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Swaidan NT, Soliman NH, Aboughalia AT, Darwish T, Almeshal RO, Al-Khulaifi AA, Taha RZ, Alanany R, Hussein AY, Salloum-Asfar S, Abdulla SA, Abdallah AM, Emara MM. CCN3, POSTN, and PTHLH as potential key regulators of genomic integrity and cellular survival in iPSCs. Front Mol Biosci 2024; 11:1342011. [PMID: 38375508 PMCID: PMC10875024 DOI: 10.3389/fmolb.2024.1342011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 02/21/2024] Open
Abstract
Reprogramming human somatic cells into a pluripotent state, achieved through the activation of well-defined transcriptional factors known as OSKM factors, offers significant potential for regenerative medicine. While OSKM factors are a robust reprogramming method, efficiency remains a challenge, with only a fraction of cells undergoing successful reprogramming. To address this, we explored genes related to genomic integrity and cellular survival, focusing on iPSCs (A53T-PD1) that displayed enhanced colony stability. Our investigation had revealed three candidate genes CCN3, POSTN, and PTHLH that exhibited differential expression levels and potential roles in iPSC stability. Subsequent analyses identified various protein interactions for these candidate genes. POSTN, significantly upregulated in A53T-PD1 iPSC line, showed interactions with extracellular matrix components and potential involvement in Wnt signaling. CCN3, also highly upregulated, demonstrated interactions with TP53, CDKN1A, and factors related to apoptosis and proliferation. PTHLH, while upregulated, exhibited interactions with CDK2 and genes involved in cell cycle regulation. RT-qPCR validation confirmed elevated CCN3 and PTHLH expression in A53T-PD1 iPSCs, aligning with RNA-seq findings. These genes' roles in preserving pluripotency and cellular stability require further exploration. In conclusion, we identified CCN3, POSTN, and PTHLH as potential contributors to genomic integrity and pluripotency maintenance in iPSCs. Their roles in DNA repair, apoptosis evasion, and signaling pathways could offer valuable insights for enhancing reprogramming efficiency and sustaining pluripotency. Further investigations are essential to unravel the mechanisms underlying their actions.
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Affiliation(s)
- Nuha T. Swaidan
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Nada H. Soliman
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ahmed T. Aboughalia
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Toqa Darwish
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ruba O. Almeshal
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Azhar A. Al-Khulaifi
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Rowaida Z. Taha
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Rania Alanany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Salam Salloum-Asfar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Sara A. Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Abdallah M. Abdallah
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Mohamed M. Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
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Swaidan NT, Salloum-Asfar S, Palangi F, Errafii K, Soliman NH, Aboughalia AT, Wali AHS, Abdulla SA, Emara MM. Identification of potential transcription factors that enhance human iPSC generation. Sci Rep 2020; 10:21950. [PMID: 33319795 PMCID: PMC7738555 DOI: 10.1038/s41598-020-78932-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Although many factors have been identified and used to enhance the iPSC reprogramming process, its efficiency remains quite low. In addition, reprogramming efficacy has been evidenced to be affected by disease mutations that are present in patient samples. In this study, using RNA-seq platform we have identified and validated the differential gene expression of five transcription factors (TFs) (GBX2, NANOGP8, SP8, PEG3, and ZIC1) that were associated with a remarkable increase in the number of iPSC colonies generated from a patient with Parkinson's disease. We have applied different bioinformatics tools (Gene ontology, protein-protein interaction, and signaling pathways analyses) to investigate the possible roles of these TFs in pluripotency and developmental process. Interestingly, GBX2, NANOGP8, SP8, PEG3, and ZIC1 were found to play a role in maintaining pluripotency, regulating self-renewal stages, and interacting with other factors that are involved in pluripotency regulation including OCT4, SOX2, NANOG, and KLF4. Therefore, the TFs identified in this study could be used as additional transcription factors that enhance reprogramming efficiency to boost iPSC generation technology.
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Affiliation(s)
- Nuha T Swaidan
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Salam Salloum-Asfar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Freshteh Palangi
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar
| | - Khaoula Errafii
- Genomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nada H Soliman
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ahmed T Aboughalia
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Abdul Haseeb S Wali
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Sara A Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation (QF), Doha, Qatar.
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar. .,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar.
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