J Nutr 2024:10.1007/s00394-024-03324-y. [PMID: 38300291 DOI: 10.1007/s00394-024-03324-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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
PURPOSE Vitamins and polyunsaturated fatty acids (PUFAs) have been studied extensively as safe and manageable nutrient interventions for mild cognitive impairment (MCI). The purpose of the current meta-analysis was to examine the effects of vitamins and PUFAs on cognition and to compare the effects of single and multiple nutrient subgroups in patients with MCI. METHODS Randomized controlled trials (RCTs) written in English and Chinese were retrieved from eight databases, namely, PubMed, CENTRAL, Embase, CINAHL, Web of Science, SinoMed, CNKI, and Wanfang Data, from their respective dates of inception until 16 July 2023. The quality of the included studies was assessed using the Cochrane Risk of Bias Tool 2.0. Meta-analyses were performed to determine the standardized mean differences (SMDs) in global cognitive function, memory function, attention, visuospatial skills, executive function, and processing speed between the supplement and control groups using 95% confidence intervals (CI) and I2. Prospero registration number: CRD42021292360. RESULTS Sixteen RCTs that studied different types of vitamins and PUFAs were included. The meta-analysis revealed that vitamins affected global cognitive function (SMD = 0.58, 95% CI = [0.20, 0.96], P = 0.003), memory function (SMD = 2.55, 95% CI = [1.01, 4.09], P = 0.001), and attention (SMD = 3.14, 95% CI = [1.00, 5.28], P = 0.004) in patients with MCI, and PUFAs showed effects on memory function (SMD = 0.65, 95% CI = [0.32, 0.99], P < 0.001) and attention (SMD = 2.98, 95% CI = [2.11, 3.84], P < 0.001). Single vitamin B (folic acid [FA]: SMD = 1.21, 95% CI = [0.87, 1.55]) supplementation may be more effective than multiple nutrients (FA and vitamin B12: SMD = 0.71, 95% CI = [0.41, 1.01]; and FA combined with docosahexaenoic acid [DHA]: SMD = 0.58, 95% CI = [0.34, 0.83]) in global cognitive function. CONCLUSIONS FA, vitamin B6, vitamin B12, and vitamin D may improve global cognitive function, memory function, and attention in patients with MCI. Eicosapentaenoic acid (EPA) and DHA may improve memory function and attention. We also noted that FA may exert a greater effect than a vitamin B combination (FA and vitamin B12) or the combination of FA and DHA. However, because of the low evidence-based intensity, further trials are necessary to confirm these findings.
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Affiliation(s)
- Jing Chang
- School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, Jiangsu, China
| | - Minhui Liu
- School of Nursing, Ningxia Medical University, 1160 Shengli South Street of Xingqing District, Yinchuan, 750001, China
| | - Chang Liu
- School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, Jiangsu, China
| | - Shiyu Zhou
- School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, Jiangsu, China
| | - Yuchen Jiao
- School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, Jiangsu, China
| | - Hongyu Sun
- School of Nursing, Peking University, 38 College Road, Haidian District, Beijing, 100191, China.
| | - Yan Ji
- School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, Jiangsu, China.
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Jiao Y, Jiang YH, Liu B, Mi RH, Bi LJ, Xu QX. [Analysis of the clinical characteristics of acute myeloid leukemia related to the treatment of hematological and solid tumors]. Zhonghua Zhong Liu Za Zhi 2024; 46:86-95. [PMID: 38246784 DOI: 10.3760/cma.j.cn112152-20231024-00249] [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: 01/23/2024]
Abstract
Objective: To compare and analyze the clinical characteristics of acute myeloid leukemia (AML) related to the treatment of hematological tumors and solid tumors. Methods: The laboratory and clinical data of 41 patients with treatment-related AML (t-AML) in the Department of Hematology, Henan Cancer Hospital from January 2014 to December 2021 were retrospectively analyzed, and they were divided into hematological tumor group and solid tumor group. Survival analysis was performed using the Kaplan-Meier method and Log rank test. Results: The median interval from the first tumor diagnosis to t-AML in 41 patients was 21.0 (16.5-46.0) months; 24 (58.5%) had abnormal expression of lymphoid antigen, 28 (68.3%) had abnormal karyotype, 18 cases (43.9%) were positive for fusion gene, and 28 cases (68.3%) were positive for gene mutation; the median recurrence-free survival (RFS) was 11.0 months, and the median overall survival (OS) was 11.5 months. The proportion of acute promyelocytic leukemia ([APL], 0.0, 0/13), complete response ([CR],18.2%, 2/11), median OS (4.5 months) and median RFS (2.5 months) of t-AML patients in the hematological tumor group were significantly lower than those in the solid tumor group (35.7%, 10/28; 68.0%, 17/25; not reach; not reach), but the proportion of M4 /M5 (93.2%,12/13) was significantly higher than that in the solid tumor group (53.6%,15/18; all P values<0.05). Through subgroup analysis, the proportion of patients with positive PML-RARa and good prognosis karyotypes in the solid tumor group (35.7%, 10/28; 46.4%, 13/28) was significantly higher than that in the hematological tumor group (0.0, 0/13; 0.0, 0/13; P<0.05), while the proportion of patients with intermediate karyotypes (42.9%, 12/28) was significantly lower than that in the hematological tumor group (84.6%, 11/13; P<0.05), the difference was statistically significant. The CR rate (90.0%, 9/10), median OS (not reach) and median RFS (not reach) in the t-APL group were higher than those in the t-AML (without t-APL) group (38.5%, 10/26; 6 months; 8 months; P<0.05). After excluding the effect of t-APL patients, there was no significant difference in the CR rate, median OS and median RFS between the solid tumor group (8; 9 months; not reach) and the hematological tumor group (2; 4 months; 2 months; P>0.05). Univariate analysis showed that the primary tumor belongs to hematological tumor was a common risk factor for OS and RFS in t-AML patients (P<0.10). Conclusions: Compared with patients with t-AML secondary to solid tumors, patients with t-AML secondary to hematological tumors have poorer treatment effects and poorer prognosis. After excluding the effect of t-APL patients, there are no significant differences in the treatment efficacy and prognosis between the two types of t-AML patients.
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Affiliation(s)
- Y Jiao
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou Key Laboratory of Digestive Tumor Markers, Zhengzhou 450008, China
| | - Y H Jiang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou Key Laboratory of Digestive Tumor Markers, Zhengzhou 450008, China
| | - B Liu
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou Key Laboratory of Digestive Tumor Markers, Zhengzhou 450008, China
| | - R H Mi
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - L J Bi
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Q X Xu
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou Key Laboratory of Digestive Tumor Markers, Zhengzhou 450008, China
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Jiao Y, Xu R, Xiao W, Wang Y, Dong SQ. [Femtosecond laser assisted cataract surgery in a complicated cataract patient with reverse implantable collamer len: a case report]. Zhonghua Yan Ke Za Zhi 2023; 59:1038-1041. [PMID: 38061905 DOI: 10.3760/cma.j.cn112142-20230811-00036] [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: 12/18/2023]
Abstract
The patient is a 33-year-old female who, 11 years ago, underwent bilateral posterior chamber phakic intraocular lens (pIOL) implantation due to myopia. She presented with a 2-year history of declining vision in her right eye and sought medical attention. She received femtosecond laser-assisted cataract surgery combined with pIOL extraction. Anterior segment optical coherence tomography and ultrasound biomicroscopy both showed an inverted pIOL in the right eye. Good visual results were achieved, and there were no complications during the six-month follow-up.
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Affiliation(s)
- Y Jiao
- Aier Eye Hospital of Wuhan University, Wuhan 430063, China
| | - R Xu
- Aier Eye Hospital of Wuhan University, Wuhan 430063, China
| | - W Xiao
- Aier Eye Hospital of Wuhan University, Wuhan 430063, China
| | - Y Wang
- Aier Eye Hospital of Wuhan University, Wuhan 430063, China
| | - S Q Dong
- Aier Eye Hospital of Wuhan University, Wuhan 430063, China
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Yang Y, Liu Y, Xu R, Jiao Y, Hao J, Sun YE, Gu XP, Zhang W. [The predictive values of platelet mitochondrial mass and quantity during the perioperative period in elderly patients on the occurrence of postoperative delirium]. Zhonghua Yi Xue Za Zhi 2023; 103:3258-3262. [PMID: 37926568 DOI: 10.3760/cma.j.cn112137-20230627-01085] [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: 11/07/2023]
Abstract
Objective: To investigate the changes of platelet mitochondrial mass and quantity during perioperative period in elderly patients, and assess their predictive values on the occurrence of postoperative delirium (POD). Methods: In this prospective study, 162 elderly patients scheduled for abdominal surgery under general anesthesia were enrolled from November 2021 to January 2022 in Nanjing Drum Tower Hospital Affiliated to Nanjing University Medical School. Among them, 20 patients [10 males, 10 females, aged (71.4±6.8) years] developed POD within 3 days after surgery (POD group), and another 20 patients[12 males, 8 females, aged (67.7±5.3) years] who did not develope POD were selected as controls (control group) using propensity score matching method. Blood samples were collected preoperatively, at the end of surgery and on the first postoperative day. Platelets were extracted and mitochondrial mass was detected with flow cytometry. Transmission electron microscopy was used to determine mitochondrial quantity. The receiver operating characteristic (ROC) curve was drawn to analyze the value of mitochondrial mass and quantity in predicting the occurrence of POD. Results: The mean fluorescence intensities of platelet mitochondrial mass were 193±46, 236±61, 264±53 preoperatively, at the end of surgery and on the first postoperative day in the POD group, respectively. The corresponding values were 209±61, 191±67 and 201±56 in the control group. The platelet mitochondrial mass of patients in the POD group was significantly increased on the first postoperative day compared to preoperative levels (P<0.001). In contrast, there was no significant difference in the control group (P=0.410). Patients in the POD group had higher platelet mitochondrial mass than patients in the control group on the first postoperative day(P=0.002). Meanwhile, platelets from patients in the POD group showed significantly higher number of mitochondria than platelets from patients in the control group [3 (2, 4) vs 2 (1, 2), P<0.001]. According to the ROC curve of platelet on the first postoperative day, at a mitochondrial mass cut-off value of>275.35, the sensitivity, specificity and area under the ROC curve to detect the occurrence of POD were 55%, 90% and 0.800 (95%CI: 0.666-0.934, P<0.001). At a mitochondrial quantity cut-off value of>2, the sensitivity, specificity and area under the ROC curve to detect the occurrence of POD were 53%, 78% and 0.680 (95%CI: 0.584-0.776, P<0.001). Conclusions: Patients who developed POD show higher platelet mitochondrial mass after surgery compared to preoperative levels. The mitochondrial mass of platelets on the first postoperative day has good predictive value on the occurrence of POD.
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Affiliation(s)
- Y Yang
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Y Liu
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - R Xu
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Y Jiao
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - J Hao
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Y E Sun
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - X P Gu
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - W Zhang
- Department of Anesthesiology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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7
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Ma WL, Ma Y, Wang WH, Ding XC, Jiao Y, Liu SW, Hai L. [Analysis of the prognosis and survival of patients with acute-on-chronic liver failure]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:1051-1055. [PMID: 38016769 DOI: 10.3760/cma.j.cn501113-20230604-00243] [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] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Objective: To explore the influencing factors and the impact of artificial liver treatment on the prognosis and survival of patients with acute-on-chronic liver failure (ACLF). Methods: Clinical data from 201 cases with ACLF from January 2016 to December 2019 was retrospectively analyzed. The survival rate was calculated by the Kaplan-Meier method, the log-rank test of univariate analysis, and the multivariate analysis of the stepwise Cox regression forward method. Results: The median survival time of patients was 6 months, and the survival rates at 6, 9, and 12 months were 51.2%, 38.3%, and 29.9%, respectively. In univariate analysis, age, presence or absence of hypertension and upper gastrointestinal bleeding, treatment method, model for end-stage liver disease (MELD) score, and cholinesterase were associated with prognosis (P < 0.05). Multivariate regression analysis results showed that MELD score was the main factor affecting the 1-year prognosis of ACLF patients (P = 0.002). Artificial liver treatment was beneficial for the 1-year prognosis of ACLF patients aged < 50 years or with a MELD score of ≥20 (P < 0.05 ). The relative risk ratio (RR) of mortality was 2.55 times higher in patients with advanced age (≥50 years old) than that of younger patients (P < 0.001). Regression analysis was performed using age as a stratification factor, and upper gastrointestinal bleeding was related to the prognosis of younger patients, while choline esterase was related to the prognosis of advanced age. Regression analysis after stratified MELD score showed that age and hypertension were related to the prognosis of patients with MELD score < 20, and treatment method and age were related to the prognosis of patients with MELD score≥20. Conclusion: Artificial liver treatment is beneficial for the 1-year prognosis of ACLF patients. Age, MELD score, hypertension, and upper gastrointestinal bleeding are independent risk factors affecting the prognosis of ACLF patients.
