1
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Ji X, Wu Q, Cao X, Liu S, Zhang J, Chen S, Shan J, Zhang Y, Li B, Zhao H. Helicobacter pylori East Asian type CagA hijacks more SHIP2 by its EPIYA-D motif to potentiate the oncogenicity. Virulence 2024; 15:2375549. [PMID: 38982595 PMCID: PMC11238919 DOI: 10.1080/21505594.2024.2375549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
CagA is a significant oncogenic factor injected into host cells by Helicobacter pylori, which is divided into two subtypes: East Asian type (CagAE), characterized by the EPIYA-D motif, and western type (CagAW), harboring the EPIYA-C motif. CagAE has been reported to have higher carcinogenicity than CagAW, although the underlying reason is not fully understood. SHIP2 is an intracellular phosphatase that can be recruited by CagA to perturb the homeostasis of intracellular signaling pathways. In this study, we found that SHIP2 contributes to the higher oncogenicity of CagAE. Co-Immunoprecipitation and Pull-down assays showed that CagAE bind more SHIP2 than CagAW. Immunofluorescence staining showed that a higher amount of SHIP2 recruited by CagAE to the plasma membrane catalyzes the conversion of PI(3,4,5)P3 into PI(3,4)P2. This alteration causes higher activation of Akt signaling, which results in enhanced IL-8 secretion, migration, and invasion of the infected cells. SPR analysis showed that this stronger interaction between CagAE and SHIP2 stems from the higher affinity between the EPIYA-D motif of CagAE and the SH2 domain of SHIP2. Structural analysis revealed the crucial role of the Phe residue at the Y + 5 position in EPIYA-D. After mutating Phe of CagAE into Asp (the corresponding residue in the EPIYA-C motif) or Ala, the activation of downstream Akt signaling was reduced and the malignant transformation of infected cells was alleviated. These findings revealed that CagAE hijacks SHIP2 through its EPIYA-D motif to enhance its carcinogenicity, which provides a better understanding of the higher oncogenic risk of H. pylori CagAE.
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Affiliation(s)
- Xiaofei Ji
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Qianwen Wu
- The Second School of Clinical Medicine, Binzhou Medical University, Yantai, Shandong, China
| | - Xinying Cao
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Shuzhen Liu
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Jianhui Zhang
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Si Chen
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Jiangfan Shan
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Ying Zhang
- The Second School of Clinical Medicine, Binzhou Medical University, Yantai, Shandong, China
| | - Boqing Li
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Huilin Zhao
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
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2
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Marasco M, Kirkpatrick J, Carlomagno T, Hub JS, Anselmi M. Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet. Comput Struct Biotechnol J 2024; 23:1169-1180. [PMID: 38510972 PMCID: PMC10951427 DOI: 10.1016/j.csbj.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.
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Affiliation(s)
- Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Kirkpatrick
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Teresa Carlomagno
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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3
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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. Proc Natl Acad Sci U S A 2024; 121:e2407159121. [PMID: 39012820 PMCID: PMC11287265 DOI: 10.1073/pnas.2407159121] [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: 04/09/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Mutations in the tyrosine phosphatase Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting autoinhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8 to 10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine-binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY10027
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY10027
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4
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Morales P, Brown AJ, Sangaré LO, Yang S, Kuihon SVNP, Chen B, Saeij JPJ. The Toxoplasma secreted effector TgWIP modulates dendritic cell motility by activating host tyrosine phosphatases Shp1 and Shp2. Cell Mol Life Sci 2024; 81:294. [PMID: 38977495 DOI: 10.1007/s00018-024-05283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 07/10/2024]
Abstract
The obligate intracellular parasite Toxoplasma gondii causes life-threatening toxoplasmosis to immunocompromised individuals. The pathogenesis of Toxoplasma relies on its swift dissemination to the central nervous system through a 'Trojan Horse' mechanism using infected leukocytes as carriers. Previous work found TgWIP, a protein secreted from Toxoplasma, played a role in altering the actin cytoskeleton and promoting cell migration in infected dendritic cells (DCs). However, the mechanism behind these changes was unknown. Here, we report that TgWIP harbors two SH2-binding motifs that interact with tyrosine phosphatases Shp1 and Shp2, leading to phosphatase activation. DCs infected with Toxoplasma exhibited hypermigration, accompanying enhanced F-actin stress fibers and increased membrane protrusions such as filopodia and pseudopodia. By contrast, these phenotypes were abrogated in DCs infected with Toxoplasma expressing a mutant TgWIP lacking the SH2-binding motifs. We further demonstrated that the Rho-associated kinase (Rock) is involved in the induction of these phenotypes, in a TgWIP-Shp1/2 dependent manner. Collectively, the data uncover a molecular mechanism by which TgWIP modulates the migration dynamics of infected DCs in vitro.
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Affiliation(s)
- Pavel Morales
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Abbigale J Brown
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Lamba Omar Sangaré
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sheng Yang
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
- Target & Protein Sciences, Johnson & Johnson, New Brunswick, USA
| | - Simon V N P Kuihon
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Jeroen P J Saeij
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.
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5
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Huang TT, Cao YX, Cao L. Novel therapeutic regimens against Helicobacter pylori: an updated systematic review. Front Microbiol 2024; 15:1418129. [PMID: 38912349 PMCID: PMC11190606 DOI: 10.3389/fmicb.2024.1418129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
Helicobacter pylori (H. pylori) is a strict microaerophilic bacterial species that exists in the stomach, and H. pylori infection is one of the most common chronic bacterial infections affecting humans. Eradicating H. pylori is the preferred method for the long-term prevention of complications such as chronic gastritis, peptic ulcers, gastric mucosa-associated lymphoid tissue lymphoma, and gastric cancer. However, first-line treatment with triple therapy and quadruple therapy has been unable to cope with increasing antibacterial resistance. To provide an updated review of H. pylori infections and antibacterial resistance, as well as related treatment options, we searched PubMed for articles published until March 2024. The key search terms were "H. pylori", "H. pylori infection", "H. pylori diseases", "H. pylori eradication", and "H. pylori antibacterial resistance." Despite the use of antimicrobial agents, the annual decline in the eradication rate of H. pylori continues. Emerging eradication therapies, such as the development of the new strong acid blocker vonoprazan, probiotic adjuvant therapy, and H. pylori vaccine therapy, are exciting. However, the effectiveness of these treatments needs to be further evaluated. It is worth mentioning that the idea of altering the oxygen environment in gastric juice for H. pylori to not be able to survive is a hot topic that should be considered in new eradication plans. Various strategies for eradicating H. pylori, including antibacterials, vaccines, probiotics, and biomaterials, are continuously evolving. A novel approach involving the alteration of the oxygen concentration within the growth environment of H. pylori has emerged as a promising eradication strategy.
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Affiliation(s)
- Ting-Ting Huang
- Department of Pharmacology, School of Basic Medical Science, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Yong-Xiao Cao
- Department of Pharmacology, School of Basic Medical Science, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Lei Cao
- Precision Medical Institute, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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6
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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.10.548257. [PMID: 37502916 PMCID: PMC10369915 DOI: 10.1101/2023.07.10.548257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY 10027
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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7
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Wang P, Han Y, Pan W, Du J, Zuo D, Ba Y, Zhang H. Tyrosine phosphatase SHP2 aggravates tumor progression and glycolysis by dephosphorylating PKM2 in gastric cancer. MedComm (Beijing) 2024; 5:e527. [PMID: 38576457 PMCID: PMC10993348 DOI: 10.1002/mco2.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 11/26/2023] [Accepted: 12/22/2023] [Indexed: 04/06/2024] Open
Abstract
Gastric cancer (GC) is among the most lethal human malignancies, yet it remains hampered by challenges in fronter of molecular-guided targeted therapy to direct clinical treatment strategies. The protein tyrosine phosphatase Src homology 2 domain-containing phosphatase 2 (SHP2) is involved in the malignant progression of GC. However, the detailed mechanisms of the posttranslational modifications of SHP2 remain poorly understood. Herein, we demonstrated that an allosteric SHP2 inhibitor, SHP099, was able to block tumor proliferation and migration of GC by dephosphorylating the pyruvate kinase M2 type (PKM2) protein. Mechanistically, we found that PKM2 is a bona fide target of SHP2. The dephosphorylation and activation of PKM2 by SHP2 are necessary to exacerbate tumor progression and GC glycolysis. Moreover, we demonstrated a strong correlation between the phosphorylation level of PKM2 and adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) in GC cells. Notably, the low phosphorylation expression of AMPK was negatively correlated with activated SHP2. Besides, we proved that cisplatin could activate SHP2 and SHP099 increased sensitivity to cisplatin in GC. Taken together, our results provide evidence that the SHP2/PKM2/AMPK axis exerts a key role in GC progression and glycolysis and could be a viable therapeutic approach for the therapy of GC.
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Affiliation(s)
- Peiyun Wang
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Yueting Han
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Wen Pan
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Jian Du
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Duo Zuo
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Yi Ba
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
| | - Haiyang Zhang
- Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerTianjin's Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin Medical UniversityTianjinChina
- The Institute of Translational MedicineTianjin Union Medical Center of Nankai UniversityTianjinChina
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8
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Cheng Y, Ouyang W, Liu L, Tang L, Zhang Z, Yue X, Liang L, Hu J, Luo T. Molecular recognition of ITIM/ITSM domains with SHP2 and their allosteric effect. Phys Chem Chem Phys 2024; 26:9155-9169. [PMID: 38165855 DOI: 10.1039/d3cp03923d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Src homology 2-domain-containing tyrosine phosphatase 2 (SHP2) is a non-receptor protein tyrosine phosphatase that is widely expressed in a variety of cells and regulates the immune response of T cells through the PD-1 pathway. However, the activation mechanism and allosteric effects of SHP2 remain unclear, hindering the development of small molecule inhibitors. For the first time, in this study, the complex structure formed by the intact PD-1 tail and SHP2 was modeled. The molecular recognition and conformational changes of inactive/active SHP2 versus ITIM/ITSM were compared based on prolonged MD simulations. The relative flexibility of the two SH2 domains during MD simulations contributes to the recruitment of ITIM/ITSM and supports the subsequent conformational change of SHP2. The binding free energy calculation shows that inactive SHP2 has a higher affinity for ITIM/ITSM than active SHP2, mainly because the former's N-SH2 refers to the α-state. In addition, a significant decrease in the contribution to the binding energy of certain residues (e.g., R32, S34, K35, T42, and K55) of conformationally transformed SHP2 contributes to the above result. These detailed changes during conformational transition will provide theoretical guidance for the molecular design of subsequent novel anticancer drugs.
