Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes
Abstract Background Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is a chronic, inflammatory, and autoimmune disease, but its specific etiology and pathogenesis are still unclear. This study aimed to better discover the causative basement membrane...
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | European Journal of Medical Research |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40001-023-01193-5 |
| _version_ | 1797774320949264384 |
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| author | Penghang Lin Jin Hua Zuhong Teng Chunlin Lin Songyi Liu Ruofan He Hui Chen Hengxin Yao Jianxin Ye Guangwei Zhu |
| author_facet | Penghang Lin Jin Hua Zuhong Teng Chunlin Lin Songyi Liu Ruofan He Hui Chen Hengxin Yao Jianxin Ye Guangwei Zhu |
| author_sort | Penghang Lin |
| collection | DOAJ |
| description | Abstract Background Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is a chronic, inflammatory, and autoimmune disease, but its specific etiology and pathogenesis are still unclear. This study aimed to better discover the causative basement membrane (BM) genes of their subtypes and their associations. Methods The differential expression of BM genes between CD and UC was analyzed and validated by downloading relevant datasets from the GEO database. We divided the samples into 3 groups for comparative analysis. Construction of PPI networks, enrichment of differential gene functions, screening of Lasso regression models, validation of ROC curves, nomogram for disease prediction and other analytical methods were used. The immune cell infiltration was further explored by ssGSEA analysis, the immune correlates of hub BM genes were found, and finally, the hub central genes were screened by machine learning. Results We obtained 6 candidate hub BM genes related to cellular immune infiltration in the CD and UC groups, respectively, and further screened the central hub genes ADAMTS17 and ADAMTS9 through machine learning. And in the ROC curve models, AUC > 0.7, indicating that this characteristic gene has a more accurate predictive effect on IBD. We also found that the pathogenicity-related BM genes of the CD and UC groups were mainly concentrated in the ADAMTS family (ADAMTS17 and ADAMTS9). Addition there are some differences between the two subtypes, and the central different hub BM genes are SPARC, POSTN, and ADAMTS2. Conclusions In the current study, we provided a nomogram model of CD and UC composed of BM genes, identified central hub genes, and clarified the similarities and differences between CD and UC. This will have potential value for preclinical, clinical, and translational guidance and differential research in IBD. |
| first_indexed | 2024-03-12T22:19:21Z |
| format | Article |
| id | doaj.art-f2fe0eae01fe47beab43da2019ee8643 |
| institution | Directory Open Access Journal |
| issn | 2047-783X |
| language | English |
| last_indexed | 2024-03-12T22:19:21Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | European Journal of Medical Research |
| spelling | doaj.art-f2fe0eae01fe47beab43da2019ee86432023-07-23T11:09:58ZengBMCEuropean Journal of Medical Research2047-783X2023-07-0128111510.1186/s40001-023-01193-5Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genesPenghang Lin0Jin Hua1Zuhong Teng2Chunlin Lin3Songyi Liu4Ruofan He5Hui Chen6Hengxin Yao7Jianxin Ye8Guangwei Zhu9Department of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery 2 Section, Institute of Abdominal Surgery, Key Laboratory of Accurate Diagnosis and Treatment of Cancer, The First Affiliated Hospital of Fujian Medical University, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical UniversityAbstract Background Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is a chronic, inflammatory, and autoimmune disease, but its specific etiology and pathogenesis are still unclear. This study aimed to better discover the causative basement membrane (BM) genes of their subtypes and their associations. Methods The differential expression of BM genes between CD and UC was analyzed and validated by downloading relevant datasets from the GEO database. We divided the samples into 3 groups for comparative analysis. Construction of PPI networks, enrichment of differential gene functions, screening of Lasso regression models, validation of ROC curves, nomogram for disease prediction and other analytical methods were used. The immune cell infiltration was further explored by ssGSEA analysis, the immune correlates of hub BM genes were found, and finally, the hub central genes were screened by machine learning. Results We obtained 6 candidate hub BM genes related to cellular immune infiltration in the CD and UC groups, respectively, and further screened the central hub genes ADAMTS17 and ADAMTS9 through machine learning. And in the ROC curve models, AUC > 0.7, indicating that this characteristic gene has a more accurate predictive effect on IBD. We also found that the pathogenicity-related BM genes of the CD and UC groups were mainly concentrated in the ADAMTS family (ADAMTS17 and ADAMTS9). Addition there are some differences between the two subtypes, and the central different hub BM genes are SPARC, POSTN, and ADAMTS2. Conclusions In the current study, we provided a nomogram model of CD and UC composed of BM genes, identified central hub genes, and clarified the similarities and differences between CD and UC. This will have potential value for preclinical, clinical, and translational guidance and differential research in IBD.https://doi.org/10.1186/s40001-023-01193-5Basement membraneIBDBiomarkersCDUCSVM-RFE |
| spellingShingle | Penghang Lin Jin Hua Zuhong Teng Chunlin Lin Songyi Liu Ruofan He Hui Chen Hengxin Yao Jianxin Ye Guangwei Zhu Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes European Journal of Medical Research Basement membrane IBD Biomarkers CD UC SVM-RFE |
| title | Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes |
| title_full | Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes |
| title_fullStr | Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes |
| title_full_unstemmed | Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes |
| title_short | Screening of hub inflammatory bowel disease biomarkers and identification of immune-related functions based on basement membrane genes |
| title_sort | screening of hub inflammatory bowel disease biomarkers and identification of immune related functions based on basement membrane genes |
| topic | Basement membrane IBD Biomarkers CD UC SVM-RFE |
| url | https://doi.org/10.1186/s40001-023-01193-5 |
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