Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus
White adipose tissue (WAT) plays a pivotal role in the onset of type 2 diabetes mellitus (T2DM) and obesity. Despite its significance the underlying pathogenesis and key genes associated with it remain elusive. In our study, we screened the differentially expressed genes (DEGs) in intra-abdominal W...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Association of Basic Medical Sciences of Federation of Bosnia and Herzegovina
2024-01-01
|
| Series: | Biomolecules & Biomedicine |
| Subjects: | |
| Online Access: | https://www.bjbms.org/ojs/index.php/bjbms/article/view/9498 |
| _version_ | 1797261374605230080 |
|---|---|
| author | Xuewei Tong Chunyan Liu Mengjie Liang Xueyan Ye Zhaohui Deng Xin Zhang |
| author_facet | Xuewei Tong Chunyan Liu Mengjie Liang Xueyan Ye Zhaohui Deng Xin Zhang |
| author_sort | Xuewei Tong |
| collection | DOAJ |
| description |
White adipose tissue (WAT) plays a pivotal role in the onset of type 2 diabetes mellitus (T2DM) and obesity. Despite its significance the underlying pathogenesis and key genes associated with it remain elusive. In our study, we screened the differentially expressed genes (DEGs) in intra-abdominal WAT of T2DM patients with obesity, as well as those with simple obesity, aiming to lay a foundational theory for an in-depth investigation of T2DM pathogenesis and the identification of novel therapeutic targets. Gene expression datasets (GSE16415 and GSE71416) were retrieved from the Gene Expression Omnibus (GEO) database. We employed R for screening DEGs and conducted a functional enrichment analysis using the Metascape database. Combined Lasso regression and Boruta feature selection algorithms were used to identify key DEGs. Subsequently, these were cross-verified using the GSE29231 dataset. Samples and medical records were collected from clinical study participants. The mRNA and protein expressions of the key DEGs were verified using qRT-PCR and western blotting, respectively. We discerned a total of 130 DEGs, with 40 being upregulated and 90 downregulated. Functional and pathway enrichment analyses illuminated that these genes are instrumental in mediating metabolite and energy production, neutrophil-mediated immunity, and other associated biological processes. This includes their involvement in the tricarboxylic acid cycle, glycolysis/gluconeogenesis, peroxisome proliferator-activated receptors, and other signalling pathways. Two genes, CIDEA and FSCN1 emerged as key DEGs. The low expression of CIDEA and high expression of FSCN1 in the T2DM and obesity group were verified in clinical samples (P < 0.05). We established that CIDEA and FSCN1 manifest significant differential expression in T2DM patients who are obese. This suggests their potential as risk assessment markers and therapeutic targets for T2DM.
|
| first_indexed | 2024-04-24T23:40:12Z |
| format | Article |
| id | doaj.art-81ec9101478f48ae98ff993e2c945176 |
| institution | Directory Open Access Journal |
| issn | 2831-0896 2831-090X |
| language | English |
| last_indexed | 2024-04-24T23:40:12Z |
| publishDate | 2024-01-01 |
| publisher | Association of Basic Medical Sciences of Federation of Bosnia and Herzegovina |
| record_format | Article |
| series | Biomolecules & Biomedicine |
| spelling | doaj.art-81ec9101478f48ae98ff993e2c9451762024-03-15T13:21:09ZengAssociation of Basic Medical Sciences of Federation of Bosnia and HerzegovinaBiomolecules & Biomedicine2831-08962831-090X2024-01-0124110.17305/bb.2023.9498Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitusXuewei Tong0https://orcid.org/0009-0007-1428-0049Chunyan Liu1https://orcid.org/0009-0002-7145-4870Mengjie Liang2https://orcid.org/0000-0003-2932-9830Xueyan Ye3https://orcid.org/0009-0003-7909-4352Zhaohui Deng4https://orcid.org/0009-0007-1428-0049Xin Zhang5https://orcid.org/0000-0003-2351-5034Department of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, China; Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, ChinaDepartment of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, ChinaDepartment of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, ChinaDepartment of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, China; Prenatal Diagnosis Center, Urumqi Maternal and Child Health Hospital, Urumqi, Xinjiang, ChinaDepartment of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, ChinaDepartment of Clinical Laboratory, the Second Affiliated Hospital of Shihezi University School of Medicine/Hospital of Xinjiang Production and Construction Corps, Urumqi, Xinjiang, China White adipose tissue (WAT) plays a pivotal role in the onset of type 2 diabetes mellitus (T2DM) and obesity. Despite its significance the underlying pathogenesis and key genes associated with it remain elusive. In our study, we screened the differentially expressed genes (DEGs) in intra-abdominal WAT of T2DM patients with obesity, as well as those with simple obesity, aiming to lay a foundational theory for an in-depth investigation of T2DM pathogenesis and the identification of novel therapeutic targets. Gene expression datasets (GSE16415 and GSE71416) were retrieved from the Gene Expression Omnibus (GEO) database. We employed R for screening DEGs and conducted a functional enrichment analysis using the Metascape database. Combined Lasso regression and Boruta feature selection algorithms were used to identify key DEGs. Subsequently, these were cross-verified using the GSE29231 dataset. Samples and medical records were collected from clinical study participants. The mRNA and protein expressions of the key DEGs were verified using qRT-PCR and western blotting, respectively. We discerned a total of 130 DEGs, with 40 being upregulated and 90 downregulated. Functional and pathway enrichment analyses illuminated that these genes are instrumental in mediating metabolite and energy production, neutrophil-mediated immunity, and other associated biological processes. This includes their involvement in the tricarboxylic acid cycle, glycolysis/gluconeogenesis, peroxisome proliferator-activated receptors, and other signalling pathways. Two genes, CIDEA and FSCN1 emerged as key DEGs. The low expression of CIDEA and high expression of FSCN1 in the T2DM and obesity group were verified in clinical samples (P < 0.05). We established that CIDEA and FSCN1 manifest significant differential expression in T2DM patients who are obese. This suggests their potential as risk assessment markers and therapeutic targets for T2DM. https://www.bjbms.org/ojs/index.php/bjbms/article/view/9498Type 2 diabetes mellitus (T2DM)obesitywhite adipose tissue (WAT)bioinformaticsdifferentially expressed genes (DEGs) |
| spellingShingle | Xuewei Tong Chunyan Liu Mengjie Liang Xueyan Ye Zhaohui Deng Xin Zhang Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus Biomolecules & Biomedicine Type 2 diabetes mellitus (T2DM) obesity white adipose tissue (WAT) bioinformatics differentially expressed genes (DEGs) |
| title | Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| title_full | Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| title_fullStr | Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| title_full_unstemmed | Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| title_short | Screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| title_sort | screening and validation of differentially expressed genes in adipose tissue of patients with obesity and type 2 diabetes mellitus |
| topic | Type 2 diabetes mellitus (T2DM) obesity white adipose tissue (WAT) bioinformatics differentially expressed genes (DEGs) |
| url | https://www.bjbms.org/ojs/index.php/bjbms/article/view/9498 |
| work_keys_str_mv | AT xueweitong screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus AT chunyanliu screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus AT mengjieliang screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus AT xueyanye screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus AT zhaohuideng screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus AT xinzhang screeningandvalidationofdifferentiallyexpressedgenesinadiposetissueofpatientswithobesityandtype2diabetesmellitus |