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Chen Y, Wang B, Zhao Y, Shao X, Wang M, Ma F, Yang L, Nie M, Jin P, Yao K, Song H, Lou S, Wang H, Yang T, Tian Y, Han P, Hu Z. Metabolomic machine learning predictor for diagnosis and prognosis of gastric cancer. Nat Commun 2024; 15:1657. [PMID: 38395893 PMCID: PMC10891053 DOI: 10.1038/s41467-024-46043-y] [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: 05/09/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Gastric cancer (GC) represents a significant burden of cancer-related mortality worldwide, underscoring an urgent need for the development of early detection strategies and precise postoperative interventions. However, the identification of non-invasive biomarkers for early diagnosis and patient risk stratification remains underexplored. Here, we conduct a targeted metabolomics analysis of 702 plasma samples from multi-center participants to elucidate the GC metabolic reprogramming. Our machine learning analysis reveals a 10-metabolite GC diagnostic model, which is validated in an external test set with a sensitivity of 0.905, outperforming conventional methods leveraging cancer protein markers (sensitivity < 0.40). Additionally, our machine learning-derived prognostic model demonstrates superior performance to traditional models utilizing clinical parameters and effectively stratifies patients into different risk groups to guide precision interventions. Collectively, our findings reveal the metabolic landscape of GC and identify two distinct biomarker panels that enable early detection and prognosis prediction respectively, thus facilitating precision medicine in GC.
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Affiliation(s)
- Yangzi Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Bohong Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yizi Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinxin Shao
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
| | - Mingshuo Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuhai Ma
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
- Department of General Surgery, Department of Gastrointestinal Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Laishou Yang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Meng Nie
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Peng Jin
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
- Department of Gastroenterology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Song
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Shenghan Lou
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Hang Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Tianshu Yang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Shanghai Qi Zhi Institute, Shanghai, 200438, China
| | - Yantao Tian
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China.
| | - Peng Han
- Department of Oncology Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
- Key Laboratory of Tumor Immunology in Heilongjiang, Harbin, 150081, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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2
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König S, Schork K, Eisenacher M. Observations from the Proteomics Bench. Proteomes 2024; 12:6. [PMID: 38390966 PMCID: PMC10885119 DOI: 10.3390/proteomes12010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data-set-wise quality control is still necessary, and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.
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Affiliation(s)
- Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, 44801 Bochum, Germany
- Core Unit for Bioinformatics (CUBiMed.RUB), Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
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3
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Shuman JHB, Lin AS, Westland MD, Bryant KN, Piazuelo MB, Reyzer ML, Judd AM, McDonald WH, McClain MS, Schey KL, Algood HMS, Cover TL. Remodeling of the gastric environment in Helicobacter pylori-induced atrophic gastritis. mSystems 2024; 9:e0109823. [PMID: 38059647 PMCID: PMC10805037 DOI: 10.1128/msystems.01098-23] [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: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 12/08/2023] Open
Abstract
Helicobacter pylori colonization of the human stomach is a strong risk factor for gastric cancer. To investigate H. pylori-induced gastric molecular alterations, we used a Mongolian gerbil model of gastric carcinogenesis. Histologic evaluation revealed varying levels of atrophic gastritis (a premalignant condition characterized by parietal and chief cell loss) in H. pylori-infected animals, and transcriptional profiling revealed a loss of markers for these cell types. We then assessed the spatial distribution and relative abundance of proteins in the gastric tissues using imaging mass spectrometry and liquid chromatography with tandem mass spectrometry. We detected striking differences in the protein content of corpus and antrum tissues. Four hundred ninety-two proteins were preferentially localized to the corpus in uninfected animals. The abundance of 91 of these proteins was reduced in H. pylori-infected corpus tissues exhibiting atrophic gastritis compared with infected corpus tissues exhibiting non-atrophic gastritis or uninfected corpus tissues; these included numerous proteins with metabolic functions. Fifty proteins localized to the corpus in uninfected animals were diffusely delocalized throughout the stomach in infected tissues with atrophic gastritis; these included numerous proteins with roles in protein processing. The corresponding alterations were not detected in animals infected with a H. pylori ∆cagT mutant (lacking Cag type IV secretion system activity). These results indicate that H. pylori can cause loss of proteins normally localized to the gastric corpus as well as diffuse delocalization of corpus-specific proteins, resulting in marked changes in the normal gastric molecular partitioning into distinct corpus and antrum regions.IMPORTANCEA normal stomach is organized into distinct regions known as the corpus and antrum, which have different functions, cell types, and gland architectures. Previous studies have primarily used histologic methods to differentiate these regions and detect H. pylori-induced alterations leading to stomach cancer. In this study, we investigated H. pylori-induced gastric molecular alterations in a Mongolian gerbil model of carcinogenesis. We report the detection of numerous proteins that are preferentially localized to the gastric corpus but not the antrum in a normal stomach. We show that stomachs with H. pylori-induced atrophic gastritis (a precancerous condition characterized by the loss of specialized cell types) exhibit marked changes in the abundance and localization of proteins normally localized to the gastric corpus. These results provide new insights into H. pylori-induced gastric molecular alterations that are associated with the development of stomach cancer.
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Affiliation(s)
- Jennifer H. B. Shuman
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Aung Soe Lin
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mandy D. Westland
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kaeli N. Bryant
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Michelle L. Reyzer
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Audra M. Judd
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - W. Hayes McDonald
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Holly M. S. Algood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Timothy L. Cover
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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Koidl L, Gentile SA, Untersmayr E. Allergen Stability in Food Allergy: A Clinician's Perspective. Curr Allergy Asthma Rep 2023; 23:601-612. [PMID: 37665560 PMCID: PMC10506954 DOI: 10.1007/s11882-023-01107-9] [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] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
PURPOSE OF REVIEW The globally rising food allergy prevalence is associated with the urgent need for new disease prevention methods, efficient treatment, and reliable risk assessment methods for characterization of food allergens. Due to inter-individual variations in the digestive system, food allergens are degraded to a different extent in each person. Food processing also influences allergen digestion. RECENT FINDINGS In this review, we provide an overview of the digestive system with focus on relevance for food allergy. Main food proteins causing allergic reactions are evaluated, and the combined role of food processing and digestion for allergen stability is highlighted. Finally, clinical implications of this knowledge are discussed. Recent literature shows that allergen digestibility is dependent on food processing, digestive conditions, and food matrix. Digestion affects proteins allergenicity. It is currently not possible to predict the immunogenicity of allergens solely based on protein stability.
