RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo
Abstract Background How AMP activated protein kinase (AMPK) signaling regulates mitochondrial functions and mitophagy in human trophoblast cells remains unclear. This study was designed to investigate potential players mediating the regulation of AMPK on mitochondrial functions and mitophagy by next...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-04-01
|
| Series: | Animal Models and Experimental Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ame2.12475 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850145964745031680 |
|---|---|
| author | Bin Wu Albert Gao Bin He Yun Chen Xiangfeng Kong Fayuan Wen Haijun Gao |
| author_facet | Bin Wu Albert Gao Bin He Yun Chen Xiangfeng Kong Fayuan Wen Haijun Gao |
| author_sort | Bin Wu |
| collection | DOAJ |
| description | Abstract Background How AMP activated protein kinase (AMPK) signaling regulates mitochondrial functions and mitophagy in human trophoblast cells remains unclear. This study was designed to investigate potential players mediating the regulation of AMPK on mitochondrial functions and mitophagy by next generation RNA‐seq. Methods We compared ATP production in protein kinase AMP‐activated catalytic subunit alpha 1/2 (PRKAA1/2) knockdown (AKD) and control BeWo cells using the Seahorse real‐time ATP rate test, then analyzed gene expression profiling by RNA‐seq. Differentially expressed genes (DEG) were examined by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then protein–protein interactions (PPI) among mitochondria related genes were further analyzed using Metascape and Ingenuity Pathway Analysis (IPA) software. Results Both mitochondrial and glycolytic ATP production in AKD cells were lower than in the control BeWo cells (CT), with a greater reduction of mitochondrial ATP production. A total of 1092 DEGs were identified, with 405 upregulated and 687 downregulated. GO analysis identified 60 genes associated with the term ‘mitochondrion’ in the cellular component domain. PPI analysis identified three clusters of mitochondria related genes, including aldo‐keto reductase family 1 member B10 and B15 (AKR1B10, AKR1B15), alanyl‐tRNA synthetase 1 (AARS1), mitochondrial ribosomal protein S6 (MRPS6), mitochondrial calcium uniporter dominant negative subunit beta (MCUB) and dihydrolipoamide branched chain transacylase E2 (DBT). Conclusions In summary, this study identified multiple mitochondria related genes regulated by AMPK in BeWo cells, and among them, three clusters of genes may potentially contribute to altered mitochondrial functions in response to reduced AMPK signaling. |
| format | Article |
| id | doaj-art-a154a27bf2994f1eab5e0247d12e7aae |
| institution | OA Journals |
| issn | 2576-2095 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Wiley |
| record_format | Article |
| series | Animal Models and Experimental Medicine |
| spelling | doaj-art-a154a27bf2994f1eab5e0247d12e7aae2025-08-20T02:27:57ZengWileyAnimal Models and Experimental Medicine2576-20952025-04-018464966110.1002/ame2.12475RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWoBin Wu0Albert Gao1Bin He2Yun Chen3Xiangfeng Kong4Fayuan Wen5Haijun Gao6Department of Reproductive Medicine Central Hospital Affiliated to Shandong First Medical University Jinan Shandong P.R. ChinaDepartment of Physiology and Biophysics, College of Medicine Howard University Washington District of Columbia USAReproductive Physiology Laboratory National Research Institute for Family Planning Beijing P.R. ChinaLandmark Bio Watertown Massachusetts USAInstitute of Subtropical Agriculture, Chinese Academy of Sciences Changsha Hunan P.R. ChinaDepartment of Biology, College of Arts and Sciences Howard University Washington District of Columbia USADepartment of Physiology and Biophysics, College of Medicine Howard University Washington District of Columbia USAAbstract Background How AMP activated protein kinase (AMPK) signaling regulates mitochondrial functions and mitophagy in human trophoblast cells remains unclear. This study was designed to investigate potential players mediating the regulation of AMPK on mitochondrial functions and mitophagy by next generation RNA‐seq. Methods We compared ATP production in protein kinase AMP‐activated catalytic subunit alpha 1/2 (PRKAA1/2) knockdown (AKD) and control BeWo cells using the Seahorse real‐time ATP rate test, then analyzed gene expression profiling by RNA‐seq. Differentially expressed genes (DEG) were examined by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then protein–protein interactions (PPI) among mitochondria related genes were further analyzed using Metascape and Ingenuity Pathway Analysis (IPA) software. Results Both mitochondrial and glycolytic ATP production in AKD cells were lower than in the control BeWo cells (CT), with a greater reduction of mitochondrial ATP production. A total of 1092 DEGs were identified, with 405 upregulated and 687 downregulated. GO analysis identified 60 genes associated with the term ‘mitochondrion’ in the cellular component domain. PPI analysis identified three clusters of mitochondria related genes, including aldo‐keto reductase family 1 member B10 and B15 (AKR1B10, AKR1B15), alanyl‐tRNA synthetase 1 (AARS1), mitochondrial ribosomal protein S6 (MRPS6), mitochondrial calcium uniporter dominant negative subunit beta (MCUB) and dihydrolipoamide branched chain transacylase E2 (DBT). Conclusions In summary, this study identified multiple mitochondria related genes regulated by AMPK in BeWo cells, and among them, three clusters of genes may potentially contribute to altered mitochondrial functions in response to reduced AMPK signaling.https://doi.org/10.1002/ame2.12475AMPKATP productiongene expressionmitochondriaRNA‐seqtrophoblast |
| spellingShingle | Bin Wu Albert Gao Bin He Yun Chen Xiangfeng Kong Fayuan Wen Haijun Gao RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo Animal Models and Experimental Medicine AMPK ATP production gene expression mitochondria RNA‐seq trophoblast |
| title | RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo |
| title_full | RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo |
| title_fullStr | RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo |
| title_full_unstemmed | RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo |
| title_short | RNA‐seq analysis of mitochondria‐related genes regulated by AMPK in the human trophoblast cell line BeWo |
| title_sort | rna seq analysis of mitochondria related genes regulated by ampk in the human trophoblast cell line bewo |
| topic | AMPK ATP production gene expression mitochondria RNA‐seq trophoblast |
| url | https://doi.org/10.1002/ame2.12475 |
| work_keys_str_mv | AT binwu rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT albertgao rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT binhe rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT yunchen rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT xiangfengkong rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT fayuanwen rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo AT haijungao rnaseqanalysisofmitochondriarelatedgenesregulatedbyampkinthehumantrophoblastcelllinebewo |