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Xu R, Yang L, Zhang Z, Liao Y, Yu Y, Zhou D, Li J, Guan H, Xiao W. Cancer-associated fibroblast related gene signature in Helicobacter pylori-based subtypes of gastric carcinoma for prognosis and tumor microenvironment estimation in silico analysis. Front Med (Lausanne) 2023; 10:1079470. [PMID: 36744128 PMCID: PMC9889637 DOI: 10.3389/fmed.2023.1079470] [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: 10/25/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Introduction Gastric cancer (GC) remains the major constituent of cancer-related deaths and a global public health challenge with a high incidence rate. Helicobacter pylori (HP) plays an essential role in promoting the occurrence and progression of GC. Cancer-associated fibroblasts (CAFs) are regarded as a significant component in the tumor microenvironment (TME), which is related to the metastasis of GC. However, the regulation mechanisms of CAFs in HP-related GC are not elucidated thoroughly. Methods HP-related genes (HRGs) were downloaded from the GSE84437 and TCGA-GC databases. The two databases were combined into one cohort for training. Furthermore, the consensus unsupervised clustering analysis was obtained to sort the training cohort into different groups for the identification of differential expression genes (DEGs). Weighted correlation network analysis (WGCNA) was performed to verify the correlation between the DEGs and cancer-associated fibroblasts which were key components in the tumor microenvironment. The least absolute shrinkage and selection operator (LASSO) was executed to find cancer-associated fibroblast-related differential expression genes (CDEGs) for the further establishment of a prognostic model. Results and discussion In this study, 52 HP-related genes (HRGs) were screened out based on the GSE84437 and TCGA-GC databases. A total of 804 GC samples were analyzed, respectively, and clustered into two HP-related subtypes. The DEGs identified from the two subtypes were proved to have a relationship with TME. After WGCNA and LASSO, the CAFs-related module was identified, from which 21 gene signatures were confirmed. Then, a CDEGs-Score was constructed and its prediction efficiency in GC patients was conducted for validation. Overall, a highly precise nomogram was established for enhancing the adaptability of the CDEGs-Score. Furthermore, our findings revealed the applicability of CDEGs-Score in the sensitivity of chemotherapeutic drugs. In general, our research provided brand-new possibilities for comprehending HP-related GC, evaluating survival, and more efficient therapeutic strategies.
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Affiliation(s)
- Ruofan Xu
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Le Yang
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Zhewen Zhang
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yuxuan Liao
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yao Yu
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Dawei Zhou
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiahao Li
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoyu Guan
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wei Xiao
- Department of Infectious Disease, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Wei Xiao,
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Sun C, Xu J, Tao J, Dong Y, Chen H, Jia Z, Ma Y, Zhang M, Wei S, Tang G, Lyu H, Jiang Y. Mobile-Based and Self-Service Tool (iPed) to Collect, Manage, and Visualize Pedigree Data: Development Study. JMIR Form Res 2022; 6:e36914. [PMID: 35737451 PMCID: PMC9264120 DOI: 10.2196/36914] [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: 01/29/2022] [Revised: 05/15/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Pedigree data (family history) are indispensable for genetics studies and the assessment of individuals' disease susceptibility. With the popularity of genetics testing, the collection of pedigree data is becoming more common. However, it can be time-consuming, laborious, and tedious for clinicians to investigate all pedigree data for each patient. A self-service robot could inquire about patients' family history in place of professional clinicians or genetic counselors. OBJECTIVE The aim of this study was to develop a mobile-based and self-service tool to collect and visualize pedigree data, not only for professionals but also for those who know little about genetics. METHODS There are 4 main aspects in the iPed construction, including interface building, data processing, data storage, and data visualization. The user interface was built using HTML, JavaScript libraries, and Cascading Style Sheets (version 3; Daniel Eden). Processing of the submitted data is carried out by PHP programming language. MySQL is used to document and manage the pedigree data. PHP calls the R script to accomplish the visualization. RESULTS iPed is freely available to all users through the iPed website. No software is required to be installed, no pedigree files need to be prepared, and no knowledge of genetics or programs is required. The users can easily complete their pedigree data collection and visualization on their own and through a dialogue with iPed. Meanwhile, iPed provides a database that stores all users' information. Therefore, when the users need to construct new pedigree trees for other genetic traits or modify the pedigree trees that have already been created, unnecessary duplication of operations can be avoided. CONCLUSIONS iPed is a mobile-based and self-service tool that could be used by both professionals and nonprofessionals at any time and from any place. It reduces the amount of time required to collect, manage, and visualize pedigree data.