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Affiliation(s)
- Larissa Koidl
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, E3Q, 1090, Vienna, Austria
| | - Salvatore Alessio Gentile
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, E3Q, 1090, Vienna, Austria
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, E3Q, 1090, Vienna, Austria.
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5
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Gao Y, Wang H. Ribosome Heterogeneity in Development and Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550527. [PMID: 37546733 PMCID: PMC10402066 DOI: 10.1101/2023.07.25.550527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The functional ribosome is composed of ∼80 ribosome proteins. With the intensity-based absolute quantification (iBAQ) value, we calculate the stoichiometry ratio of each ribosome protein. We analyze the ribosome ratio-omics (Ribosome R ), which reflects the holistic signature of ribosome composition, in various biological samples with distinct functions, developmental stages, and pathological outcomes. The Ribosome R reveals significant ribosome heterogeneity among different tissues of fat, spleen, liver, kidney, heart, and skeletal muscles. During tissue development, testes at various stages of spermatogenesis show distinct Ribosome R signatures. During in vitro neuronal maturation, the Ribosome R changes reveal functional association with certain molecular aspects of neurodevelopment. Regarding ribosome heterogeneity associated with pathological conditions, the Ribosome R signature of gastric tumors is functionally linked to pathways associated with tumorigenesis. Moreover, the Ribosome R undergoes dynamic changes in macrophages following immune challenges. Taken together, with the examination of a broad spectrum of biological samples, the Ribosome R barcode reveals ribosome heterogeneity and specialization in cell function, development, and disease. One-Sentence Summary Ratio-omics signature of ribosome deciphers functionally relevant heterogeneity in development and disease.
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6
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Gupta N, Kumar A, Verma VK. Strategies adopted by gastric pathogen Helicobacter pylori for a mature biofilm formation: Antimicrobial peptides as a visionary treatment. Microbiol Res 2023; 273:127417. [PMID: 37267815 DOI: 10.1016/j.micres.2023.127417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 06/04/2023]
Abstract
Enormous efforts in recent past two decades to eradicate the pathogen that has been prevalent in half of the world's population have been problematic. The biofilm formed by Helicobacter pylori provides resistance towards innate immune cells, various combinatorial antibiotics, and human antimicrobial peptides, despite the fact that these all are potent enough to eradicate it in vitro. Biofilm provides the opportunity to secrete various virulence factors that strengthen the interaction between host and pathogen helping in evading the innate immune system and ultimately leading to persistence. To our knowledge, this review is the first of its kind to explain briefly the journey of H. pylori starting with the chemotaxis, the mechanism for selecting the site for colonization, the stress faced by the pathogen, and various adaptations to evade these stress conditions by forming biofilm and the morphological changes acquired by the pathogen in mature biofilm. Furthermore, we have explained the human GI tract antimicrobial peptides and the reason behind the failure of these AMPs, and how encapsulation of Pexiganan-A(MSI-78A) in a chitosan microsphere increases the efficiency of eradication.
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Affiliation(s)
- Nidhi Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India.
| | - Atul Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Vijay Kumar Verma
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India.
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7
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Li L, Jiang D, Liu H, Guo C, Zhao R, Zhang Q, Xu C, Qin Z, Feng J, Liu Y, Wang H, Chen W, Zhang X, Li B, Bai L, Tian S, Tan S, Yu Z, Chen L, Huang J, Zhao JY, Hou Y, Ding C. Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes. Nat Commun 2023; 14:1751. [PMID: 36991000 PMCID: PMC10060430 DOI: 10.1038/s41467-023-37221-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
The subtypes of duodenal cancer (DC) are complicated and the carcinogenesis process is not well characterized. We present comprehensive characterization of 438 samples from 156 DC patients, covering 2 major and 5 rare subtypes. Proteogenomics reveals LYN amplification at the chromosome 8q gain functioned in the transmit from intraepithelial neoplasia phase to infiltration tumor phase via MAPK signaling, and illustrates the DST mutation improves mTOR signaling in the duodenal adenocarcinoma stage. Proteome-based analysis elucidates stage-specific molecular characterizations and carcinogenesis tracks, and defines the cancer-driving waves of the adenocarcinoma and Brunner's gland subtypes. The drug-targetable alanyl-tRNA synthetase (AARS1) in the high tumor mutation burden/immune infiltration is significantly enhanced in DC progression, and catalyzes the lysine-alanylation of poly-ADP-ribose polymerases (PARP1), which decreases the apoptosis of cancer cells, eventually promoting cell proliferation and tumorigenesis. We assess the proteogenomic landscape of early DC, and provide insights into the molecular features corresponding therapeutic targets.
