1
|
Tamkeen N, AlOmar SY, Alqahtani SAM, Al-Jurayyan A, Farooqui A, Tazyeen S, Ahmad N, Ishrat R. Identification of the Key Regulators of Spina Bifida Through Graph-Theoretical Approach. Front Genet 2021; 12:597983. [PMID: 33889172 PMCID: PMC8056047 DOI: 10.3389/fgene.2021.597983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Spina Bifida (SB) is a congenital spinal cord malformation. Efforts to discern the key regulators (KRs) of the SB protein-protein interaction (PPI) network are requisite for developing its successful interventions. The architecture of the SB network, constructed from 117 manually curated genes was found to self-organize into a scale-free fractal state having a weak hierarchical organization. We identified three modules/motifs consisting of ten KRs, namely, TNIP1, TNF, TRAF1, TNRC6B, KMT2C, KMT2D, NCOA3, TRDMT1, DICER1, and HDAC1. These KRs serve as the backbone of the network, they propagate signals through the different hierarchical levels of the network to conserve the network’s stability while maintaining low popularity in the network. We also observed that the SB network exhibits a rich-club organization, the formation of which is attributed to our key regulators also except for TNIP1 and TRDMT1. The KRs that were found to ally with each other and emerge in the same motif, open up a new dimension of research of studying these KRs together. Owing to the multiple etiology and mechanisms of SB, a combination of several biomarkers is expected to have higher diagnostic accuracy for SB as compared to using a single biomarker. So, if all the KRs present in a single module/motif are targetted together, they can serve as biomarkers for the diagnosis of SB. Our study puts forward some novel SB-related genes that need further experimental validation to be considered as reliable future biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Naaila Tamkeen
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Suliman Yousef AlOmar
- Doping Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Abdullah Al-Jurayyan
- Immunology and HLA Section, Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Anam Farooqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nadeem Ahmad
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
2
|
Zhang H, Guo Y, Gu H, Wei X, Ma W, Liu D, Yu K, Luo W, Ma L, Liu Y, Xue J, Huang J, Wang Y, Jia S, Dong N, Wang H, Yuan Z. TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis. Clin Epigenetics 2019; 11:17. [PMID: 30709423 PMCID: PMC6359777 DOI: 10.1186/s13148-018-0603-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 12/20/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are complex abnormalities associated with gene-environment interactions. The underlying cause has not been determined. METHODS Spinal cord tissues from cases with NTDs and healthy controls were collected. Methylation patterns between cases and normal individuals were compared using 450K Infinium Methylation BeadChip Illumina. DNA methylation analysis by pyrosequencing (PyroMark Q96) and mRNA and protein expression were analyzed using real-time quantitative PCR and Western blotting, respectively. Next-generation and Sanger sequencing were used to determine genetic variants in the target genes. RESULTS Spinal cord tissues from cases with NTDs had more hypomethylated than hypermethylated genes. Further evaluation showed that the exon 1 region of TRIM4 was hypomethylated, and TRIM4 mRNA and protein levels were significantly increased in NTDs compared to controls. A rare missense variant (rs76665876) in TRIM4 was found in 3 of the 14 NTD cases but was not related to TRIM4 expression. TRIM4 mRNA levels were significantly increased in cases with hypomethylation and without the rs76665876 variant. CONCLUSION These findings suggest that spinal cord tissues in cases with NTDs had a different genome-wide methylation pattern compared to controls. Abnormal methylation patterns in TRIM4 in immunity pathways might be involved in NTD pathogenesis. Genetic variants in TRIM4 genes only slightly contribute to the etiology of human NTDs.
Collapse
Affiliation(s)
- Henan Zhang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yi Guo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Kun Yu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Ling Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yusi Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Jia Xue
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Jieting Huang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yanfu Wang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Naixuan Dong
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, Key Lab of Reproduction Regulation of NPFPC in SIPPR, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China.
| |
Collapse
|