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Affiliation(s)
- W L Ma
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - Y Ma
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - W H Wang
- Department of Nutrition, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - X C Ding
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - Y Jiao
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - S W Liu
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
| | - L Hai
- Department of Infectious Diseases, Ningxia Medical University General Hospital, Yinchuan 750004, China
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8
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Gai YL, Huang HD, Zhang W, Li X, Zhang XQ, Jiao Y, Wang Q, Dong YC, Bai C. [A case of left pulmonary artery sling combined with congenital tracheal stenosis in an adult]. Zhonghua Jie He He Hu Xi Za Zhi 2023; 46:1011-1014. [PMID: 37752044 DOI: 10.3760/cma.j.cn112147-20230603-00293] [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
Pulmonary artery sling in adults is a rare congenital vascular malformation usually accompanied by tracheal and bronchial stenosis. Due to its high mortality risk and relatively poor prognosis, it has rarely been reported in adults. We reported a middle-aged patient who presented with shortness of breath, predominantly after activity, since childhood. He was diagnosed with "tracheal stenosis" in another hospital and received symptomatic treatment. The diagnosis of left pulmonary artery sling with congenital tracheal stenosis was confirmed by multi-slice spiral CT (MSCT), airway examination with flexible bronchoscope and 3D image post-processing system. Data from this case and the related literatures have been summarized and analyzed. This will help clinicians to improve their level of diagnosis and treatment.
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Affiliation(s)
- Y L Gai
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - H D Huang
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - W Zhang
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - X Li
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - X Q Zhang
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - Y Jiao
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - Q Wang
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - Y C Dong
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
| | - C Bai
- Department of Respiratory and Critical Care, First Affiliated Hospital of Naval Military Medical University, Shanghai 2004332, China
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9
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Affiliation(s)
- W Shi
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Y Jiao
- Department of General Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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10
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Wen H, Yang C, Dou D, Xu L, Jiao Y. Underwater source ranging by Siamese network aided semi-supervised learning. JASA Express Lett 2023; 3:094803. [PMID: 37712840 DOI: 10.1121/10.0020991] [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] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Underwater source ranging based on Deep Learning methods demands a considerable amount of labeled data, which is costly to collect. To alleviate this challenge, semi-supervised learning of the wrapper paradigm is introduced into this task. First, the Siamese network is used to generate pseudo labels for unlabeled data to expand the labeled dataset. A new effective confidence criterion based on similarity score and similar sample distribution is proposed to evaluate the reliability of pseudo labels. Then the model can be trained more fully with an expanded dataset. Experiments on the SwellEx-96 dataset validate that this method can effectively improve prediction accuracy.
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Affiliation(s)
- Hao Wen
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, People's Republic of , , , ,
| | - Chengzhu Yang
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, People's Republic of , , , ,
| | - Daowei Dou
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, People's Republic of , , , ,
| | - Lijun Xu
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, People's Republic of , , , ,
| | - Yuchen Jiao
- School of Information and Electronics, Beijing Institute of Technology, Beijing, 100081, People's Republic of , , , ,
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11
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Ma Y, Gan J, Bai Y, Cao D, Jiao Y. Minimal residual disease in solid tumors: an overview. Front Med 2023; 17:649-674. [PMID: 37707677 DOI: 10.1007/s11684-023-1018-6] [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: 02/22/2023] [Accepted: 06/24/2023] [Indexed: 09/15/2023]
Abstract
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Affiliation(s)
- Yarui Ma
- 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
| | - Jingbo Gan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yinlei Bai
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yuchen Jiao
- 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.
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12
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Jiao Y, Guo L, Han TL, Qi X, Gao Y, Zhang Y, Zhao JH, Li BB, Zhang Z, Sun LL. [Analysis of the characteristics of viral infections in children with diarrhea in Beijing from 2018 to 2022]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:976-982. [PMID: 37400218 DOI: 10.3760/cma.j.cn112150-20230131-00066] [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: 07/05/2023]
Abstract
Objective: To explore the characteristics of viral infections in children with diarrhea in Beijing from 2018 to 2022. Methods: Real-time PCR and enzyme-linked immunosorbent assay were used to detect viral nucleic acid of Norovirus (NoV), Sappovirus (SaV), Astrovirus (AstV), Enteric Adenovirus (AdV) or antigen of Rotavirus (RV) in 748 stool samples collected from Beijing Capital Institute of Pediatrics from January 2018 to December 2021. Subsequently, the reverse transcription PCR or PCR method was used to amplify the target gene of the positive samples after the initial screening, followed by sequencing, genotyping and evolution analysis, so as to obtain the characteristics of these viruses. Phylogenetic analysis was performed using Mega 6.0. Results: From 2018 to 2021, the overall detection rate of the above five common viruses was 37.6%(281/748)in children under 5 years old in Beijing. NoV, Enteric AdV and RV were still the top three diarrhea-related viruses, followed by AstV and SaV, accounting for 41.6%, 29.2%, 27.8%, 8.9% and 7.5%, respectively. The detection rate of co-infections with two or three diarrhea-related viruses was 4.7% (35/748). From the perspective of annual distribution, the detection rate of Enteric AdV was the highest in 2021, while NoV was predominant in the other 4 years. From the perspective of genetic characteristics, NoV was predominant by GII.4, and after the first detection of GII.4[P16] in 2020, it occupied the first two gene groups together with GII.4[P31]. Although the predominant RV was G9P[8], the rare epidemic strain G8P[8] was first detected in 2021. The predominant genotypes of Enteric AdV and AstV were Ad41 and HAstV-1. SaV was sporadic spread with a low detection rate. Conclusion: Among the diarrhea-related viruses infected children under 5 years of age in Beijing, the predominant strains of NoV and RV have changed and new sub-genotypes have been detected for the first time, while the predominant strains of AstV and Enteric AdV are relatively stable.
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Affiliation(s)
- Y Jiao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - L Guo
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - T L Han
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - X Qi
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Y Gao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Y Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - J H Zhao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - B B Li
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Z Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - L L Sun
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
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13
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Zhao L, Song J, Sun Y, Ju Q, Mu H, Dong X, Ding J, Liu Y, Wang X, Sun L, Wu J, Jiao Y, Lu S, Zhao X. Tumor-derived proliferative CTCs and CTC clusters predict aggressiveness and early recurrence in hepatocellular carcinoma patients. Cancer Med 2023. [PMID: 37337648 DOI: 10.1002/cam4.5946] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 03/20/2023] [Accepted: 04/02/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Circulating tumor cells (CTCs), an indispensable liquid biopsy classifier, can provide extra information for the diagnosis and prognosis of hepatocellular carcinoma (HCC). METHODS We systematically analyzed the peripheral blood of preoperative HCC patients (n = 270) for CTC number, Ki67 index reflecting the proliferative CTC percentage (PCP), and CTC clusters correlated with the characteristics of malignant HCC tumors. RESULTS Driver gene mutations were found with high levels of consistency between CTCs and primary tumors (n = 73). CTC number and PCP were associated with tumor size, microvascular invasion (MVI), presence or absence of multiple tumors, and thrombosis significantly. CTC number and PCP robustly separated patients with and without relapse, with a sensitivity of 88.89%/81.48% and a specificity of 72.73%/94.81% in the training set (n = 104) and corresponding values of 80.00%/86.67% and 78.38%/89.19% in the validation set (n = 52), showing a better performance than that associated with the alpha-fetoprotein (AFP) level. CTC number, PCP, CTC clusters, and MVI were independent significant risk factors for HCC recurrence (P = 0.0375, P < 0.0001, P = 0.0017, and P = 0.0157). A nomogram model based on these risk factors showed a considerable prediction ability for HCC recurrence (area under the curve = 0.947). PCP (training: log-rank P < 0.0001; hazard ratio [HR] 30.13, 95% confidence interval [CI] = 11.12-81.62; validation: log-rank P < 0.0001; HR 25.73, 95% CI = 5.28-106.60) and CTC clusters (training: log-rank P < 0.0001; HR 17.34, 95% CI = 7.46-40.30; validation: log-rank P < 0.0001; HR 9.92, 95% CI = 2.55-38.58) were more significantly correlated with worse recurrence-free survival than CTC number (training: log-rank P < 0.0001; HR 14.93, 95% CI = 4.48-49.78; validation: log-rank P = 0.0007; HR 9.03, 95% CI = 2.53-32.24). CONCLUSION PCP and CTC clusters may predict HCC recurrence and improve the performance of the serum biomarker AFP.
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Affiliation(s)
- Lina 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, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jinge Song
- 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, China
| | - Yulin 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, Beijing, China
| | - Qiang Ju
- 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, China
| | - Hong Mu
- 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, China
| | - Xiu Dong
- 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, China
| | - Jing Ding
- Department of Hepatobiliary Surgery and You-an liver Transplant Center, Beijing You-An Hospital, Capital Medical University, Beijing, China
| | - Yunhe Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuebing Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases (NCRC-DD), Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Liying Sun
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases (NCRC-DD), Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- 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, China
| | - Shichun Lu
- Department of Hepatobiliary Surgery and You-an liver Transplant Center, Beijing You-An Hospital, Capital Medical University, Beijing, China
- Department of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaohang 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, China
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14
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Luo L, Jiao Y, Yang P, Li Y, Huang WY, Ke XY, Zou DH, Jing HM. [Efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation treatment for T lymphoblastic leukemia/lymphoma]. Zhonghua Xue Ye Xue Za Zhi 2023; 44:388-394. [PMID: 37550188 PMCID: PMC10440623 DOI: 10.3760/cma.j.issn.0253-2727.2023.05.006] [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: 08/13/2022] [Indexed: 08/09/2023]
Abstract
Objective: To analyze the efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for treating T lymphoblastic leukemia/lymphoma (T-ALL/LBL) . Methods: This study retrospectively evaluated 119 adolescent and adult patients with T-ALL/LBL from January 2006 to January 2020 at Peking University Third Hospital and Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences. Patients were divided into chemotherapy-only, chemotherapy followed by allo-HSCT, and chemotherapy followed by autologous hematopoietic stem cell transplantation (auto-HSCT) groups according to the consolidation regimen, and the 5-year overall survival (OS) and progression-free survival (PFS) rates of each group were compared. Results: Among 113 patients with effective follow-up, 96 (84.9%) patients achieved overall response (ORR), with 79 (69.9%) having complete response (CR) and 17 (15.0%) having partial response (PR), until July 2022. The analysis of the 96 ORR population revealed that patients without transplantation demonstrated poorer outcomes compared with the allo-HSCT group (5-year OS: 11.4% vs 55.6%, P=0.001; 5-year PFS: 8.9% vs 54.2%, P<0.001). No difference was found in 5-year OS and 5-year PFS between the allo-HSCT and auto-HSCT groups (P=0.271, P=0.197). The same results were achieved in the CR population. Allo-HSCT got better 5-year OS (37.5% vs 0) for the 17 PR cases (P=0.064). Different donor sources did not affect 5-year OS, with sibling of 61.1% vs hap-haploidentical of 63.6% vs unrelated donor of 50.0% (P>0.05). No significant difference was found in the treatment response in the early T-cell precursor acute lymphoblastic leukemia/lymphoma (ETP) and non-ETP populations. The ETP group demonstrated lower 5-year OS compared with the non-ETP group in the chemotherapy alone group (0 vs 12.6%, P=0.045), whereas no significant difference was found between the ETP and non-ETP groups in the allo-HSCT group (75.0% vs 62.9%, P=0.852). Multivariate analysis revealed that high serum lactate dehydrogenase level, without transplantation, and no CR after chemotherapy induction were independently associated with inferior outcomes (P<0.05) . Conclusion: Allo-HSCT could be an effective consolidation therapy for adult and adolescent patients with T-ALL/LBL. Different donor sources did not affect survival. Allo-HSCT may overcome the adverse influence of ETP-ALL/LBL on OS.