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Affiliation(s)
- Lingling Li
- 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
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hui Liu
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Chunmei Guo
- 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
| | - Rui Zhao
- Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua HospitalShanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Qiao 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
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhaoyu Qin
- 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
| | - Jinwen Feng
- 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
| | - Yang Liu
- 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
| | - Haixing Wang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Weijie Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xue Zhang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Bin Li
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lin Bai
- 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
| | - Sha Tian
- 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
| | - Subei Tan
- 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
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jie Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Yuan Zhao
- Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua HospitalShanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
- Department of Anatomy and Neuroscience Research Institute, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, 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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8
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Li L, Jiang D, Zhang Q, Liu H, Xu F, Guo C, Qin Z, Wang H, Feng J, Liu Y, Chen W, Zhang X, Bai L, Tian S, Tan S, Xu C, Song Q, Liu Y, Zhong Y, Chen T, Zhou P, Zhao JY, Hou Y, Ding C. Integrative proteogenomic characterization of early esophageal cancer. Nat Commun 2023; 14:1666. [PMID: 36966136 PMCID: PMC10039899 DOI: 10.1038/s41467-023-37440-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is malignant while the carcinogenesis is still unclear. Here, we perform a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 ESCC patients, covering 9 histopathological stages and 3 phases. Proteogenomics elucidates cancer-driving waves in ESCC progression, and reveals the molecular characterization of alcohol drinking habit associated signatures. We discover chromosome 3q gain functions in the transmit from nontumor to intraepithelial neoplasia phases, and find TP53 mutation enhances DNA replication in intraepithelial neoplasia phase. The mutations of AKAP9 and MCAF1 upregulate glycolysis and Wnt signaling, respectively, in advanced-stage ESCC phase. Six major tracks related to different clinical features during ESCC progression are identified, which is validated by an independent cohort with another 256 samples. Hyperphosphorylated phosphoglycerate kinase 1 (PGK1, S203) is considered as a drug target in ESCC progression. This study provides insight into the understanding of ESCC molecular mechanism and the development of therapeutic targets.
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Affiliation(s)
- Lingling Li
- 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
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Qiao 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
| | - Hui Liu
- 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
| | - Fujiang Xu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Chunmei Guo
- 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
| | - Zhaoyu Qin
- 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
| | - Haixing Wang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Jinwen Feng
- 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
| | - Yang Liu
- 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
| | - Weijie Chen
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Xue Zhang
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Lin Bai
- 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
| | - Sha Tian
- 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
| | - Subei Tan
- 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
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Qi Song
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Yalan Liu
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Yunshi Zhong
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Tianyin Chen
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, China
| | - Pinghong Zhou
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital Fudan University, Shanghai, 200032, China.
| | - Jian-Yuan Zhao
- 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.
- 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.
- Department of Anatomy and Neuroscience Research Institute , School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital Fudan University, Shanghai, 200032, 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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9
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Wang T, Min L, Gao Y, Zhao M, Feng S, Wang H, Wang Y, Zheng Y. SUMOylation of TUFT1 is essential for gastric cancer progression through AKT/mTOR signaling pathway activation. Cancer Sci 2022; 114:533-545. [PMID: 36380570 PMCID: PMC9899612 DOI: 10.1111/cas.15618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tuftelin (TUFT1) is highly expressed in various tumor types and promotes tumor growth and metastasis by activating AKT and other core signaling pathways. However, the effects of post-translational modifications of TUFT1 on its oncogenic function remain unexplored. In this study, we found that TUFT1 was SUMOylated at K79. SUMOylation deficiency significantly impaired the ability of TUFT1 to promote the proliferation, migration, and invasion of gastric cancer (GC) cells by blocking AKT/mTOR signaling pathway activation. SUMOylation of TUFT1 is mediated by the E3 SUMO ligase tripartite motif-containing protein 27 (TRIM27), and these two proteins regulate the malignant behavior of GC cells and AKT activation in the same pathway. TUFT1 binds to TRIM27 through its N-terminus, and decreased binding affinity of TUFT1 to TRIM27 significantly impairs its oncogenic effect. In addition, data collected from GC clinical samples indicated that the combined detection of TUFT1 and TRIM27 expression reflected tumor malignancy and patient survival with higher precision. In addition, we proved that SUMOylated TUFT1 is not only an upstream signal for AKT activation but also directly activates mTOR by forming a complex with Rab GTPase activating protein 1, which further inhibits Rab GTPases and promotes the perinuclear accumulation of mTORC1. Altogether, these data indicate that SUMOylated TUFT1 is the active form that affects GC progression through the AKT/mTOR signaling pathway and might be a promising therapeutic target or biomarker for GC progression.
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Affiliation(s)
- Tianning Wang
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina,Research Center of Translational MedicineJinan Central Hospital, Shandong UniversityJinanChina
| | - Lingyuan Min
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Yan Gao
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Mengmeng Zhao
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina,Research Center of Translational MedicineJinan Central Hospital, Shandong UniversityJinanChina
| | - Shaojie Feng
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina,Research Center of Translational MedicineJinan Central Hospital, Shandong UniversityJinanChina
| | - Huiyun Wang
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Yunshan Wang
- Research Center of Translational MedicineJinan Central Hospital, Shandong UniversityJinanChina
| | - Yan Zheng
- Research Center of Translational MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinanChina,Research Center of Translational MedicineJinan Central Hospital, Shandong UniversityJinanChina
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10
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Jiang S, Shi J, Li Y, Zhang Z, Chang L, Wang G, Wu W, Yu L, Dai E, Zhang L, Lyu Z, Xu P, Zhang Y. Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis. Front Microbiol 2022; 13:1015140. [PMID: 36312923 PMCID: PMC9597629 DOI: 10.3389/fmicb.2022.1015140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC2 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC2 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics.
