Epigenetic and genetic burden measures are associated with tumor characteristics in invasive breast carcinoma

The development and progression of invasive breast cancer is characterized by alterations to the genome and epigenome. However, the relationship between breast tumor characteristics, disease subtypes, and patient outcomes with the cumulative burden of these molecular alterations are not well characterized. We determined the average departure of tumor DNA methylation from adjacent normal breast DNA methylation using Illumina 450K methylation data from 700 invasive breast tumors and 90 adjacent normal breast tissues in The Cancer Genome Atlas. From this we generated a novel summary measure of altered DNA methylation, the DNA methylation dysregulation index (MDI), and examined the relation of MDI with tumor characteristics and summary measures that quantify cumulative burden of genetic mutation and copy number alterations. Our analysis revealed that MDI was significantly associated with tumor stage (P = 0.017). Across invasive breast tumor subtypes we observed significant differences in genome-wide DNA MDIs (P = 4.9E–09) and in a fraction of the genome with copy number alterations (FGA) (P = 4.6E–03). Results from a linear regression adjusted for subject age, tumor stage, and estimated tumor purity indicated a positive significant association of MDI with both MCB and FGA (P = 0.036 and P < 2.2E–16). A recursively partitioned mixture model of all 3 somatic alteration burden measures resulted in classes of tumors whose epigenetic and genetic burden profile were associated with the PAM50 subtype and mutations in TP53, PIK3CA, and CDH1. Together, our work presents a novel framework for characterizing the epigenetic burden and adds to the understanding of the aggregate impact of epigenetic and genetic alterations in breast cancer.     

Amiloride-sensitive NaCl taste responses are associated with genetic variation of ENaC alpha-subunit in mice

An epithelial Na(+) channel (ENaC) is expressed in taste cells and may be involved in the salt taste transduction. ENaC activity is blocked by amiloride, which in several mammalian species also inhibits taste responses to NaCl. In mice, lingual application of amiloride inhibits NaCl responses in the chorda tympani (CT) gustatory nerve much stronger in the C57BL/6 (B6) strain than in the 129P3/J (129) strain. We examined whether this strain difference is related to gene sequence variation or mRNA expression of three ENaC subunits (alpha, beta, gamma). Real-time RT-PCR and in situ hybridization detected no significant strain differences in expression of all three ENaC subunits in fungiform papillae. Sequences of the beta- and gammaENaC subunit genes were also similar in the B6 and 129 strains, but alphaENaC gene had three single nucleotide polymorphisms (SNPs). One of these SNPs resulted in a substitution of arginine in the B6 strain to tryptophan in the 129 strain (R616W) in the alphaENaC protein. To examine association of this SNP with amiloride sensitivity of CT responses to NaCl, we produced F(2) hybrids between B6 and 129 strains. Amiloride inhibited CT responses to NaCl in F(2) hybrids with B6/129 and B6/B6 alphaENaC R616W genotypes stronger than in F(2) hybrids with 129/129 genotype. This suggests that the R616W variation in the alphaENaC subunit affects amiloride sensitivity of the ENaC channel and provides evidence that ENaC is involved in amiloride-sensitive salt taste responses in mice.     

Interferon regulatory factor 5 genetic variants are associated with cardiovascular disease in patients with rheumatoid arthritis

Introduction

Rheumatoid arthritis (RA) is a complex polygenic inflammatory disease associated with accelerated atherosclerosis and increased cardiovascular (CV) disease risk. Interferon regulatory factor 5 (IRF5) is a regulator of type I interferon induction. Recently, researchers have described an association between multiple single-nucleotide polymorphisms of the IRF5 gene and some rheumatic disorders. In this study, we aimed to evaluate whether three different haplotype blocks within the IRF5 locus which have been shown to alter the protein function are involved in the risk of CV events occurring in Spanish RA patients.