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Affiliation(s)
- L Luo
- Department of Hematology, Peking University Third Hospital, Beijing 100191, China
| | - Y Jiao
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, National Clinical Research Center for Blood Diseases, State Key Laboratory of Experimental Hematology, Tianjin 300020, China
| | - P Yang
- Department of Hematology, Peking University Third Hospital, Beijing 100191, China
| | - Y Li
- Department of Hematology, Peking University Third Hospital, Beijing 100191, China
| | - W Y Huang
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, National Clinical Research Center for Blood Diseases, State Key Laboratory of Experimental Hematology, Tianjin 300020, China
| | - X Y Ke
- Department of Hematology, Peking University Third Hospital, Beijing 100191, China
| | - D H Zou
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, National Clinical Research Center for Blood Diseases, State Key Laboratory of Experimental Hematology, Tianjin 300020, China
| | - H M Jing
- Department of Hematology, Peking University Third Hospital, Beijing 100191, China
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15
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Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Babu JM, Zheng L, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Niknafs N, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, Wood LD. Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions. bioRxiv 2023:2023.01.27.525553. [PMID: 36747709 PMCID: PMC9900989 DOI: 10.1101/2023.01.27.525553] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents a critical opportunity for cancer interception. However, the number, size, shape, and connectivity of PanINs in human pancreatic tissue samples are largely unknown. In this study, we quantitatively assessed human PanINs using CODA, a novel machine-learning pipeline for 3D image analysis that generates quantifiable models of large pieces of human pancreas with single-cell resolution. Using a cohort of 38 large slabs of grossly normal human pancreas from surgical resection specimens, we identified striking multifocality of PanINs, with a mean burden of 13 spatially separate PanINs per cm3 of sampled tissue. Extrapolating this burden to the entire pancreas suggested a median of approximately 1000 PanINs in an entire pancreas. In order to better understand the clonal relationships within and between PanINs, we developed a pipeline for CODA-guided multi-region genomic analysis of PanINs, including targeted and whole exome sequencing. Multi-region assessment of 37 PanINs from eight additional human pancreatic tissue slabs revealed that almost all PanINs contained hotspot mutations in the oncogene KRAS, but no gene other than KRAS was altered in more than 20% of the analyzed PanINs. PanINs contained a mean of 13 somatic mutations per region when analyzed by whole exome sequencing. The majority of analyzed PanINs originated from independent clonal events, with distinct somatic mutation profiles between PanINs in the same tissue slab. A subset of the analyzed PanINs contained multiple KRAS mutations, suggesting a polyclonal origin even in PanINs that are contiguous by rigorous 3D assessment. This study leverages a novel 3D genomic mapping approach to describe, for the first time, the spatial and genetic multifocality of human PanINs, providing important insights into the initiation and progression of pancreatic neoplasia.
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Affiliation(s)
- Alicia M Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ashley L Kiemen
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mia P Grahn
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - André Forjaz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Jaanvi Mahesh Babu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lily Zheng
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
| | - Liping Jiang
- State Key Lab 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, China
| | - Haixia Cheng
- State Key Lab 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, China
| | - Qianqian Song
- State Key Lab 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, China
| | - Rebecca Reichel
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sarah Graham
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander I Damanakis
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Catherine G Fischer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephanie Mou
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cameron Metz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Julie Granger
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiao-Ding Liu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Niklas Bachmann
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cristina Almagro-Pérez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Ann Chenyu Jiang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Jeonghyun Yoo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Bridgette Kim
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Scott Du
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Eli Foster
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Jocelyn Y Hsu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Paula Andreu Rivera
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Linda C Chu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Fengze Liu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elliot K Fishman
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alan Yuille
- Department of Computer Science, Johns Hopkins University, Baltimore, MD
| | - Nicholas J Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elizabeth D Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Robert B Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Toby C Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Yuchen Jiao
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
| | - Rachel Karchin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Denis Wirtz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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16
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Liu Z, Zhao Y, Kong P, Liu Y, Huang J, Xu E, Wei W, Li G, Cheng X, Xue L, Li Y, Chen H, Wei S, Sun R, Cui H, Meng Y, Liu M, Li Y, Feng R, Yu X, Zhu R, Wu Y, Li L, Yang B, Ma Y, Wang J, Zhu W, Deng D, Xi Y, Wang F, Li H, Guo S, Zhuang X, Wang X, Jiao Y, Cui Y, Zhan Q. Integrated multi-omics profiling yields a clinically relevant molecular classification for esophageal squamous cell carcinoma. Cancer Cell 2023; 41:181-195.e9. [PMID: 36584672 DOI: 10.1016/j.ccell.2022.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [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: 02/07/2022] [Revised: 07/31/2022] [Accepted: 12/06/2022] [Indexed: 12/30/2022]
Abstract
Integrated molecular analysis of human cancer has yielded molecular classification for precise management of cancer patients. Here, we analyzed the whole genomic, epigenomic, transcriptomic, and proteomic data of 155 esophageal squamous cell carcinomas (ESCCs). Multi-omics analysis led to the classification of ESCCs into four subtypes: cell cycle pathway activation, NRF2 oncogenic activation, immune suppression (IS), and immune modulation (IM). IS and IM cases were highly immune infiltrated but differed in the type and distribution of immune cells. IM cases showed better response to immune checkpoint blockade therapy than other subtypes in a clinical trial. We further developed a classifier with 28 features to identify the IM subtype, which predicted anti-PD-1 therapy response with 85.7% sensitivity and 90% specificity. These results emphasize the clinical value of unbiased molecular classification based on multi-omics data and have the potential to further improve the understanding and treatment of ESCC.
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Affiliation(s)
- 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.
| | - Yahui 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, China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Cancer Institute, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen 518107, China
| | - Yuhao 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
| | - Jing Huang
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Enwei Xu
- Department of Pathology, Shanxi Province Cancer Hospital, Taiyuan, Shanxi 030001, China
| | - Wenqing 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, China
| | - Guangyu Li
- Center for Bioinformatics, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Liyan Xue
- 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, China
| | - Yi Li
- 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
| | - 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
| | - Shuqing Wei
- Department of Thoracic Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Heyang Cui
- Institute of Cancer Research, Shenzhen Bay Laboratory, Cancer Institute, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen 518107, China
| | - Yongsheng Meng
- Department of Tumor Biobank, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Meilin Liu
- Department of Tumor Biobank, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Yang Li
- 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
| | - Riyue Feng
- 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
| | - Xiao Yu
- 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
| | - Rui Zhu
- 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
| | - Yenan Wu
- 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
| | - Lei Li
- 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
| | - Bin Yang
- Department of Thoracic Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Yanchun Ma
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jiawei Wang
- Mingma Technologies Co., Ltd., Shanghai 200131, China
| | - Wenjie Zhu
- Mingma Technologies Co., Ltd., Shanghai 200131, China
| | - Dongjie Deng
- Mingma Technologies Co., Ltd., Shanghai 200131, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Province Cancer Hospital, Taiyuan, Shanxi 030001, China
| | - Fang Wang
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Hongyi Li
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Shiping Guo
- Department of Thoracic Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Xiaofei Zhuang
- Department of Thoracic Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030013, China
| | - Xiaoyue Wang
- Center for Bioinformatics, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Jiao
- 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.
| | - Yongping Cui
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Cancer Institute, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen 518107, China.
| | - Qimin Zhan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Cancer Institute, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen 518107, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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17
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Li T, Du D, Zhang D, Lin Y, Ma J, Zhou M, Meng W, Jin Z, Chen Z, Yuan H, Wang J, Dong S, Sun S, Ye W, Li B, Liu H, Zhang Z, Jiao Y, Xie Z, Qiu W, Liu Y. CRISPR-based targeted haplotype-resolved assembly of a megabase region. Nat Commun 2023; 14:22. [PMID: 36596772 PMCID: PMC9810730 DOI: 10.1038/s41467-022-35389-w] [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: 01/28/2022] [Accepted: 11/29/2022] [Indexed: 01/04/2023] Open
Abstract
Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
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Affiliation(s)
- Taotao Li
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Duo Du
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Dandan Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yicheng Lin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Jiakang Ma
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Mengyu Zhou
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Zelin Jin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Haozhe Yuan
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Jue Wang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Shulong Dong
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Shaoyang Sun
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
| | - Bosen Li
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Houbao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhao Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuchen Jiao
- 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, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenqing Qiu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China. .,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China. .,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.
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18
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He S, Zeng F, Yin H, Wang P, Bai Y, Song Q, Chu J, Huang Z, Liu Y, Liu H, Chen Q, Liu L, Zhou J, Hu H, Li X, Li T, Wang G, Cai J, Jiao Y, Zhao H. Molecular diagnosis of pancreatobiliary tract cancer by detecting mutations and methylation changes in bile samples. EClinicalMedicine 2023; 55:101736. [PMID: 36425869 PMCID: PMC9678809 DOI: 10.1016/j.eclinm.2022.101736] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Patients with pancreatobiliary tract cancer usually have a poor clinical outcome, with a 5-year overall survival rate below 20%. This is mainly associated with the late diagnosis. In addition, the standard-of-care for patients with malignant biliary stenosis involves a major surgery, the Whipple procedure. An accurate preoperative diagnosis, including differentiation from benign diseases, is critical to avoid unnecessary treatment. Here we developed BileScreen, a sensitive detection modality for the diagnosis of pancreatobiliary tract cancer based on massively parallel sequencing mutation and methylation changes in bile samples. METHODS A total of 338 patients, from five hospitals in China, with pancreatobiliary system disorders were enrolled in this study between November 2018 and October 2020, and 259 were included for the analysis of BileScreen. We profiled 23 gene mutations and 44 genes with methylation modifications in parallel from bile samples, and set up a model for the detection of malignancy based on multi-level biomarkers. FINDINGS We applied the BileScreen assay in a training cohort (n = 104) to set up the model and algorithm. The model was further evaluated in a validation cohort (n = 105), resulting in 92% sensitivity and 98% specificity. The performance of BileScreen was further assessed in a prospective test cohort (n = 50) of patients diagnosed with suspicious or negative pathology by endoscopic retrograde cholangiopancreatography and were confirmed in follow-up. BileScreen yielded 90% sensitivity and 80% specificity, and outcompeted serum carbohydrate antigen 19-9 in detecting pancreatobiliary tract cancer in all three cohorts, especially in terms of specificity. INTERPRETATION Taken together, BileScreen has the ability to interrogate mutations and methylation changes in bile samples in parallel, thus rendering it a potentially sensitive detection method to help in the diagnosis of pancreatobiliary tract cancer in a safe, convenient and less-invasive manner. FUNDING This study was supported by the Capital's Funds for Health Improvement and Research (2020-2-4025 to S.H.), the National Natural Science Foundation of China (81972311 to H.Z.), CAMS Innovation Fund for Medical Sciences (CIFMS) (2017-12M-4-002 to H.Z.), the CAMS Innovation Fund for Medical Sciences(CIFMS) (2021-I2M-1-066 to CJQ), the Non-profit Central Research Institution Fund of Chinese Academy of Medical Sciences (2019PT310026 to H.Z.) and Sanming Project of Medicine in Shenzhen (SZSM202011010 to H.Z.).
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Affiliation(s)
- Shun He
- Department of Endoscopy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan province, China
| | - Huihui Yin
- 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, China
| | - Pei Wang
- 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, China
| | - Yinlei Bai
- Jinchenjunchuang Clinical Laboratory, Hangzhou, Zhejiang, China
| | - Qianqian Song
- 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, China
| | - Jiangtao Chu
- Department of Endoscopy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen Huang
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yumeng Liu
- Department of Endoscopy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Liu
- Department of Hepatobiliary Surgery, Dazhou Central Hospital, Dazhou, Sichuan province, China
| | - Qichen Chen
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Liu
- Jinchenjunchuang Clinical Laboratory, Hangzhou, Zhejiang, China
| | - Jun Zhou
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan province, China
| | - Hanjie Hu
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingchen Li
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tengyan Li
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guiqi Wang
- Department of Endoscopy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Corresponding author. National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan South Lane, Chaoyang District, Beijing, China.
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Corresponding author. National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan South Lane, Chaoyang District, Beijing, China.
| | - Yuchen Jiao
- 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, China
- Corresponding author. National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan South Lane, Chaoyang District, Beijing, China.
| | - Hong Zhao
- Department of Hepatobiliary Surgery, 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, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Corresponding author. National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan South Lane, Chaoyang District, Beijing, China.
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Jiao Y, Zhang J, Yang X, Zhan T, Wu Z, Li Y, Zhao S, Li H, Weng J, Huo R, Wang J, Xu H, Sun Y, Wang S, Cao Y. Artificial Intelligence-Assisted Evaluation of the Spatial Relationship between Brain Arteriovenous Malformations and the Corticospinal Tract to Predict Postsurgical Motor Defects. AJNR Am J Neuroradiol 2023; 44:17-25. [PMID: 36549849 PMCID: PMC9835926 DOI: 10.3174/ajnr.a7735] [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: 03/18/2022] [Accepted: 11/07/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND PURPOSE Preoperative evaluation of brain AVMs is crucial for the selection of surgical candidates. Our goal was to use artificial intelligence to predict postsurgical motor defects in patients with brain AVMs involving motor-related areas. MATERIALS AND METHODS Eighty-three patients who underwent microsurgical resection of brain AVMs involving motor-related areas were retrospectively reviewed. Four artificial intelligence-based indicators were calculated with artificial intelligence on TOF-MRA and DTI, including FN5mm/50mm (the proportion of fiber numbers within 5-50mm from the lesion border), FN10mm/50mm (the same but within 10-50mm), FP5mm/50mm (the proportion of fiber voxel points within 5-50mm from the lesion border), and FP10mm/50mm (the same but within 10-50mm). The association between the variables and long-term postsurgical motor defects was analyzed using univariate and multivariate analyses. Least absolute shrinkage and selection operator regression with the Pearson correlation coefficient was used to select the optimal features to develop the machine learning model to predict postsurgical motor defects. The area under the curve was calculated to evaluate the predictive performance. RESULTS In patients with and without postsurgical motor defects, the mean FN5mm/50mm, FN10mm/50mm, FP5mm/50mm, and FP10mm/50mm were 0.24 (SD, 0.24) and 0.03 (SD, 0.06), 0.37 (SD, 0.27) and 0.06 (SD, 0.08), 0.06 (SD, 0.10) and 0.01 (SD, 0.02), and 0.10 (SD, 0.12) and 0.02 (SD, 0.05), respectively. Univariate and multivariate logistic analyses identified FN10mm/50mm as an independent risk factor for long-term postsurgical motor defects (P = .002). FN10mm/50mm achieved a mean area under the curve of 0.86 (SD, 0.08). The mean area under the curve of the machine learning model consisting of FN10mm/50mm, diffuseness, and the Spetzler-Martin score was 0.88 (SD, 0.07). CONCLUSIONS The artificial intelligence-based indicator, FN10mm/50mm, can reflect the lesion-fiber spatial relationship and act as a dominant predictor for postsurgical motor defects in patients with brain AVMs involving motor-related areas.
