1
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He D, Liu Y, Dong S, Shen D, Yang X, Hao M, Yin X, He X, Li Y, Wang Y, Liu M, Wang J, Chen X, Cui L. The prognostic value of systematic genetic screening in amyotrophic lateral sclerosis patients. J Neurol 2024; 271:1385-1396. [PMID: 37980296 DOI: 10.1007/s00415-023-12079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with complex genetic architecture. Emerging evidence has indicated comorbidity between ALS and autoimmune conditions, suggesting a potential shared genetic basis. The objective of this study is to assess the prognostic value of systematic screening for rare deleterious mutations in genes associated with ALS and aberrant inflammatory responses. METHODS A discovery cohort of 494 patients and a validation cohort of 69 patients were analyzed in this study, with population-matched healthy subjects (n = 4961) served as controls. Whole exome sequencing (WES) was performed to identify rare deleterious variants in 50 ALS genes and 1177 genes associated with abnormal inflammatory responses. Genotype-phenotype correlation was assessed, and an integrative prognostic model incorporating genetic and clinical factors was constructed. RESULTS In the discovery cohort, 8.1% of patients carried confirmed ALS variants, and an additional 15.2% of patients carried novel ALS variants. Gene burden analysis revealed 303 immune-implicated genes with enriched rare variants, and 13.4% of patients harbored rare deleterious variants in these genes. Patients with ALS variants exhibited a more rapid disease progression (HR 2.87 [95% CI 2.03-4.07], p < 0.0001), while no significant effect was observed for immune-implicated variants. The nomogram model incorporating genetic and clinical information demonstrated improved accuracy in predicting disease outcomes (C-index, 0.749). CONCLUSION Our findings enhance the comprehension of the genetic basis of ALS within the Chinese population. It also appears that rare deleterious mutations occurring in immune-implicated genes exert minimal influence on the clinical trajectories of ALS patients.
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Affiliation(s)
- Di He
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Dongcheng District, Beijing, China
| | - Yining Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Siqi Dong
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Dongcheng District, Beijing, China
| | - Xunzhe Yang
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Dongcheng District, Beijing, China
| | - Meng Hao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Xianhong Yin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Xinyi He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Mingsheng Liu
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Dongcheng District, Beijing, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China.
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China.
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China.
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Dongcheng District, Beijing, China.
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2
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Qu Y, Yao Z, Xu N, Shi G, Su J, Ye S, Chang K, Li K, Wang Y, Tan S, Pei X, Chen Y, Qin Z, Feng J, Lv J, Zhu J, Ma F, Tang S, Xu W, Tian X, Anwaier A, Tian S, Xu W, Wu X, Zhu S, Zhu Y, Cao D, Sun M, Gan H, Zhao J, Zhang H, Ye D, Ding C. Plasma proteomic profiling discovers molecular features associated with upper tract urothelial carcinoma. Cell Rep Med 2023; 4:101166. [PMID: 37633276 PMCID: PMC10518597 DOI: 10.1016/j.xcrm.2023.101166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/16/2023] [Accepted: 08/01/2023] [Indexed: 08/28/2023]
Abstract
Upper tract urothelial carcinoma (UTUC) is often diagnosed late and exhibits poor prognosis. Limited data are available on potential non-invasive biomarkers for disease monitoring. Here, we investigate the proteomic profile of plasma in 362 UTUC patients and 239 healthy controls. We present an integrated tissue-plasma proteomic approach to infer the signature proteins for identifying patients with muscle-invasive UTUC. We discover a protein panel that reflects lymph node metastasis, which is of interest in identifying UTUC patients with high risk and poor prognosis. We also identify a ten-protein classifier and establish a progression clock predicting progression-free survival of UTUC patients. Finally, we further validate the signature proteins by parallel reaction monitoring assay in an independent cohort. Collectively, this study portrays the plasma proteomic landscape of a UTUC cohort and provides a valuable resource for further biological and diagnostic research in UTUC.
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Affiliation(s)
- Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Zhenmei Yao
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Ning Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Shiqi Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Kai Li
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Yunzhi Wang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Subei Tan
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Xiaoru Pei
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Yijiao Chen
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Zhaoyu Qin
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Jinwen Feng
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Jiacheng Lv
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Jiajun Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Fahan Ma
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Shaoshuai Tang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Sha Tian
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Wenbo Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Xinqiang Wu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Shuxuan Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Dalong Cao
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Menghong Sun
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China; Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China; Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jianyuan Zhao
- Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China.
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai 200032, China.
| | - Chen Ding
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China.