Methods

Three IRF5 polymorphisms (rs2004640, rs2070197 and rs10954213) representative of each haplotype group were genotyped by performing TaqMan assays using a 7900HT Fast Real-Time PCR System with tissue from a total of 2,137 Spanish patients diagnosed with RA. Among them, 390 (18.2%) had experienced CV events. The relationship of IRF5 genotypes and haplotypes to CV events was tested using Cox regression.

Results

Male sex, age at RA diagnosis and most traditional risk factors (hypertension, dyslipidemia and smoking habit) were associated with increased risk for CV events in the RA population. Interestingly, a protective effect of both IRF5 rs2004640 GG and IRF5 rs10954213 GG genotypes against the risk for CV events after adjusting the results for sex, age at RA diagnosis and traditional CV disease risk factors was observed (hazard ratio (HR) = 0.6, 95% confidence interval (CI) = 0.38 to 0.92, P = 0.02; and HR = 0.58, 95% CI = 0.36 to 0.95, P = 0.03, respectively). Moreover, we detected a protective effect of the GTG haplotype against the risk for CV events after adjusting the results for potential confounding factors (HR = 0.72, 95% CI = 0.56 to 0.93, P = 0.012).

Conclusions

Our results reveal that IRF5 gene variants are associated with risk of CV events in patients with RA.     

Common genetic variants are associated with accelerated bone mineral density loss after hematopoietic cell transplantation

Background

Bone mineral density (BMD) loss commonly occurs after hematopoietic cell transplantation (HCT). Hypothesizing that genetic variants may influence post-HCT BMD loss, we conducted a prospective study to examine the associations of single nucleotide polymorphisms (SNP) in bone metabolism pathways and acute BMD loss after HCT.

Methods and Findings

We genotyped 122 SNPs in 45 genes in bone metabolism pathways among 121 autologous and allogeneic HCT patients. BMD changes from pre-HCT to day +100 post-HCT were analyzed in relation to these SNPs in linear regression models. After controlling for clinical risk factors, we identified 16 SNPs associated with spinal or femoral BMD loss following HCT, three of which have been previously implicated in genome-wide association studies of bone phenotypes, including rs2075555 in COL1A1, rs9594738 in RANKL, and rs4870044 in ESR1. When multiple SNPs were considered simultaneously, they explained 5–35% of the variance in post-HCT BMD loss. There was a significant trend between the number of risk alleles and the magnitude of BMD loss, with patients carrying the most risk alleles having the greatest loss.

Conclusion

Our data provide the first evidence that common genetic variants play an important role in BMD loss among HCT patients similar to age-related BMD loss in the general population. This infers that the mechanism for post-HCT bone loss is a normal aging process that is accelerated during HCT. A limitation of our study comes from its small patient population; hence future larger studies are warranted to validate our findings.     

Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 ×10⁻⁷), hip circumference (p = 3.4 × 10⁻⁸), and weight (p = 9.1 × 10⁻⁷). In Sardinia, homozygotes for the rare “G” allele of this SNP (minor allele frequency = 0.46) were 1.3 BMI units heavier than homozygotes for the common “A” allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 × 10⁻⁶). Homozygotes for the rare “A” allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common “G” allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496) and in Hispanic Americans (N = 839), we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare “A” allele were, on average, 1.0–3.0 BMI units heavier than homozygotes for the more common “G” allele. In summary, we have completed a whole genome–association scan for three obesity-related quantitative traits and report that common genetic variants in the FTO gene are associated with substantial changes in BMI, hip circumference, and body weight. These changes could have a significant impact on the risk of obesity-related morbidity in the general population.     

Common genetic variations in the NALP3 inflammasome are associated with delayed apoptosis of human neutrophils

Background

Neutrophils are key-players in the innate host defense and their programmed cell death and removal are essential for efficient resolution of inflammation. These cells recognize a variety of pathogens, and the NOD-like receptors (NLRs) have been suggested as intracellular sensors of microbial components and cell injury/stress. Some NLR will upon activation form multi-protein complexes termed inflammasomes that result in IL-1β production. NLR mutations are associated with auto-inflammatory syndromes, and our previous data propose NLRP3 (Q705K)/CARD-8 (C10X) polymorphisms to contribute to increased risk and severity of inflammatory disease by acting as genetic susceptibility factors. These gene products are components of the NALP3 inflammasome, and approximately 6.5% of the Swedish population are heterozygote carriers of these combined gene variants. Since patients carrying the Q705K/C10X polymorphisms display leukocytosis, the aim of the present study was to find out whether the inflammatory phenotype was related to dysfunctional apoptosis and impaired clearance of neutrophils by macrophages.