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Affiliation(s)
- Yan Cheng
- Breast Disease Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China.
- Multi-omics Laboratory of Breast Diseases, State Key Laboratory of Biotherapy, National Collaborative, Innovation Center for Biotherapy, West China Hospital, Sichuan University, China
| | - Weiwei Ouyang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Ling Liu
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Lingkai Tang
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Zhigang Zhang
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Xinru Yue
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Breast Disease Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China.
- Multi-omics Laboratory of Breast Diseases, State Key Laboratory of Biotherapy, National Collaborative, Innovation Center for Biotherapy, West China Hospital, Sichuan University, China
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9
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Chen S, Zhao H, Tian Y, Wu Q, Zhang J, Liu S, Zhang Y, Wu Y, Li B, Chen S, Wang Z, Xiao R, Ji X. Antagonizing roles of SHP1 in the pathogenesis of Helicobacter pylori infection. Helicobacter 2024; 29:e13066. [PMID: 38468575 DOI: 10.1111/hel.13066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND SHP1 has been documented as a tumor suppressor and it was thought to play an antagonistic role in the pathogenesis of Helicobacter pylori infection. In this study, the exact mechanism of this antagonistic action was studied. MATERIALS AND METHODS AGS, MGC803, and GES-1 cells were infected with H. pylori, intracellular distribution changes of SHP1 were first detected by immunofluorescence. SHP1 overexpression and knockdown were then constructed in these cells to investigate its antagonistic roles in H. pylori infection. Migration and invasion of infected cells were detected by transwell assay, secretion of IL-8 was examined via ELISA, the cells with hummingbird-like alteration were determined by microexamination, and activation of JAK2/STAT3, PI3K/Akt, and ERK pathways were detected by immunoblotting. Mice infection model was established and gastric pathological changes were evaluated. Finally, the SHP1 activator sorafenib was used to analyze the attenuating effect of SHP1 activation on H. pylori pathogenesis in vitro and in vivo. RESULTS The sub-localization of SHP1 changed after H. pylori infection, specifically that the majority of the cytoplasmic SHP1 was transferred to the cell membrane. SHP1 inhibited H. pylori-induced activation of JAK2/STAT3 pathway, PI3K/Akt pathway, nuclear translocation of NF-κB, and then reduced EMT, migration, invasion, and IL-8 secretion. In addition, SHP1 inhibited the formation of CagA-SHP2 complex by dephosphorylating phosphorylated CagA, reduced ERK phosphorylation and the formation of CagA-dependent hummingbird-like cells. In the mice infection model, gastric pathological changes were observed and increased IL-8 secretion, indicators of cell proliferation and EMT progression were also detected. By activating SHP1 with sorafenib, a significant curative effect against H. pylori infection was obtained in vitro and in vivo. CONCLUSIONS SHP1 plays an antagonistic role in H. pylori pathogenesis by inhibiting JAK2/STAT3 and PI3K/Akt pathways, NF-κB nuclear translocation, and CagA phosphorylation, thereby reducing cell EMT, migration, invasion, IL-8 secretion, and hummingbird-like changes.
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Affiliation(s)
- Si Chen
- Binzhou Medical University, Yantai, China
| | | | - Yue Tian
- Binzhou Medical University, Yantai, China
- Binzhou People's Hospital, Binzhou, China
| | - Qianwen Wu
- Binzhou Medical University, Yantai, China
| | | | | | - Ying Zhang
- Binzhou Medical University, Yantai, China
| | - Yulong Wu
- Binzhou Medical University, Yantai, China
| | - Boqing Li
- Binzhou Medical University, Yantai, China
| | - Shu Chen
- Binzhou Medical University, Yantai, China
| | | | - Ruoyu Xiao
- Binzhou Medical University, Yantai, China
| | - Xiaofei Ji
- Binzhou Medical University, Yantai, China
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10
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Tran SC, Bryant KN, Cover TL. The Helicobacter pylori cag pathogenicity island as a determinant of gastric cancer risk. Gut Microbes 2024; 16:2314201. [PMID: 38391242 PMCID: PMC10896142 DOI: 10.1080/19490976.2024.2314201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Helicobacter pylori strains can be broadly classified into two groups based on whether they contain or lack a chromosomal region known as the cag pathogenicity island (cag PAI). Colonization of the human stomach with cag PAI-positive strains is associated with an increased risk of gastric cancer and peptic ulcer disease, compared to colonization with cag PAI-negative strains. The cag PAI encodes a secreted effector protein (CagA) and components of a type IV secretion system (Cag T4SS) that delivers CagA and non-protein substrates into host cells. Animal model experiments indicate that CagA and the Cag T4SS stimulate a gastric mucosal inflammatory response and contribute to the development of gastric cancer. In this review, we discuss recent studies defining structural and functional features of CagA and the Cag T4SS and mechanisms by which H. pylori strains containing the cag PAI promote the development of gastric cancer and peptic ulcer disease.
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Affiliation(s)
- Sirena C Tran
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kaeli N Bryant
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy L Cover
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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11
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Anselmi M, Hub JS. Atomistic ensemble of active SHP2 phosphatase. Commun Biol 2023; 6:1289. [PMID: 38129686 PMCID: PMC10739809 DOI: 10.1038/s42003-023-05682-5] [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: 07/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76K almost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
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Affiliation(s)
- Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
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12
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Usui Y, Momozawa Y. Personalized medicine with germline pathogenic variants: Importance of population- and region-wide evidence. Cancer Sci 2023; 114:3816-3824. [PMID: 37530079 PMCID: PMC10551596 DOI: 10.1111/cas.15922] [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: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
Rare germline pathogenic variants in cancer-predisposing genes have a high impact and potential for clinical utility. In the last 30 years, based on evidence of cancer risk associated with germline pathogenic variants, several measures have been suggested for personalized medicine, including the development of novel treatments, treatment stratification, risk reduction by surgical measures, chemoprevention, removal of environmental factors, and surveillance for early detection among specific high-risk individuals. However, this evidence is mainly based on evaluations of European populations. Our large-scale analyses of more than 100,000 individuals, including 14 disease cases and non-cancer controls in the Japanese population, suggest some discrepancies in the associations between cancer-predisposing genes and diseases, expansion of the targeted diseases of BRCA1 and BRCA2, and a potential novel risk-reduction measure for gastric cancer. They are likely to be explained by population and region variations; therefore, more population-wide and region-wide research could provide improved personalized medicine as well as a better understanding of disease mechanisms. This review summarizes current personalized medicine and discusses the potential use of germline pathogenic variants.
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Affiliation(s)
- Yoshiaki Usui
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Yukihide Momozawa
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesYokohamaJapan
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13
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Ailloud F, Gottschall W, Suerbaum S. Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori. Commun Biol 2023; 6:839. [PMID: 37573385 PMCID: PMC10423294 DOI: 10.1038/s42003-023-05218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023] Open
Abstract
The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation implied that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection may shape both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.
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Affiliation(s)
- Florent Ailloud
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Wilhelm Gottschall
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sebastian Suerbaum
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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14
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Usui Y, Matsuo K, Momozawa Y. Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer. Reply. N Engl J Med 2023; 389:379-381. [PMID: 37494497 DOI: 10.1056/nejmc2306877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
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15
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Marasco M, Kirkpatrick J, Carlomagno T, Hub JS, Anselmi M. Experiment-guided molecular simulations define a heterogeneous structural ensemble for the PTPN11 tandem SH2 domains. Chem Sci 2023; 14:5743-5755. [PMID: 37265738 PMCID: PMC10231330 DOI: 10.1039/d3sc00746d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/04/2023] [Indexed: 06/03/2023] Open
Abstract
SHP2 plays an important role in regulating cellular processes, and its pathogenic mutations cause developmental disorders and are linked to cancer. SHP2 is a multidomain protein, comprising two SH2 domains arranged in tandem, a catalytic PTP domain, and a disordered C-terminal tail. SHP2 is activated upon binding two linked phosphopeptides to its SH2 domains, and the peptide orientation and spacing between binding sites are critical for enzymatic activation. For decades, the tandem SH2 has been extensively studied to identify the relative orientation of the two SH2 domains that most effectively binds effectors. So far, neither crystallography nor experiments in solution have provided conclusive results. Using experiment-guided molecular simulations, we determine the heterogeneous structural ensemble of the tandem SH2 in solution in agreement with experimental data from small-angle X-ray scattering and NMR residual dipolar couplings. In the solution ensemble, N-SH2 adopts different orientations and positions relative to C-SH2. We suggest that the intrinsic structural plasticity of the tandem SH2 allows SHP2 to respond to external stimuli and is essential for its functional activity.