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Affiliation(s)
- Songhao Jiang
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Jiahui Shi
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Yanchang Li
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Zhenpeng Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Lei Chang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Guibin Wang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Wenhui Wu
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Liyan Yu
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Erhei Dai
- The Fifth Hospital of Shijiazhuang, School of Public Health, Shijiazhuang, China
| | - Lixia Zhang
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Haihe Hospital, Tianjin University, Tianjin, China
| | - Zhitang Lyu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Zhitang Lyu
| | - Ping Xu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Ping Xu
| | - Yao Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Yao Zhang
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11
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Aziz S, Rasheed F, Akhter TS, Zahra R, König S. Microbial Proteins in Stomach Biopsies Associated with Gastritis, Ulcer, and Gastric Cancer. Molecules 2022; 27:molecules27175410. [PMID: 36080177 PMCID: PMC9458002 DOI: 10.3390/molecules27175410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Gastric cancer (GC) is the fourth leading cause of cancer-related deaths worldwide. Helicobacter pylori infection is a major risk factor, but other microbial species may also be involved. In the context of an earlier proteomics study of serum and biopsies of patients with gastroduodenal diseases, we explored here a simplified microbiome in these biopsies (H. pylori, Acinetobacter baumannii, Escherichia coli, Fusobacterium nucleatum, Bacteroides fragilis) on the protein level. (2) Methods: A cohort of 75 patients was divided into groups with respect to the findings of the normal gastric mucosa (NGM) and gastroduodenal disorders such as gastritis, ulcer, and gastric cancer (GC). The H. pylori infection status was determined. The protein expression analysis of the biopsy samples was carried out using high-definition mass spectrometry of the tryptic digest (label-free data-independent quantification and statistical analysis). (3) Results: The total of 304 bacterial protein matches were detected based on two or more peptide hits. Significantly regulated microbial proteins like virulence factor type IV secretion system protein CagE from H. pylori were found with more abundance in gastritis than in GC or NGM. This finding could reflect the increased microbial involvement in mucosa inflammation in line with current hypotheses. Abundant proteins across species were heat shock proteins and elongation factors. (4) Conclusions: Next to the bulk of human proteins, a number of species-specific bacterial proteins were detected in stomach biopsies of patients with gastroduodenal diseases, some of which, like those expressed by the cag pathogenicity island, may provide gateways to disease prevention without antibacterial intervention in order to reduce antibiotic resistance.
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Affiliation(s)
- Shahid Aziz
- Patients Diagnostic Lab, Isotope Application Division, Pakistan Institute of Nuclear Science and Technology (PINSTECH), Islamabad 44000, Pakistan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence: or
| | - Faisal Rasheed
- Patients Diagnostic Lab, Isotope Application Division, Pakistan Institute of Nuclear Science and Technology (PINSTECH), Islamabad 44000, Pakistan
| | - Tayyab Saeed Akhter
- The Centre for Liver and Digestive Diseases, Holy Family Hospital, Rawalpindi 46300, Pakistan
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
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12
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Wang X, Yin J, Hu J, Nie S, Xie M. Gastroprotective polysaccharide from natural sources: Review on structure, mechanism, and structure–activity relationship. FOOD FRONTIERS 2022. [DOI: 10.1002/fft2.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Xiao‐Yin Wang
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang 330047 China
- School of Public Health and Health Management Gannan Medical University Ganzhou 341000 China
| | - Jun‐Yi Yin
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang 330047 China
| | - Jie‐Lun Hu
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang 330047 China
| | - Shao‐Ping Nie
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang 330047 China
| | - Ming‐Yong Xie
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang 330047 China
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13
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Tang M, Zhao Y, Zhao J, Wei S, Liu M, Zheng N, Geng D, Han S, Zhang Y, Zhong G, Li S, Zhang X, Wang C, Yan H, Cao X, Li L, Bai X, Ji J, Feng XH, Qin J, Liang T, Zhao B. Liver cancer heterogeneity modeled by in situ genome editing of hepatocytes. SCIENCE ADVANCES 2022; 8:eabn5683. [PMID: 35731873 PMCID: PMC9216519 DOI: 10.1126/sciadv.abn5683] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mechanistic study and precision treatment of primary liver cancer (PLC) are hindered by marked heterogeneity, which is challenging to recapitulate in any given liver cancer mouse model. Here, we report the generation of 25 mouse models of PLC by in situ genome editing of hepatocytes recapitulating 25 single or combinations of human cancer driver genes. These mouse tumors represent major histopathological types of human PLCs and could be divided into three human-matched molecular subtypes based on transcriptomic and proteomic profiles. Phenotypical characterization identified subtype- or genotype-specific alterations in immune microenvironment, metabolic reprogramming, cell proliferation, and expression of drug targets. Furthermore, single-cell analysis and expression tracing revealed spatial and temporal dynamics in expression of pyruvate kinase M2 (Pkm2). Tumor-specific knockdown of Pkm2 by multiplexed genome editing reversed the Warburg effect and suppressed tumorigenesis in a genotype-specific manner. Our study provides mouse PLC models with defined genetic drivers and characterized phenotypical heterogeneity suitable for mechanistic investigation and preclinical testing.
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Affiliation(s)
- Mei Tang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Jianhui Zhao
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shumei Wei
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Didi Geng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shixun Han
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yuchao Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Guoxuan Zhong
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuaifeng Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiuming Zhang
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Chenliang Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Huan Yan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaolei Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Li
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xueli Bai
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tingbo Liang
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Corresponding author. (T.L.); (B.Z.)
| | - Bin Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Shaoxing Institute, Zhejiang University, Shaoxing 321000, China
- Corresponding author. (T.L.); (B.Z.)
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14
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Aziz S, Rasheed F, Zahra R, König S. Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures. Molecules 2022; 27:molecules27092857. [PMID: 35566209 PMCID: PMC9099457 DOI: 10.3390/molecules27092857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: A gastric cancer (GC) diagnosis relies on histopathology. Endoscopy rates are increasing. Helicobacter pylori infection is a major GC risk factor. In an effort to elucidate abundant blood biomarkers, and potentially reduce the number of diagnostic surgical interventions, we investigated sera and biopsies from a cohort of 219 H. pylori positive and negative patients diagnosed with GC, gastritis, and ulcers. This allowed the comparative investigation of the different gastroduodenal diseases, and the exclusion of protein changes resulting from bacterial infection or inflammation of the gastric mucosa when searching for GC-dependent proteins. Methods: High-definition mass spectrometry-based expression analysis of tryptically digested proteins was performed, followed by multivariate statistical and network analyses for the different disease groups, with respect to H. pylori infection status. Significantly regulated proteins differing more than two-fold between groups were shortlisted, and their role in gastritis and GC discussed. Results: We present data of comparative protein analyses of biopsies and sera from patients suffering from mild to advanced gastritis, ulcers, and early to advanced GC, in conjunction with a wealth of metadata, clinical information, histopathological evaluation, and H. pylori infection status. We used samples from pre-malignant stages to extract prospective serum markers for early-stage GC, and present a 29-protein marker panel containing, amongst others, integrin β-6 and glutathione peroxidase. Furthermore, ten serum markers specific for advanced GC, independent of H. pylori infection, are provided. They include CRP, protein S100A9, and kallistatin. The majority of these proteins were previously discussed in the context of cancer or GC. In addition, we detected hypoalbuminemia and increased fibrinogen serum levels in gastritis. Conclusion: Two protein panels were suggested for the development of multiplex tests for GC serum diagnostics. For most of the elements contained in these panels, individual commercial tests are available. Thus, we envision the design of multi-protein assays, incorporating several to all of the panel members, in order to gain a level of specificity that cannot be achieved by testing a single protein alone. As their development and validation will take time, gastritis diagnosis based on the fibrinogen to albumin serum ratio may be a quick way forward. Its determination at the primary/secondary care level for early diagnosis could significantly reduce the number of referrals to endoscopy. Preventive measures are in high demand. The protein marker panels presented in this work will contribute to improved GC diagnostics, once they have been transferred from a research result to a practical tool.
