In Silico Analysis of the Molecular-Level Impact of NPM۱ Protein Variants on Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a rapidly progressing cancer of the blood and bone marrow, characterized by the abnormal proliferation of immature white blood cells. Genetic mutations in a wide range of proteins lead to AML and one highly relevant protein associated with AML is Nucleophosmin۱ (NPM۱). Nucleophosmin۱, which is a pentamer with NES, NLS, and NoLS motifs for each subunit, is a multifunctional nucleolar protein involved in various cellular processes, including ribosome biogenesis, genome stability, cell growth, and apoptosis. NPM۱ has a main regulatory role in the ARF-p۵۳-tumor-suppressor pathway. Under stressful situations for cells, the nucleolar proteins, NPM۱ and ARF are released from nucleoli to the nucleoplasm and engaged to activate p۵۳, which is required for the apoptosis of damaged cells. NPM۱ is important for ARF stability, and it protects ARF from degradation. Mutations in the NPM۱ gene are known as one of the most frequent genetic alterations in AML progression. Through the identification and understanding of genetic mutations in the NPM۱ protein, this study aims to provide a way to help with diagnosis, prognosis, and treatment strategies. Methods: We collected information about the sequence, structure, and ۱۵ missense mutations of NPM۱ from NCBI, Uniprot, and HGMD datasets. We used bioinformatic tools such as SIFT, PolyPhen۲, PROVEAN, PANTHER, I-Mutant, and MUpro to predict the pathogenicity and stability change of the mutations. To confirm the severity of variations, we used Project HOPE. Results: Out of ۱۵ missense mutations in the NPM۱ protein, ۵ (۳۳%) were simultaneously predicted as deleterious and damaging in the six prediction tools mentioned above. These mutations (p.Asp۲۴۶Gly, p.Pro۱۵۲Ala, p.Lys۱۹۳Asn, p.Trp۲۸۸Cys, and p.Trp۲۹۰Glu) were analyzed by Project HOPE to identify the changes of the wild-type protein after variations. P.Asp۲۴۶Gly mutation, is located in the C-terminal domain of NPM۱. Because of the smaller size and neutral charge of the mutant residue(Gly), this mutation leads to a loss of interactions and hydrogen bonds; thus, the protein function can be disturbed. The location of p.Pro۱۵۲Ala in NPM۱ is known as the region required for interaction with other proteins. Prolines are very rigid and forceful for the formation of specific conformations. This mutation may cause the structural deformation of the protein and, as a result, change its function. P.Lys۱۹۳Asn occurs in an important motif called: the Nuclear Localization Signal (NLS); therefore, it is very conserved among the homologous sequences. Mutations in this region can be damaging. Based on Project HOPE and Uniprot databases, the Nucleolar Localization Signal (NoLS) motif on exon ۱۲ has two highly conserved tryptophan residues (at positions ۲۸۸ and ۲۹۰) which can cause relocalization of NPM۱ and other damaging consequences, when mutated. Therefore, these mutations (p.Trp۲۸۸Cys and p.Trp۲۹۰Glu), in which mutant residues are smaller in size and more hydrophilic than the wild-type residues, were highly damaging according to all the bioinformatic tools used in this article. Conclusion: In this article, we tried to pave the way for diagnosis and genetic treatment by personalized medicine for AML patients, using In-Silico analysis of missense mutations affecting the structure and function of the NPM۱ protein that can cause disease.

کلیدواژه ها:

Missense mutations ، NPM۱ ، Acute myeloid leukemia (AML) ، Bioinformatics