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Affiliation(s)
- Y Jiao
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - J Zhang
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - X Yang
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - T Zhan
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - Z Wu
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - Y Li
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - S Zhao
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - H Li
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - J Weng
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - R Huo
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - J Wang
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - H Xu
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - Y Sun
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - S Wang
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
| | - Y Cao
- From the Department of Neurosurgery (Y.J., J.Z., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases (Y.J., J.Z., X.Y., T.Z., Z.W., Y.L., S.Z., H.L., J. Weng, R.H., J. Wang, H.X., Y.S., S.W., Y.C.), Beijing, China
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Zhang J, Sun L, Withanage M, Ganesan S, Williamson M, Marchesan J, Jiao Y, Teles F, Yu N, Liu Y, Wu D, Moss K, Mangalam A, Zeng E, Lei Y, Zhang S. TRAF3IP2-IL-17 Axis Strengthens the Gingival Defense against Pathogens. J Dent Res 2023; 102:103-115. [PMID: 36281065 PMCID: PMC9780753 DOI: 10.1177/00220345221123256] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recent genome-wide association studies have suggested novel risk loci associated with periodontitis, which is initiated by dysbiosis in subgingival plaque and leads to destruction of teeth-supporting structures. One such genetic locus was the tumor necrosis factor receptor-associated factor 3 interacting protein 2 (TRAF3IP2), a gene encoding the gate-keeping interleukin (IL)-17 receptor adaptor. In this study, we first determined that carriers of the lead exonic variant rs13190932 within the TRAF3IP2 locus combined with a high plaque microbial burden was associated with more severe periodontitis than noncarriers. We then demonstrated that TRAF3IP2 is essential in the IL-17-mediated CCL2 and IL-8 chemokine production in primary gingival epithelial cells. Further analysis suggested that rs13190932 may serve a surrogate variant for a genuine loss-of-function variant rs33980500 within the same gene. Traf3ip2 null mice (Traf3ip2-/-) were more susceptible than wild-type (WT) mice to the Porphyromonas gingivalis-induced periodontal alveolar bone loss. Such bone loss was associated with a delayed P. gingivalis clearance and an attenuated neutrophil recruitment in the gingiva of Traf3ip2-/- mice. Transcriptomic data showed decreased expression of antimicrobial genes, including Lcn2, S100a8, and Defb1, in the Traf3ip2-/- mouse gingiva in comparison to WT mice prior to or upon P. gingivalis oral challenge. Further 16S ribosomal RNA sequencing analysis identified a distinct microbial community in the Traf3ip2-/- mouse oral plaque, which was featured by a reduced microbial diversity and an overabundance of Streptococcus genus bacteria. More P. gingivalis was observed in the Traf3ip2-/- mouse gingiva than WT control animals in a ligature-promoted P. gingivalis invasion model. In agreement, neutrophil depletion resulted in more local gingival tissue invasion by P. gingivalis. Thus, we identified a homeostatic IL-17-TRAF3IP2-neutrophil axis underpinning host defense against a keystone periodontal pathogen.
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Affiliation(s)
- J. Zhang
- Iowa Institute of Oral Health Research, University of Iowa College of Dentistry, Iowa City, IA, USA,Periodontics, University of Iowa College of Dentistry, Iowa City, IA, USA,S. Zhang, Iowa Institute of Oral Health Research, Periodontics Department, University of Iowa College of Dentistry, Room 401 Dental Science Building, 801 Newton Road, Iowa City, IA 52242, USA.
| | - L. Sun
- Department of Microbiology & Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M.H.H. Withanage
- Division of Biostatistics and Computational Biology, University of Iowa College of Dentistry, Iowa City, IA, USA
| | - S.M. Ganesan
- Iowa Institute of Oral Health Research, University of Iowa College of Dentistry, Iowa City, IA, USA,Periodontics, University of Iowa College of Dentistry, Iowa City, IA, USA
| | - M.A. Williamson
- Iowa Institute of Oral Health Research, University of Iowa College of Dentistry, Iowa City, IA, USA,Periodontics, University of Iowa College of Dentistry, Iowa City, IA, USA
| | - J.T. Marchesan
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Y. Jiao
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - F.R. Teles
- Department of Basic & Translational Sciences, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - N. Yu
- The Forsyth Institute, Cambridge, MA, USA
| | - Y. Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D. Wu
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K.L. Moss
- Department of Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A.K. Mangalam
- Department of Pathology, University of Iowa College of Medicine, Iowa City, IA, USA
| | - E. Zeng
- Division of Biostatistics and Computational Biology, University of Iowa College of Dentistry, Iowa City, IA, USA
| | - Y.L. Lei
- Department of Periodontics & Oral Medicine, University of Michigan School of Dentistry, Ann Harbor, MI, USA
| | - S. Zhang
- Iowa Institute of Oral Health Research, University of Iowa College of Dentistry, Iowa City, IA, USA,Periodontics, University of Iowa College of Dentistry, Iowa City, IA, USA
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21
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Wang P, Song Q, Ren J, Zhang W, Wang Y, Zhou L, Wang D, Chen K, Jiang L, Zhang B, Chen W, Qu C, Zhao H, Jiao Y. Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection. Sci Transl Med 2022; 14:eabp8704. [PMID: 36417488 DOI: 10.1126/scitranslmed.abp8704] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cell-free DNA (cfDNA)-based liquid biopsy is a promising approach for the early detection of cancer. A major hurdle is the limited yield of cfDNA from one blood draw, limiting the use of most samples to one test of either mutation or methylation. Here, we develop a technology, Mutation Capsule Plus (MCP), which enables multiplex profiling of one cfDNA sample, including simultaneous detection of genetic and epigenetic alterations and genome-wide discovery of methylation markers. With this technology, we performed de novo screening of methylation markers on cfDNA samples from 30 hepatocellular carcinoma (HCC) cases and 30 non-HCC controls. The methylation markers enriched in HCC cfDNA were further profiled in parallel with a panel of mutations on a training cohort of 60 HCC and 60 non-HCC cases, resulting in an HCC detection model. We validated the model in an independent retrospective cohort with 58 HCC and 198 non-HCC cases and got 90% sensitivity with 94% specificity. Furthermore, we applied the model to a prospective cohort of 311 asymptomatic hepatitis B virus carriers with normal liver ultrasonography and serum AFP concentration. The model detected four of the five HCC cases in the cohort, showing 80% sensitivity and 94% specificity. These findings demonstrate that the MCP technology has potential for the discovery and validation of multiomics biomarkers for the noninvasive detection of cancer. This study also provides a comprehensive database of genetic and epigenetic alterations in the cfDNA of a large cohort of HCC cases and high-risk non-HCC individuals.
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Affiliation(s)
- Pei Wang
- 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
| | - Qianqian Song
- 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
| | - Jie Ren
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Weilong Zhang
- 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.,Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuting Wang
- 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.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Lin Zhou
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Dongmei Wang
- 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.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Kun Chen
- Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Liping Jiang
- 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
| | - Bochao Zhang
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Wanqing Chen
- Office of Cancer Screening, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17 Pan-jia-yuan South Lane, Chaoyang District, Beijing 100021, China
| | - Chunfeng Qu
- 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.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuchen Jiao
- 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
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Kashi AA, van der Tol JJGM, Williams KA, Jiao Y. Efficient and fabrication error tolerant grating couplers on the InP membrane on silicon platform. Appl Opt 2022; 61:9926-9936. [PMID: 36606824 DOI: 10.1364/ao.473271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
In order to couple light between photonic integrated circuits and optical fibers, grating couplers are commonly employed. This paper describes the design and fabrication of deep and shallow-etched grating couplers with a metal back-reflector with record low insertion losses in InP-based platforms. The measured insertion losses for deep and shallow-etched gratings are 2.4 and 2.6 dB, respectively. Additionally, fabrication error tolerances in shallow etched grating couplers have been examined experimentally, which showed high tolerance of this structure toward the grating period and fill factor.
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Braxton AM, Kiemen A, Karchin R, Jiao Y, Wu PH, Hruban RH, Wirtz D, Wood LD. Abstract B027: Three-dimensional genomic analysis of human pancreatic intraepithelial neoplasia (PanIN) reveals striking multifocality and genetic heterogeneity. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b027] [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: 11/17/2022]
Abstract
Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Short Talks from Proffered Abstracts section (PR007) of the Conference Proceedings.
Citation Format: Alicia M. Braxton, Ashley Kiemen, Rachel Karchin, Yuchen Jiao, Pei-Hsun Wu, Ralph H Hruban, Denis Wirtz, Laura D. Wood. Three-dimensional genomic analysis of human pancreatic intraepithelial neoplasia (PanIN) reveals striking multifocality and genetic heterogeneity [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B027.
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Affiliation(s)
| | | | | | - Yuchen Jiao
- 3Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Mainland)
| | - Pei-Hsun Wu
- 2The Johns Hopkins University, Baltimore, MD,
| | | | - Denis Wirtz
- 2The Johns Hopkins University, Baltimore, MD,
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Braxton AM, Kiemen A, Karchin R, Jiao Y, Wu PH, Hruban RH, Wirtz D, Wood LD. Abstract PR007: Three-dimensional genomic analysis of human pancreatic intraepithelial neoplasia (PanIN) reveals striking multifocality and genetic heterogeneity. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-pr007] [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: 11/17/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a 5 year survival rate of 11%. PDAC arises from precursor lesions, the most common of which is pancreatic intraepithelial neoplasia (PanIN). Molecular analysis of human PanINs is critical to understand early pancreatic tumorigenesis, which could inform risk stratification, early detection, and cancer prevention approaches. Because PanINs are microscopic, it is challenging to determine their full extent and anatomic relationships using two dimensional histological sections. To determine the density and connectivity of PanINs, we utilized a novel machine learning algorithm (CODA) for three-dimensional (3D) reconstruction and cellular quantification. Large blocks of grossly normal pancreas were harvested from 39 surgical pancreatectomy specimens, followed by formalin fixation, paraffin-embedding, and complete serial sectioning. 3D reconstruction using CODA revealed striking multifocality of PanINs within the pancreata of most analyzed patients, with more than 600 spatially PanINs being modeled. Next, to determine whether these multifocal PanINs arose as independent neoplasms or via intraductal spread of a single PanIN, we assessed their clonal relationships using somatic multi-region DNA next generation sequencing (NGS). To do so, 8 additional blocks of grossly normal pancreatic tissue were harvested and 3D modeled, yielding 37 anatomically distinct PanINs for genomic analysis. Each spatially unconnected PanIN was separately microdissected in five different regions to assess both intra-PanIN and inter-PanIN genetic heterogeneity. 99 samples from the 37 PanIN lesions underwent targeted NGS using a panel covering major drivers of pancreatic ductal neoplasia. For PanINs with sufficient DNA, whole exome sequencing and deep sequencing of KRAS was also performed. Across the 8 blocks, 10 PanINs shared no mutations with other PanINs in the same block, indicating independent clonal origin. In addition, 8 PanINs shared only KRAS hotspot mutations with numerous other unshared mutations, likely indicating independent PanINs that shared hotspot mutations by chance. Six spatially separate low grade PanINs shared both driver and passenger mutations with at least one other spatially unconnected PanIN, demonstrating the ability of PanIN cells to dissociate from one lesion and establish unconnected, genetically related PanINs nearby. Furthermore, 5 PanINs harbored multiple KRAS mutations within a single PanIN, suggesting a polyclonal origin. One PanIN lacked any driver gene mutations. The genetic origins of the remaining 7 spatially separate PanINs could not be resolved due to a lack of discrete mutations found by targeted sequencing. Our 3D genomic analysis of anatomically distinct PanINs demonstrates that the unexpectedly large number of PanINs in normal pancreas most often arise independently, providing new foundations for our understanding of early pancreatic tumorigenesis. Determining the mechanisms for this multifocal neoplasia is an important direction for future research.
Citation Format: Alicia M. Braxton, Ashley Kiemen, Rachel Karchin, Yuchen Jiao, Pei-Hsun Wu, Ralph H Hruban, Denis Wirtz, Laura D. Wood. Three-dimensional genomic analysis of human pancreatic intraepithelial neoplasia (PanIN) reveals striking multifocality and genetic heterogeneity [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR007.