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Affiliation(s)
- Shahid Aziz
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Faisal Rasheed
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence:
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15
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Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer. Proteome Sci 2022; 20:5. [PMID: 35397555 PMCID: PMC8994365 DOI: 10.1186/s12953-022-00188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/24/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer.
Methods
In this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC).
Results
We identified ~ 6000 proteins and > 10,000 phosphosites in single trace FFPE samples. Comparative analysis disclosed the diverse proteomic features of tumor tissues compared with paired normal tissue of EESCC and EDAC, and revealed the difference of EESCC and EDAC was derived from their origin normal tissue. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic.
Conclusion
We disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic.
Graphical Abstract
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16
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Liu Y, Lin Y, Yang W, Lin Y, Wu Y, Zhang Z, Lin N, Wang X, Tong M, Yu R. Application of individualized differential expression analysis in human cancer proteome. Brief Bioinform 2022; 23:6562685. [DOI: 10.1093/bib/bbac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Liquid chromatography–mass spectrometry-based quantitative proteomics can measure the expression of thousands of proteins from biological samples and has been increasingly applied in cancer research. Identifying differentially expressed proteins (DEPs) between tumors and normal controls is commonly used to investigate carcinogenesis mechanisms. While differential expression analysis (DEA) at an individual level is desired to identify patient-specific molecular defects for better patient stratification, most statistical DEP analysis methods only identify deregulated proteins at the population level. To date, robust individualized DEA algorithms have been proposed for ribonucleic acid data, but their performance on proteomics data is underexplored. Herein, we performed a systematic evaluation on five individualized DEA algorithms for proteins on cancer proteomic datasets from seven cancer types. Results show that the within-sample relative expression orderings (REOs) of protein pairs in normal tissues were highly stable, providing the basis for individualized DEA for proteins using REOs. Moreover, individualized DEA algorithms achieve higher precision in detecting sample-specific deregulated proteins than population-level methods. To facilitate the utilization of individualized DEA algorithms in proteomics for prognostic biomarker discovery and personalized medicine, we provide Individualized DEP Analysis IDEPAXMBD (XMBD: Xiamen Big Data, a biomedical open software initiative in the National Institute for Data Science in Health and Medicine, Xiamen University, China.) (https://github.com/xmuyulab/IDEPA-XMBD), which is a user-friendly and open-source Python toolkit that integrates individualized DEA algorithms for DEP-associated deregulation pattern recognition.
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Affiliation(s)
- Yachen Liu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
| | - Yalan Lin
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
| | - Wenxian Yang
- Aginome Scientific, Xiamen, Fujian 316005, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yujuan Wu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
| | - Zheyang Zhang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Nuoqi Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xianlong Wang
- Department of Bioinformatics, School of Medical Technology and Engineering, Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Mengsha Tong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Rongshan Yu
- School of Informatics, Xiamen University, Xiamen, Fujian 316000, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 316005, China
- Aginome Scientific, Xiamen, Fujian 316005, China
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17
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Jiang Z, Li M, McClements DJ, Liu X, Liu F. Recent advances in the design and fabrication of probiotic delivery systems to target intestinal inflammation. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107438] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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19
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Li X, Zheng NR, Wang LH, Li ZW, Liu ZC, Fan H, Wang Y, Dai J, Ni XT, Wei X, Liu MW, Li K, Li ZX, Zhou T, Zhang Y, Zhang JY, Kadeerhan G, Huang S, Wu WH, Liu WD, Wu XZ, Zhang LF, Xu JM, Gerhard M, You WC, Pan KF, Li WQ, Qin J. Proteomic profiling identifies signatures associated with progression of precancerous gastric lesions and risk of early gastric cancer. EBioMedicine 2021; 74:103714. [PMID: 34818622 PMCID: PMC8617343 DOI: 10.1016/j.ebiom.2021.103714] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
Background Molecular features underlining the multistage progression of gastric lesions and development of early gastric cancer (GC) are poorly understood, restricting the ability to GC prevention and management. Methods We portrayed proteomic landscape and explored proteomic signatures associated with progression of gastric lesions and risk of early GC. Tissue proteomic profiling was conducted for a total of 324 subjects. A case-control study was performed in the discovery stage (n=169) based on populations from Linqu, a known high-risk area for GC in China. We then conducted two-stage validation, including a cohort study from Linqu (n = 56), with prospective follow-up for progression of gastric lesions (280–473 days), and an independent case-control study from Beijing (n = 99). Findings There was a clear distinction in proteomic features for precancerous gastric lesions and GC. We derived four molecular subtypes of gastric lesions and identified subtype-S4 with the highest progression risk. We found 104 positively-associated and 113 inversely-associated proteins for early GC, with APOA1BP, PGC, HPX and DDT associated with the risk of gastric lesion progression. Integrating these proteomic signatures, the ability to predict progression of gastric lesions was significantly strengthened (areas-under-the-curve=0.88 (95%CI: 0.78–0.99) vs. 0.56 (0.36–0.76), Delong's P = 0.002). Immunohistochemistry assays and examination at mRNA level validated the findings for four proteins. Interpretation We defined proteomic signatures for progression of gastric lesions and risk of early GC, which may have translational significance for identifying particularly high-risk population and detecting GC at an early stage, improving potential for targeted GC prevention. Funding The funders are listed in the Acknowledgement.