Methods and Findings

Patients carrying the Q705K/C10X polymorphisms displayed significantly delayed spontaneous as well as microbe-induced apoptosis compared to matched controls. Western blotting revealed increased levels and phosphorylation of Akt and Mcl-1 in the patients'' neutrophils. In contrast to macrophages from healthy controls, macrophages from the patients produced lower amounts of TNF; suggesting impaired macrophage clearance response.

Conclusions

The Q705K/C10X polymorphisms are associated with delayed apoptosis of neutrophils. These findings are explained by altered involvement of different regulators of apoptosis, resulting in an anti-apoptotic profile. Moreover, the macrophage response to ingestion of microbe-induced apoptotic neutrophils is altered in the patients. Taken together, the patients display impaired turnover and clearance of apoptotic neutrophils, pointing towards a dysregulated innate immune response that influences the resolution of inflammation. The future challenge is to understand how microbes affect the activation of inflammasomes, and why this interaction will develop into severe inflammatory disease in certain individuals.     

Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders

With the availability of a large amount of genomic data it is expected that the influence of single nucleotide variations (SNVs) in many biological phenomena will be elucidated. Here, we approached the problem of how SNVs affect alternative splicing. First, we observed that SNVs and exonic splicing regulators (ESRs) independently show a biased distribution in alternative exons. More importantly, SNVs map more frequently in ESRs located in alternative exons than in ESRs located in constitutive exons. By looking at SNVs associated with alternative exon/intron borders (by their common presence in the same cDNA molecule), we observed that a specific type of ESR, the exonic splicing silencers (ESSs), are more frequently modified by SNVs. Our results establish a clear association between genetic diversity and alternative splicing involving ESSs.     

Fitness costs associated with low genetic variation are reduced in a harsher environment in amphibian island populations

A basic premise of conservation geneticists is that low levels of genetic variation are associated with fitness costs in terms of reduced survival and fecundity. These fitness costs may frequently vary with environmental factors and should increase under more stressful conditions. However, there is no consensus on how fitness costs associated with low genetic variation change under natural conditions in relation to the stressfulness of the environment. On the Swedish west coast, natterjack toad Bufo calamita populations show a strong population genetic structure and large variation in the amount of within-population genetic variation. We experimentally examined the survival of natterjack larvae from six populations with different genetic variation in three thermal environments corresponding to (a) the mean temperature of natural ponds (stable, laboratory), (b) a high temperature environment occurring in desiccating ponds (stable, laboratory) and (c) an outdoor treatment mimicking the natural, variable thermal conditions (fluctuating, semi-natural). We found that larvae in the outdoor treatment had poorer survival than larvae in the stable environments suggesting that the outdoor treatment was more stressful. Overall, populations with higher genetic variation had higher larval survival. However, a significant interaction between treatments and genetic variation indicated that fitness costs associated with low genetic variation were less severe in the outdoor treatment. Thus, we found no support for the hypothesis that fitness costs associated with low genetic variation increase under more stressful conditions. Our results suggest that natural thermal stress may mask fitness losses associated with low genetic variation in these populations.     