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Affiliation(s)
| | | | | | - Yuchen Jiao
- 3Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Mainland)
| | - Pei-Hsun Wu
- 2The Johns Hopkins University, Baltimore, MD,
| | | | - Denis Wirtz
- 2The Johns Hopkins University, Baltimore, MD,
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Xu C, Cheng S, Chen K, Song Q, Liu C, Fan C, Zhang R, Zhu Q, Wu Z, Wang Y, Fan J, Zheng H, Lu L, Chen T, Zhao H, Jiao Y, Qu C. Sex Differences in Genomic Features of Hepatitis B-Associated Hepatocellular Carcinoma With Distinct Antitumor Immunity. Cell Mol Gastroenterol Hepatol 2022; 15:327-354. [PMID: 36272708 PMCID: PMC9772570 DOI: 10.1016/j.jcmgh.2022.10.009] [Citation(s) in RCA: 4] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND & AIMS Aflatoxin exposure increases the risk for hepatocellular carcinoma (HCC) in hepatitis B virus (HBV)-infected individuals, particularly males. We investigated sex-based differences in the HCC genome and antitumor immunity. METHODS Whole-genome, whole-exome, and RNA sequencing were performed on 101 HCC patient samples (47 males, 54 females) that resulted from HBV infection and aflatoxin exposure from Qidong. Androgen on the expression of aflatoxin metabolism-related genes and nonhomologous DNA end joining (NHEJ) factors were examined in HBV-positive HCC cell lines, and further tested in tumor-bearing syngeneic mice. RESULTS Qidong HCC differed between males and females in genomic landscape and transcriptional dysfunction pathways. Compared with females, males expressed higher levels of aflatoxin metabolism-related genes, such as AHR and CYP1A1, and lower levels of NHEJ factors, such as XRCC4, LIG4, and MRE11, showed a signature of up-regulated type I interferon signaling/response and repressed antitumor immunity. Treatment with AFB1 in HBV-positive cells, the addition of 2 nmol/L testosterone to cultures significantly increased the expression of aflatoxin metabolism-related genes, but reduced NHEJ factors, resulting in more nuclear DNA leakage into cytosol to activate cGAS-STING. In syngeneic tumor-bearing mice that were administrated tamoxifen daily via oral gavage, favorable androgen signaling repressed NHEJ factor expression and activated cGAS-STING in tumors, increasing T-cell infiltration and improving anti-programmed cell death protein 1 treatment effect. CONCLUSIONS Androgen signaling in the context of genotoxic stress repressed DNA damage repair. The alteration caused more nuclear DNA leakage into cytosol to activate the cGAS-STING pathway, which increased T-cell infiltration into tumor mass and improved anti-programmed cell death protein 1 immunotherapy in HCCs.
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Affiliation(s)
- Chungui Xu
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Shaoyan Cheng
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kun Chen
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qianqian Song
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chang Liu
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chunsun Fan
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, Jiangsu Province, China
| | - Ruochan Zhang
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qing Zhu
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhiyuan Wu
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yuting Wang
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jian Fan
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, Jiangsu Province, China
| | - Hongwei Zheng
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, Jiangsu Province, China
| | - Lingling Lu
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, Jiangsu Province, China
| | - Taoyang Chen
- Qidong Liver Cancer Institute, Qidong People's Hospital, Qidong, Jiangsu Province, China
| | - Hong Zhao
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Hong Zhao, MD, Department of Hepatobiliary Surgery, State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Yuchen Jiao, MD, PhD, State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.
| | - Chunfeng Qu
- State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Immunology Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,Correspondence Address correspondence to: Chunfeng Qu, MD, PhD, State Key Lab of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.
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Jiao Y, Liu C, Chang J, Zhou S, Ji Y. Self-management preferences in patients with mild cognitive impairment: A qualitative study. Front Psychol 2022; 13:955960. [DOI: 10.3389/fpsyg.2022.955960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
PurposePatients with mild cognitive impairment (MCI) require self-management, yet current self-management compliance is low. Taking patients’ preferences into account can improve the self-management situation. The purpose of this study is to look into MCI patients’ preferences for self-management in China.MethodsA qualitative research was conducted using semi-structured in-depth interviews with 21 patients recently diagnosed with MCI who were chosen by purposive sampling. These interviews were analyzed through thematic analysis and identified emerging themes.ResultsFive themes of self-management preference were identified: (1) Preference for acquiring disease knowledge; (2) Preference for participating in drug therapy; (3) Preference for participating in exercise; (4) Preference for applying memory compensation strategy; (5) Preferences for emotional expression and response.ConclusionOur study identified the specific preferences of MCI patients in China for the main self-management items. The findings are valuable insights for knowing MCI patients’ self-management content and preferences and provide better guidance for health practitioners to improve self-management compliance.
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Liu C, Yang H, Jiao Y, Liu Y, Chang J, Ji Y. Preferences of people with mild cognitive impairment for physical activity interventions in China: protocol for a discrete choice experiment study. BMJ Open 2022; 12:e064153. [PMID: 36241356 PMCID: PMC9577920 DOI: 10.1136/bmjopen-2022-064153] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
INTRODUCTION Exercise interventions are important non-pharmacological interventions for patients with mild cognitive impairment (MCI), but patients with MCI have poor compliance and there is no consistent strategy for exercise interventions. Understanding the needs and preferences of MCI patients allows for the development of effective and acceptable exercise intervention programmes that achieve the goals of patient-centred care. This study uses a discrete choice experiment (DCE) to measure and quantify MCI patients' preferences for exercise interventions, and aims at (1) identifying and exploring which elements of exercise intervention programmes are essential for MCI patients; (2) measuring MCI patients' preferences for exercise interventions and summarising relevant characteristics that may influence preference choices and (3) determining whether these preferences vary by participant characteristics and classifying the population types based on the sociodemographic characteristics of the participants. METHODS AND ANALYSIS A DCE will be conducted to explore MCI patients' preferences for exercise interventions. We conducted a systematic literature review and extensive qualitative work to select the best attributes to develop the design of DCE. A partial factorial survey design was generated through an orthogonal experimental design. We will conduct a questionnaire survey in one city each in the eastern (Nanjing), western (Xining), southern (Zhuhai) and northern (Beijing) parts of China and reach the planned sample size (n=278). Final data will be analysed using a mixed logit model and a latent class model. ETHICS AND DISSEMINATION This study was approved by the Ethics Committee of Nanjing Medical University (2021-666). All participants will be required to provide informed consent. Our findings will be disseminated and shared with interested patient groups and the general public through online blogs, policy briefs, national and international conferences and peer-reviewed journals.
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Affiliation(s)
- Chang Liu
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Hong Yang
- Department of General Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Yuchen Jiao
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Yunyue Liu
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Jing Chang
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Yan Ji
- School of Nursing, Nanjing Medical University, Nanjing, China
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Wu Z, Jiao Y, Liu F, Ai Z, Zhang Q. Reducing temperature sensitivity of gas measurement using chirped-modulated photoacoustic spectroscopy. Rev Sci Instrum 2022; 93:094902. [PMID: 36182511 DOI: 10.1063/5.0106669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Resonance frequency drift caused by a change in temperature greatly limits the application of high-Q resonators with high temperature sensitivity in photoacoustic (PA) gas detection systems. In this work, a chirp-wavelength combined modulation method was designed by incorporating a real-time frequency scanning in wavelength-modulated PA spectroscopy to reduce the influence of temperature changes on measurement. Theoretical analysis shows that the chirp rate depends on the precision requirements and the cutoff frequency of the cascaded low-pass filter. Trace acetylene measurement experiment at varying temperature verified that the proposed method can significantly reduce the temperature sensitivity within a preset temperature range. Thus, this method can effectively reduce the temperature sensitivity of a high-Q resonator for improving the measurement accuracy and detection limit in trace gas detection.
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Affiliation(s)
- Z Wu
- State Key Laboratory of Electric Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Y Jiao
- State Key Laboratory of Electric Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - F Liu
- State Key Laboratory of Electric Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Z Ai
- State Key Laboratory of Electric Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Q Zhang
- State Key Laboratory of Electric Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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Cheng FF, Ma HH, Jiao Y, Wei A, Lian HY, Wang D, Yang Y, Zhao XX, Li ZG, Wang TY, Zhang R. [Efficacy and safety of modified hemophagocytic lymphohistiocytosis 04 regimen in Beijing Children's Hospital]. Zhonghua Er Ke Za Zhi 2022; 60:804-809. [PMID: 35922192 DOI: 10.3760/cma.j.cn112140-20211109-00939] [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: 06/15/2023]
Abstract
Objective: To evaluate the efficacy and safety of Beijing Children's Hospital (BCH) modified hemophagocytic lymphohistiocytosis (HLH) 04 regimen in the treatment of childhood HLH. Methods: A retrospective cohort study was conducted. From January 2016 to December 2017, 110 children with HLH who were treated with the modified HLH-04 regimen (replacing dexamethasone with methylprednisolone during the induction period, reducing the dose and frequency of etoposide, and not using cyclosporine except for autoimmune-related HLH) at the Hematology Oncology Center of Beijing Children's Hospital were selected as the modified group, while 102 children treated with the standard HLH-04 regimen from January 2012 to December 2015 were selected as the control group. The early remission rate, survival rate and adverse reactions of two groups were compared. Rank sum test and chi square test were used for comparison between groups. Results: The age of onset in the modified group was 1.9 (1.1, 3.5) years, with 65 males and 45 females. The age of onset in the control group was 2.0 (1.2, 4.6) years, with 47 males and 55 females. No significant difference was found in age and gender between 2 groups (both P>0.05). Except for fibrinogen (1.3 (1.0, 1.7) vs. 1.1 (0.8, 1.4) g/L, Z=-2.67, P=0.008) and natural killer cell activity (13.9 (13.4, 16.3) % vs.14.9 (12.0, 16.1) %, Z=-2.34, P=0.028), there were no statistically significant differences in etiology, disease duration, first clinical presentation, or laboratory tests between 2 groups (all P>0.05). At 2 months and 3 years, there were no statistically significant differences in overall survival between 2 groups (84.5% (93/110) vs.76.5% (78/102), 78.2% (86/110) vs. 67.6% (69/102), χ2=2.28, 3.07, P=0.131, 0.080). The first 3 weeks were the most common time for bone marrow suppression in the modified group, with a lower incidence than in the control group (47.3% (52/110) vs. 62.7% (64/102), χ2=5.11, P=0.024). The modified group had a lower rate of fungal infections than the control group (3.6% (4/110) vs. 13.7% (14/102), χ2=6.93, P=0.008). Compared with the control group, fewer children in the modified group died as a result of side effects from chemotherapy (8.0% (2/25) vs.30.3% (10/33), χ2=4.31, P=0.038). Conclusion: The BCH modified HLH-04 regimen reduced the intensity of chemotherapy, with overall efficacy no worse than the standard HLH-04 regimen, and significantly reduced the rate of chemotherapy-related myelosuppression, fungal infection and mortality.
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Affiliation(s)
- F F Cheng
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - H H Ma
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - Y Jiao
- Postgraduate Research Institute, Statistics of Renmin University of China, Beijing 100045, China
| | - A Wei
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - H Y Lian
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - D Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - Y Yang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - X X Zhao
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - Z G Li
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - T Y Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
| | - R Zhang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Disease Laboratory of Beijing Pediatric Research Institute, Beijing 100045, China
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Li L, Song Q, Cao D, Jiao Y, Yuan G, Song Y. Whole-Exome Sequencing Could Distinguish Primary Pulmonary Squamous Cell Carcinoma From Lung Metastases in Individuals With Cervical Squamous Cell Carcinoma. Pathol Oncol Res 2022; 28:1610325. [PMID: 35645619 PMCID: PMC9130473 DOI: 10.3389/pore.2022.1610325] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022]
Abstract
Aims: Metastatic cervical carcinoma is hard to cure using traditional treatment and new therapeutic approaches are needed. However, the process of clonal evolution and the molecular alterations that contribute to tumor progression from primary to metastatic carcinoma remain unclear. It is currently difficult to distinguish between the primary pulmonary squamous cell carcinoma (PPSCC) and metastatic cervical squamous cell carcinoma (CSCC). Methods: Paired primary CSCC and lung/lymph nodes metastatic lesions from eight patients were analyzed by whole-exome sequencing (WES). WES data of matched specimens and normal samples were aligned to the human reference genome and analyzed to identify somatic mutations in primary and metastatic lesions. Results: A total of 1,254 somatic variants were identified. All the primary lesions and metastatic lesions shared mutations, the percentage of shared mutations between primary lesions and corresponding metastatic lesions varied significantly, ranging from 6% to 70%. In other words, all the metastatic lesions are clonally related to primary lesions, confirming WES could prove they are metastatic from the cervix but not PPSCC. We tried to apply a gene panel to help distinguish PPSCC and metastatic CSCC but failed because the mutations were widely distributed in CSCC. Interestingly, lymph nodes metastasis (LNM) harbored fewer cancer driver mutations than primary CSCC specimens with a significant difference. Besides this, there was no significant difference in somatic mutations and copy number variation (CNV) between primary and metastatic CSCC. Conclusion: Our data demonstrate that WES is an additional helpful tool in distinguishing PPSCC and metastatic CSCC, especially for certain difficult cases.
