A Common Copy Number Variation (CNV) Polymorphism in the CNTNAP4 Gene: Association with Aging in Females

Background

Aging is a biological process strongly determined by genetics. However, only a few single nucleotide polymorphisms (SNPs) have been reported to be consistently associated with aging. While investigating whether copy number variations (CNVs) could fill this gap, we focused on CNVs that have not been studied in previous SNP-based searches via tagging SNPs.

Methods

TaqMan qPCR assays were developed to quantify 20 common CNVs in 222 senior American Caucasians in order to reveal possible association with longevity. The replication study was comprised of 1283 community-dwelling senior European Caucasians. Replicated CNVs were further investigated for association with healthy aging and aging-related diseases, while association with longevity was additionally tested in Caenorhabditis elegans.

Results

In the discovery study of ≥80 vs.<80 years old seniors, a homozygous intronic CNV deletion in the CNTNAP4 gene was inversely associated with survival to the age of 80 (OR=0.51, 95%CI 0.29-0.87, p=0.015 before correction for multiple testing). After stratification by sex, association remained significant in females (OR=0.41, 95%CI 0.21-0.77, p=0.007), but not in males (OR=0.97, 95%CI 0.33-2.79, p=1). The finding was validated in a replication study (OR=0.66, 95%CI 0.48-0.90, p=0.011 for females). CNTNAP4 association with longevity was supported by a marked 25% lifespan change in C. elegans after knocking down the ortholog gene. An inverse association of the CNV del/del variant with female healthy aging was observed (OR=0.39, 95%CI 0.19-0.76, p=0.006). A corresponding positive association with aging-related diseases was revealed for cognitive impairment (OR=2.17, 95%CI 1.11-4.22, p=0.024) and, in independent studies, for Alzheimer’s (OR=4.07, 95%CI 1.17-14.14, p=0.036) and Parkinson’s (OR=1.59, 95%CI 1.03-2.42, p=0.041) diseases.

Conclusion

This is the first demonstration for association of the CNTNAP4 gene and one of its intronic CNV polymorphisms with aging. Association with particular aging-related diseases awaits replication and independent validation.     

Chemical synthesis of dolichyl phosphates, their analogues and derivatives and application of these compounds in biochemical assays

Several methods for simple and efficient chemical synthesis of dolichyl phosphates and their analogues and derivatives are briefly summarized with a special emphasis on chemical modification of phosphoryl group and preparation of dolichyl phosphates labelled at the omega-end and at the gamma-isoprene unit of the isoprene chain by fluorescent groups, 2-aminopyridine and 1-aminonaphtalene residues. Additionally, data on biochemical assays with application of the compounds mentioned above are presented.     

Uncoupling light quality from light irradiance effects in Helianthus annuus shoots: putative roles for plant hormones in leaf and internode growth

An attempt has been made to uncouple the effects of the two primary components of shade light, a reduced red to far-red (R/FR) ratio and low photosynthetically active radiation (PAR), on the elongation of the youngest internode of sunflower (Helianthus annuus) seedlings. Maximal internode growth (length and biomass) was induced by a shade light having a reduced R/FR ratio (0.85) under the low PAR of 157 micromol m(-2) s(-1). Reducing the R/FR ratio under normal PAR (421 micromol m(-2) s(-1)) gave similar growth trends, albeit with a reduced magnitude of the response. Leaf area growth showed a rather different pattern, with maximal growth occurring at the higher (normal) PAR of 421 micromol m(-2) s(-1)), but with variable effects being seen with changes in light quality. Reducing the R/FR ratio (by enrichment with FR) gave significant increases in gibberellin A(1) (GA(1)) and indole-3-acetic acid (IAA) contents in both internodes and leaves. By contrast, a lower PAR irradiance had no significant effect on GA(1) and IAA levels in internodes or leaves, but did increase the levels of other GAs, including two precursors of GA(1). Interestingly, both leaf and internode hormone content (GAs, IAA) are positively and significantly correlated with growth of the internode, as are leaf levels of abscisic acid (ABA). However, changes in these three hormones bear little relationship to leaf growth. By implication, then, the leaf may be the major source of GAs and IAA, at least, for the rapidly elongating internode. Several other hormones were also assessed in leaves for plants grown under varying R/FR ratios and PARs. Leaf ethylene production was not influenced by changes in R/FR ratio, but was significantly reduced under the normal (higher) PAR, the irradiance treatment which increased leaf growth. Levels of the growth-active free base and riboside cytokinins were significantly increased in leaves under a reduced R/FR ratio, but only at the higher (normal) PAR irradiance; other light quality treatments evoked no significant changes. Taken in toto, these results indicate that both components of shade light can influence the levels of a wide range of endogenous hormones in internodes and leaves while evoking increased internode elongation and biomass accumulation. However, it is light quality changes (FR enrichment) which are most closely tied to increased hormone content, and especially with increased GA and IAA levels. Finally, the increases seen in internode and leaf GA content with a reduced R/FR ratio are consistent with FR enrichment inducing an overall increase in sunflower seedling GA biosynthesis.     