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Affiliation(s)
- Chen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junxian Tao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yu Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haiyan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhe Jia
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yingnan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guoping Tang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Hongchao Lyu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Liatsos C, Papaefthymiou A, Kyriakos N, Galanopoulos M, Doulberis M, Giakoumis M, Petridou E, Mavrogiannis C, Rokkas T, Kountouras J. Helicobacter pylori, gastric microbiota and gastric cancer relationship: Unrolling the tangle. World J Gastrointest Oncol 2022; 14:959-972. [PMID: 35646287 PMCID: PMC9124990 DOI: 10.4251/wjgo.v14.i5.959] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/12/2021] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori infection (Hp-I) represents a typical microbial agent intervening in the complex mechanisms of gastric homeostasis by disturbing the balance between the host gastric microbiota and mucosa-related factors, leading to inflammatory changes, dysbiosis and eventually gastric cancer. The normal gastric microbiota shows diversity, with Proteobacteria [Helicobacter pylori (H. pylori) belongs to this family], Firmicutes, Actinobacteria, Bacteroides and Fusobacteria being the most abundant phyla. Most studies indicate that H. pylori has inhibitory effects on the colonization of other bacteria, harboring a lower diversity of them in the stomach. When comparing the healthy with the diseased stomach, there is a change in the composition of the gastric microbiome with increasing abundance of H. pylori (where present) in the gastritis stage, while as the gastric carcinogenesis cascade progresses to gastric cancer, the oral and intestinal-type pathogenic microbial strains predominate. Hp-I creates a premalignant environment of atrophy and intestinal metaplasia and the subsequent alteration in gastric microbiota seems to play a crucial role in gastric tumorigenesis itself. Successful H. pylori eradication is suggested to restore gastric microbiota, at least in primary stages. It is more than clear that Hp-I, gastric microbiota and gastric cancer constitute a challenging tangle and the strong interaction between them makes it difficult to unroll. Future studies are considered of crucial importance to test the complex interaction on the modulation of the gastric microbiota by H. pylori as well as on the relationships between the gastric microbiota and gastric carcinogenesis.
