| Literature DB >> 30918758 |
Suhong Fu1, Yongqun Zhang1, Jing Shi1, Doudou Hao1, Pengfei Zhang1.
Abstract
Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein-protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What's more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.Entities:
Keywords: Functional network analysis; KEGG pathway; Naringenin; PPI network; Prostate cancer
Year: 2019 PMID: 30918758 PMCID: PMC6430101 DOI: 10.7717/peerj.6611
Source DB: PubMed Journal: PeerJ ISSN: 2167-8359 Impact factor: 2.984
Figure 1The structure of naringenin.
Identification of direct protein targets of naringenin using DrugBank.
| No. | Uniprot ID | Uniprot name | Gene name |
|---|---|---|---|
| 1 | P03372 | Estrogen receptor | ESR1 |
| 2 | Q04828 | Aldo-keto reductase family 1 member C1 | AKR1C1 |
| 3 | Q16678 | Cytochrome P450 1B1 | CYP1B1 |
| 4 | Q9P2N6 | KAT8 regulatory NSL complex subunit 3 | KANSL3 |
| 5 | P04278 | Sex hormone-binding globulin | SHBG |
| 6 | P11511 | Aromatase | CYP19A1 |
| 7 | Q92731 | Estrogen receptor beta | ESR2 |
Figure 2The interactions of naringenin and its DPTs.
Figure 3PPI network of naringenin-mediated proteins.
The nodes indicate proteins and the edges indicate interaction between proteins. High node degree value was represented by big size and low node degree value was represented by small size.
The list of top 10 proteins ranked by degree value.
| No. | Gene name | Node degree | No. | Gene name | Node degree |
|---|---|---|---|---|---|
| 1 | ESR1 | 51 | 6 | HPGDS | 38 |
| 2 | CYP19A1 | 48 | 7 | ESR2 | 35 |
| 3 | HSD17B6 | 44 | 8 | JUN | 34 |
| 4 | CYP1A1 | 43 | 9 | HSD3B2 | 34 |
| 5 | CYP3A4 | 38 | 10 | UGT1A6 | 33 |
Top 15 enriched KEGG pathways identified using DAVID.
| Pathway description | Gene count | Gene | |
|---|---|---|---|
| Steroid hormone biosynthesis | 33 | CYP3A4, HSD3B2, CYP3A5, HSD3B1, CYP1B1, HSD17B2, HSD17B1, CYP11B1, COMT, UGT1A7, AKR1C3, UGT1A6, UGT1A9, UGT1A3, UGT1A4, UGT2A1, HSD17B6, HSD17B3, SRD5A1, UGT2A3, SULT1E1, HSD17B7, AKR1C1, CYP19A1, HSD17B8, CYP1A1, UGT1A1, UGT1A10, UGT2B17, CYP17A1, UGT2B15, AKR1D1, UGT2B7 | 4.86 |
| Metabolism of xenobiotics by cytochrome P450 | 26 | GSTA1, CYP3A4, CYP3A5, CYP1B1, SULT2A1, CYP1A1, EPHX1, GSTT1, UGT1A1, DHDH, GSTM1, UGT1A7, UGT1A10, GSTM2, UGT1A6, UGT1A9, UGT2B17, GSTM3, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT2B7, AKR1C1, GSTP1 | 3.29 |
| Chemical carcinogenesis | 24 | GSTA1, CYP3A4, CYP3A5, CYP1B1, SULT2A1, CYP1A1, EPHX1, GSTT1, UGT1A1, UGT1A7, GSTM1, UGT1A10, UGT1A6, GSTM2, UGT1A9, UGT2B17, GSTM3, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT2B7, GSTP1 | 8.08 |
| Drug metabolism-cytochrome P450 | 20 | GSTA1, CYP3A4, CYP3A5, GSTT1, UGT1A1, UGT1A7, GSTM1, UGT1A10, UGT1A6, GSTM2, UGT1A9, UGT2B17, GSTM3, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, GSTP1, UGT2B7 | 6.4 |
| Retinol metabolism | 16 | CYP3A4, CYP3A5, CYP1A1, UGT1A1, UGT1A7, UGT1A6, UGT1A10, UGT1A9, UGT2B17, UGT1A3, UGT1A4, UGT2A1, HSD17B6, UGT2A3, UGT2B15, UGT2B7 | 3.57E-16 |
