Causal Path of COPD Progression-Associated Genes in Different Biological Samples
Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease with pulmonary and extra-pulmonary complications. Due to the disease’s systemic nature, many investigations investigated the genetic alterations in various biological samples. We aimed to infer causal genes in COPD’s...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2022-12-01
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| Series: | COPD |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15412555.2022.2081541 |
| _version_ | 1797403959533502464 |
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| author | Shayan Mostafaei Hojat Borna Alireza Emamvirdizadeh Masoud Arabfard Ali Ahmadi Jafar Salimian Mahmood Salesi Sadegh Azimzadeh Jamalkandi |
| author_facet | Shayan Mostafaei Hojat Borna Alireza Emamvirdizadeh Masoud Arabfard Ali Ahmadi Jafar Salimian Mahmood Salesi Sadegh Azimzadeh Jamalkandi |
| author_sort | Shayan Mostafaei |
| collection | DOAJ |
| description | Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease with pulmonary and extra-pulmonary complications. Due to the disease’s systemic nature, many investigations investigated the genetic alterations in various biological samples. We aimed to infer causal genes in COPD’s pathogenesis in different biological samples using elastic-net logistic regression and the Structural Equation Model. Samples of small airway epithelial cells, bronchoalveolar lavage macrophages, lung tissue biopsy, sputum, and blood samples were selected (135, 70, 235, 143, and 226 samples, respectively). Elastic-net Logistic Regression analysis was implemented to identify the most important genes involved in COPD progression. Thirty-three candidate genes were identified as essential factors in the pathogenesis of COPD and regulation of lung function. Recognized candidate genes in small airway epithelial (SAE) cells have the highest area under the ROC curve (AUC = 97%, SD = 3.9%). Our analysis indicates that macrophages and epithelial cells are more influential in COPD progression at the transcriptome level. |
| first_indexed | 2024-03-09T02:47:12Z |
| format | Article |
| id | doaj.art-463f050c1439469399095c92752d0298 |
| institution | Directory Open Access Journal |
| issn | 1541-2555 1541-2563 |
| language | English |
| last_indexed | 2024-03-09T02:47:12Z |
| publishDate | 2022-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | COPD |
| spelling | doaj.art-463f050c1439469399095c92752d02982023-12-05T16:09:50ZengTaylor & Francis GroupCOPD1541-25551541-25632022-12-0119129029910.1080/15412555.2022.20815412081541Causal Path of COPD Progression-Associated Genes in Different Biological SamplesShayan Mostafaei0Hojat Borna1Alireza Emamvirdizadeh2Masoud Arabfard3Ali Ahmadi4Jafar Salimian5Mahmood Salesi6Sadegh Azimzadeh Jamalkandi7Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesDepartment of Molecular Genetics, Faculty of Bio Sciences, Tehran North Branch, Islamic Azad UniversityChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesMolecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesChronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease with pulmonary and extra-pulmonary complications. Due to the disease’s systemic nature, many investigations investigated the genetic alterations in various biological samples. We aimed to infer causal genes in COPD’s pathogenesis in different biological samples using elastic-net logistic regression and the Structural Equation Model. Samples of small airway epithelial cells, bronchoalveolar lavage macrophages, lung tissue biopsy, sputum, and blood samples were selected (135, 70, 235, 143, and 226 samples, respectively). Elastic-net Logistic Regression analysis was implemented to identify the most important genes involved in COPD progression. Thirty-three candidate genes were identified as essential factors in the pathogenesis of COPD and regulation of lung function. Recognized candidate genes in small airway epithelial (SAE) cells have the highest area under the ROC curve (AUC = 97%, SD = 3.9%). Our analysis indicates that macrophages and epithelial cells are more influential in COPD progression at the transcriptome level.http://dx.doi.org/10.1080/15412555.2022.2081541copdcandidate genesstructure equation modelelastic-net logistic regression |
| spellingShingle | Shayan Mostafaei Hojat Borna Alireza Emamvirdizadeh Masoud Arabfard Ali Ahmadi Jafar Salimian Mahmood Salesi Sadegh Azimzadeh Jamalkandi Causal Path of COPD Progression-Associated Genes in Different Biological Samples COPD copd candidate genes structure equation model elastic-net logistic regression |
| title | Causal Path of COPD Progression-Associated Genes in Different Biological Samples |
| title_full | Causal Path of COPD Progression-Associated Genes in Different Biological Samples |
| title_fullStr | Causal Path of COPD Progression-Associated Genes in Different Biological Samples |
| title_full_unstemmed | Causal Path of COPD Progression-Associated Genes in Different Biological Samples |
| title_short | Causal Path of COPD Progression-Associated Genes in Different Biological Samples |
| title_sort | causal path of copd progression associated genes in different biological samples |
| topic | copd candidate genes structure equation model elastic-net logistic regression |
| url | http://dx.doi.org/10.1080/15412555.2022.2081541 |
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