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3
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Yao Z, Xu N, Shang G, Wang H, Tao H, Wang Y, Qin Z, Tan S, Feng J, Zhu J, Ma F, Tian S, Zhang Q, Qu Y, Hou J, Guo J, Zhao J, Hou Y, Ding C. Proteogenomics of different urothelial bladder cancer stages reveals distinct molecular features for papillary cancer and carcinoma in situ. Nat Commun 2023; 14:5670. [PMID: 37704624 PMCID: PMC10499981 DOI: 10.1038/s41467-023-41139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
The progression of urothelial bladder cancer (UC) is a complicated multi-step process. We perform a comprehensive multi-omics analysis of 448 samples from 190 UC patients, covering the whole spectrum of disease stages and grades. Proteogenomic integration analysis indicates the mutations of HRAS regulated mTOR signaling to form urothelial papilloma rather than papillary urothelial cancer (PUC). DNA damage is a key signaling pathway in the progression of carcinoma in situ (CIS) and related to APOBEC signature. Glucolipid metabolism increase and lower immune cell infiltration are associated with PUC compared to CIS. Proteomic analysis distinguishes the origins of invasive tumors (PUC-derived and CIS-derived), related to distinct clinical prognosis and molecular features. Additionally, loss of RBPMS, associated with CIS-derived tumors, is validated to increase the activity of AP-1 and promote metastasis. This study reveals the characteristics of two distinct branches (PUC and CIS) of UC progression and may eventually benefit clinical practice.
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Grants
- National Natural Science Foundation of China (National Science Foundation of China)
- the National Key Research and Development Program of China (2022YFA1303200 [C.D.], 2022YFA1303201 [C.D.], 2020YFE0201600 [C.D.], 2018YFE0201600 [C.D.], 2018YFE0201603 [C.D.], 2018YFA0507500 [C.D.], 2018YFA0507501 [C.D.], 2017YFA0505100 [C.D.], 2017YFA0505102 [C.D.], 2017YFA0505101 [C.D.], 2017YFC0908404 [C.D.], and 2016YFA0502500 [C.D.]), Program of Shanghai Academic/Technology Research Leader (22XD1420100 [C.D.]), Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission (19SG02 [C.D.]),the Major Project of Special Development Funds of Zhangjiang National Independent Innovation Demonstration Zone (ZJ2019‐ZD‐004 [C.D.]), the Science and Technology Commission of Shanghai Municipality (2017SHZDZX01 [C.D.]).
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Affiliation(s)
- Zhenmei Yao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Ning Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Guoguo Shang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Haixing Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Hui Tao
- Department of Cardiothoracic Surgery, Second Hospital of Anhui Medical University, and Cardiovascular Research Center, Anhui Medical University, Hefei, 230601, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Subei Tan
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jiajun Zhu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Fahan Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Jun Hou
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
| | - Jianming Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yingyong Hou
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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4
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Ji S, Feng L, Fu Z, Wu G, Wu Y, Lin Y, Lu D, Song Y, Cui P, Yang Z, Sang C, Song G, Cai S, Li Y, Lin H, Zhang S, Wang X, Qiu S, Zhang X, Hua G, Li J, Zhou J, Dai Z, Wang X, Ding L, Wang P, Gao D, Zhang B, Rodriguez H, Fan J, Clevers H, Zhou H, Sun Y, Gao Q. Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology. Sci Transl Med 2023; 15:eadg3358. [PMID: 37494474 PMCID: PMC10949980 DOI: 10.1126/scitranslmed.adg3358] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Organoid models have the potential to recapitulate the biological and pharmacotypic features of parental tumors. Nevertheless, integrative pharmaco-proteogenomics analysis for drug response features and biomarker investigation for precision therapy of patients with liver cancer are still lacking. We established a patient-derived liver cancer organoid biobank (LICOB) that comprehensively represents the histological and molecular characteristics of various liver cancer types as determined by multiomics profiling, including genomic, epigenomic, transcriptomic, and proteomic analysis. Proteogenomic profiling of LICOB identified proliferative and metabolic organoid subtypes linked to patient prognosis. High-throughput drug screening revealed distinct response patterns of each subtype that were associated with specific multiomics signatures. Through integrative analyses of LICOB pharmaco-proteogenomics data, we identified the molecular features associated with drug responses and predicted potential drug combinations for personalized patient treatment. The synergistic inhibition effect of mTOR inhibitor temsirolimus and the multitargeted tyrosine kinase inhibitor lenvatinib was validated in organoids and patient-derived xenografts models. We also provide a user-friendly web portal to help serve the biomedical research community. Our study is a rich resource for investigation of liver cancer biology and pharmacological dependencies and may help enable functional precision medicine.