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Affiliation(s)
- Lihong 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, China
| | - Qianqian Song
- State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Genetron Health (Beijing) Co. Ltd., Beijing, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangwen Yuan
- Department of Gynecology Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medvdical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Song
- 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, China
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Wang L, Zhu Y, Zhang B, Wang X, Mo H, Jiao Y, Xu J, Huang J. Prognostic and predictive impact of neutrophil-to-lymphocyte ratio and HLA-I genotyping in advanced esophageal squamous cell carcinoma patients receiving immune checkpoint inhibitor monotherapy. Thorac Cancer 2022; 13:1631-1641. [PMID: 35437954 PMCID: PMC9161342 DOI: 10.1111/1759-7714.14431] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/03/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 01/02/2023] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have become standard‐of‐care in patients with pretreated advanced esophageal squamous cell carcinoma (ESCC). However, reliable biomarkers for clinical outcomes are lacking for ICIs. The exploration of effective biomarkers is therefore needed to optimize patient benefit in the treatment of ESCC. Methods Sixty‐nine patients with advanced ESCC enrolled at one center from two prospective trials were consecutively analyzed. NLR was dynamically collected and high‐resolution HLA‐I genotyping were performed on genomic DNA. Overall response rate (ORR), median progression‐free survival (mPFS) and median overall survival (mOS) were investigated. Results Thirty‐three (47.8%) of 69 patients with baseline NLR ≥4 demonstrated significantly worse clinical outcomes (ORR 9.1% vs. 36.1%, p = 0.018; mPFS 1.8 vs. 3.2 months, hazard ratio [HR] 1.79, p = 0.026; mOS 7.4 vs. 11.0 months, HR 2.28, p = 0.008). An NLR decrease ≥20% at the first radiological evaluation was associated with longer OS (median, 14.0 vs. 7.9 months, p = 0.038). Eleven (15.9%) patients with HLA‐I homozygosity presented poorer clinical outcomes (ORR 0 vs. 27.6%, p = 0.056; mPFS 1.8 vs. 2.4 months, HR 3.37, p = 0.010; mOS 5.6 vs. 10.5 months, HR 3.97, p = 0.004). Patients with baseline NLR ≥4 and HLA‐I homozygosity had the worst outcome (ORR 0; mPFS 1.4 months; mOS 1.8 months) among all. The association between NLR, HLA‐I genotyping and clinical outcomes was independent of programmed death receptor ligand‐1 expression. Conclusions NLR and HLA‐I genotyping could have predictive and prognostic value in patients with advanced ESCC receiving camrelizumab, and the combination of biomarkers may help to identify more patient benefit from immunotherapy.
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Affiliation(s)
- Lin Wang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yanrong Zhu
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Zhang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xi Wang
- Daycare Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongnan Mo
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Huang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Zhao L, Jiang L, Liu Y, Wang X, Song J, Sun Y, Bai Y, Dong X, Sun L, Wu J, Jiao Y, Zhao X. Integrated analysis of circulating tumour cells and circulating tumour DNA to detect minimal residual disease in hepatocellular carcinoma. Clin Transl Med 2022; 12:e793. [PMID: 35384341 PMCID: PMC8982315 DOI: 10.1002/ctm2.793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Affiliation(s)
- Lina 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, China
| | - Liping Jiang
- 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, China
| | - Yunhe Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuebing Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Liver Transplantation Center, National Clinical Research Center for Digestive Diseases (NCRC-DD), Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jinge Song
- 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, China
| | - Yulin 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, Beijing, China
| | - Yinlei Bai
- Jinchenjunchuang Clinical Laboratory, Hangzhou, China
| | - Xiu Dong
- 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, China
| | - Liying Sun
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Liver Transplantation Center, National Clinical Research Center for Digestive Diseases (NCRC-DD), Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- 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, China
| | - Xiaohang 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, China
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Liu W, Li Y, Tang Y, Song Q, Wang J, Li N, Chen S, Shi J, Wang S, Li Y, Jiao Y, Zeng Y, Jin J. Response prediction and risk stratification of patients with rectal cancer after neoadjuvant therapy through an analysis of circulating tumour DNA. EBioMedicine 2022; 78:103945. [PMID: 35306340 PMCID: PMC8933829 DOI: 10.1016/j.ebiom.2022.103945] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/11/2022] Open
Abstract
Background Multiple approaches based on cell-free DNA (cfDNA) have been applied to detect minimal residual disease (MRD) and to predict prognosis or recurrence. However, a comparison of the approaches used in different cohorts and studies is difficult. We aimed to compare multiple approaches for MRD analysis after neoadjuvant therapy (NAT) in patients with locally advanced rectal cancer (LARC). Methods Sixty patients with LARC from a multicentre, phase II/III randomized trial were included, with tissue and blood samples collected. For each cfDNA sample, we profiled MRD using 3 approaches: personalized assay targeting tumour-informed mutations, universal panel of genes frequently mutated in colorectal cancer (CRC), and low depth sequencing for copy number alterations (CNAs). Findings Positive MRD based on post-NAT personalized assay was significantly associated with an increased risk of recurrence (HR = 27.38; log-rank P < 0.0001). MRD analysis based on universal panel (HR = 5.18; log-rank P = 0.00086) and CNAs analysis (HR = 9.24; log-rank P = 0.00017) showed a compromised performance in predicting recurrence. Both the personalized assay and universal panel showed complementary pattern to CNAs analysis in detecting cases with recurrence and the combination of the two types of biomarkers may lead to better performance. Interpretation The combination of mutation profiling and CNA profiling can improve the detection of MRD, which may help optimize the treatment strategies for patients with LARC.
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Ma Y, Zhu Q, Wang X, Liu M, Chen Q, Jiang L, Chi Y, Zeng YX, Zhao H, Jiao Y. Synthetic lethal screening identifies DHODH as a target for MEN1-mutated tumor cells. Cell Res 2022; 32:596-599. [PMID: 35169281 DOI: 10.1038/s41422-022-00613-1] [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] [Received: 07/17/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yarui Ma
- 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, China.,Department of Medical Oncology, Beijing Hospital, National Center of Gerontology and Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qing Zhu
- 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, China.,Department of Clinical Laboratory Diagnostics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaobing Wang
- 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, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei 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, China
| | - Qichen Chen
- Department of Hepatobiliary Surgery, 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, China
| | - Liming Jiang
- Department of Diagnostic Imaging, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yihebali Chi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Hong Zhao
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Department of Hepatobiliary Surgery, 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, China.
| | - Yuchen Jiao
- 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, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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35
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JIANG S, Jiao Y, Yu T, Zou G, Gao H, Zhuo L, Li W. POS-333 Local activation of complement C3 in kidney tissue mediates diabetic tubulointerstitial injury. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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36
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Zhu Q, Ma Y, Liang J, Wei Z, Li M, Zhang Y, Liu M, He H, Qu C, Cai J, Wang X, Zeng Y, Jiao Y. Correction: AHR mediates the Aflatoxin B1 toxicity associated with hepatocellular carcinoma. Signal Transduct Target Ther 2021; 6:432. [PMID: 34924560 PMCID: PMC8685275 DOI: 10.1038/s41392-021-00794-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Qing Zhu
- 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, China
| | - Yarui Ma
- 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, China
| | - Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhewen Wei
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mo Li
- 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, China
| | - Ying Zhang
- 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, China
| | - Mei 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, China
| | - Huan He
- 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, China
| | - Chunfeng Qu
- 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, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- 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, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Yixin Zeng
- 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, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yuchen Jiao
- 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, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China. .,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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37
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Jiao Y, Qi X, Han TL, Gao Y, Zhang Y, Zhao JH, Sun LL. [Study on the genetic characteristics of enteric viral pathogens of sporadic adult diarrhea in Chaoyang district, Beijing in 2019]. Zhonghua Yu Fang Yi Xue Za Zhi 2021; 55:1404-1409. [PMID: 34963236 DOI: 10.3760/cma.j.cn112150-20210224-00182] [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: 06/14/2023]
Abstract
Objective: To analyze the distribution and genetic characteristics of sporadic adult diarrhea virus in Chaoyang District, Beijing. Methods: Fecal samples from 177 adult patients with sporadic diarrhea were collected from 4 enteric outpatient clinics in Chaoyang District, Beijing from May to December 2019. Nucleic acid detection of Norovirus, Sappovirus, Rotavirus, Enteric Adenovirus and Astrovirus in the samples was performed by real-time quantitative PCR. The positive samples were amplified by RT-PCR/PCR and sequenced. The phylogenetic analysis was performed by neighbor-Joining (NJ) methods of Mega 6.0 software. Results: There were 60 of 177 (33.90%) adult sporadic diarrhea samples positive for enteric viral pathogens. Among them, 47 cases were infected with single virus, including 29 cases of Norovirus, 9 cases of Sappovirus, 8 cases of Astrovirus and 1 case of Enteric Adenovirus, in addition with 13 cases of multiple infections. None of rotavirus was detected. Partial sequences were successfully obtained for analysis, including 16 cases of GI Norovirus (7 subtypes and GI.3[P13] predominant), 10 cases of GII Norovirus (5 subtypes and GII.6[P7] predominant), 12 cases of Sappovirus (4 subtypes and GI.2 predominant), and 7 cases of Astrovirus (2 subtypes and AST-1 predominant). Conclusion: Norovirus, Astrovirus and Sappovirus are main pathogens among sporadic adult diarrhea in Beijing in 2019, and and different pathogenic gene subtypes show diverse characteristics.
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Affiliation(s)
- Y Jiao
- Department of Microbiological Inspection, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - X Qi
- Department of Infectious Diseases and Endemic Diseases Preventiou, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - T L Han
- Department of Microbiological Inspection, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - Y Gao
- Department of Microbiological Inspection, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - Y Zhang
- Department of Infectious Diseases and Endemic Diseases Preventiou, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - J H Zhao
- Department of Microbiological Inspection, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
| | - L L Sun
- Department of Microbiological Inspection, Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing 100021, China
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38
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Jia SS, Wang XC, Jiao Y, Jiang DY, Zhao J. [Research advances on skin wounds suturing techniques and their clinical application]. Zhonghua Shao Shang Za Zhi 2021; 37:1099-1104. [PMID: 34794263 DOI: 10.3760/cma.j.cn501120-20200701-00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Stitching skin wounds is one of the essential skills of a surgeon. Whether it is a traumatic wound or a surgical incision, choosing the most appropriate closure technique according to its characteristics is an important factor for good healing. Various skin wounds suturing techniques have been created and improved over the years, which have advantages of simple operation, precise alignment, reducing tension of the wound edges, and reducing scar formation, etc. Although these techniques provide more options for wound suture, they also put forward requirements for the judgment and operation ability of the operators. This article summarizes the advantages and disadvantages of the different skin wounds suturing techniques and their clinical application.
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Affiliation(s)
- S S Jia
- Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - X C Wang
- Department of Plastic and Burn Surgery, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Y Jiao
- Department of Emergency, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - D Y Jiang
- Department of Emergency, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - J Zhao
- Department of Emergency, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
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39
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Tian S, Jiao Y, Gao Z, Xu Y, Fu L, Fu H, Zhou W, Hu C, Liu G, Wang M, Ma D. Catalytic Amination of Polylactic Acid to Alanine. J Am Chem Soc 2021; 143:16358-16363. [PMID: 34591468 DOI: 10.1021/jacs.1c08159] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In comparison to the traditional petroleum-based plastics, polylactic acid, the most popular biodegradable plastic, can be decomposed into carbon dioxide and water in the environment. However, the natural degradation of polylactic acid requires a substantial period of time and, more importantly, it is a carbon-emitting process. Therefore, it is highly desirable to develop a novel transformation process that can upcycle the plastic trash into value-added products, especially with high chemical selectivity. Here we demonstrate a one-pot catalytic method to convert polylactic acid into alanine by a simple ammonia solution treatment using a Ru/TiO2 catalyst. The process has a 77% yield of alanine at 140 °C, and an overall selectivity of 94% can be reached by recycling experiments. Importantly, no added hydrogen is used in this process. It has been verified that lactamide and ammonium lactate are the initial intermediates and that the dehydrogenation of ammonium lactate initiates the amination, while Ru nanoparticles are essential for the dehydrogenation/rehydrogenation and amination steps. The process demonstrated here could expand the application of polylactic acid waste and inspire new upcycling strategies for different plastic wastes.