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Affiliation(s)
- Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center New York NY USA
| | - John Kirkpatrick
- School of Biosciences, University of Birmingham Edgbaston B15 2TT Birmingham UK
| | - Teresa Carlomagno
- School of Biosciences, University of Birmingham Edgbaston B15 2TT Birmingham UK
- Institute of Cancer and Genomic Sciences, University of Birmingham Edgbaston B15 2TT Birmingham UK
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University 66123 Saarbrücken Germany
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University 66123 Saarbrücken Germany
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16
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Welsh CL, Allen S, Madan LK. Setting sail: Maneuvering SHP2 activity and its effects in cancer. Adv Cancer Res 2023; 160:17-60. [PMID: 37704288 PMCID: PMC10500121 DOI: 10.1016/bs.acr.2023.03.003] [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] [Indexed: 09/15/2023]
Abstract
Since the discovery of tyrosine phosphorylation being a critical modulator of cancer signaling, proteins regulating phosphotyrosine levels in cells have fast become targets of therapeutic intervention. The nonreceptor protein tyrosine phosphatase (PTP) coded by the PTPN11 gene "SHP2" integrates phosphotyrosine signaling from growth factor receptors into the RAS/RAF/ERK pathway and is centrally positioned in processes regulating cell development and oncogenic transformation. Dysregulation of SHP2 expression or activity is linked to tumorigenesis and developmental defects. Even as a compelling anti-cancer target, SHP2 was considered "undruggable" for a long time owing to its conserved catalytic PTP domain that evaded drug development. Recently, SHP2 has risen from the "undruggable curse" with the discovery of small molecules that manipulate its intrinsic allostery for effective inhibition. SHP2's unique domain arrangement and conformation(s) allow for a truly novel paradigm of inhibitor development relying on skillful targeting of noncatalytic sites on proteins. In this review we summarize the biological functions, signaling properties, structural attributes, allostery and inhibitors of SHP2.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Sarah Allen
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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17
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Usui Y, Taniyama Y, Endo M, Koyanagi YN, Kasugai Y, Oze I, Ito H, Imoto I, Tanaka T, Tajika M, Niwa Y, Iwasaki Y, Aoi T, Hakozaki N, Takata S, Suzuki K, Terao C, Hatakeyama M, Hirata M, Sugano K, Yoshida T, Kamatani Y, Nakagawa H, Matsuda K, Murakami Y, Spurdle AB, Matsuo K, Momozawa Y. Helicobacter pylori, Homologous-Recombination Genes, and Gastric Cancer. N Engl J Med 2023; 388:1181-1190. [PMID: 36988593 DOI: 10.1056/nejmoa2211807] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
BACKGROUND Helicobacter pylori infection is a well-known risk factor for gastric cancer. However, the contribution of germline pathogenic variants in cancer-predisposing genes and their effect, when combined with H. pylori infection, on the risk of gastric cancer has not been widely evaluated. METHODS We evaluated the association between germline pathogenic variants in 27 cancer-predisposing genes and the risk of gastric cancer in a sample of 10,426 patients with gastric cancer and 38,153 controls from BioBank Japan. We also assessed the combined effect of pathogenic variants and H. pylori infection status on the risk of gastric cancer and calculated the cumulative risk in 1433 patients with gastric cancer and 5997 controls from the Hospital-based Epidemiologic Research Program at Aichi Cancer Center (HERPACC). RESULTS Germline pathogenic variants in nine genes (APC, ATM, BRCA1, BRCA2, CDH1, MLH1, MSH2, MSH6, and PALB2) were associated with the risk of gastric cancer. We found an interaction between H. pylori infection and pathogenic variants in homologous-recombination genes with respect to the risk of gastric cancer in the sample from HERPACC (relative excess risk due to the interaction, 16.01; 95% confidence interval [CI], 2.22 to 29.81; P = 0.02). At 85 years of age, persons with H. pylori infection and a pathogenic variant had a higher cumulative risk of gastric cancer than noncarriers infected with H. pylori (45.5% [95% CI, 20.7 to 62.6] vs. 14.4% [95% CI, 12.2 to 16.6]). CONCLUSIONS H. pylori infection modified the risk of gastric cancer associated with germline pathogenic variants in homologous-recombination genes. (Funded by the Japan Agency for Medical Research and Development and others.).
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Affiliation(s)
- Yoshiaki Usui
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yukari Taniyama
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Mikiko Endo
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yuriko N Koyanagi
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yumiko Kasugai
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Isao Oze
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Hidemi Ito
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Issei Imoto
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Tsutomu Tanaka
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Masahiro Tajika
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yasumasa Niwa
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yusuke Iwasaki
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Tomomi Aoi
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Nozomi Hakozaki
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Sadaaki Takata
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Kunihiko Suzuki
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Chikashi Terao
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Masanori Hatakeyama
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Makoto Hirata
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Kokichi Sugano
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Teruhiko Yoshida
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yoichiro Kamatani
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Hidewaki Nakagawa
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Koichi Matsuda
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yoshinori Murakami
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Amanda B Spurdle
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Keitaro Matsuo
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
| | - Yukihide Momozawa
- From the Laboratories for Genotyping Development (Y.U., M.E., Y.I., T.A., N.H., S.T., K. Suzuki, Y. Momozawa), Statistical and Translational Genetics (C.T.), and Cancer Genomics (H.N.), RIKEN Center for Integrative Medical Sciences, Yokohama, the Divisions of Cancer Information and Control (Y.U., Y.T., Y.N.K., H.I.) and Cancer Epidemiology and Prevention (Y. Kasugai, I.O., K. Matsuo), Department of Preventive Medicine, Aichi Cancer Center, the Divisions of Cancer Epidemiology (Y. Kasugai, K. Matsuo) and Descriptive Cancer Epidemiology (H.I.), Nagoya University Graduate School of Medicine, Aichi Cancer Center Research Institute (I.I.), and the Department of Endoscopy (T.T., M.T.), Aichi Cancer Center Hospital (Y.N.), Nagoya, the Department of Hematology, Oncology, and Respiratory Medicine, Okayama University Medical School, Okayama (Y.U.), the Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (M. Hatakeyama), the Department of Genetic Medicine and Services, National Cancer Center Hospital (M. Hirata, K. Sugano, T.Y.), the Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science (M. Hirata, Y. Murakami), and the Laboratories of Complex Trait Genomics (Y. Kamatani) and Clinical Genome Sequencing (K. Matsuda), Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, and the Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation (K. Sugano), Tokyo, and the Research Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo (M. Hatakeyama) - all in Japan; and the Population Health Program, QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute, Brisbane, Australia (A.B.S.)
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18
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Thrift AP, Wenker TN, El-Serag HB. Global burden of gastric cancer: epidemiological trends, risk factors, screening and prevention. Nat Rev Clin Oncol 2023; 20:338-349. [PMID: 36959359 DOI: 10.1038/s41571-023-00747-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
Abstract
Gastric cancer remains a major cause of cancer-related mortality worldwide. The temporal trends for this malignancy, however, are dynamic, and reports from the past decade indicate important declines in some regions and demographic groups, as well as a few notable exceptions in which gastric cancer rates are either stable or increasing. Two main anatomical subtypes of gastric cancer exist, non-cardia and cardia, with different temporal trends and risk factors (such as obesity and reflux for cardia gastric cancer and Helicobacter pylori infection for non-cardia gastric cancer). Shifts in the distribution of anatomical locations have been detected in several high-incidence regions. H. pylori is an important aetiological factor for gastric cancer; importantly, the anticipated long-term findings from studies examining the effect of H. pylori eradication on the risk of (re)developing gastric cancer have emerged in the past few years. In this Review, we highlight the latest trends in incidence and mortality using an evidence-based approach. We make the best possible inferences, including clinical and public health inference, on the basis of the quality of the evidence available, and highlight burning questions as well as gaps in knowledge and public health practice that need to be addressed to reduce gastric cancer burden worldwide.
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Affiliation(s)
- Aaron P Thrift
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Theresa Nguyen Wenker
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Hashem B El-Serag
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA.
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19
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Senda M, Senda T. Crystal Structure Analysis of SH2 Domains in Complex with Phosphotyrosine Peptides. Methods Mol Biol 2023; 2705:39-58. [PMID: 37668968 DOI: 10.1007/978-1-0716-3393-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
While the number of tertiary structures solved by cryoelectron microscopy has rapidly increased, X-ray crystallography is still a popular method to determine the tertiary structure of proteins at atomic resolution. However, there are still problems associated with X-ray crystallography, including crystallization and crystal twinning. Indeed, we encountered crystallization and twinning problems in the crystal structure analysis of the SH2 domains complexed with a phosphorylated peptide derived from the oncoprotein CagA. In this chapter, we describe the methods used to overcome these problems. In addition, we provide details of the optimization of the crystallization conditions and cryo-conditions, which are usually not given in published crystal structure analyses.
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Affiliation(s)
- Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
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20
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Hatakeyama M. Impact of the Helicobacter pylori Oncoprotein CagA in Gastric Carcinogenesis. Curr Top Microbiol Immunol 2023; 444:239-257. [PMID: 38231221 DOI: 10.1007/978-3-031-47331-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Helicobacter pylori CagA is the first and only bacterial oncoprotein etiologically associated with human cancer. Upon delivery into gastric epithelial cells via bacterial type IV secretion, CagA acts as a pathogenic/pro-oncogenic scaffold that interacts with and functionally perturbs multiple host proteins such as pro-oncogenic SHP2 phosphatase and polarity-regulating kinase PAR1b/MARK2. Although H. pylori infection is established during early childhood, gastric cancer generally develops in elderly individuals, indicating that oncogenic CagA activity is effectively counteracted at a younger age. Moreover, the eradication of cagA-positive H. pylori cannot cure established gastric cancer, indicating that H. pylori CagA-triggered gastric carcinogenesis proceeds via a hit-and-run mechanism. In addition to its direct oncogenic action, CagA induces BRCAness, a cellular status characterized by replication fork destabilization and loss of error-free homologous recombination-mediated DNA double-strand breaks (DSBs) by inhibiting cytoplasmic-to-nuclear localization of the BRCA1 tumor suppressor. This causes genomic instability that leads to the accumulation of excess mutations in the host cell genome, which may underlie hit-and-run gastric carcinogenesis. The close connection between CagA and BRCAness was corroborated by a recent large-scale case-control study that revealed that the risk of gastric cancer in individuals carrying pathogenic variants of genes that induce BRCAness (such as BRCA1 and BRCA2) dramatically increases upon infection with cagA-positive H. pylori. Accordingly, CagA-mediated BRCAness plays a crucial role in the development of gastric cancer in conjunction with the direct oncogenic action of CagA.
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Affiliation(s)
- Masanori Hatakeyama
- Institute of Microbial Chemistry, Laboratory of Microbial Carcinogenesis, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-Ku, Tokyo, 141-0021, Japan.
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-Ku, Sapporo, 060-0815, Japan.
