Pathway analysis of sepsis-induced changes gene expression
Abstract Background Sepsis reaction is a response to an infection composed of genetic elements. This research aims to better understand how sepsis affects the molecular pathways in whole blood samples. Methods Whole blood samples from healthy controls (n = 18), sepsis nonsurvivors (n = 9), and sepsi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-09-01
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| Series: | Egyptian Journal of Medical Human Genetics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43042-022-00352-3 |
| _version_ | 1818016898588082176 |
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| author | Abdallah Ahmed Elbakkoush Anas Khaleel Albakush Nura Ahmed Mohamed Ahmad Alathamneh |
| author_facet | Abdallah Ahmed Elbakkoush Anas Khaleel Albakush Nura Ahmed Mohamed Ahmad Alathamneh |
| author_sort | Abdallah Ahmed Elbakkoush |
| collection | DOAJ |
| description | Abstract Background Sepsis reaction is a response to an infection composed of genetic elements. This research aims to better understand how sepsis affects the molecular pathways in whole blood samples. Methods Whole blood samples from healthy controls (n = 18), sepsis nonsurvivors (n = 9), and sepsis survivors (n = 26) were retrieved from the gene expression omnibus (GEO) collection of the national center for biotechnology information (NCBI) (accession number GSE54514). The NCBI's GEO2R program was used to determine differential expression, and the ingenuity pathway analysis (IPA) software was utilized to do a pathway analysis. Results In sepsis patients, 2672 genes were substantially differently expressed (p value 0.05). One thousand three hundred four genes were overexpressed, and one thousand three hundred sixty-eight were under-expressed. The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were the most significant canonical pathways identified by ingenuity pathway analysis (IPA). The IPA upstream analysis predicted the ESR1, SIRT1, and PTPRR proteins, and the drugs filgrastim and fluticasone were top transcriptional regulators. Conclusions The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were highlighted as essential pathways of inflammation by IPA, indicating widespread cancer owing to sepsis. Our data imply that sepsis considerably influences gene pathways in whole blood samples, pointing to possible targets for sepsis treatment. |
| first_indexed | 2024-04-14T07:19:33Z |
| format | Article |
| id | doaj.art-2d17802d3738434eb9f2d1ae8217745f |
| institution | Directory Open Access Journal |
| issn | 2090-2441 |
| language | English |
| last_indexed | 2024-04-14T07:19:33Z |
| publishDate | 2022-09-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Egyptian Journal of Medical Human Genetics |
| spelling | doaj.art-2d17802d3738434eb9f2d1ae8217745f2022-12-22T02:06:13ZengSpringerOpenEgyptian Journal of Medical Human Genetics2090-24412022-09-012311810.1186/s43042-022-00352-3Pathway analysis of sepsis-induced changes gene expressionAbdallah Ahmed Elbakkoush0Anas Khaleel1Albakush Nura Ahmed Mohamed2Ahmad Alathamneh3Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical UniversityDepartment of Pharmacology and Biomedical Sciences, Faculty of Pharmacy, Petra UniversityDepartment of Zoology, Faculty of Sciences, Misurata UniversityDepartment of Nutrition, Faculty of Pharmacy and Medical Sciences, Petra UniversityAbstract Background Sepsis reaction is a response to an infection composed of genetic elements. This research aims to better understand how sepsis affects the molecular pathways in whole blood samples. Methods Whole blood samples from healthy controls (n = 18), sepsis nonsurvivors (n = 9), and sepsis survivors (n = 26) were retrieved from the gene expression omnibus (GEO) collection of the national center for biotechnology information (NCBI) (accession number GSE54514). The NCBI's GEO2R program was used to determine differential expression, and the ingenuity pathway analysis (IPA) software was utilized to do a pathway analysis. Results In sepsis patients, 2672 genes were substantially differently expressed (p value 0.05). One thousand three hundred four genes were overexpressed, and one thousand three hundred sixty-eight were under-expressed. The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were the most significant canonical pathways identified by ingenuity pathway analysis (IPA). The IPA upstream analysis predicted the ESR1, SIRT1, and PTPRR proteins, and the drugs filgrastim and fluticasone were top transcriptional regulators. Conclusions The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were highlighted as essential pathways of inflammation by IPA, indicating widespread cancer owing to sepsis. Our data imply that sepsis considerably influences gene pathways in whole blood samples, pointing to possible targets for sepsis treatment.https://doi.org/10.1186/s43042-022-00352-3Gene expressionSepsisIngenuity pathway analysisWhole blood samples |
| spellingShingle | Abdallah Ahmed Elbakkoush Anas Khaleel Albakush Nura Ahmed Mohamed Ahmad Alathamneh Pathway analysis of sepsis-induced changes gene expression Egyptian Journal of Medical Human Genetics Gene expression Sepsis Ingenuity pathway analysis Whole blood samples |
| title | Pathway analysis of sepsis-induced changes gene expression |
| title_full | Pathway analysis of sepsis-induced changes gene expression |
| title_fullStr | Pathway analysis of sepsis-induced changes gene expression |
| title_full_unstemmed | Pathway analysis of sepsis-induced changes gene expression |
| title_short | Pathway analysis of sepsis-induced changes gene expression |
| title_sort | pathway analysis of sepsis induced changes gene expression |
| topic | Gene expression Sepsis Ingenuity pathway analysis Whole blood samples |
| url | https://doi.org/10.1186/s43042-022-00352-3 |
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