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Affiliation(s)
- Shuheng Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yuchen Jiao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Zirui Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yao Xu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Linke Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Wu Zhou
- School of Physical Sciences and CAS Key Laboratory of Vacuum Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chaoquan Hu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,Nanjing IPE Institute of Green Manufacturing Industry, Nanjing 211135, People's Republic of China
| | - Guosheng Liu
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Meng Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Ding Ma
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
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40
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Liu C, Su M, Jiao Y, Ji Y, Zhu S. Effects of Dance Interventions on Cognition, Psycho-Behavioral Symptoms, Motor Functions, and Quality of Life in Older Adult Patients With Mild Cognitive Impairment: A Meta-Analysis and Systematic Review. Front Aging Neurosci 2021; 13:706609. [PMID: 34616285 PMCID: PMC8488360 DOI: 10.3389/fnagi.2021.706609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 05/07/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Dance interventions are considered beneficial for older patients with mild cognitive impairment in many aspects. We conducted a comprehensive systematic review and meta-analysis to assess the effects of dance on different aspects (cognitive function, emotions, physical function, and quality of life) of this population. Methods: A systematic search of PubMed, Web of Science, the Cochrane Central Register of Controlled Trials, Embase, American Psychological Association PsycInfo, ProQuest, Scopus, Cumulative Index to Nursing and Allied Health Literature, the Chinese BioMedical Literature Database, the VIP Database for Chinese Technical Periodicals, China National Knowledge Infrastructure, and Wanfang Data database was performed. Two reviewers independently assessed the study quality. Results: Fourteen studies were retrieved from the databases for analysis. The pooled results showed that dance interventions significantly improved global cognition (standardized mean difference [SMD] = 0.73, 95% confidence interval [CI]: 0.47 to 0.99, P < 0.00001), rote memory (mean difference [MD] = -2.12, 95% CI: -4.02 to -0.21, P = 0.03), immediate recall (SMD = 0.54, 95% CI: 0.30 to 0.78, P < 0.0001), delayed recall (SMD = 0.56, 95% CI: 0.26 to 0.86, P = 0.0002) and attention (SMD = 0.38, 95% CI: 0.13 to 0.64, P = 0.003). No significant improvement was found in executive function, language, depression, anxiety, dementia-related behavioral symptoms, motor function, and quality of life. Conclusion: Dance interventions benefit most aspects of cognitive functions. The evidence for the effects of dance on psycho-behavioral symptoms, motor function and quality of life remains unclear. More trials with rigorous study designs are necessary to provide this evidence.
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Affiliation(s)
- Chang Liu
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Mengyu Su
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Yuchen Jiao
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Yan Ji
- School of Nursing, Nanjing Medical University, Nanjing, China
| | - Shuqin Zhu
- School of Nursing, Nanjing Medical University, Nanjing, China
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Zhang S, Yin H, Zhang J, Yang L, Yang G, Jia J, Jiao Y, Ying J, Wang Y. Novel genetic characteristics in low-grade fetal adenocarcinoma of the lung. Thorac Cancer 2021; 12:2789-2795. [PMID: 34464028 PMCID: PMC8520817 DOI: 10.1111/1759-7714.14126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/22/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 01/24/2023] Open
Abstract
Background Low‐grade fetal adenocarcinoma of the lung (L‐FLAC) is a rare subtype of lung adenocarcinoma with undetermined histological features and genetic abnormalities. In this study, we attempted to investigate the pathological characteristics and genomic profiles of L‐FLAC. Methods Among 9839 cases of primary lung adenocarcinoma resected at Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College between January 2011 and June 2016, three cases diagnosed with L‐FLAC were selected. An immunohistochemical profile and whole exome sequencing (WES) using tumor and normal tissues was conducted. The last follow‐up date of patients was January 2021. Results Three cases diagnosed with L‐FLAC were finally screened, suggesting a percentage of 0.03%. All three patients were male and diagnosed as stage I following radical lobectomy. The missense variant was found to be the major gene mutation type using WES. CTNNB1 and DICER1 were the two most frequent gene mutations. All cases demonstrated positive TTF‐1 expression. In addition, two patients showed positive expression of β‐catenin (nuclear/cytoplasmic expression), CgA and Sny. Negative expression of PD‐L1 in tumor cells was observed in all three cases. One case with a relatively high tumor mutation burden (TMB) (2.18 mut/Mb) had an inferior overall survival of 11.5 months. However, the other two cases with a lower TMB (0.12 and 0.74 mut/Mb) still acquired disease‐free status up to the last follow‐up date. Conclusions L‐FLAC has a specific molecular background which is different from lung adenocarcinoma. Furthermore, gene heterogeneity was found and might be the reason for a dramatically different prognosis in these L‐FLAC patients.
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Affiliation(s)
- Shuyang Zhang
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huihui Yin
- 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, China
| | - Jing Zhang
- 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, China.,Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Lu Yang
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangjian Yang
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia Jia
- 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, China
| | - Yuchen Jiao
- 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, China
| | - Jianming Ying
- 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, China
| | - Yan Wang
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Zhu Q, Ma Y, Liang J, Wei Z, Li M, Zhang Y, Liu M, He H, Qu C, Cai J, Wang X, Zeng Y, Jiao Y. AHR mediates the aflatoxin B1 toxicity associated with hepatocellular carcinoma. Signal Transduct Target Ther 2021; 6:299. [PMID: 34373448 PMCID: PMC8352983 DOI: 10.1038/s41392-021-00713-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/31/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Aflatoxin exposure is a crucial factor in promoting the development of primary hepatocellular carcinoma (HCC) in individuals infected with the hepatitis virus. However, the molecular pathways leading to its bioactivation and subsequent toxicity in hepatocytes have not been well-defined. Here, we carried out a genome-wide CRISPR-Cas9 genetic screen to identify aflatoxin B1 (AFB1) targets. Among the most significant hits was the aryl hydrocarbon receptor (AHR), a ligand-binding transcription factor regulating cell metabolism, differentiation, and immunity. AHR-deficient cells tolerated high concentrations of AFB1, in which AFB1 adduct formation was significantly decreased. AFB1 triggered AHR nuclear translocation by directly binding to its N-terminus. Furthermore, AHR mediated the expression of P450 induced by AFB1. AHR expression was also elevated in primary tumor sections obtained from AFB1-HCC patients, which paralleled the upregulation of PD-L1, a clinically relevant immune regulator. Finally, anti-PD-L1 therapy exhibited greater efficacy in HCC xenografts derived from cells with ectopic expression of AHR. These results demonstrated that AHR was required for the AFB1 toxicity associated with HCC, and implicate the immunosuppressive regimen of anti-PD-L1 as a therapeutic option for the treatment of AFB1-associated HCCs.
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Affiliation(s)
- Qing Zhu
- 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, China
| | - Yarui Ma
- 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, China
| | - Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhewen Wei
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mo Li
- 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, China
| | - Ying Zhang
- 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, China
| | - Mei 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, China
| | - Huan He
- 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, China
| | - Chunfeng Qu
- 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, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- 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, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Yixin Zeng
- 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, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yuchen Jiao
- 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, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China. .,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Du Y, Ma Y, Zhu Q, Liu T, Jiao Y, Yuan P, Wang X. An m6A-Related Prognostic Biomarker Associated With the Hepatocellular Carcinoma Immune Microenvironment. Front Pharmacol 2021; 12:707930. [PMID: 34248650 PMCID: PMC8263919 DOI: 10.3389/fphar.2021.707930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/11/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background: N6-methyladenosine (m6A) is related to the progression of multiple cancers. However, the underlying influences of m6A-associated genes on the tumor immune microenvironment in hepatocellular carcinoma (HCC) remain poorly understood. Therefore, we sought to construct a survival prediction model using m6A-associated genes to clarify the molecular and immune characteristics of HCC. Methods: HCC case data were downloaded from The Cancer Genome Atlas (TCGA). Then, by applying consensus clustering, we identified two distinct HCC clusters. Next, four m6A-related genes were identified to construct a prognostic model, which we validated with Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC) datasets. Additionally, the molecular and immune characteristics in different subgroups were analyzed. Results: m6A RNA methylation regulators were differentially expressed between HCC and normal samples and linked with immune checkpoint expression. Using consensus clustering, we divided HCC samples into two subtypes with distinct clinical features. Cluster 2 was associated with unfavorable prognosis, higher immune checkpoint expression and immune cell infiltration levels. In addition, the immune and carcinogenic signaling pathways were enriched in cluster 2. Furthermore, we constructed a risk model using four m6A-associated genes. Patients with different risk scores had distinct survival times, expression levels of immunotherapy biomarkers, TP53 mutation rates, and sensitivities to chemotherapy and targeted therapy. Similarly, the model exhibited an identical impact on overall survival in the validation cohorts. Conclusion: The constructed m6A-based signature may be promising as a biomarker for prognostics and to distinguish immune characteristics in HCC.
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Affiliation(s)
- Yingxi Du
- 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, China
| | - Yarui Ma
- 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, China
| | - Qing Zhu
- 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, China
| | - Tongzheng Liu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Yuchen Jiao
- 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, China
| | - Peng Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- 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, China
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Yin H, Yang L, Peng G, Yang K, Mi Y, Hu X, Hao X, Jiao Y, Wang X, Wang Y. The commensal consortium of the gut microbiome is associated with favorable responses to anti-programmed death protein 1 (PD-1) therapy in thoracic neoplasms. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0450. [PMID: 33960176 PMCID: PMC8610161 DOI: 10.20892/j.issn.2095-3941.2020.0450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/09/2020] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVE Immune checkpoint inhibitors have revolutionized cancer therapy for multiple types of solid tumors, but as expected, a large percentage of patients do not show durable responses. Biomarkers that can predict clinical responses to immunotherapies at diagnosis are therefore urgently needed. Herein, we determined the associations between baseline gut commensal microbes and the clinical treatment efficiencies of patients with thoracic neoplasms during anti-programmed death protein 1 (PD-1) therapy. METHODS Forty-two patients with advanced thoracic carcinoma who received anti-PD-1 treatment were enrolled in the study. Baseline and time-serial stool samples were analyzed using 16S ribosomal RNA gene sequencing. Tumor responses, patient progression-free survival, and overall survival were used to measure clinical outcomes. RESULTS The diversities of the baseline gut microbiota were similar between responders (n = 23) and nonresponders (n = 19). The relative abundances of the Akkermansiaceae, Enterococcaceae, Enterobacteriaceae, Carnobacteriaceae and Clostridiales Family XI bacterial families were significantly higher in the responder group. These 5 bacterial families acted as a commensal consortium and better stratified patients according to clinical responses (P = 0.014). Patients with a higher abundance of commensal microbes had prolonged PFS (P = 0.00016). Using multivariable analysis, the abundance of the commensal consortium was identified as an independent predictor of anti-PD-1 immunotherapy in thoracic neoplasms (hazard ratio: 0.17; 95% confidence interval: 0.05-0.55; P = 0.003). CONCLUSIONS Baseline gut microbiota may have a critical impact on anti-PD-1 treatment in thoracic neoplasms. The abundance of gut commensal microbes at diagnosis might be useful for the early prediction of anti-PD-1 immunotherapy responses.
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Affiliation(s)
- Huihui Yin
- 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
| | - Lu Yang
- Department of Medical 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
| | - Gongxin Peng
- Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100021, China
| | - Ke Yang
- Department of Medical Oncology, Cancer Hospital of Huanxing Chaoyang District Beijing, Beijing 100122, China
| | - Yuling Mi
- Department of Medical Oncology, Chaoyang Sanhuan Cancer Hospital, Beijing 100021, China
| | - Xingsheng Hu
- Department of Medical 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
| | - Xuezhi Hao
- Department of Medical 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
| | - Yuchen Jiao
- 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
| | - Xiaobing Wang
- 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
| | - Yan Wang
- Department of Medical 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
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Fujikura K, Hosoda W, Felsenstein M, Song Q, Reiter JG, Zheng L, Beleva Guthrie V, Rincon N, Dal Molin M, Dudley J, Cohen JD, Wang P, Fischer CG, Braxton AM, Noë M, Jongepier M, Fernández-del Castillo C, Mino-Kenudson M, Schmidt CM, Yip-Schneider MT, Lawlor RT, Salvia R, Roberts NJ, Thompson ED, Karchin R, Lennon AM, Jiao Y, Wood LD. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut 2021; 70:928-939. [PMID: 33028669 PMCID: PMC8262510 DOI: 10.1136/gutjnl-2020-321217] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/06/2020] [Accepted: 08/09/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursor lesions that can progress to invasive pancreatic cancer and are classified as low-grade or high-grade based on the morphology of the neoplastic epithelium. We aimed to compare genetic alterations in low-grade and high-grade regions of the same IPMN in order to identify molecular alterations underlying neoplastic progression. DESIGN We performed multiregion whole exome sequencing on tissue samples from 17 IPMNs with both low-grade and high-grade dysplasia (76 IPMN regions, including 49 from low-grade dysplasia and 27 from high-grade dysplasia). We reconstructed the phylogeny for each case, and we assessed mutations in a novel driver gene in an independent cohort of 63 IPMN cyst fluid samples. RESULTS Our multiregion whole exome sequencing identified KLF4, a previously unreported genetic driver of IPMN tumorigenesis, with hotspot mutations in one of two codons identified in >50% of the analyzed IPMNs. Mutations in KLF4 were significantly more prevalent in low-grade regions in our sequenced cases. Phylogenetic analyses of whole exome sequencing data demonstrated diverse patterns of IPMN initiation and progression. Hotspot mutations in KLF4 were also identified in an independent cohort of IPMN cyst fluid samples, again with a significantly higher prevalence in low-grade IPMNs. CONCLUSION Hotspot mutations in KLF4 occur at high prevalence in IPMNs. Unique among pancreatic driver genes, KLF4 mutations are enriched in low-grade IPMNs. These data highlight distinct molecular features of low-grade and high-grade dysplasia and suggest diverse pathways to high-grade dysplasia via the IPMN pathway.