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21
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Calligari P, Stella L, Bocchinfuso G. Computational Evaluation of Peptide-Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains. Methods Mol Biol 2023; 2705:113-133. [PMID: 37668972 DOI: 10.1007/978-1-0716-3393-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Many biological functions are mediated by protein-protein interactions (PPIs), often involving specific structural modules, such as SH2 domains. Inhibition of PPIs is a pharmaceutical strategy of growing importance. However, a major challenge in the design of PPI inhibitors is the large interface involved in these interactions, which, in many cases, makes inhibition by small organic molecules ineffective. Peptides, which cover a wide range of dimensions and can be opportunely designed to mimic protein sequences at PPI interfaces, represent a valuable alternative to small molecules. Computational techniques able to predict the binding affinity of peptides for the target domain or protein represent a crucial stage in the workflow for the design of peptide-based drugs. This chapter describes a protocol to obtain the potential of mean force (PMF) for peptide-SH2 domain binding, starting from umbrella sampling (US) molecular dynamics (MD) simulations. The PMF profiles can be effectively used to predict the relative standard binding free energies of different peptide sequences.
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Affiliation(s)
- Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy.
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22
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Hayashi T, Hatakeyama M. Exploring Allosteric Inhibitors of Protein Tyrosine Phosphatases Through High-Throughput Screening. Methods Mol Biol 2023; 2691:235-245. [PMID: 37355550 DOI: 10.1007/978-1-0716-3331-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
High-throughput screening (HTS) using a natural or synthetic chemical or natural product library is a powerful technique for discovering novel small-molecular-weight compounds in order to develop drugs that specifically inhibit or activate molecular targets, malfunctioning of which underlies the development of diseases, especially malignant neoplasms. In contrast to a large number of successful cases in obtaining inhibitors against protein tyrosine kinases (PTKs) using HTS, however, the development of selective inhibitors for protein tyrosine phosphatases (PTPs) has lagged since PTP family members share highly conserved catalytic domain structures. Here, in this chapter we describe a novel method for exploring seed compounds of allosteric PTP inhibitors from a chemical/natural product library through HTS.
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Affiliation(s)
- Takeru Hayashi
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Masanori Hatakeyama
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo, Japan.
- Center of Infection-Associated Cancer, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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23
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Ishioka M, Osawa H, Hirasawa T, Kawachi H, Nakano K, Fukushima N, Sakaguchi M, Tada T, Kato Y, Shibata J, Ozawa T, Tajiri H, Fujisaki J. Performance of an artificial intelligence-based diagnostic support tool for early gastric cancers: Retrospective study. Dig Endosc 2022; 35:483-491. [PMID: 36239483 DOI: 10.1111/den.14455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/12/2022] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Endoscopists' abilities to diagnose early gastric cancers (EGCs) vary, especially between specialists and nonspecialists. We developed an artificial intelligence (AI)-based diagnostic support tool "Tango" to differentiate EGCs and compared its performance with that of endoscopists. METHODS The diagnostic performances of Tango and endoscopists (34 specialists, 42 nonspecialists) were compared using still images of 150 neoplastic and 165 non-neoplastic lesions. Neoplastic lesions included EGCs and adenomas. The primary outcome was to show the noninferiority of Tango (based on sensitivity) over specialists. The secondary outcomes were the noninferiority of Tango (based on accuracy) over specialists and the superiority of Tango (based on sensitivity and accuracy) over nonspecialists. The lower limit of the 95% confidence interval (CI) of the difference between Tango and the specialists for sensitivity was calculated, with >-10% defined as noninferiority and >0% defined as superiority in the primary outcome. The comparable differences between Tango and the endoscopists for each performance were calculated, with >10% defined as superiority and >0% defined as noninferiority in the secondary outcomes. RESULTS Tango achieved superiority over the specialists based on sensitivity (84.7% vs. 65.8%, difference 18.9%, 95% CI 12.3-25.3%) and demonstrated noninferiority based on accuracy (70.8% vs. 67.4%). Tango achieved superiority over the nonspecialists based on sensitivity (84.7% vs. 51.0%) and accuracy (70.8% vs. 58.4%). CONCLUSIONS The AI-based diagnostic support tool for EGCs demonstrated a robust performance and may be useful to reduce misdiagnosis.
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Affiliation(s)
- Mitsuaki Ishioka
- Department of Gastroenterology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroyuki Osawa
- Division of Gastroenterology, Department of Medicine, Jichi Medical University, Tochigi, Japan
| | - Toshiaki Hirasawa
- Department of Gastroenterology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroshi Kawachi
- Department of Pathology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kaoru Nakano
- Department of Pathology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Mio Sakaguchi
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Tomohiro Tada
- AI Medical Service Inc., Tokyo, Japan.,Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Tada Tomohiro Institute of Gastroenterology and Proctology, Saitama, Japan
| | | | - Junichi Shibata
- AI Medical Service Inc., Tokyo, Japan.,Tada Tomohiro Institute of Gastroenterology and Proctology, Saitama, Japan
| | - Tsuyoshi Ozawa
- AI Medical Service Inc., Tokyo, Japan.,Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisao Tajiri
- The Jikei University School of Medicine, Tokyo, Japan
| | - Junko Fujisaki
- Department of Gastroenterology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
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24
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Structural Insights into the Binding Propensity of Human SHIP2 SH2 to Oncogenic CagA Isoforms from Helicobacter pylori. Int J Mol Sci 2022; 23:ijms231911299. [PMID: 36232599 PMCID: PMC9569640 DOI: 10.3390/ijms231911299] [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: 08/30/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
SHIP2 is a multi-domain inositol 5-phosphatase binding to a variety of phosphotyrosine (pY)-containing proteins through its SH2 domain, so as to regulate various cell signaling pathways by modulating the phosphatidylinositol level in the plasma membrane. Unfavorably, Helicobacter pylori can hijack SHIP2 through the CagA protein to induce gastric cell carcinogenesis. To date, the interaction between SHIP2 and CagA was not analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Tyr-phosphorylated peptides from four EPIYA motifs (A/B/C/D) in CagA was studied using NMR spectroscopy. The results showed that EPIYA-C and -D bind to a similar interface of SHIP2-SH2, including a pY-binding pocket and a hydrophobic pocket, to achieve high affinity, while EPIYA-A and -B bind to a smaller interface of SHIP2-SH2 with weak affinity. By summarizing the interface and affinity of SHIP2-SH2 for CagA EPIYA-A/B/C/D, c-MET and FcgR2B ITIM, it was proposed that, potentially, SHIP2-SH2 has a selective preference for L > I > V for the aliphatic residues at the pY+3 position in its ligand. This study reveals the rule of the ligand sequence bound by SHIP2-SH2 and the mechanism by which CagA protein hijacks SHIP2, which will help design a peptide inhibitor against SHIP2-SH2.
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25
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Liu Y, Baba Y, Ishimoto T, Gu X, Zhang J, Nomoto D, Okadome K, Baba H, Qiu P. Gut microbiome in gastrointestinal cancer: a friend or foe? Int J Biol Sci 2022; 18:4101-4117. [PMID: 35844804 PMCID: PMC9274484 DOI: 10.7150/ijbs.69331] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/04/2022] [Indexed: 12/07/2022] Open
Abstract
The impact of the gut microbiome on host health is becoming increasingly recognized. To date, there is growing evidence that the complex characteristics of the microbial community play key roles as potential biomarkers and predictors of responses in cancer therapy. Many studies have shown that altered commensal bacteria lead to cancer susceptibility and progression in diverse pathways. In this review, we critically assess the data for gut microbiota related to gastrointestinal cancer, including esophageal, gastric, pancreatic, colorectal cancer, hepatocellular carcinoma and cholangiocarcinoma. Importantly, the underlying mechanisms of gut microbiota involved in cancer occurrence, prevention and treatment are elucidated. The purpose of this review is to provide novel insights for applying this understanding to the development of new therapeutic strategies in gastrointestinal cancer by targeting the microbial community.
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Affiliation(s)
- Yang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning province, China
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Department of Next-Generation Surgical Therapy Development, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Gastrointestinal Cancer Biology, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Xi Gu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning province, China
| | - Jun Zhang
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Gastrointestinal Cancer Biology, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Daichi Nomoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuo Okadome
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Peng Qiu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning Province, China
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26
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Zeng X, Xiong L, Wang W, Zhao Y, Xie Y, Wang Q, Zhang Q, Li L, Jia C, Liao Y, Zhou J. Whole-genome sequencing and comparative analysis of Helicobacter pylori GZ7 strain isolated from China. Folia Microbiol (Praha) 2022; 67:923-934. [PMID: 35829852 DOI: 10.1007/s12223-022-00989-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 07/01/2022] [Indexed: 11/04/2022]
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative pathogen as a carcinogen of the class Ι, with unique genetic diversity and wide geographic differences. The high incidence of gastric cancer in East Asia may be related to the bacterial genotype. It is of great significance that the genome of H. pylori in East Asia is widely collected. Therefore, we combined two sequencing technologies (PacBio and Illumina HiSeq 4000) and multiple databases to sequence and annotate the whole genome of H. pylori GZ7 isolated from a gastric cancer patient in Guizhou, China. Furthermore, this sequence was further compared with the genome sequence of 23 H. pylori strains isolated from different regions through collinearity comparison, specific gene analysis, phylogenetic tree construction, etc. The results showed that the genome of H. pylori GZ7 consists of 1,579,995 bp circle chromosomes with a GC content of 39.51%. This chromosome has 1,572 coding sequences, three antibiotic resistance genes, five prophages, and 198 virulence genes. The comparative genome analyses showed that H. pylori GZ7 has 53 specific genes compared to the other 23 strains. Most of these specific genes have not been annotated and characterized until now, whose research may provide insights into the biological activities of this strain. H. pylori GZ7 has the closest genetic relationship with H. pylori F30, and the farthest genetic relationship with H. pylori ELS37, which indicates that H. pylori genomes have geographical differences. This information may provide a molecular basis and guidance for constructing diagnostic methods for H. pylori and researching subsequent experiments.
