In silico identification of microRNAs predicted to regulate N-myristoyltransferase and Methionine Aminopeptidase 2 functions in cancer and infectious diseases

Abstract

Protein myristoylation is a key protein modification carried out by N-Myristoyltransferase (NMT) after Methionine aminopeptidase 2 (MetAP2) removes methionine from the amino-terminus of the target protein. Protein myristoylation by NMT augments several signaling pathways involved in a myriad of cellular processes, including developmental pathways and pathways that when dysregulated lead to cancer or immune dysfunction. The emerging evidence pointing to NMT-mediated myristoylation as a major cellular regulator underscores the importance of understanding the framework of this type of signaling event. Various studies have investigated the role that myristoylation plays in signaling dysfunction by examining differential gene or protein expression between normal and diseased states, such as cancers or following HIV-1 infection, however no study exists that addresses the role of microRNAs (miRNAs) in the regulation of myristoylation. By performing a large scale bioinformatics and functional analysis of the miRNAs that target key genes involved in myristoylation (NMT1, NMT2, MetAP2), we have narrowed down a list of promising candidates for further analysis. Our condensed panel of miRNAs identifies 35 miRNAs linked to cancer, 21 miRNAs linked to developmental and immune signaling pathways, and 14 miRNAs linked to infectious disease (primarily HIV). The miRNAs panel that was analyzed revealed several NMT-targeting mRNAs (messenger RNA) that are implicated in diseases associated with NMT signaling alteration, providing a link between the realms of miRNA and myristoylation signaling. These findings verify miRNA as an additional facet of myristoylation signaling that must be considered to gain a full perspective. This study provides the groundwork for future studies concerning NMT-transcript-binding miRNAs, and will potentially lead to the development of new diagnostic/prognostic biomarkers and therapeutic targets for several important diseases.

Fig 1. Schematic representation of protein N-myristoylation.

Fig 2. The distribution of microRNAs (miRNAs) that target N-myristoyltransferase (NMT1/2) and methionine aminopeptidase 2 (MetAP2) genes.

The miRNAs that target either NMT or MetAP2, or both genes are illustrated in the Venn diagram. Seven miRNAs target both NMT1/2 and MetAP2 genes.

Fig 3. ErbB signaling pathway that is enriched with target genes of microRNAs (miRNAs) which negatively regulate N-myristoyltransferase (NMT1/2) and methionine aminopeptidase 2 (MetAP2) genes.

The figure illustrates ErbB signaling pathway that contain genes that are targeted by miRNAs which regulate NMT gene. (EGF, epidermal growth factor; TGF, transforming growth factor; BTC, betacellulin; HB-EGF, heparin-binding epidermal growth factor (EGF)-like growth factor; EREG, epiregulin; NRG1, neuregulin-1; NRG2, neuregulin-2; NRG3, neuregulin-3; NRG4, neuregulin-4; PLCγ, phospholipase C type gamma; CAMK2B, calcium/calmodulin dependent protein kinase; PRKCB, Protein kinase C-beta; STAT5, Signal transducer and activator of transcription 5; src, Rous sarcoma virus gene; CRK, C T10 regulator of a tyrosine kinase; NCL, NCK Adaptor Protein 2; PTK2, PTK2 protein tyrosine kinase 2; ABL2, V-Abl Abelson Murine Leukemia Viral Oncogene Homolog 2; PAK2, P21 (RAC1) Activated Kinase 2; MAP2K4, Mitogen-Activated Protein Kinase Kinase 4; MAPK10, Mitogen-Activated Protein Kinase 10; SOS1, SOS Ras/Rac Guanine Nucleotide Exchange Factor 1; Grb2, Growth Factor Receptor Bound Protein 2; SHC4, Src Homology 2 Domain-Containing-Transforming Protein C4; PIK3C4, Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit; AKT3, KT Serine/Threonine Kinase 3; mTOR, Mechanistic Target Of Rapamycin Kinase; BCL2, BCL2 Associated Agonist Of Cell Death; GSK3B, Glycogen Synthase Kinase 3 Beta; CDKN1A, Cyclin Dependent Kinase Inhibitor 1A; EIF4EBP1, Eukaryotic Translation Initiation Factor 4E Binding Protein 1; BRAF, B-Raf Proto-Oncogene, Serine/Threonine Kinase; RPS6KB1, Ribosomal Protein S6 Kinase B1; KRAS, KRAS Proto-Oncogene, GTPase; JUN, Jun Proto-Oncogene, AP-1 Transcription Factor Subunit; ELK, ETS Transcription Factor; Myc, MYC Proto-Oncogene, BHLH Transcription Factor; ER, endoplasmic reticulum. DNA, deoxyribonucleic acid).

Fig 4. Colorectal cancer and prostate cancer pathways that are enriched with target genes of microRNAs (miRNAs) which negatively regulate N-myristoyltransferase (NMT1/2) and methionine aminopeptidase 2 (MetAP2) genes.