Mitochondrial NADH:ubiquinone oxidoreductase alterations are associated with endometriosis

Genetic alterations and aberrant expression of ‘mitochondrial membrane complex I’ (MMC-I) underlie several complex human disorders, but no reports are documented to date in endometriosis. Sequencing of mitochondrially encoded MMC-I subunits revealed 72 mutations of which 2 missense (G10398A; A13603A/G) mutations and 1 synonymous (T10400C) mutation showed higher prevalence in patients. In silico functional analysis predicted A13603A/G, a novel heteroplasmy as a ‘damaging variant’. Our results indicate higher endometriosis risk for haplotype ‘10398A/10400C/13603AG’ and haplogroup ‘N’. Immunohistochemical analysis revealed elevated MMC-I expression in eutopic endometria of patients compared to controls. In conclusion, MMC-I alterations may constitute an inheritable risk factor for endometriosis.     

Identification of genetic variants in TNF receptor 2 which are associated with the development of cervical carcinoma

Cervical cancer is one of the most common malignancies among women in India. Beside HPV, other factors present in host also put their role in the progression of cervical tumerogenesis. In present study, we screened 300 subjects to identify variations in TNFR2 gene by PCR-dHPLC method followed by direct sequencing. We identified six known and four novel variations in six different exons of TNFR2 gene. Out of these identified variations, five known variations were found to be significantly associated with the risk of cervical cancer (p?<?0.0001). On construction of haplotypes, one haplotype (TTGCC) was emerged as a major protective type while two (CAAGC?+?CTGCC) were revealed as major risk haplotypes. In conclusion, postmenopausal women having CAAGC?+?CTGCC haplotypes in TNFR2 gene along with HPV infection and tobacco consumption may lead to the development of cervical cancer.     

Somatic point mutations in mtDNA control region are influenced by genetic background and associated with healthy aging: a GEHA study

Tissue specific somatic mutations occurring in the mtDNA control region have been proposed to provide a survival advantage. Data on twins and on relatives of long-lived subjects suggested that the occurrence/accumulation of these mutations may be genetically influenced. To further investigate control region somatic heteroplasmy in the elderly, we analyzed the segment surrounding the nt 150 position (previously reported as specific of Leukocytes) in various types of leukocytes obtained from 195 ultra-nonagenarians sib-pairs of Italian or Finnish origin collected in the frame of the GEHA Project. We found a significant correlation of the mtDNA control region heteroplasmy between sibs, confirming a genetic influence on this phenomenon. Furthermore, many subjects showed heteroplasmy due to mutations different from the C150T transition. In these cases heteroplasmy was correlated within sibpairs in Finnish and northern Italian samples, but not in southern Italians. This suggested that the genetic contribution to control region mutations may be population specific. Finally, we observed a possible correlation between heteroplasmy and Hand Grip strength, one of the best markers of physical performance and of mortality risk in the elderly. Our study provides new evidence on the relevance of mtDNA somatic mutations in aging and longevity and confirms that the occurrence of specific point mutations in the mtDNA control region may represent a strategy for the age-related remodelling of organismal functions.     

Self-organization and emergence are some irrelevant concepts without their association with the concepts of hetero-organization and immergence

There are many reasons for questioning the relevance of the concepts of self-organization (SO) and emergence. By studying three types of SO, respectively related to ontogeny, phylogeny and formalized models, we show that we always have to suppose an associated hetero-organization and preconceived immergence, unconsciously present in the authors mind. In order to understand how these unusual couples are working, they must be considered as agonistic antagonistic couples. Heteroorganization and immergence put constraints on the system so that SO and emergence will produce new patterns and forms, depending on these constraints. Besides, such couples (SO and heteroorganization, emergence and immergence) seem to belong to a series of couples of the same type, allowing us to define a kind of model of life.The concept of self-organization has been presented as the main concept defining systemics, and second order cybernetics. This concept has been accepted also in general Biological Theory (BT) where authors endowed the key to many phenomena until then poorly understood.Nevertheless, we question the validity of this concept, or more precisely point out that the concept contains non explicit elements which were neglected. We propose a frame in which this concept-and the associated concept of emergence-remains available, but can no longer claim to give an account for the features they are said to explain by themselves alone.     

