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. 2024 Sep 28;14(1):22537.
doi: 10.1038/s41598-024-73779-w.

Determination of key hub genes in Leishmaniasis as potential factors in diagnosis and treatment based on a bioinformatics study

Mohsen Safaei  1 , Arash Goodarzi  1 , Zahra Abpeikar  2 , Ahmad Reza Farmani  1 , Seyed Amin Kouhpayeh  3 , Sohrab Najafipour  4 , Mohammad Hassan Jafari Najaf Abadi  5   6
Affiliations

Determination of key hub genes in Leishmaniasis as potential factors in diagnosis and treatment based on a bioinformatics study

Mohsen Safaei et al. Sci Rep. .

Abstract

Leishmaniasis is an infectious disease caused by protozoan parasites from different species of leishmania. The disease is transmitted by female sandflies that carry these parasites. In this study, datasets on leishmaniasis published in the GEO database were analyzed and summarized. The analysis in all three datasets (GSE43880, GSE55664, and GSE63931) used in this study has been performed on the skin wounds of patients infected with a clinical form of leishmania (Leishmania braziliensis), and biopsies have been taken from them. To identify differentially expressed genes (DEGs) between leishmaniasis patients and controls, the robust rank aggregation (RRA) procedure was applied. We performed gene functional annotation and protein-protein interaction (PPI) network analysis to demonstrate the putative functionalities of the DEGs. The study utilized Molecular Complex Detection (MCODE), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) to detect molecular complexes within the protein-protein interaction (PPI) network and conduct analyses on the identified functional modules. The CytoHubba plugin's results were paired with RRA analysis to determine the hub genes. Finally, the interaction between miRNAs and hub genes was predicted. Based on the RRA integrated analysis, 407 DEGs were identified (263 up-regulated genes and 144 down-regulated genes). The top three modules were listed after creating the PPI network via the MCODE plug. Seven hub genes were found using the CytoHubba app and RRA: CXCL10, GBP1, GNLY, GZMA, GZMB, NKG7, and UBD. According to our enrichment analysis, these functional modules were primarily associated with immune pathways, cytokine activity/signaling pathways, and inflammation pathways. However, a UBD hub gene is interestingly involved in the ubiquitination pathways of pathogenesis. The mirNet database predicted the hub gene's interaction with miRNAs, and results revealed that several miRNAs, including mir-146a-5p, crucial in fighting pathogenesis. The key hub genes discovered in this work may be considered as potential biomarkers in diagnosis, development of agonists/antagonist, novel vaccine design, and will greatly contribute to clinical studies in the future.

Keywords: Differentially expressed genes; GEO database; Leishmaniasis; Microarray; RRA method.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Flowchart for dataset retrieval and selection.
Fig. 2
Fig. 2
Volcano maps of the three datasets. The location of up-regulated and down-regulated genes is indicated in the Figure. Red points indicate genes with no significant difference. The Figure was obtained by R software.
Fig. 3
Fig. 3
The heatmap diagram. DEGs Clustering between the control/normal (Red color) and leishmaniasis groups (Turquoise blue color). The Figure was obtained by R software.
Fig. 4
Fig. 4
Heatmap exhibiting the top 20 DEGs (up-regulated or down-regulated) found in the RRA analysis. Red indicates a relatively high expression of genes in Leishmania patients, and green indicates a relatively low expression of genes in Leishmania patients. The values in the heatmap indicate the logarithmic fold change in each dataset, as estimated by R software. The Figure was obtained by R software.
Fig. 5
Fig. 5
GO analysis of DEGs: (A) Functional enrichment analysis of down-regulated genes. (B) Functional enrichment analysis of up-regulated genes. WIKIpath enrichment analysis of DEGs: (C) Functional enrichment analysis of downregulated genes. (D) Functional enrichment analysis of up-regulated genes. KEGG pathway enrichment analysis for DEGs,: (E) The functional enrichment analysis of down-regulated genes. (F) Functional enrichment analysis of up-regulated genes. The Figures were obtained by R software.
Fig. 6
Fig. 6
Representation and module determination for the PPI network. (A) Cytoscape software was used to map 407 DEGs. The MCODE plug-in identified three modules of the PPI networks. (B) Module 1 comprised IFI44, ISG15, IFIT2, IFI44L, PARP14, SAMD9L, MX1, IFI6, OAS2, IFIT3, RSAD2, XAF1, STAT1, EPSTI1, OASL, GBP1, GBP4, LAP3, CXCL10 with the seed gene TRIM22; (C) module 2 contained CD3D, GZMB, CXCR6, ITK, GZMH, CD6, CCL8, IL2RB, CD2, SH2D1A, FASLG, NKG7, CTSW, CXCL11, CXCL9, ICOS, CST7, SAMD3, EOMES, CD96, CD247, CXCR3, GPSM3, CD3E, GNLY, CCR1, GZMK, CXCL13, PRF1,CCR7,CD3G with the seed gene KLRB1; (D) module 3 consisted of KRTAP17-1, KRT32, KRT15, KRT35, KRT71, KRT19, KRTAP9-8, KRT25, KRT27, KRTAP9-4, KRT31, KRTAP19-1 with the seed gene KRTAP9-3. The red points indicate up-regulated genes, while the green points indicate down-regulated genes.
Fig. 7
Fig. 7
Functional enrichment analysis for the genes in module 1: (A) GO analysis for DEGs. (B) The KEGG analysis for DEGs. (C) The WIKIpath analysis for DEGs. Functional enrichment analysis for the genes in module 2: (D) GO analysis for DEGs. (E) The KEGG analysis for DEGs. (F) The WIKIpath analysis for DEGs. Functional enrichment analysis for the genes in module 3: (G) GO analysis for DEGs. (H) The KEGG analysis for DEGs. (I) The WIKIpath analysis for DEGs,. The Figures were obtained by R software.
Fig. 8
Fig. 8
The interaction of miRNAs and selected Hub genes using the the miRNet database.
Fig. 9
Fig. 9
ROC curve analysis of selected genes obtained from sharing three sets of genes (up-regulated DEGs, down-regulated DEGs, and hub genes) in the early vs. late phase related to the GSE55664 dataset. 2 genes out of 4 obtained genes are members of hub genes and are significant at the P < 0.05 (CXCL10 and GBP1).
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References

    1. Abpeikar, Z., Safaei, M., Alizadeh, A. A., Goodarzi, A. & Hatam, G. The novel treatments based on tissue engineering, cell therapy and nanotechnology for cutaneous leishmaniasis. Int. J. Pharm. 2023, 122615 (2023). - PubMed
    1. de Menezes, J. P. B. et al. Advances in development of new treatment for leishmaniasis. BioMed. Res. int. 2015, 56 (2015). - PMC - PubMed
    1. Eshetu, E. & Bassa, A. A. T. The Public Health significance of Leishmaniasis: an overview. J. Nat. Sci. Res. 6, 48–57 (2016).
    1. Mukbel, R. M. et al. Human immune response to salivary proteins of wild-caught Phlebotomus papatasi. Parasitol. Res. 115, 3345–3355 (2016). - PubMed
    1. Niroumand, U. et al. Preparation and characterization of artemether-loaded niosomes in Leishmania major-induced cutaneous leishmaniasis. Sci. Rep. 14, 10073 (2024). - PMC - PubMed