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Affiliation(s)
- Xiaoyan Zeng
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Lin Xiong
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi), Fenghuang Road 98, Zunyi, 563099, China
| | - Wenling Wang
- GuiZhou Cancer Hospital, Beijing Road 9, Guiyang, 550004, China
| | - Yan Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Yuan Xie
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Leilei Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Cencen Jia
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Yonghui Liao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China
| | - Jianjiang Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Beijing Road 9, GuizhouGuiyang, 550004, China.
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27
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Saha K, Sarkar D, Khan U, Karmakar BC, Paul S, Mukhopadhyay AK, Dutta S, Bhattacharya S. Capsaicin Inhibits Inflammation and Gastric Damage during H pylori Infection by Targeting NF-kB–miRNA Axis. Pathogens 2022; 11:pathogens11060641. [PMID: 35745495 PMCID: PMC9227394 DOI: 10.3390/pathogens11060641] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/26/2022] Open
Abstract
Helicobacter pylori (H. pylori) infection is considered as one of the strongest risk factors for gastric disorders. Infection triggers several host pathways to elicit inflammation, which further proceeds towards gastric complications. The NF-kB pathway plays a central role in the upregulation of the pro-inflammatory cytokines during infection. It also regulates the transcriptional network of several inflammatory cytokine genes. Hence, targeting NF-kB could be an important strategy to reduce pathogenesis. Moreover, treatment of H. pylori needs attention as current therapeutics lack efficacy due to antibiotic resistance, highlighting the need for alternative therapeutic approaches. In this study, we investigated the effects of capsaicin, a known NF-kB inhibitor in reducing inflammation and gastric complications during H. pylori infection. We observed that capsaicin reduced NF-kB activation and upregulation of cytokine genes in an in vivo mice model. Moreover, it affected NF-kB–miRNA interplay to repress inflammation and gastric damages. Capsaicin reduced the expression level of mir21 and mir223 along with the pro-inflammatory cytokines. The repression of miRNA further affected downstream targets such as e-cadherin and Akt. Our data represent the first evidence that treatment with capsaicin inhibits inflammation and induces antimicrobial activity during H. pylori infection. This alternative approach might open a new avenue in treating H. pylori infection, thus reducing gastric problems.
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Affiliation(s)
- Kalyani Saha
- Department of Biochemistry, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research (ICMR-NICED), P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (K.S.); (D.S.); (U.K.)
| | - Deotima Sarkar
- Department of Biochemistry, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research (ICMR-NICED), P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (K.S.); (D.S.); (U.K.)
| | - Uzma Khan
- Department of Biochemistry, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research (ICMR-NICED), P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (K.S.); (D.S.); (U.K.)
| | - Bipul Chandra Karmakar
- Department of Microbiology, National Institute of Cholera and Enteric Diseases (ICMR-NICED), Indian Council of Medical Research, P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (B.C.K.); (S.P.); (A.K.M.)
| | - Sangita Paul
- Department of Microbiology, National Institute of Cholera and Enteric Diseases (ICMR-NICED), Indian Council of Medical Research, P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (B.C.K.); (S.P.); (A.K.M.)
| | - Asish K. Mukhopadhyay
- Department of Microbiology, National Institute of Cholera and Enteric Diseases (ICMR-NICED), Indian Council of Medical Research, P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (B.C.K.); (S.P.); (A.K.M.)
| | - Shanta Dutta
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research (ICMR-NICED), P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India;
| | - Sushmita Bhattacharya
- Department of Biochemistry, National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research (ICMR-NICED), P-33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata 700010, India; (K.S.); (D.S.); (U.K.)
- Correspondence: ; Tel.: +91-97179-96740
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Koizumi Y, Ahmad S, Ikeda M, Yashima-Abo A, Espina G, Sugimoto R, Sugai T, Iwaya T, Tamura G, Koeda K, Liotta LA, Takahashi F, Nishizuka SS. Helicobacter pylori modulated host immunity in gastric cancer patients with S-1 adjuvant chemotherapy. J Natl Cancer Inst 2022; 114:1149-1158. [PMID: 35437596 PMCID: PMC9360472 DOI: 10.1093/jnci/djac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Paradoxically, Helicobacter pylori-positive (HP+) advanced gastric cancer patients have a better prognosis than those who are HP-negative (HP-). Immunologic and statistical analyses can be used to verify whether systemic mechanisms modulated by HP are involved in this more favorable outcome. METHODS A total of 658 advanced gastric cancer patients who underwent gastrectomy were enrolled. HP infection, mismatch repair, programmed death-ligand 1 (PD-L1), and CD4/CD8 proteins, and microsatellite instability were analyzed. Overall survival (OS) and relapse free survival (RFS) rates were analyzed after stratifying clinicopathological factors. Cox proportional hazards regression analysis was performed to identify independent prognostic factors. RESULTS Among 491 cases that were analyzed, 175 (36%) and 316 (64%) cases were HP+ and HP⁻, respectively. Analysis of RFS indicated an interaction of HP status among the subgroups for S-1 dose (Pinteraction=0.0487) and PD-L1 (P = .016). HP+ patients in the PD-L1⁻ group had significantly higher five-year OS and RFS than HP- patients (81% vs. 68%; P = .0011; HR 0.477; 95% CI, 0.303-0.751 and 76% vs. 63% P = .0011; HR 0.508; 95% CI, 0.335-0.771, respectively). The five-year OS and RFS was also significantly higher for HP+ compared to HP- patients in the PD-L1-/S-1-reduced group (86% vs. 46%; P = .0014; HR 0.205; 95% CI, 0.07-0.602 and 83% vs. 34%; P = .001; HR 0.190; 95% CI, 0.072-0.498, respectively). Thus, HP status was identified as one of the most potentially important independent factors to predict prolonged survival. CONCLUSION This retrospective study suggests that an HP-modulated host immune system may contribute to prolonged survival in the absence of immune escape mechanisms of gastric cancer.
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Affiliation(s)
- Yuka Koizumi
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Sheny Ahmad
- Aspirating Scientists Summer Internship Program, George Mason University, Manassas, VA USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Miyuki Ikeda
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Akiko Yashima-Abo
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Ginny Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Takeshi Iwaya
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine
| | - Gen Tamura
- Department of Laboratory Medicine, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Keisuke Koeda
- Department of Medical Safety Science, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Fumiaki Takahashi
- Division of Medical Engineering, Department of Information Science, Iwate Medical University, Yahaba, Japan
| | - Satoshi S Nishizuka
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
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Brasil-Costa I, Souza CDO, Monteiro LCR, Santos MES, Oliveira EHCD, Burbano RMR. H. pylori Infection and Virulence Factors cagA and vacA (s and m Regions) in Gastric Adenocarcinoma from Pará State, Brazil. Pathogens 2022; 11:pathogens11040414. [PMID: 35456089 PMCID: PMC9028951 DOI: 10.3390/pathogens11040414] [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: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/23/2022] Open
Abstract
H. pylori shows a great variability in genes associated with virulence, which may influence properties related to gastric adenocarcinoma initiation and progression. Among them, cagA and vacA show a strong positive association with the disease. Therefore, a cross-sectional study was carried out with 281 samples of gastric adenocarcinoma, collected at a cancer reference center in the Brazilian Amazon. Detection of H. pylori was proceeded by PCR of the ureA and 16S genes. Positive samples were subjected to the cagA detection and vacA typing. The bacteria were observed in 32.03% of the samples. Positivity for H. pylori was associated with advanced age (p = 0.0093) and metastases (p = 0.0073). Among the positive cases, 80% (72/90) had the cagA gene. For the “s” position of the vacA gene, 98.8% (83/84) of the bacteria had genotype s1 and 1.2% (1/84) were genotyped as s2. For the “m” position, the results were: 63.6% (56/88) with m1 genotype, 2.3% (2/88) genotyped as m2 and 34.1% (30/88) m1/m2. Virulence factors did not impact an increase in the association with age or metastases. In conclusion, H. pylori infection is associated with malignant phenotype cases of gastric adenocarcinoma, involving metastases. The virulence factors related to the cagA and vacA genes showed a high prevalence in the Brazilian Amazon.
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Affiliation(s)
- Igor Brasil-Costa
- Laboratório de Imunologia, Seção de Virologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Correspondence: ; Tel.: +55-91-3214-2005
| | - Cintya de Oliveira Souza
- Laboratório de Enteroinfecções Bacterianas, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil; (C.d.O.S.); (L.C.R.M.)
| | - Leni Célia Reis Monteiro
- Laboratório de Enteroinfecções Bacterianas, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil; (C.d.O.S.); (L.C.R.M.)
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30
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Sun H, He T, Wu Y, Yuan H, Ning J, Zhang Z, Deng X, Li B, Wu C. Cytotoxin-Associated Gene A-Negative Helicobacter pylori Promotes Gastric Mucosal CX3CR1+CD4+ Effector Memory T Cell Recruitment in Mice. Front Microbiol 2022; 13:813774. [PMID: 35154057 PMCID: PMC8829513 DOI: 10.3389/fmicb.2022.813774] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background Helicobacter pylori can cause many kinds of gastric disorders, ranging from gastritis to gastric cancer. Cytotoxin-associated gene A (CagA)+H. pylori is more likely to cause gastric histopathologic damage than CagA–H. pylori. However, the underlying mechanism needs to be further investigated. Materials and methods Mice were intragastrically administered equal amounts of CagA+ or CagA–H. pylori. Four weeks later, 24 chemokines in stomachs were measured using a mouse chemokine array, and the phenotypes of the recruited gastric CD4+ T cells were analyzed. The migration pathway was evaluated. Finally, the correlation between each pair among the recruited CD4+ T cell sub-population, H. pylori colonization level, and histopathologic damage score were determined by Pearson correlation analysis. Results The concentration of chemokines, CCL3 and CX3CL1, were significantly elevated in CagA–H. pylori-infected gastric mucosa than in CagA+H. pylori-infected gastric mucosa. Among them, CX3CL1 secreted by gastric epithelial cells, which was elicited more effectively by CagA–H. pylori than by the CagA+ strain, dramatically promoted mucosal CD4+ T cell migration. The expression of CX3CR1, the only known receptor of CX3CL1, was upregulated on the surface of gastric CD4+ T cells in CagA–H. pylori-infected stomach. In addition, most of the CX3CR1-positive gastric CD4+ T cells were CD44+CD69–CCR7– effector memory T cells (Tem). Pearson correlation analysis showed that the recruited CX3CR1+CD4+ Tem cell population was negatively correlated with H. pylori colonization level and histopathologic damage score. Conclusion CagA–H. pylori promotes gastric mucosal CX3CR1+CD4+ Tem recruitment in mice.