The figure illustrates A) colorectal cancer pathway and B) prostate cancer pathway that contain genes that are targeted by miRNAs which regulate NMT gene. (Rac1, Rac family small GTPase 1; Wnt, Wingless-related integration site; FOS, Fos Proto-Oncogene, AP-1 Transcription Factor Subunit; APC, Adenomatosis Polyposis Coli Tumor Suppressor; AXIN2, Axis Inhibition Protein 2; CTNNB1, Catenin Beta 1; CASP3, Caspase 3; APPL, Adaptor Protein, Phosphotyrosine Interacting With PH Domain And Leucine Zipper 1; CCND1, Cyclin D1; RALGDS, Ral Guanine nucleotide dissociation stimulator; MSH6, MutS homolog 6; BCL2, B-Cell CLL/Lymphoma 2; TGFBR2, Transforming Growth Factor Beta Receptor 2; SMAD, SMAD Family Member 3 (mothers against decapentaplegic); Myc, MYC Proto-Oncogene; BAX, BCL2 Associated X, Apoptosis Regulator; CYCS, Cytochrome C, DCC, Deleted In Colorectal Carcinoma; LEF, lymphoid enhancer binding factor 1; P53, Phosphoprotein-53. AR, androgen receptor; FOXO1, Forkhead Box O1; PTEN, Phosphatase And Tensin Homolog; GSTP1, Glutathione S-Transferase Pi 1; CDK2, Cyclin Dependent Kinase 2; Rb1, Retinoblastoma 1; E2F3, E2F Transcription Factor 3; EGF, Epidermal Growth Factor; SRD5A2, Steroid 5 Alpha-Reductase 2; PSA, Kallikrein 3; MDM2, RING-Type E3 Ubiquitin Transferase Mdm2; PDK1, Pyruvate Dehydrogenase Kinase 1; CDKN1A, Cyclin Dependent Kinase Inhibitor 1A; CREBBP, CREB Binding Protein; CREB3L1, AMP Responsive Element Binding Protein 3 Like 1).

Fig 5. T-cell and B-cell receptor pathways that are enriched with target genes of microRNAs (miRNAs) which negatively regulate N-myristoyltransferase (NMT1/2) and methionine aminopeptidase 2 (MetAP2) genes.

The figure illustrates two cellular pathways A) T cell receptor signaling and B) B cell receptor signaling that contains genes that are targeted by miRNAs, which regulate NMT1/2 gene. (PD1, programmed cell death-1; ZAP70, Zeta Chain Of T-Cell Receptor Associated Protein Kinase 70; LAT, Linker for Activation Of T-Cells; ICOS, Inducible T-Cell Co-stimulator; DLG1, Discs Large MAGUK Scaffold Protein 1; NCK2, NCK Adaptor Protein 2; LCP2, Lymphocyte Cytosolic Protein 2; GM-CSF, Granulocyte-macrophage colony-stimulating factor; IFN-γ, Interferon gamma; TNFα, Tumor Necrosis Factor alpha; IL, Interleukin; NFKB1, Nuclear Factor Kappa B Subunit 1; CDK4, Cyclin Dependent Kinase 4; PPP3R2, Protein Phosphatase 3 Regulatory Subunit B, Beta; CTLA4, Cytotoxic T-lymphocyte Associated Protein; PKC8, protein kinase C-8; FYN, FYN Proto-Oncogene, Src Family Tyrosine Kinase; Raf-1, Raf-1 Proto-Oncogene, Serine/Threonine Kinase. CD, cluster of differentiation; BCR, break-point cluster region; BTK, Bruton Tyrosine Kinase; DAPP1, Dual Adaptor Of Phosphotyrosine And 3-Phosphoinositides 1; VAV3, Vav Guanine Nucleotide Exchange Factor 3; SHIP, SH2 Domain-Containing Inositol 5-Phosphatase; Rac1, Rac Family Small GTPase 1; SYK, Spleen Associated Tyrosine Kinase; NFATC1, Nuclear Factor of activated T-cells 1; PPP3R2, Protein Phosphatase 3 Regulatory Subunit B, Beta; RASGRP3, RAS Guanyl Releasing Protein 3; MALT1, Mucosa Associated Lymphoid Tissue Lymphoma Translocation; Lyn, LYN Proto-oncogene src family tyrosine kinase).

Fig 6. The clustering of microRNAs (miRNAs) targeting N-myristoyltransferase (NMT) genes.

The figure illustrates clustering of the miRNAs that target NMT1/2 genes based on normalized expression values obtained from “GSE62037”. Data suggest miRNA regulon model is similar to the RNA regulon model. Green color shows positive Pearson correlation coefficient (PCC) values (0.5 ≤ r ≤ 1) and red color shows inverse/negative PCC values (-0.5 ≤ r ≤ 1). Heatmap shows that most of miRNAs have high PCC values, and these miRNAs co-express with each other to regulate common biological processes.