When enough is enough: genetic diseases associated with transcriptional derepression

For many human genetic diseases, the underlying genetic defect has been determined. Thus, although traditionally a field only for researchers in medicine or human genetics, human diseases are now opening up to molecular biologists, cell biologists and biochemists. Here we discuss four human genetic disorders, Familial Alzheimer's disease, Rett syndrome, Klippel-Trenaunay syndrome and Facioscapulohumeral muscular dystrophy, and how investigations into these diseases are providing important lessons about human biology.     

Shell mats associated with microsporida in Biomphalaria glabrata: genetic studies

Multilayered mats have been observed lining the shell of some Biomphalaria glabrata infected with Steinhausia brachynema. Occurrence of the mats is associated with extensive infection with the microsporidia in these snails, in contrast to most B. glabrata in which infection appears restricted to the intestinal wall. Observations suggest that this variation in pathology may be influenced by a genetic difference in the host snails.     

CYP17 and CYP19 genetic variants are not associated with age at natural menopause in Polish women

The aim of the study was to investigate associations between two common polymorphisms of CYP17 and CYP19, encoding key enzymes of estrogen biosynthesis, and age at menopause in Polish women. One hundred fifty women after menopause (49.5 ± 3.8 years), with no previous history of hormone replacement therapy took part in the study. The genetic control group consisted of 150 newborns from the same population. We investigated an association between the age at menopause and the single nucleotide polymorphism T → C in the 5′ untranslated region (promoter) of the CYP17 gene (c.-34T>C; rs743572 – MspA1) or the number of tetranucleotide repeats [TTTA]_n (rs60271534) including deletion/insertion (D/I) of a 3 bp sequence in intron 4 of the CYP19 gene. CYP17 polymorphism was analyzed by PCR-RFLP and CYP19 by PCR and capillary electrophoresis. In the case of CYP17 polymorphism, 28.7% and 36.7% wild homozygous (TT), 50.7% and 46.0% heterozygous (TC), as well as 20.6% and 17.3% mutated homozygous (CC) types were identified in the subjects and controls, respectively. The frequency of mutated alleles (C) was 46.0% vs. 40.3% (p = 0.19). In the case of CYP19 polymorphism, 34.0% and 32.0% of homozygotes (1_1), 50.7% and 51.3% of heterozygotes (1_2), 15.3% and 16.7% of homozygotes (2_2) were identified in the subjects and controls, respectively. No association between the studied CYP17 or CYP19 polymorphisms and age at menopause was found in Polish women.     

Exogenous visual orienting is associated with specific neurotransmitter genetic markers: a population-based genetic association study

Background

Currently, there is a sense that the spatial orienting of attention is related to genotypic variations in cholinergic genes but not to variations in dopaminergic genes. However, reexamination of associations with both cholinergic and dopaminergic genes is warranted because previous studies used endogenous rather than exogenous cues and costs and benefits were not analyzed separately. Examining costs (increases in response time following an invalid pre-cue) and benefits (decreases in response time following a valid pre-cue) separately could be important if dopaminergic genes (implicated in disorders such as attention deficit disorder) independently influence the different processes of orienting (e.g., disengage, move, engage).

Methodology/Principal Findings

We tested normal subjects (N = 161) between 18 and 61 years. Participants completed a computer task in which pre-cues preceded the presence of a target. Subjects responded (with a key press) to the location of the target (right versus left of fixation). The cues could be valid (i.e., appear where the target would appear) or invalid (appear contralateral to where the target would appear). DNA sequencing assays were performed on buccal cells to genotype known genetic markers and these were examined for association with task scores. Here we show significant associations between visual orienting and genetic markers (on COMT, DAT1, and APOE; R²s from 4% to 9%).

Conclusions/Significance

One measure in particular – the response time cost of a single dim, invalid cue – was associated with dopaminergic markers on COMT and DAT1. Additionally, variations of APOE genotypes based on the ε2/ε3/ε4 alleles were also associated with response time differences produced by simultaneous cues with unequal luminances. We conclude that individual differences in visual orienting are related to several dopaminergic markers as well as to a cholinergic marker. These results challenge the view that orienting is not associated with genotypic variation in dopaminergic genes.