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Affiliation(s)
- Xue Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Nai-Ren Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lin-Heng Wang
- Department of Gastroenterology, Second Clinical Medical College of Beijing University of Chinese Medicine (Dongfang Hospital), Beijing 100078, China
| | - Zhong-Wu Li
- Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zong-Chao Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Hua Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jin Dai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiao-Tian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xin Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ming-Wei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Kai Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhe-Xuan Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Tong Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jing-Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Gaohaer Kadeerhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Sha Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wen-Hui Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wei-Dong Liu
- Linqu County Public Health Bureau, Shandong 262600, China
| | - Xiu-Zhen Wu
- Linqu County People's Hospital, Shandong 262600, China
| | - Lan-Fu Zhang
- Linqu County People's Hospital, Shandong 262600, China
| | - Jian-Ming Xu
- Department of Gastrointestinal Oncology, The Fifth Medical Center, General Hospital of PLA, Beijing 100071, China
| | - Markus Gerhard
- PYLOTUM Key joint laboratory for upper GI cancer, Technische Universität München/Peking University Cancer Hospital & Institute, Munich/Beijing, Germany/ China
| | - Wei-Cheng You
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China; PYLOTUM Key joint laboratory for upper GI cancer, Technische Universität München/Peking University Cancer Hospital & Institute, Munich/Beijing, Germany/ China
| | - Kai-Feng Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China; PYLOTUM Key joint laboratory for upper GI cancer, Technische Universität München/Peking University Cancer Hospital & Institute, Munich/Beijing, Germany/ China.
| | - Wen-Qing Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing 100142, China; PYLOTUM Key joint laboratory for upper GI cancer, Technische Universität München/Peking University Cancer Hospital & Institute, Munich/Beijing, Germany/ China.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
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20
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Mao Y, Wang X, Huang P, Tian R. Spatial proteomics for understanding the tissue microenvironment. Analyst 2021; 146:3777-3798. [PMID: 34042124 DOI: 10.1039/d1an00472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human body comprises rich populations of cells, which are arranged into tissues and organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and are often organized as a heterogeneous but sophisticatedly regulated ecosystem - tissue microenvironment, inside which every cell interacts with and is reciprocally influenced by its surroundings through its life span. Therefore, it is critical to comprehensively explore the cellular machinery and biological processes in the tissue microenvironment, which is best exemplified by the tumor microenvironment (TME). The past decade has seen increasing advances in the field of spatial proteomics, the main purpose of which is to characterize the abundance and spatial distribution of proteins and their post-translational modifications in the microenvironment of diseased tissues. Herein, we outline the achievements and remaining challenges of mass spectrometry-based tissue spatial proteomics. Exciting technology developments along with important biomedical applications of spatial proteomics are highlighted. In detail, we focus on high-quality resources built by scalpel macrodissection-based region-resolved proteomics, method development of sensitive sample preparation for laser microdissection-based spatial proteomics, and antibody recognition-based multiplexed tissue imaging. In the end, critical issues and potential future directions for spatial proteomics are also discussed.
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Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China. and Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China and Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Peiwu Huang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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21
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Yuan J, Li Z, Li F, Lin Z, Yao S, Zhou H, Liu W, Yu H, Liu Y, Liu F, Li F, Ran H, Zhang J, Huang Y, Fu Q, Wang L, Liu J. Proteomics reveals the potential mechanism of Mrps35 controlling Listeria monocytogenes intracellular proliferation in macrophages. Proteomics 2021; 21:e2000262. [PMID: 33763969 DOI: 10.1002/pmic.202000262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/10/2022]
Abstract
Macrophages are sentinels in the organism which can resist and destroy various bacteria through direct phagocytosis. Here, we reported that expression level of mitochondrial ribosomal protein S35 (Mrps35) continued to decrease over infection time after Listeria monocytogenes (L. monocytogenes) infected macrophages. Our results indicated that knockdown Mrps35 increased the load of L. monocytogenes in macrophages. This result supported that Mrps35 played the crucial roles in L. monocytogenes infection. Moreover, we performed the comprehensive proteomics to analyze the differentially expressed protein of wild type and Mrps35 Knockdown Raw264.7 cells by L. monocytogenes infection over 6 h. Based on the results of mass spectrometry, we presented a wide variety of hypotheses about the mechanism of Mrps35 controlling the L. monocytogenes intracellular proliferation. Among them, experiments confirmed that Mrps35 and 60S ribosomal protein L22-like 1 (Rpl22l1) were a functional correlation or potentially a compensatory mechanism during L. monocytogenes infection. This study provided new insights into understanding that L. monocytogenes infection changed the basic synthesis or metabolism-related proteins of host cells.