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Affiliation(s)
- Kohei Fujikura
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Waki Hosoda
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Matthäus Felsenstein
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Surgery, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Qianqian Song
- State Key Lab 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
| | - Johannes G. Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA,Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, CA, USA,Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lily Zheng
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Natalia Rincon
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marco Dal Molin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan Dudley
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joshua D. Cohen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pei Wang
- State Key Lab 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
| | - Catherine G. Fischer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alicia M. Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michaël Noë
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martine Jongepier
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - C. Max Schmidt
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Rita T. Lawlor
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Department, The Pancreas Institute and Hospital Trust of Verona, Verona, Italy
| | - Nicholas J. Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth D. Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Marie Lennon
- Department of Medicine, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Correspondence: Laura D. Wood, MD, PhD, CRB2 Room 345, 1550 Orleans Street, Baltimore, MD 21231, Phone: 410-955-3511, Fax: 410-614-0671, , Yuchen Jiao, PhD, 4104 Laobingfanglou, 17 Panjiayuannanli, Beijing, China, 100021, Phone: 86-10-87787662,
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Lasky R, Chaudhuri S, Jiao Y, Larkin MS J, Monaghan C, Winter A, Raimann J, Neri L, Kotanko P, Hymes J, Lee S, Usvyat L, Kooman J, Maddux F. POS-534 TRAJECTORIES OF CLINICAL AND LABORATORY CHARACTERISTICS ASSOCIATED WITH COVID-19 IN HEMODIALYSIS PATIENTS BY SURVIVAL. Kidney Int Rep 2021. [PMCID: PMC8049706 DOI: 10.1016/j.ekir.2021.03.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Xu Y, Ma X, Ai X, Gao J, Liang Y, Zhang Q, Ma T, Mao K, Zheng Q, Wang S, Jiao Y, Zhang X, Li H. A Urine-Based Liquid Biopsy Method for Detection of Upper Tract Urinary Carcinoma. Front Oncol 2021; 10:597486. [PMID: 33634022 PMCID: PMC7901537 DOI: 10.3389/fonc.2020.597486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/21/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Background Conventional clinical detection methods such as CT, urine cytology, and ureteroscopy display low sensitivity and/or are invasive in the diagnosis of upper tract urinary carcinoma (UTUC), a factor precluding their use. Previous studies on urine biopsy have not shown satisfactory sensitivity and specificity in the application of both gene mutation or gene methylation panels. Therefore, these unfavorable factors call for an urgent need for a sensitive and non-invasive method for the diagnosis of UTUC. Methods In this study, a total of 161 hematuria patients were enrolled with (n = 69) or without (n = 92) UTUC. High-throughput sequencing of 17 genes and methylation analysis for ONECUT2 CpG sites were combined as a liquid biopsy test panel. Further, a logistic regression prediction model that contained several significant features was used to evaluate the risk of UTUC in these patients. Results In total, 86 UTUC− and 64 UTUC+ case samples were enrolled for the analysis. A logistic regression analysis of significant features including age, the mutation status of TERT promoter, and ONECUT2 methylation level resulted in an optimal model with a sensitivity of 94.0%, a specificity of 93.1%, the positive predictive value of 92.2% and a negative predictive value of 94.7%. Notably, the area under the curve (AUC) was 0.957 in the training dataset while internal validation produced an AUC of 0.962. It is worth noting that during follow-up, a patient diagnosed with ureteral inflammation at the time of diagnosis exhibiting both positive mutation and methylation test results was diagnosed with ureteral carcinoma 17 months after his enrollment. Conclusion This work utilized the epigenetic biomarker ONECUT2 for the first time in the detection of UTUC and discovered its superior performance. To improve its sensitivity, we combined the biomarker with high-throughput sequencing of 17 genes test. It was found that the selected logistic regression model diagnosed with ureteral cancer can evaluate upper tract urinary carcinoma risk of patients with hematuria and outperform other existing panels in providing clinical recommendations for the diagnosis of UTUC. Moreover, its high negative predictive value is conducive to rule to exclude patients without UTUC.
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Affiliation(s)
- Yansheng Xu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China.,Department of Urology, The Sixth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xin Ma
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xing Ai
- Department of Urology, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiangping Gao
- Department of Urology, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yiming Liang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Qin Zhang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Tonghui Ma
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Kaisheng Mao
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Qiaosong Zheng
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Sizhen Wang
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Yuchen Jiao
- State Key Lab 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, China
| | - Xu Zhang
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hongzhao Li
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
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Mattox AK, Yang B, Douville C, Lo SF, Sciubba D, Wolinsky JP, Gokaslan ZL, Robison J, Blair C, Jiao Y, Bettegowda C. The mutational landscape of spinal chordomas and their sensitive detection using circulating tumor DNA. Neurooncol Adv 2021; 3:vdaa173. [PMID: 33543146 PMCID: PMC7850091 DOI: 10.1093/noajnl/vdaa173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 11/29/2022] Open
Abstract
Background Chordomas are the most common primary spinal column malignancy in the United States. The aim of this study was to determine whether chordomas may be detected by evaluating mutations in circulating tumor DNA (ctDNA). Methods Thirty-two patients with a biopsy-confirmed diagnosis of chordoma had blood drawn pre-operatively and/or at follow-up appointments. Mutations in the primary tumor were identified by whole exome sequencing and liquid biopsy by ddPCR and/or RACE-Seq was used to detect one or more of these mutations in plasma ctDNA at concurrent or later time points. Results At the time of initial blood draw, 87.1% of patients were ctDNA positive (P <.001). Follow-up blood draws in twenty of the patients suggest that ctDNA levels may reflect the clinical status of the disease. Patients with positive ctDNA levels were more likely to have greater mutant allele frequencies in their primary tumors (P = .004) and undergo radiotherapy (P = .02), and the presence of ctDNA may correlate with response to systemic chemotherapy and/or disease recurrence. Conclusions Detection of ctDNA mutations may allow for the detection and monitoring of disease progression for chordomas.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Beibei Yang
- State Key Lab 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, China
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sheng-Fu Lo
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Sciubba
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jean Paul Wolinsky
- Department of Neurosurgery, Northwestern University School of Medicine, Chicago, Illinois, USA
| | - Ziya L Gokaslan
- Department of Neurosurgery, Brown University School of Medicine, Providence, Rhode Island, USA
| | - Jamie Robison
- Department of Neurosurgery, Mayo Clinic, Jacksonville, Florida, USA
| | - Cherie Blair
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yuchen Jiao
- State Key Lab 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, China
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Wang Y, Wang M, Li H, Chen K, Zeng H, Bi X, Zhu Z, Jiao Y, Wang Y, Zhu J, Zhao H, Liu X, Dai C, Fan C, Zhao C, Guo D, Zhao H, Zhou J, Wang D, Wu Z, Zhao X, Cui W, Zhang X, Cai J, Chen W, Qu C. A male-ABCD algorithm for hepatocellular carcinoma risk prediction in HBsAg carriers. Chin J Cancer Res 2021; 33:352-363. [PMID: 34321832 PMCID: PMC8286891 DOI: 10.21147/j.issn.1000-9604.2021.03.07] [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: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 11/28/2022] Open
Abstract
Objective Hepatocellular carcinoma (HCC) development among hepatitis B surface antigen (HBsAg) carriers shows gender disparity, influenced by underlying liver diseases that display variations in laboratory tests. We aimed to construct a risk-stratified HCC prediction model for HBsAg-positive male adults. Methods HBsAg-positive males of 35−69 years old (N=6,153) were included from a multi-center population-based liver cancer screening study. Randomly, three centers were set as training, the other three centers as validation. Within 2 years since initiation, we administrated at least two rounds of HCC screening using B-ultrasonography and α-fetoprotein (AFP). We used logistic regression models to determine potential risk factors, built and examined the operating characteristics of a point-based algorithm for HCC risk prediction. Results With 2 years of follow-up, 302 HCC cases were diagnosed. A male-ABCD algorithm was constructed including participant’s age, blood levels of GGT (γ-glutamyl-transpeptidase), counts of platelets, white cells, concentration of DCP (des-γ-carboxy-prothrombin) and AFP, with scores ranging from 0 to 18.3. The area under receiver operating characteristic was 0.91 (0.90−0.93), larger than existing models. At 1.5 points of risk score, 26.10% of the participants in training cohort and 14.94% in validation cohort were recognized at low risk, with sensitivity of identifying HCC remained 100%. At 2.5 points, 46.51% of the participants in training cohort and 33.68% in validation cohort were recognized at low risk with 99.06% and 97.78% of sensitivity, respectively. At 4.5 points, only 20.86% of participants in training cohort and 23.73% in validation cohort were recognized at high risk, with positive prediction value of 22.85% and 12.35%, respectively. Conclusions Male-ABCD algorithm identified individual’s risk for HCC occurrence within short term for their HCC precision surveillance.
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Affiliation(s)
- Yuting Wang
- State Key Lab 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
| | - Minjie Wang
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - He Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kun Chen
- State Key Lab 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
| | - Hongmei Zeng
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xinyu Bi
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zheng Zhu
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuchen Jiao
- State Key Lab 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
| | - Yong Wang
- Department of Ultrasonography, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Zhu
- Qidong Liver Cancer Institute & Qidong People's Hospital, Qidong 226200, China
| | - Hui Zhao
- Lingbi Center for Disease Control and Prevention, Suzhou 234200, China
| | - Xiang Liu
- Mengcheng Center for Disease Control and Prevention, Bozhou 233500, China
| | - Chunyun Dai
- Sheyang Center for Disease Control and Prevention, Yancheng 224300, China
| | - Chunsun Fan
- Qidong Liver Cancer Institute & Qidong People's Hospital, Qidong 226200, China
| | - Can Zhao
- Shenqiu County Center for Disease Control and Prevention, Zhoukou 411624, China
| | - Deyin Guo
- Dancheng Center for Disease Control and Prevention, Zhoukou 477150, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jianguo Zhou
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Dongmei Wang
- State Key Lab 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
| | - Zhiyuan Wu
- State Key Lab 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
| | - Xinming Zhao
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wei Cui
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Department of Nutrition, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wanqing Chen
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Chunfeng Qu
- State Key Lab 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
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Zhang W, Yang B, Weng L, Li J, Bai J, Wang T, Wang J, Ye J, Jing H, Jiao Y, Chen X, Liu H, Zeng YX. Single cell sequencing reveals cell populations that predict primary resistance to imatinib in chronic myeloid leukemia. Aging (Albany NY) 2020; 12:25337-25355. [PMID: 33226961 PMCID: PMC7803567 DOI: 10.18632/aging.104136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/06/2020] [Accepted: 09/20/2020] [Indexed: 01/12/2023]
Abstract
The treatment of chronic myeloid leukemia (CML), a disease caused by t(9;22)(q34;q11) reciprocal translocation, has advanced largely through the use of targeted tyrosine kinase inhibitors (TKIs). To identify molecular differences that might distinguish TKI responders from non-responders, we performed single cell RNA sequencing on cells (n = 41,723 cells) obtained from the peripheral blood of four CML patients at different stages of treatment to generate single cell expression profiles. Analysis of our single cell expression profiles in conjunction with those previously obtained from the bone marrow of additional CML patients and healthy donors (total = 69,263 cells) demonstrated that imatinib treatment significantly altered leukocyte population compositions in both responders and non-responders, and affected the expression profiles of multiple cell populations, including non-neoplastic cell types. Notably, in imatinib poor-responders, patient-specific pre-treatment unique stem/progenitor cells became enriched in peripheral blood compared to the responders. These results indicate that resistance to TKIs might be intrinsic in some CML patients rather than acquired, and that non-neoplastic immune cell types may also play vital roles in dispersing the responsiveness of patients to TKIs. Furthermore, these results demonstrated the potential utility of peripheral blood as a diagnostic tool in the TKI sensitivity of CML patients.
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Affiliation(s)
- Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China.,State Key Lab 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
| | - Beibei Yang
- State Key Lab 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
| | - Linqian Weng
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jiangtao Li
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jiefei Bai
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Ting Wang
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jingwen Wang
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jin Ye
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuchen Jiao
- State Key Lab 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
| | - Xixi Chen
- Genetron Health (Beijing) Co. Ltd., Beijing 102206, China.,Children’s Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Hui Liu
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yi-Xin Zeng
- State Key Lab 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.,Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
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