Systems biology approach: identification of hub genes, signaling pathways, and molecular docking of COL1A1 gene in cervical insufficiency

Sushma Shah; Pooja Trivedi; Mohammadfesal Ghanchi; Gaurang Sindhav; Haresh Doshi; Ramtej J Verma

doi:10.1007/s40203-024-00218-z

Systems biology approach: identification of hub genes, signaling pathways, and molecular docking of COL1A1 gene in cervical insufficiency

In Silico Pharmacol. 2024 May 14;12(1):45. doi: 10.1007/s40203-024-00218-z. eCollection 2024.

Authors

Sushma Shah¹, Pooja Trivedi², Mohammadfesal Ghanchi², Gaurang Sindhav², Haresh Doshi³, Ramtej J Verma²

Affiliations

¹ Smt. NHL Municipal Medical College, Pritan Rai Cross Road, Ellise Bridge, Paldi, Ahmedabad, Gujarat 380006 India.
² Department of Zoology, BMT, HGC and WBC, University School of Sciences, Gujarat University, Ahmedabad, 09 Gujarat India.
³ FICOG, Diploma (USG), PGCML, PGDMLS, PGDCR, PGDHHM Prof. & HOD ObGy, GCSMCH & RC, Opp. DRM Office, Chamunda Bridge, Naroda Road, Ahmedabad, 380025 India.

PMID: 38756679
PMCID: PMC11093961 (available on 2025-05-14)
DOI: 10.1007/s40203-024-00218-z

Abstract

The collagen type I alpha 1 (COL1A1, OMIM #120,150) gene, encoding the alpha-1 chain of type I collagen (UniProt #P02452), plays a key role in life-homeostasis due to its remarkable involvement in collagen synthesis. It is a promising candidate gene implicated in the pathogenesis of cervical insufficiency (CI). This study aimed to identify genetic variations within the COL1A1 gene that contribute to the development of CI. Polymerase chain reaction (PCR) and amplicon sequencing were implemented for single nucleotide polymorphisms (SNPs) detection (+ 1245G/T, SP1 rs1800012), which revealed wild-type sequence for targeted SNPs in enrolled proband indicated negative results regarding COL1A1 gene involvement for current form of CI. It allows further investigation of other closely connected genes probed in this study. Computational approaches viz. Protein-protein interaction (PPI), gene ontology (GO), and pathway participation were used to identify the crucial hub genes and signaling pathways for COL1A1 and CI. Using the Yet Another Scientific Artificial Reality Application (YASARA) software, molecular docking, and molecular dynamic (MD) simulation with the oxytocin (CID 439,302), estradiol (CID 129,728,744), progesterone (CID 5994) and hydroxyprogesterone (CID 150,788) were done. Interactive bioinformatics analysis demonstrated that the COL1A1 and more than 10 collagen sister genes had a strong connection with CI. In sum, the findings of this study provide insights into a modus operandi that can be utilized to illuminate the path toward studying sister genes and smooth diagnosis of CI. These findings have implications for understanding the foundational process of the condition and potentially developing screening, diagnostic, and therapeutic interventions.

Keywords: COL1A1; Cervical insufficiency; Molecular docking; SNPs.

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