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Affiliation(s)
- Heqiang Sun
- Department of Laboratory Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Taojun He
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yanan Wu
- Peking University People’s Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Hanmei Yuan
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jie Ning
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zhenhua Zhang
- Department of Gastroenterology of the 305 Hospital of Chinese People’s Liberation Army, Beijing, China
| | - Xinli Deng
- Department of Laboratory Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Bin Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Bin Li,
| | - Chao Wu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- *Correspondence: Chao Wu,
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31
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Retnakumar R, Nath AN, Nair GB, Chattopadhyay S. Gastrointestinal microbiome in the context of Helicobacter pylori infection in stomach and gastroduodenal diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:53-95. [DOI: 10.1016/bs.pmbts.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Bobone S, Pannone L, Biondi B, Solman M, Flex E, Canale VC, Calligari P, De Faveri C, Gandini T, Quercioli A, Torini G, Venditti M, Lauri A, Fasano G, Hoeksma J, Santucci V, Cattani G, Bocedi A, Carpentieri G, Tirelli V, Sanchez M, Peggion C, Formaggio F, den Hertog J, Martinelli S, Bocchinfuso G, Tartaglia M, Stella L. Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions. J Med Chem 2021; 64:15973-15990. [PMID: 34714648 PMCID: PMC8591604 DOI: 10.1021/acs.jmedchem.1c01371] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2-20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein-protein interactions in the function of SHP2.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | - Maja Solman
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Elisabetta Flex
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Viviana Claudia Canale
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Chiara De Faveri
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Tommaso Gandini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Andrea Quercioli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giuseppe Torini
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Jelmer Hoeksma
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Valerio Santucci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giada Cattani
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alessio Bocedi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giovanna Carpentieri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Valentina Tirelli
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Massimo Sanchez
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Jeroen den Hertog
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Simone Martinelli
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
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Calligari P, Santucci V, Stella L, Bocchinfuso G. Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state. Comput Struct Biotechnol J 2021; 19:6125-6139. [PMID: 34900129 PMCID: PMC8632847 DOI: 10.1016/j.csbj.2021.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/31/2021] [Accepted: 10/31/2021] [Indexed: 11/07/2022] Open
Abstract
The Src-homology 2 domain containing phosphatase 2 (SHP2) plays a critical role in crucial signaling pathways and is involved in oncogenesis and in developmental disorders. Its structure includes two SH2 domains (N-SH2 and C-SH2), and a protein tyrosine phosphatase (PTP) domain. Under basal conditions, SHP2 is auto-inhibited, with the N-SH2 domain blocking the PTP active site. Activation involves a rearrangement of the domains that makes the catalytic site accessible, coupled to the association between the SH2 domains and cognate proteins containing phosphotyrosines. Several aspects of this transition are debated and competing mechanistic models have been proposed. A crystallographic structure of SHP2 in an active state has been reported (PDB code 6crf), but several lines of evidence suggests that it is not fully representative of the conformations populated in solution. To clarify the structural rearrangements involved in SHP2 activation, enhanced sampling simulations of the autoinhibited and active states have been performed, for wild type SHP2 and its pathogenic E76K variant. Our results demonstrate that the crystallographic conformation of the active state is unstable in solution, and multiple interdomain arrangements are populated, thus allowing association to bisphosphorylated sequences. Contrary to a recent proposal, activation is coupled to the conformational changes of the N-SH2 binding site, which is significantly more accessible in the active sate, rather than to the structure of the central β-sheet of the domain. In this coupling, a previously undescribed role for the N-SH2 BG loop emerged.
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Key Words
- BTLA, B and T lymphocyte attenuator
- CTLA-4, cytotoxic T lymphocyte-associated antigen 4
- FRET, Förster resonance energy transfer
- Inter-domain dynamics
- JMML, juvenile myelomonocytic leukemia
- MD, molecular dynamics
- NS, Noonan syndrome
- NSML, Noonan syndrome with multiple lentigines
- PD-1, programmed cell death protein 1
- PDB, protein data bank
- PMF, potential of mean force
- PTP, protein tyrosine phosphatase
- Protein flexibility
- REMD, replica exchange molecular dynamics
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- RTK, receptor tyrosine kinase
- Replica exchange molecular dynamics simulations
- SASA, solvent accessible surface area
- SAXS, small angle X-ray scattering
- SH2, Src homology 2
- SHP2 regulatory mechanism
- SHP2, Src homology 2 domain-containing phosphatase 2
- SIRPalpha, signal regulatory protein alpha
- pY, phosphorylated tyrosine
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Affiliation(s)
- Paolo Calligari
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Valerio Santucci
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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Lifestyles, genetics, and future perspectives on gastric cancer in east Asian populations. J Hum Genet 2021; 66:887-899. [PMID: 34267306 PMCID: PMC8384627 DOI: 10.1038/s10038-021-00960-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
The prevalence of gastric cancer (GC) differs among regions worldwide, with the highest occurrence in east Asia. Thus, its etiology, with respect to ethnic background, environmental factors, and lifestyles, is also thought to differ essentially. In addition, etiology of GC is speculated to be changing due to the recent decrease in the Helicobacter pylori (H. pylori) infection in Japan. State-of-the-art somatic/germline cancer genomics has clarified the etiologies of gastric carcinogenesis. In this review article, we summarize past and present milestones in our understanding of GC achieved through genomic approaches, including a recent report that revealed higher-than-expected frequencies of GCs attributed to east Asian-specific germline variants in ALDH2 or CDH1 in combination with lifestyles. Based on this updated knowledge, we also discuss the possible impact of and high-risk approaches for GCs in the upcoming "H. pylori-negative era."
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Abstract
In the United States, the incidence of gastric cancer has decreased over the past five decades. However, despite overall decreasing trends in incidence rates of gastric cancer, rates of noncardia gastric cancer among adults aged less than 50 years in the United States are increasing, and most cases of gastric cancer still present with advanced disease and poor resultant survival. Epidemiologic studies have identified the main risk factors for gastric cancer, including increasing age, male sex, non-White race, Helicobacter pylori infection, and smoking. This article summarizes the current epidemiologic evidence with implications for primary and secondary prevention of gastric cancer.
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Affiliation(s)
- Aaron P Thrift
- Section of Epidemiology and Population Sciences, Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Theresa H Nguyen
- Baylor Clinic, 6620 Main Street, MS: BCM620, Room 110D, Houston, TX, 77030, USA
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Imai S, Ooki T, Murata-Kamiya N, Komura D, Tahmina K, Wu W, Takahashi-Kanemitsu A, Knight CT, Kunita A, Suzuki N, Del Valle AA, Tsuboi M, Hata M, Hayakawa Y, Ohnishi N, Ueda K, Fukayama M, Ushiku T, Ishikawa S, Hatakeyama M. Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis. Cell Host Microbe 2021; 29:941-958.e10. [PMID: 33989515 DOI: 10.1016/j.chom.2021.04.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/17/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Infection with CagA-producing Helicobacter pylori plays a causative role in the development of gastric cancer. Upon delivery into gastric epithelial cells, CagA deregulates prooncogenic phosphatase SHP2 while inhibiting polarity-regulating kinase PAR1b through complex formation. Here, we show that CagA/PAR1b interaction subverts nuclear translocation of BRCA1 by inhibiting PAR1b-mediated BRCA1 phosphorylation. It hereby induces BRCAness that promotes DNA double-strand breaks (DSBs) while disabling error-free homologous recombination-mediated DNA repair. The CagA/PAR1b interaction also stimulates Hippo signaling that circumvents apoptosis of DNA-damaged cells, giving cells time to repair DSBs through error-prone mechanisms. The DSB-activated p53-p21Cip1 axis inhibits proliferation of CagA-delivered cells, but the inhibition can be overcome by p53 inactivation. Indeed, sequential pulses of CagA in TP53-mutant cells drove somatic mutation with BRCAness-associated genetic signatures. Expansion of CagA-delivered cells with BRCAness-mediated genome instability, from which CagA-independent cancer-predisposing cells arise, provides a plausible "hit-and-run mechanism" of H. pylori CagA for gastric carcinogenesis.
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Affiliation(s)
- Satoshi Imai
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Takuya Ooki
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Naoko Murata-Kamiya
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan.
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Kamrunnesa Tahmina
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Weida Wu
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | | | - Christopher Takaya Knight
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Nobumi Suzuki
- Department of Gastroenterology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Adriana A Del Valle
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Mayo Tsuboi
- Department of Gastroenterology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Masahiro Hata
- Department of Gastroenterology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Naomi Ohnishi
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Koji Ueda
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan
| | - Masanori Hatakeyama
- Department of Microbiology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-0033, Japan.
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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation. Proc Natl Acad Sci U S A 2021; 118:2025107118. [PMID: 33888588 DOI: 10.1073/pnas.2025107118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Src-homology-2 domain-containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key "allosteric switch" driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the allosteric switch model, we critically reviewed structural data of SHP2, and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central β-sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.
