Variation of the encoding hyaluronic receptors Hyaluronan-mediated motility receptor (rs299295) and Stabilin-2 (rs2271637) genes with prostate neoplasms risk: A case-control and in silico study

Abstract

Background: Hyaluronan-mediated motility receptor (HMMR) and Stabilin-2 (STAB2), known as extracellular matrix cell surface protein's receptors, bind to hyaluronic acid and lead to various cell functions.

Objective: The study aims to investigate the relationship between the HMMR-rs299295 (C $>$ T/ A485V) and STAB2-rs2271637 (C $>$ G/ L2401V) gene variants and the risk of prostate neoplasms in the Mazandaran population, North of Iran.

Materials and methods: This study was conducted based on a case-control and in silico approach. Genomic DNA was extracted from 598 intravenous blood samples, collected from 250 benign prostatic hyperplasia (case group I) and 250 malignant prostate (case group II) neoplasms as cases, and 98 healthy men as control. The HMMR-rs299295 and STAB2-rs2271637 genotypes were identified using the polymerase chain reaction-restriction fragment length polymorphism method. Bioinformatics analyses were conducted using PolyPhen-2, GOR IV, and GeneMANIA free web tools.

Results: The study found that the mutant T allele in HMMR-rs299295 and the G allele in STAB2-rs2271637 are associated with an increased risk of prostate neoplasm, including benign prostatic hyperplasia and prostate cancer (p $<$ 0.001). Bioinformatic analyses revealed structural changes and potential damage from these variants. The HMMR-A485V variant might impair interaction with family with sequence similarity 83 member D, and the STAB2-L2401V variant could disrupt domain 7 of FAS1, together they may affect the protein's physical interactions, especially with mitogen-activated protein kinase 1.

Conclusion: The mutant alleles of T in HMMR-rs299295 and the G in STAB2-rs2271637 may disrupt protein structures and probably contribute to prostate neoplasm progression.

Keywords: Fasciclin-like; HMMR, MAPK1; Prostate neoplasm; STAB2.; FAM83D.

Figure 1

HMMR-rs299295 and SATB2-rs2271637 gene variants loci, RFLP maps, agarose gel profiling of PCR products digestion, and DNA sequencing results: a and e) The location of HMMR (chromosome 5) and STAB2 (chromosome 12) genes which include exons 13 and 65 for HMMR-rs299295 and SATB2-rs2271637 variants, respectively, b and f) Schematic RFLP maps of HMMR-rs299295 and STAB2-rs2271637 showing restriction enzyme cleavage sites, c and g) Digestion with AciI and MwoI restriction enzymes revealed distinct band patterns on a 2% agarose gel. These patterns corresponded to the genotypes of HMMR-rs299295 (CC, CT, TT) and STAB2-rs2271637 (CC, CG, GG), respectively. M denotes 100 bp DNA marker (SinaColon Co., Iran), d and h) Sequencing chromatograms represented HMMR-rs299295 and STAB2-rs2271637 genotypes.

Figure 2

Predicted changes by GOR IV server in protein secondary structure for HMMR-rs299295 and STAB2-rs2271637 variants: a) GOR IV predicts slight alpha helix and random coil content changes for the HMMR-rs299295 variant (alanine vs. valine), b) GOR IV predicts the wild-type STAB2 protein (leucine) to have 18.5% alpha helix, 20.5% extended strand, and 61.0% random coil. The mutant (valine) shows a slight decrease in alpha helix and a small increase in the extended strand and random coil.

Figure 3

Rosetta LDDT prediction for HMMR-rs299295 and STAB2-rs2271637 variants: a) The predicted structure of the HMMR-rs299295 variant showed the mutant valine residue (blue) has a higher LDDT score than the wild-type alanine (red), indicating a better predicted local structural accuracy, b) The predicted structure of the STAB2-rs2271637 variant represented the wild-type leucine (red) has a higher LDDT score than the mutant valine (blue), suggesting a better predicted local structural accuracy for the wild-type protein.

Figure 4

Protein physical interactions network of HMMR and STAB2: a) The network demonstrated that HMMR and STAB2 proteins, directly and indirectly, interact with nearly 20 other proteins, b) HMMR interacts both directly and physically interacts with 12 other proteins, c) STAB2 directly interacts with 6 proteins. HMMR: Hyaluronan mediated motility receptor, STAB2: Stabilin 2, TPX2: TPX2 microtubule nucleation factor, ANKRD26: Ankyrin repeat domain containing 26, TMSB4X: Thymosin beta 4 X-linked, BACH1: BTB domain and CNC homolog 1, AURKA: Aurora kinase A, BRCA1: BRCA1 DNA repair associated, APOB: Apolipoprotein B, FAM83D: Family with sequence similarity 83 member D, NDC80: NDC80 kinetochore complex component, POSTN: Periostin, TGFBI: Transforming growth factor beta-induced, MAPK1: Mitogen-activated protein kinase 1, MAD2L1: Mitotic arrest deficient 2 like 1, STAB1: Stabilin 1, MKI67: Marker of proliferation Ki-67, RAB28: RAB28, member RAS oncogene family, SLC9A1: Solute carrier family 9 member A1, HYAL2: Hyaluronidase 2, ABCC5: ATP binding cassette subfamily C member 5, KIF15: Kinesin family member 15.