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Affiliation(s)
- Jiangbei Yuan
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong province, China
| | - Zhangfu Li
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong province, China
| | - Fang Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Zewei Lin
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Siyu Yao
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Hang Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenhu Liu
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fei Li
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Haiying Ran
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Junying Zhang
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Qihuan Fu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Jikui Liu
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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22
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Xian J, Wang S, Jiang Y, Li L, Cai L, Chen P, Liu Y, Zeng X, Chen G, Ding C, Hoffman RM, Jia L, Zhao H, Zhang Y. Overexpressed NEDD8 as a potential therapeutic target in esophageal squamous cell carcinoma. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0484. [PMID: 33733647 PMCID: PMC9088192 DOI: 10.20892/j.issn.2095-3941.2020.0484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/24/2020] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE The hyperactivated neddylation pathway plays an important role in tumorigenesis and is emerging as a promising anticancer target. We aimed to study whether NEDD8 (neural precursor cell expressed, developmentally down-regulated 8) might serve as a therapeutic target in esophageal squamous cell carcinoma (ESCC). METHODS The clinical relevance of NEDD8 expression was evaluated by using The Cancer Genome Atlas (TCGA) database and tissue arrays. NEDD8-knockdown ESCC cells generated with the CRISPR/Cas9 system were used to explore the anticancer effects and mechanisms. Quantitative proteomic analysis was used to examine the variations in NEDD8 knockdown-induced biological pathways. The cell cycle and apoptosis were assessed with fluorescence activated cell sorting. A subcutaneous-transplantation mouse tumor model was established to investigate the anticancer potential of NEDD8 silencing in vivo. RESULTS NEDD8 was upregulated at both the mRNA and protein expression levels in ESCC, and NEDD8 overexpression was associated with poorer overall patient survival (mRNA level: P = 0.028, protein level: P = 0.026, log-rank test). Downregulation of NEDD8 significantly suppressed tumor growth both in vitro and in vivo. Quantitative proteomic analysis revealed that downregulation of NEDD8 induced cell cycle arrest, DNA damage, and apoptosis in ESCC cells. Mechanistic studies demonstrated that NEDD8 knockdown led to the accumulation of cullin-RING E3 ubiquitin ligases (CRLs) substrates through inactivation of CRLs, thus suppressing the malignant phenotype by inducing cell cycle arrest and apoptosis in ESCC. Rescue experiments demonstrated that the induction of apoptosis after NEDD8 silencing was attenuated by DR5 knockdown. CONCLUSIONS Our study elucidated the anti-ESCC effects and underlying mechanisms of NEDD8 knockdown, and validated NEDD8 as a potential target for ESCC therapy.
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Affiliation(s)
- Jingrong Xian
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
- Research Center on Aging and Medicine, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China
| | - Shiwen Wang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
- Research Center on Aging and Medicine, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China
| | - Yanyu Jiang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lihui Li
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lili Cai
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Ping Chen
- Department of Basic Science of Oncology, College of Basic Medical Sciences, Zhengzhou University, Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou 450001, China
| | - Yue Liu
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
- Research Center on Aging and Medicine, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China
| | - Xiaofei Zeng
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoan Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Robert M. Hoffman
- Department of Surgery, University of California, San Diego 92101, USA
- Anticancer Inc., San Diego 92101, USA
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
- Research Center on Aging and Medicine, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China
| | - Yanmei Zhang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
- Research Center on Aging and Medicine, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China
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23
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Nie L, Wang C, Li N, Feng X, Lee N, Su D, Tang M, Yao F, Chen J. Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation. Mol Cell Proteomics 2020; 19:2015-2030. [PMID: 32958691 PMCID: PMC7710139 DOI: 10.1074/mcp.ra120.002290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 12/28/2022] Open
Abstract
Specific E3 ligases target tumor suppressors for degradation. Inhibition of such E3 ligases may be an important approach to cancer treatment. RNF146 is a RING domain and PARylation-dependent E3 ligase that functions as an activator of the β-catenin/Wnt and YAP/Hippo pathways by targeting the degradation of several tumor suppressors. Tankyrases 1 and 2 (TNKS1/2) are the only known poly-ADP-ribosyltransferases that require RNF146 to degrade their substrates. However, systematic identification of RNF146 substrates have not yet been performed. To uncover substrates of RNF146 that are targeted for degradation, we generated RNF146 knockout cells and TNKS1/2-double knockout cells and performed proteome profiling with label-free quantification as well as transcriptome analysis. We identified 160 potential substrates of RNF146, which included many known substrates of RNF146 and TNKS1/2 and 122 potential TNKS-independent substrates of RNF146. In addition, we validated OTU domain-containing protein 5 and Protein mono-ADP-ribosyltransferase PARP10 as TNKS1/2-independent substrates of RNF146 and SARDH as a novel substrate of TNKS1/2 and RNF146. Our study is the first proteome-wide analysis of potential RNF146 substrates. Together, these findings not only demonstrate that proteome profiling can be a useful general approach for the systemic identification of substrates of E3 ligases but also reveal new substrates of RNF146, which provides a resource for further functional studies.
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Affiliation(s)
- Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Namsoo Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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24
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Di Meo A, Sohaei D, Batruch I, Alexandrou P, Prassas I, Diamandis EP. Proteomic Profiling of the Human Tissue and Biological Fluid Proteome. J Proteome Res 2020; 20:444-452. [PMID: 33107741 DOI: 10.1021/acs.jproteome.0c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In-depth analysis of the human genome sequence has led to the annotation of approximately 20,000 human protein-coding genes. Although mass spectrometry (MS)-based workflows have made a great headway in achieving near genome-wide coverage, an equivalent complete map of the human proteome remains elusive. Delineating the spatial distribution of all human proteins at the organ, tissue, and cellular level can offer insight into health and disease and represents an excellent reference for the discovery of biomarkers and therapeutic targets. Here, we performed label-free liquid chromatography coupled to tandem MS (LC-MS/MS) to profile the normal human proteome. In total, we analyzed 117 samples from 46 normal tissues and organs at autopsy. Our high-resolution MS approach allowed for the quantification of 10,438 unique proteins. In order to expand our coverage of the human proteome, we combined our previously published biological fluid proteomic data from healthy individuals. We considered data from seven biological fluids, including urine, cerebrospinal fluid, synovial fluid, seminal plasma, sweat, cervical vaginal fluid, and nipple aspirate fluid. Overall, we generated tandem mass spectra corresponding to 13,028 unique human protein-coding genes. Although our analysis did not accomplish complete proteome coverage, it should be an important complementary resource for future biomarker discovery.