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Affiliation(s)
- Christos Liatsos
- Department of Gastroenterology, 401 General Military Hospital of Athens, Athens 11525, Greece
| | - Apostolis Papaefthymiou
- Department of Gastroenterology, 401 General Military Hospital of Athens, Athens 11525, Greece
- Gastroenterology, University Hospital of Larissa, Larissa 41336, Greece
| | - Nikolaos Kyriakos
- Department of Gastroenterology, 401 General Military Hospital of Athens, Athens 11525, Greece
| | - Michail Galanopoulos
- Department of Gastroenterology, 401 General Military Hospital of Athens, Athens 11525, Greece
| | - Michael Doulberis
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, Aarau 1234, Switzerland
| | - Marios Giakoumis
- Department of Gastroenterology, 401 General Military Hospital of Athens, Athens 11525, Greece
| | - Evangelia Petridou
- Department of Microbiology, “Agia Sofia” Paediatric Hospital, Goudi, Athens 11527, Greece
| | - Christos Mavrogiannis
- Gastrointestinal and Liver Unit, Faculty of Nursing, Kifissia General and Oncology Hospital, Kaliftaki, N.Kifisia 14564, Greece
| | - Theodore Rokkas
- Gastroenterological Clinic, Henry Dunant Hospital, Athens 11525, Greece
| | - Jannis Kountouras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki 41336, Macedonia, Greece
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Schisandrin B suppresses gastric cancer cell growth and enhances the efficacy of chemotherapy drug 5-FU in vitro and in vivo. Eur J Pharmacol 2022; 920:174823. [DOI: 10.1016/j.ejphar.2022.174823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/23/2022]
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Teufel A, Quante M, Kandulski A, Hirth M, Zhan T, Eckardt M, Thieme R, Kusnik A, Yesmembetov K, Wiest I, Riemann JF, Schlitt HJ, Gockel I, Malfertheiner P, Ebert MP. [Prevention of gastrointestinal cancer]. ZEITSCHRIFT FUR GASTROENTEROLOGIE 2021; 59:964-982. [PMID: 34507375 DOI: 10.1055/a-1540-7539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Throughout the past decades, considerable progress has been made in the (early) diagnosis and treatment of gastrointestinal cancers. However, the prognosis for advanced stages of gastrointestinal tumors remains limited for many patients and approximately one third of all tumor patients die as a result of gastrointestinal tumors. The prevention and early detection of gastrointestinal tumors is therefore of great importance.For this reason, we summarize the current state of knowledge and recommendations for the primary, secondary and tertiary prevention of esophageal, stomach, pancreas, liver and colorectal cancer in the following.
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Affiliation(s)
- Andreas Teufel
- II. Medizinische Klinik, Sektion Hepatologie, Medizinische Fakultät Mannheim, Universität Heidelberg, Universitätsklinikum Mannheim, Mannheim.,Klinische Kooperationseinheit Healthy Metabolism, Zentrum für Präventivmedizin und Digitale Gesundheit Baden-Württemberg, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim
| | - Michael Quante
- Klinik für Innere Medizin II, Medizinische Universitätsklinik, Universitätsklinikum Freiburg, Freiburg im Breisgau
| | - Arne Kandulski
- Klinik und Poliklinik für Innere Medizin I, Universitätsklinikum Regensburg, Regensburg
| | - Michael Hirth
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim
| | - Tianzuo Zhan
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim
| | - Maximilian Eckardt
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim
| | - René Thieme
- Klinik und Poliklinik für Viszeral-, Transplantations-, Thorax- und Gefäßchirurgie, Department für Operative Medizin (DOPM), Universitatsklinikum Leipzig, Leipzig
| | - Alexander Kusnik
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim
| | - Kakharman Yesmembetov
- Klinik für Gastroenterologie, Stoffwechselerkrankungen und Internistische Intensivmedizin (Med. III), RWTH Universitätsklinikum Aachen, Aachen
| | - Isabella Wiest
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim
| | | | - Hans Jürgen Schlitt
- Klinik und Poliklinik für Chirurgie, Universitatsklinikum Regensburg, Regensburg
| | - Ines Gockel
- Klinik und Poliklinik für Viszeral-, Transplantations-, Thorax- und Gefäßchirurgie, Department für Operative Medizin (DOPM), Universitatsklinikum Leipzig, Leipzig
| | - Peter Malfertheiner
- Klinik für Gastroenterologie, Hepatologie und Infektiologie, Medizinische Fakultät Magdeburg, Magdeburg
| | - Matthias Philip Ebert
- II. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Universitätsklinikum Mannheim, Mannheim.,Klinische Kooperationseinheit Healthy Metabolism, Zentrum für Präventivmedizin und Digitale Gesundheit Baden-Württemberg, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim
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Kim N. Reversal of the Methylation-Associated Regulation of miR-200a/b by Helicobacter pylori Eradication Contributes to the Chemoprevention of Gastric Carcinogenesis. Gut Liver 2020; 14:533-534. [PMID: 32921637 PMCID: PMC7492488 DOI: 10.5009/gnl20251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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