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Affiliation(s)
- Shuyi Ji
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Li Feng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zile Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Gaohua Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Dayun Lu
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuanli Song
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peng Cui
- Burning Rock Biotech, Shanghai 201114, China
| | - Zijian Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Chen Sang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Shangli Cai
- Burning Rock Biotech, Shanghai 201114, China
| | | | - Hanqing Lin
- D1 Medical Technology, Shanghai 200235, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Shuangjian Qiu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xiaoming Zhang
- Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoqiang Hua
- Department of Radiation Oncology, and Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Junqiang Li
- D1 Medical Technology, Shanghai 200235, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhi Dai
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital Institute for Clinical Science, Fudan University Shanghai Medical College, Shanghai, China
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University, St. Louis, MO 63108, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029, USA
| | - Daming Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Department of Radiation Oncology, and Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Current Address: Roche Pharma Research and Early Development (pRED), Basel, Switzerland
| | - Hu Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Gao
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai 200433, China
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5
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Xiang H, Zhang B, Wang Y, Xu N, Zhang F, Luo R, Ji M, Ding C. Region-resolved multi-omics of the mouse eye. Cell Rep 2023; 42:112121. [PMID: 36790928 DOI: 10.1016/j.celrep.2023.112121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/19/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
The eye is a complex organ consisting of multiple compartments with unique and specialized properties, and small disturbances in one eye region can result in impaired vision and blindness. Although there have been advancements in ocular research, the hierarchical molecular network in region-wide resolution, indicating the division of labor and crosstalk among different eye regions, is not yet comprehensively illuminated. Here, we present an atlas of region-resolved proteome and lipidome of mouse eye. Multiphoton microscopy-guided laser microdissection combined with in-depth label-free proteomics identifies 13,536 proteins across various mouse eye regions. Further integrative analysis of spectral imaging, label-free proteome, and imaging mass spectrometry of the lipidome and phosphoproteome reveals distinctive molecular features, including proteins and lipids of various anatomical mouse eye regions. These deposited datasets and our open proteome server integrating all information provide a valuable resource for future functional and mechanistic studies of mouse eye and ocular disease.
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Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Bohan Zhang
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Multiscale Research Institute of Complex Systems, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Ning Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Fan Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, China
| | - Minbiao Ji
- State Key Laboratory of Surface Physics and Department of Physics, Human Phenome Institute, Multiscale Research Institute of Complex Systems, Academy for Engineering and Technology, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China.
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6
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Wu X, Li C, Wang Z, Zhang Y, Liu S, Chen S, Chen S, Liu W, Liu X. A bioinformatic analysis study of m 7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma. BMC Cancer 2022; 22:729. [PMID: 35788194 PMCID: PMC9251941 DOI: 10.1186/s12885-022-09791-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Glioblastoma is one of the most common brain cancers in adults, and is characterized by recurrence and little curative effect. An effective treatment for glioblastoma patients remains elusive worldwide. 7-methylguanosine (m7G) is a common RNA modification, and its role in tumors has become a research hotspot. Methods By searching for differentially expressed genes related to m7G, we generated a prognostic signature via cluster analysis and established classification criteria of high and low risk scores. The effectiveness of classification was validated using the Non-negative matrix factorization (NMF) algorithm, and repeatedly verified using training and test groups. The dimension reduction method was used to clearly show the difference and clinical significance of the data. All analyses were performed via R (version 4.1.2). Results According to the signature that included four genes (TMOD2, CACNG2, PLOD3, and TMSB10), glioblastoma patients were divided into high and low risk score groups. The survival rates between the two groups were significantly different, and the predictive abilities for 1-, 3-, and 5-year survivals were effective. We further established a Nomogram model to further examine the signature,as well as other clinical factors, with remaining significant results. Our signature can act as an independent prognostic factor related to immune-related processes in glioblastoma. Conclusions Our research addresses the gap in knowledge in the m7G and glioblastoma research fields. The establishment of a prognostic signature and the extended analysis of the tumor microenvironment, immune correlation, and tumor mutation burden further suggest the important role of m7G in the development and development of this disease. This work will provide support for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09791-y.
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Affiliation(s)
- Xinrui Wu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China.,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhisu Wang
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Yundi Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shifan Liu
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Siqi Chen
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Shuai Chen
- Department of measurement and control technology and instruments, School of mechanical engineering, Nantong University, Nantong, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China. .,Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoman Liu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China. .,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China.
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