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Affiliation(s)
- Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Dorsa Sohaei
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Pantelis Alexandrou
- Department of Forensic Medicine and Toxicology, School of Medicine, University of Athens, Athens 157 72, Greece
| | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
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25
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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26
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Liu X, Hui X, Kang H, Fang Q, Chen A, Hu Y, Lu D, Chen X, Wang Y. A Multi-Gene Model Effectively Predicts the Overall Prognosis of Stomach Adenocarcinomas With Large Genetic Heterogeneity Using Somatic Mutation Features. Front Genet 2020; 11:940. [PMID: 33005171 PMCID: PMC7479248 DOI: 10.3389/fgene.2020.00940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Background Stomach adenocarcinoma (STAD) is one of the most common malignancies worldwide with poor prognosis. It remains unclear whether the prognosis is associated with somatic gene mutations. Methods In this research, we collected two independent STAD cohorts with both genetic profiling and clinical follow-up data, systematically investigated the association between the prognosis and somatic mutations, and analyzed the influence of heterogeneity on the prognosis-genetics association. Results Typical association was identified between somatic mutations and overall prognosis for individual cohorts. In The Cancer Genome Atlas (TCGA) cohort, a list of 24 genes was also identified that tended to mutate within cases of the poorest prognosis. The association showed apparent heterogeneity between different cohorts, although common signatures could be identified. A machine-learning model was trained with 20 common genes that showed a similar mutation rate difference between prognostic groups in the two cohorts, and it classified the cases in each cohort into two groups with significantly different prognosis. The model outperformed both single-gene models and TNM-based staging system significantly. Conclusion The study made a systematic analysis on the association between STAD prognosis and somatic mutations, identified signature genes that showed mutation preference in different prognostic groups, and developed an effective multi-gene model that can effectively predict the overall prognosis of STAD in different cohorts.
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Affiliation(s)
- Xianming Liu
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Xinjie Hui
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Huayu Kang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Qiongfang Fang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Aiyue Chen
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Yueming Hu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Desheng Lu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Xianxiong Chen
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
| | - Yejun Wang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, China
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27
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Dong H, Liu Y, Zeng WF, Shu K, Zhu Y, Chang C. A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data. Proteomics 2020; 20:e1900344. [PMID: 32643271 DOI: 10.1002/pmic.201900344] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/21/2020] [Indexed: 12/11/2022]
Abstract
Since the launch of Chinese Human Proteome Project (CNHPP) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), large-scale mass spectrometry (MS) based proteomic profiling of different kinds of human tumor samples have provided huge amount of valuable data for both basic and clinical researchers. Accurate prediction for tumor and non-tumor samples, as well as the tumor types has become a key step for biological and medical research, such as biomarker discovery, diagnosis, and monitoring of diseases. The traditional MS-based classification strategy mainly depends on the identification and quantification results of MS data, which has some inherent limitations, such as the low identification rate of MS data. Here, a deep learning-based tumor classifier directly using MS raw data is proposed, which is independent of the identification and quantification results of MS data. The potential precursors with intensities and retention times from MS data as input is first detected and extracted. Then, a deep learning-based classifier is trained, which can accurately distinguish between the tumor and non-tumor samples. Finally, it is demonstrated the deep learning-based classifier has a good performance compared with other machine learning methods and may help researchers find the potential biomarkers which are likely to be missed by the traditional strategy.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.,Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Yi Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100023, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunxian Shu
- School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.,Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
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28
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Guo G, Gao Z, Tong M, Zhan D, Wang G, Wang Y, Qin J. NQO1 is a determinant for cellular sensitivity to anti-tumor agent Napabucasin. Am J Cancer Res 2020; 10:1442-1454. [PMID: 32509390 PMCID: PMC7269777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023] Open
Abstract
Napabucasin (NAPA) is thought to be a potent cancer stemness inhibitor in different types of cancer cell lines. While it has shown promising activity in early phase clinical trials, two recent phase III NAPA clinical trials failed to meet the primary endpoint of overall survival. The reason for the failure is not clear, but a possible way to revive the clinical trial is to stratify patients with biomarkers that could predict NAPA response. Here, we report the identification of NAD(P)H dehydrogenase 1 (NQO1) as a major determinant of NAPA efficacy. A proteomic profiling of cancer cell lines revealed that NQO1 abundance is negatively correlated with IC50; in vitro assays showed that NAPA is a substrate for NQO1, which mediates the generation of ROS that leads to cell death. Furthermore, activation of an NQO1 transcription factor NRF2 by chemicals, including an FDA approved drug, can increase the NAPA cytotoxicity. Our findings suggest a potential use of NQO1 expression as a companion diagnostic test to identify patients in future NAPA trials and a combination strategy to expand the application of NAPA-based regimens for cancer therapy.
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Affiliation(s)
- Gaigai Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
| | - Zhouyong Gao
- Joint Center for Translational Medical Medicine, Baodi HospitalTianjin 301800, China
| | - Mengsha Tong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
- School of Life Sciences, Tsinghua UniversityBeijing 100084, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
- Center for Bioinformatics, East China Normal UniversityShanghai 200241, China
| | - Guangshun Wang
- Joint Center for Translational Medical Medicine, Baodi HospitalTianjin 301800, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
- Joint Center for Translational Medical Medicine, Baodi HospitalTianjin 301800, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijing 102206, China
- Joint Center for Translational Medical Medicine, Baodi HospitalTianjin 301800, China
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29
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Abstract
Gastric cancer is the third deadliest cancer in the world, and the absolute number of cases is increasing every year due to aging and growing of high-risk populations. This disease is a consequence of the complex interaction of microbial agents, with environmental and host factors, resulting in the dysregulation of multiple oncogenic and tumor-suppressing signaling pathways. Despite the advances in our understanding of carcinogenesis, there are still reduced therapeutic options for patients with gastric cancer. In recent years, genomic analyses of gastric tumors have emphasized their molecular heterogeneity. The distinction of gastric cancer molecular subtypes may be a key to identify novel therapeutic targets, to predict patient outcome and response to therapy, and to guide early diagnosis strategies. In this review, we summarize the most recent updates on the relationship between microbial agents and gastric cancer, in particular, Helicobacter pylori, the non-H pylori microbiome, and Epstein-Barr virus. We also highlight the main advances made in the past year regarding the molecular characterization of gastric cancer, especially the signatures with potential clinical utility.
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Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ceu Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Jose C Machado
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
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