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Marasco M, Kirkpatrick J, Nanna V, Sikorska J, Carlomagno T. Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network. Comput Struct Biotechnol J 2021; 19:2398-2415. [PMID: 34025932 PMCID: PMC8113834 DOI: 10.1016/j.csbj.2021.04.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
SHP2 is a ubiquitous protein tyrosine phosphatase, whose activity is regulated by phosphotyrosine (pY)-containing peptides generated in response to extracellular stimuli. Its crystal structure reveals a closed, auto-inhibited conformation in which the N-terminal Src homology 2 (N-SH2) domain occludes the catalytic site of the phosphatase (PTP) domain. High-affinity mono-phosphorylated peptides promote catalytic activity by binding to N-SH2 and disrupting the interaction with the PTP. The mechanism behind this process is not entirely clear, especially because N-SH2 is incapable of accommodating complete peptide binding when SHP2 is in the auto-inhibited state. Here, we show that pY performs an essential role in this process; in addition to its contribution to overall peptide-binding energy, pY-recognition leads to enhanced dynamics of the N-SH2 EF and BG loops via an allosteric communication network, which destabilizes the N-SH2-PTP interaction surface and simultaneously generates a fully accessible binding pocket for the C-terminal half of the phosphopeptide. Subsequently, full binding of the phosphopeptide is associated with the stabilization of activated SHP2. We demonstrate that this allosteric network exists only in N-SH2, which is directly involved in the regulation of SHP2 activity, while the C-terminal SH2 domain (C-SH2) functions primarily to recruit high-affinity bidentate phosphopeptides.
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Affiliation(s)
- Michelangelo Marasco
- Leibniz University Hannover, Center of Biomolecular Drug Research and Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany
| | - John Kirkpatrick
- Leibniz University Hannover, Center of Biomolecular Drug Research and Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany
- Helmholtz Center for Infection Research, Group of NMR-based Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Vittoria Nanna
- Leibniz University Hannover, Center of Biomolecular Drug Research and Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany
| | - Justyna Sikorska
- Helmholtz Center for Infection Research, Group of NMR-based Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Center of Biomolecular Drug Research and Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany
- Helmholtz Center for Infection Research, Group of NMR-based Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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40
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Tagoe EA, Awandare GA, Quaye O, Asmah RH, Archampong TN, Osman MA, Brown CA. Helicobacter Pylori Variants with ABC-Type Tyrosine Phosphorylation Motif in Gastric Biopsies of Ghanaian Patients. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6616059. [PMID: 33860041 PMCID: PMC8026283 DOI: 10.1155/2021/6616059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Helicobacter pylori pathogenicity and disease severity are determined by the tyrosine phosphorylation motifs of CagA protein. This study is aimed at detecting the presence of H. pylori and identifying the CagA tyrosine phosphorylation motifs in Ghanaian patients. Material and Methods. A total of 94 archival genomic DNA samples from gastric biopsies were used for the study, and H. pylori was detected by amplifying the 16S rRNA gene. The 3'-end variable region of the cagA gene was amplified, and the entire 3'-end was sequenced and translated into amino acids. RESULTS H. pylori was detected in 53.2% (50/94) of the samples, and all the detected bacteria harboured the cagA gene. Two variants of the bacteria were identified based on the size of the amplified cagA gene: 207 bp and 285 bp. The 207 bp and 285 bp variants accounted for 74% and 22%, respectively, and 4% showed both fragments. Translated amino acid sequence of the cagA gene showed EPIYA-A, EPIYA-B, and EPIYA-C (ABC type) motifs, indicating the Western variant. The CagA protein C-terminal showed insertion of amino acids in the sequence flanking the EPIYA-A motif at the N-terminal and a complete deletion of the EPIYA-CC and EPIYA-CCC motifs together with the flanking sequences. CONCLUSIONS H. pylori identified were Western variant (ABC type) with unique amino acid insertions, suggesting unique variants in Ghanaian patients. Further investigation is however required to understand the role of the molecular diversity of the variant in gastric disease outcome.
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Affiliation(s)
- Emmanuel A. Tagoe
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)/Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Richard H. Asmah
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Allied Health Sciences, Ho, Ghana
| | - Timothy N. Archampong
- Department of Medicine, University of Ghana Medical School, University of Ghana, Korle Bu, Accra, Ghana
| | - Mahasin A. Osman
- Departments of Medicine, College of Medicine and Life Sciences, University of Toledo, OH 34614, USA
| | - Charles A. Brown
- Department of Medical Laboratory Sciences, University of Ghana, Korle Bu, Accra, Ghana
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41
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Tao Y, Xie J, Zhong Q, Wang Y, Zhang S, Luo F, Wen F, Xie J, Zhao J, Sun X, Long H, Ma J, Zhang Q, Long J, Fang X, Lu Y, Li D, Li M, Zhu J, Sun B, Li G, Diao J, Liu C. A novel partially open state of SHP2 points to a "multiple gear" regulation mechanism. J Biol Chem 2021; 296:100538. [PMID: 33722610 PMCID: PMC8054191 DOI: 10.1016/j.jbc.2021.100538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/03/2021] [Accepted: 03/10/2021] [Indexed: 11/14/2022] Open
Abstract
The protein tyrosine phosphatase SHP2 mediates multiple signal transductions in various cellular pathways, controlled by a variety of upstream inputs. SHP2 dysregulation is causative of different types of cancers and developmental disorders, making it a promising drug target. However, how SHP2 is modulated by its different regulators remains largely unknown. Here, we use single-molecule fluorescence resonance energy transfer and molecular dynamics simulations to investigate this question. We identify a partially open, semiactive conformation of SHP2 that is intermediate between the known open and closed states. We further demonstrate a “multiple gear” regulatory mechanism, in which different activators (e.g., insulin receptor substrate-1 and CagA), oncogenic mutations (e.g., E76A), and allosteric inhibitors (e.g., SHP099) can shift the equilibrium of the three conformational states and regulate SHP2 activity to different levels. Our work reveals the essential role of the intermediate state in fine-tuning the activity of SHP2, which may provide new opportunities for drug development for relevant cancers.
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Affiliation(s)
- Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jingfei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Qinglu Zhong
- University of the Chinese Academy of Sciences, Beijing, China; Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yongyao Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Feng Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Fengcai Wen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jingjing Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Jiawei Zhao
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoou Sun
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Houfang Long
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Lu
- University of the Chinese Academy of Sciences, Beijing, China; Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Li
- University of the Chinese Academy of Sciences, Beijing, China; Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guohui Li
- University of the Chinese Academy of Sciences, Beijing, China; Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China.
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42
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Wang Q, Zhao WC, Fu XQ, Zheng QC. Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations. Molecules 2021; 26:molecules26040837. [PMID: 33562680 PMCID: PMC7916045 DOI: 10.3390/molecules26040837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/25/2023] Open
Abstract
CagA is a major virulence factor of Helicobacter pylori. H. pylori CagA is geographically subclassified into East Asian CagA and Western CagA, which are characterized by the presence of a EPIYA-D or EPIYA-C segment. The East Asian CagA is more closely associated with gastric cancer than the Western CagA. In this study, molecular dynamic (MD) simulations were performed to investigate the binding details of SHP2 and EPIYA segments, and to explore the allosteric regulation mechanism of SHP2. Our results show that the EPIYA-D has a stronger binding affinity to the N-SH2 domain of SHP2 than EPIYA-C. In addition, a single EPIYA-D binding to N-SH2 domain of SHP2 can cause a deflection of the key helix B, and the deflected helix B could squeeze the N-SH2 and PTP domains to break the autoinhibition pocket of SHP2. However, a single EPIYA-C binding to the N-SH2 domain of SHP2 cannot break the autoinhibition of SHP2 because the secondary structure of the key helix B is destroyed. However, the tandem EPIYA-C not only increases its binding affinity to SHP2, but also does not significantly break the secondary structure of the key helix B. Our study can help us better understand the mechanism of gastric cancer caused by Helicobacter pylori infection.
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Affiliation(s)
- Quan Wang
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun 130023, China; (Q.W.); (W.-C.Z.)
| | - Wen-Cheng Zhao
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun 130023, China; (Q.W.); (W.-C.Z.)
| | - Xue-Qi Fu
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun 130023, China; (Q.W.); (W.-C.Z.)
- Correspondence: (X.-Q.F.); (Q.-C.Z.)
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, China
- Correspondence: (X.-Q.F.); (Q.-C.Z.)
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43
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Wang Q, Zhao WC, Fu XQ, Zheng QC. Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations. Front Chem 2020; 8:597495. [PMID: 33330386 PMCID: PMC7719740 DOI: 10.3389/fchem.2020.597495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022] Open
Abstract
The Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2, encoded by PTPN11) is a critical allosteric phosphatase for many signaling pathways. Programmed cell death 1 (PD-1) could be phosphorylated at its immunoreceptor tyrosine-based inhibitory motif (ITIM) and immunoreceptor tyrosine-based switch motif (ITSM) and can bind to SHP2 to initiate T cell inactivation. Although the interaction of SHP2-PD-1 plays an important role in the immune process, the complex structure and the allosteric regulation mechanism remain unknown. In this study, molecular dynamics (MD) simulations were performed to study the binding details of SHP2 and PD-1, and explore the allosteric regulation mechanism of SHP2. The results show that ITIM has a preference to bind to the N-SH2 domain and ITSM has almost the same binding affinity to the N-SH2 and C-SH2 domain. Only when ITIM binds to the N-SH2 domain and ITSM binds to the C-SH2 domain can the full activation of SHP2 be obtained. The binding of ITIM and ITSM could change the motion mode of SHP2 and switch it to the activated state.
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Affiliation(s)
- Quan Wang
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Wen-Cheng Zhao
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Xue-Qi Fu
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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44
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Anselmi M, Hub JS. An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase. Sci Rep 2020; 10:18530. [PMID: 33116231 PMCID: PMC7595171 DOI: 10.1038/s41598-020-75409-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022] Open
Abstract
SHP2 is a protein tyrosine phosphatase (PTP) involved in multiple signaling pathways. Mutations of SHP2 can result in Noonan syndrome or pediatric malignancies. Inhibition of wild-type SHP2 represents a novel strategy against several cancers. SHP2 is activated by binding of a phosphopeptide to the N-SH2 domain of SHP2, thereby favoring dissociation of the N-SH2 domain and exposing the active site on the PTP domain. The conformational transitions controlling ligand affinity and PTP dissociation remain poorly understood. Using molecular simulations, we revealed an allosteric interaction restraining the N-SH2 domain into a SHP2-activating and a stabilizing state. Only ligands selecting for the activating N-SH2 conformation, depending on ligand sequence and binding mode, are effective activators. We validate the model of SHP2 activation by rationalizing modified basal activity and responsiveness to ligand stimulation of several N-SH2 variants. This study provides mechanistic insight into SHP2 activation and may open routes for SHP2 regulation.
