Combined Genotype Effects of TP53 and PAI-1 Polymorphisms in Breast Cancer Susceptibility: Multifactor Dimensionality Reduction and in silico Analysis

Introduction: Breast cancer is a heterogeneous and multifactorial disease. TP53 and PAI-1 as important tumor suppressor genes are involved in the development, invasion, and metastasis of many cancers. This study’s objective was to demonstrate the combined genotype effects of these 2 genes by investigating their single nucleotide polymorphisms. Methods: In this case-control study, 200 individuals with breast cancer and 179 healthy individuals were studied. The genotypes were determined using the tetra-ARMS method. For data analysis, MDR, online javstat statistics package, and SPSS v.24 software were used. Also, in silico studies on the estimated effects of each of these polymorphisms were performed. Results: We showed a novel gene-gene interaction of these 2 genes and demonstrated a strong synergistic interaction for TP53/PAI-1, moderate synergistic interaction for PAI-1/age, and correlation for TP53/age. On the other hand, there was no association between the allelic and genotype frequency alone and in combination, with case-control status, using the parametric method, between TP53 and PAI-1. Discussion/Conclusion: Our findings suggest that the polymorphism of codon 72 of the TP53 gene was significantly associated with tumor stage (p < 0.023). In conclusion, we showed a gene-gene interaction between TP53 and PAI-1, in combination, using the MDR method.

The fat mass and obesity-associated (FTO) gene allele rs9939609 and glucose tolerance, hepatic and total insulin sensitivity, in adults with obesity

The objective of the study was to assess associations of the rs9939609 FTO allele to glucose tolerance, hepatic and total insulin sensitivity (IS) in individuals with obesity. From a low-dose hyperinsulinemic euglycemic clamp with glucose-tracer, hepatic IS was assessed by rates of basal and suppressed glucose appearance (Ra), a measure of endogenous glucose production (EGP), and the hepatic insulin resistance index (HIR). Total IS was assessed by rates of glucose infusion (GIR), disappearance (Rd), and metabolic clearance (MCR). From a meal test we assessed IS by the Matsuda index and glucose tolerance by glucose and insulin measurements in the fasted state and postprandially for 2.5 h. The meal test was performed in 97 healthy individuals with BMI ≥35 in similar-sized risk-allele groups (n = 32 T/T, 31 A/T, and 34 A/A), and 79 of them performed the clamp. We analyzed outcomes separately for males and females, and adjusted glucose Ra, Rd, MCR, GIR, and HIR for fat mass. We did not find genotype effects on EGP. Among males, genotype A/A was associated with a significantly lower glucose Rd, MCR, and Matsuda index score relative to genotype T/T. Glucose tolerance was significantly lower in males with genotype A/T vs. T/T and A/A. For females, there were no genotype effects on hepatic or total IS, or on glucose tolerance. Independently of genotypes, females displayed a significantly better hepatic and total IS, and better glucose tolerance than males. We conclude that in subjects with similar obesity we did not register any FTO risk-allele effect on hepatic IS. A FTO risk-allele effect on total IS was registered in males only, findings which need to be reproduced in further studies. Results confirm marked differences in IS between the biological sexes and extend present knowledge by demonstrating a lower endogenous glucose production in females vs. males in uniformly obese individuals.

Development and validation of functional markers from Dw1 and Dw2 loci to assistant predict apple rootstock dwarfing ability

Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2, for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’(Malus × domestica Borkh.) trees grafted on 1123 hybrids from ‘Malus baccata Borkh.’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 (Md Lateral organ boundaries domain 3)and MdARF6 (Md Auxin response factor 6) were predicted as potential candidate genes from Dw1, while MdG3OX3 (Md Gibberellin 3-beta-dioxygenase 3) was a possible candidate gene from Dw2. An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 (Md WRKY transcription factor 2)and caused increased expression of MdLBD3. Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 (Md Abscisic acid insensitive 5), leading to higher expression of MdG3OX3. At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdGAMYB (Md transcription factor GAMYB)and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion: The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that hormone (ABA, Auxin, GA, and zeatin signals) is one of the regulation pathways in controlling apple rootstock dwarfing mechanisms.

Development and validation of functional markers from Dw1 and Dw2 loci to accurately predict apple rootstock dwarfing ability

Background: ‘M9’ is a widely used apple dwarfing rootstock due to the outstanding effects on both precocity and vigorous control. Two quantitative trait loci (QTLs), Dw1 and Dw2, for the dwarfing effect were previously mapped on ‘M9’, but the genetic variations that underpin the dwarfing ability have not been elucidated to date. Result: By using ‘Red Fuji’ trees grafted on 1123 hybrids from ‘Malus baccata’ × ‘M9’, the intervals of Dw1 and Dw2 were narrowed down. MdLBD3 (Md Lateral organ boundaries domain 3)and MdARF6 (Md Auxin response factor 6) were predicted as potential candidate genes from Dw1, while MdG3OX3 (Md Gibberellin 3-beta-dioxygenase 3) was a possible candidate gene from Dw2. An 11 bp deletion at -339 bp upstream of the transcription start site (TSS) of MdLBD3 generated a new cis-element binding site with MdWRKY2 (Md WRKY transcription factor 2)and caused increased expression of MdLBD3. Coincidently, a ten bp deletion at -278 bp upstream of the TSS of MdG3OX3 created an additional binding site of MdABI5 (Md Abscisic acid insensitive 5), leading to higher expression of MdG3OX3. At -954 bp of the MdARF6 promoter, a 14 bp insertion destroyed the binding ability by MdGAMYB (Md transcription factor GAMYB)and reduced MdARF6 expression. The genotype effects of these insertion and deletions as diagnostic markers on dwarfing traits (tree height, trunk diameter, and canopy width) were estimated in 108 F1 hybrids. The genomic predicted genetic values (GEGV) were calculated by adding up the genotype effects of the three markers and the population mean phenotype. The GEGV of the dwarfing traits exhibited high correlation coefficients of 0.93, 0.94, and 0.93 in terms of tree height, trunk diameter, and canopy width for the observed phenotype values, respectively. The predictability of GEGV was validated in 64 Malus accessions. Conclusion: The development of the three functional markers, Ld/Li, Ad/Ai, and Gd/Gi, ensures the accurate genomic assisted prediction of dwarfing ability in apple rootstock breeding. The data also suggested that ABA, auxin, GA, and zeatin signals may be involved in the regulation of apple rootstock dwarfing mechanism.