| Pentose and glucuronate interconversions | 13 | UGT1A7, UGT1A10, UGT1A6, UGT1A9, UGT2B17, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT1A1, DHDH, UGT2B7 | 1.02 |
| Ascorbate and aldarate metabolism | 12 | UGT1A7, UGT1A10, UGT1A6, UGT1A9, UGT2B17, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT1A1, UGT2B7 | 3.81 |
| Ovarian steroidogenesis | 14 | AKR1C3, HSD3B2, IGF1R, CYP17A1, HSD3B1, CYP1B1, CYP1A1, HSD17B2, INS, HSD17B1, IGF1, GNAS, HSD17B7, CYP19A1 | 6.86 |
| Drug metabolism-other enzymes | 13 | CYP3A4, UGT1A7, UGT1A10, UGT1A6, UGT1A9, UGT2B17, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT1A1, UGT2B7 | 1.01 |
| Porphyrin and chlorophyl metabolism | 12 | UGT1A7, UGT1A10, UGT1A6, UGT1A9, UGT2B17, UGT1A3, UGT1A4, UGT2A1, UGT2A3, UGT2B15, UGT1A1, UGT2B7 | 1.10 |
| Prolactin signaling pathway | 12 | AKT1, MAPK1, FOS, CYP17A1, CCND1, INS, ESR1, PIK3CA, MAPK11, ESR2, PRL, SRC | 4.99 |
| Thyroid hormone signaling pathway | 12 | AKT1, MAPK1, NCOA1, CCND1, NCOA2, NCOA3, ESR1, PIK3CA, NCOR1, MYC, SRC, MED1 | 9.09 |
| Estrogen signaling pathway | 10 | AKT1, MAPK1, FOS, JUN, ESR1, PIK3CA, NOS3, GNAS, ESR2, SRC | 2.26 |
| Metabolic pathways | 32 | CYP3A4, HSD3B2, CYP3A5, HSD3B1, HSD17B2, HSD17B1, CYP11B1, COMT, AKR1C3, UGT1A7, UGT1A6, UGT1A9, POLE4, UGT1A3, UGT1A4, UGT2A1, HSD17B6, HSD17B3, NOS3, UGT2A3, HPGDS, HSD17B7, CYP19A1, HSD17B8, CYP1A1, UGT1A1, UGT1A10, UGT2B17, CYP17A1, UGT2B15, AKR1D1, UGT2B7 | 1.18 |
| Prostate cancer | 8 | AKT1, MAPK1, IGF1R, AR, CCND1, INS, PIK3CA, IGF1 | 7.70 |
Figure 4Overview of changes on ESR1, PIK3CA, AKT1, and MAPK1 genes in genomics data sets available in 16 different prostate cancer studies.
Figure 5A visual summary of alteration across a set of prostate samples (data taken from the NEPC studies, Nat Med 2016) (Beltran et al., 2016) based on a query of four genes ESR1, PIK3CA, AKT1, and MAPK1.
Different genomic alterations are summarized and color coded presented by % changes in particular affected genes in individual tumor samples. Each row represents a gene, and each column represents a tumor sample.
Mutual exclusivity analysis of four selected genes (ESR1, AKT1, PIK3CA, MAPK1) in NEPC study.
| Gene A | Gene B | Log2 odds ratio | Association | |
|---|---|---|---|---|
| ESR1 | AKT1 | <0.001 | >3 | Tendency toward co-occurrence |
| ESR1 | PIK3CA | <0.001 | >3 | Tendency toward co-occurrence |
| ESR1 | MAPK1 | 0.003 | >3 | Tendency toward co-occurrence |
| PIK3CA | AKT1 | <0.001 | 2.733 | Tendency toward co-occurrence |
| AKT1 | MAPK1 | 0.002 | >3 | Tendency toward co-occurrence |
| PIK3CA | MAPK1 | 0.005 | >3 | Tendency toward co-occurrence |
Figure 6A visual display of the gene network connected to ESR1/PIK3CA/AKT1/MAPK1 in prostate adenocarcinoma (based on the NEPC study, Nat Med 2016) (Beltran et al., 2016).
(A) Cross-cancer alteration summary for ESR1/PIK3CA/AKT1/MAPK1 mined from the cBioPortal for Cancer Genomics. Multidimensional genomic details are shown for seed genes ESR1, PIK3CA, AKT1, and MAPK1. A darker shade of red indicates increased frequency of alteration in prostate cancer. (B) Neighboring genes connected to the four query genes, filtered by alterations (45%).