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Affiliation(s)
- Massimiliano Anselmi
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, 37077, Göttingen, Germany. .,Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123, Saarbrücken, Germany
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Ansari S, Yamaoka Y. Helicobacter pylori Virulence Factor Cytotoxin-Associated Gene A (CagA)-Mediated Gastric Pathogenicity. Int J Mol Sci 2020; 21:ijms21197430. [PMID: 33050101 PMCID: PMC7582651 DOI: 10.3390/ijms21197430] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori causes persistent infection in the gastric epithelium of more than half of the world’s population, leading to the development of severe complications such as peptic ulcer diseases, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) lymphoma. Several virulence factors, including cytotoxin-associated gene A (CagA), which is translocated into the gastric epithelium via the type 4 secretory system (T4SS), have been indicated to play a vital role in disease development. Although infection with strains harboring the East Asian type of CagA possessing the EPIYA-A, -B, and -D sequences has been found to potentiate cell proliferation and disease pathogenicity, the exact mechanism of CagA involvement in disease severity still remains to be elucidated. Therefore, we discuss the possible role of CagA in gastric pathogenicity.
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Affiliation(s)
- Shamshul Ansari
- Department of Microbiology, Chitwan Medical College, Bharatpur 44200, Nepal;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita 879-5593, Japan
- Global Oita Medical Advanced Research Center for Health (GO-MARCH), Yufu, Oita 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
- Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
- Correspondence: ; Tel.: +81-97-586-5740; Fax: +81-97-586-5749
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46
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Phosphatase-independent functions of SHP2 and its regulation by small molecule compounds. J Pharmacol Sci 2020; 144:139-146. [PMID: 32921395 DOI: 10.1016/j.jphs.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene in human. Clinically, SHP2 has been identified as a causal factor of several diseases, such as Noonan syndrome, LEOPARD syndrome as well as myeloid malignancies. Interestingly, both loss-of-function and gain-of-function mutations occur in the PTPN11 gene. Analyses by biochemical and cell biological means as well as probing with small molecule compounds have demonstrated that SHP2 has both phosphatase-dependent and independent functions. In comparison with its phosphatase activity, the non-phosphatase-like function of SHP2 has not been well introduced or summarized. This review mainly focuses on the phosphatase-independent functions and its regulation by small molecule compounds as well as their use for disease therapy.
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47
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Anselmi M, Calligari P, Hub JS, Tartaglia M, Bocchinfuso G, Stella L. Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. J Chem Inf Model 2020; 60:3157-3171. [PMID: 32395997 PMCID: PMC8007070 DOI: 10.1021/acs.jcim.0c00307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Indexed: 11/28/2022]
Abstract
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by PTPN11, plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in PTPN11 are associated with different rare diseases and hematologic malignancies, and recent studies have individuated SHP2 as a central node in oncogenesis and cancer drug resistance. The SHP2 structure includes two Src homology 2 domains (N-SH2 and C-SH2) followed by a catalytic protein tyrosine phosphatase (PTP) domain. Under basal conditions, the N-SH2 domain blocks the active site, inhibiting phosphatase activity. Association of the N-SH2 domain with binding partners containing short amino acid motifs comprising a phosphotyrosine residue (pY) leads to N-SH2/PTP dissociation and SHP2 activation. Considering the relevance of SHP2 in signaling and disease and the central role of the N-SH2 domain in its allosteric regulation mechanism, we performed microsecond-long molecular dynamics (MD) simulations of the N-SH2 domain complexed to 12 different peptides to define the structural and dynamical features determining the binding affinity and specificity of the domain. Phosphopeptide residues at position -2 to +5, with respect to pY, have significant interactions with the SH2 domain. In addition to the strong interaction of the pY residue with its conserved binding pocket, the complex is stabilized hydrophobically by insertion of residues +1, +3, and +5 in an apolar groove of the domain and interaction of residue -2 with both the pY and a protein surface residue. Additional interactions are provided by hydrogen bonds formed by the backbone of residues -1, +1, +2, and +4. Finally, negatively charged residues at positions +2 and +4 are involved in electrostatic interactions with two lysines (Lys89 and Lys91) specific for the SHP2 N-SH2 domain. Interestingly, the MD simulations illustrated a previously undescribed conformational flexibility of the domain, involving the core β sheet and the loop that closes the pY binding pocket.
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Affiliation(s)
- Massimiliano Anselmi
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Paolo Calligari
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Jochen S. Hub
- Theoretical
Physics and Center for Biophysics, Saarland
University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Marco Tartaglia
- Genetics
and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Gianfranco Bocchinfuso
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
| | - Lorenzo Stella
- Department
of Chemical Science and Technologies, University
of Rome Tor Vergata, 00133, Rome, Italy
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Association Between Helicobacter pylori Infection and Short-segment/Long-segment Barrett's Esophagus in a Japanese Population: A Large Cross-Sectional Study. J Clin Gastroenterol 2020; 54:439-444. [PMID: 31524650 DOI: 10.1097/mcg.0000000000001264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GOAL The goal of this study was to investigate the relationship between Helicobacter pylori (H. pylori) infection and short-segment and long-segment Barrett's esophagus (SSBE and LSBE). BACKGROUND H. pylori infection is reported to be inversely associated with Barrett's esophagus (BE) in western countries. However, the impact of BE segment length on the association between BE and H. pylori infection has scarcely been investigated. MATERIALS AND METHODS The study subjects were 41,065 asymptomatic Japanese individuals who took medical surveys between October 2010 and September 2017. Using this large database of healthy Japanese subjects, we investigated the association between H. pylori infection and SSBE/LSBE. We used multivariable logistic regression analysis to estimate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS Among the study subjects, 36,615 were eligible for the analysis. H. pylori seropositivity was significantly associated with a lower rate of LSBE (OR: 0.42; 95% CI: 0.16-0.91) and a higher rate of SSBE (OR: 1.66; 95% CI: 1.56-1.78) after multivariate adjustment. In the subgroup analysis, H. pylori seropositivity was significantly associated with a high rate of SSBE in subjects without reflux esophagitis (RE) (OR: 1.73; 95% CI: 1.61-1.85). However, H. pylori seropositivity was not associated with SSBE in subjects with RE (OR: 1.07; 95% CI: 0.84-1.37). CONCLUSION In a Japanese population, H. pylori infection was inversely associated with LSBE but significantly associated with SSBE only in subjects without RE. H. pylori may be a risk factor for SSBE, especially in individuals without RE.
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Mechanisms of the Epithelial-Mesenchymal Transition and Tumor Microenvironment in Helicobacter pylori-Induced Gastric Cancer. Cells 2020; 9:cells9041055. [PMID: 32340207 PMCID: PMC7225971 DOI: 10.3390/cells9041055] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) is one of the most common human pathogens, affecting half of the world’s population. Approximately 20% of the infected patients develop gastric ulcers or neoplastic changes in the gastric stroma. An infection also leads to the progression of epithelial–mesenchymal transition within gastric tissue, increasing the probability of gastric cancer development. This paper aims to review the role of H. pylori and its virulence factors in epithelial–mesenchymal transition associated with malignant transformation within the gastric stroma. The reviewed factors included: CagA (cytotoxin-associated gene A) along with induction of cancer stem-cell properties and interaction with YAP (Yes-associated protein pathway), tumor necrosis factor α-inducing protein, Lpp20 lipoprotein, Afadin protein, penicillin-binding protein 1A, microRNA-29a-3p, programmed cell death protein 4, lysosomal-associated protein transmembrane 4β, cancer-associated fibroblasts, heparin-binding epidermal growth factor (HB-EGF), matrix metalloproteinase-7 (MMP-7), and cancer stem cells (CSCs). The review summarizes the most recent findings, providing insight into potential molecular targets and new treatment strategies for gastric cancer.
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50
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Mi Y, Dong H, Sun X, Ren F, Tang Y, Zheng P. The association of Helicobacter pylori CagA EPIYA motifs and vacA genotypes with homologous recombination repair markers during the gastric precancerous cascade. Int J Biol Markers 2020; 35:49-55. [PMID: 32286927 DOI: 10.1177/1724600820914935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Helicobacter pylori-induced DNA damage and impaired homologous recombination repair are vital molecular mechanisms for gastric cancer, which mainly count on its virulence factors cytotoxic-associated gene A (CagA) and vacuolating cytotoxin A (VacA). However, the relationship between H. pylori CagA EPIYA motifs and vacA genotypes with DNA damage and homologous recombination repair markers is still not clear. METHODS H. pylori positive and negative gastric biopsies were taken from 165 subjects with different gastric precancerous pathologic stages, and DNA damage marker γH2AX and key homologous recombination repair proteins (CtIP and Rad51) were investigated for their association with H. pylori CagA EPIYA motifs and vacAs-, m-, i-, and d-region genotypes and histology (Sydney classification). RESULTS Out of 165 patients, 78 were identified as H. pylori-positive. CagA EPIYA motifs were identified as AB, ABC, and ABD in 2 (3.3%), 21 (35%), and 37 (61.7%) patients, respectively, while vacA alleles were identified as: s1, s2, m1, m2, i1, i2, d1, and d2 in 50 (89.3%), 6 (10.7%), 24 (42.9%), 32 (57.1%), 45 (80.4%), 11 (19.6%), 40 (71.4%), and 16 (28.6%) patients, respectively. vacAs1m1i1d1, s1m2i1d1, and s1m2i2d2 were the most prevailing genotypes. γH2AX was highly localized in H. pylori-positive tissues with corresponding CagA EPIYA motifs and vacA genotypes, while Rad51 and CtIP signals were weak. CONCLUSION H. pylori were positively correlated with the DNA damage marker in precancerous lesions, but were negatively correlated with the key homologous recombination repair proteins, which may be due to the specific CagA EPIYA motifs and vacA genotypes.
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Affiliation(s)
- Yang Mi
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Haibin Dong
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Tshinghua Changgung Hospital, Tsinghua University, Beijing, P.R. China
| | - Xiangdong Sun
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Feifei Ren
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Youcai Tang
- Department of Pediatrics, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Pengyuan Zheng
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
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