The development of human sera tests for HDL-bound serum PON1 and its lipolactonase activity

Serum paraoxonase (PON1) is a lipolactonase that associates with HDL-apolipoprotein A-I (HDL-apoA-I) and thereby plays a role in the prevention of atherosclerosis. Current sera tests make use of promiscuous substrates and provide no indications regarding HDL-PON1 complex formation. We developed new enzymatic tests that detect total PON1 levels, irrespective of HDL status and R/Q polymorphism, as well as the degree of catalytic stimulation and increased stability that follow PON1's tight binding to HDL-apoA-I. The tests are based on measuring total PON1 levels with a fluorogenic phosphotriester, measuring the lipolactonase activity with a chromogenic lactone, and assaying the enzyme's chelator-mediated inactivation rate. The latter two are affected by tight HDL binding and thereby derive the levels of the serum PON1-HDL complex. We demonstrate these new tests with a group of healthy individuals (n=54) and show that the levels of PON1-HDL vary by a factor of 12. Whereas the traditionally applied paraoxonase and arylesterase tests weakly reflect PON1-HDL levels (R=0.64), the lipolactonase test provides better correlation (R=0.80). These new tests indicate the levels and activity of PON1 in a physiologically relevant context as well as the levels and quality of the HDL particles with which the enzyme is associated.     

Converting the prion protein: what makes the protein infectious

The discovery of prion disease transmission in mammals, as well as a non-Mendelian type of inheritance in yeast, has led to the establishment of a new concept in biology, the prion hypothesis. The prion hypothesis postulates that an abnormal protein conformation propagates itself in an autocatalytic manner via recruitment of the normal isoform of the same protein as a substrate, and thereby acts either as a transmissible agent of disease (in mammals) or as a heritable determinant of phenotype (in yeast and fungus). Although reconstitution of fully infectious PrP(Sc)in vitro from synthetic components has not yet been achieved, numerous lines of evidence indicate that the prion protein is the major and essential component, if not the only one, of the prion infectious agent. This article summarizes our current knowledge about the chemical nature of the prion infectious agent, describes potential strategies and challenges related to the generation of prion infectivity de novo, proposes new hypotheses to explain the apparently low infectivity observed in the first synthetic mammalian prions, and describes plausible effects of chemical modifications on prion conversion.     

Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking in two subsets of rheumatoid arthritis

Gene-gene and gene-environment interactions are key features in the development of rheumatoid arthritis (RA) and other complex diseases. The aim of this study was to use and compare three different definitions of interaction between the two major genetic risk factors of RA--the HLA-DRB1 shared epitope (SE) alleles and the PTPN22 R620W allele--in three large case-control studies: the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA) study, the North American RA Consortium (NARAC) study, and the Dutch Leiden Early Arthritis Clinic study (in total, 1,977 cases and 2,405 controls). The EIRA study was also used to analyze interactions between smoking and the two genes. "Interaction" was defined either as a departure from additivity, as interaction in a multiplicative model, or in terms of linkage disequilibrium--for example, deviation from independence of penetrance of two unlinked loci. Consistent interaction, defined as departure from additivity, between HLA-DRB1 SE alleles and the A allele of PTPN22 R620W was seen in all three studies regarding anti-CCP-positive RA. Testing for multiplicative interactions demonstrated an interaction between the two genes only when the three studies were pooled. The linkage disequilibrium approach indicated a gene-gene interaction in EIRA and NARAC, as well as in the pooled analysis. No interaction was seen between smoking and PTPN22 R620W. A new pattern of interactions is described between the two major known genetic risk factors and the major environmental risk factor concerning the risk of developing anti-CCP-positive RA. The data extend the basis for a pathogenetic hypothesis for RA involving genetic and environmental factors. The study also raises and illustrates principal questions concerning ways to define interactions in complex diseases.     

Direct evidence for specific interactions of the fibrinogen alphaC-domains with the central E region and with each other

The carboxyl-terminal regions of the fibrinogen Aalpha chains (alphaC regions) form compact alphaC-domains tethered to the bulk of the molecule with flexible alphaC-connectors. It was hypothesized that in fibrinogen two alphaC-domains interact intramolecularly with each other and with the central E region preferentially through its N-termini of Bbeta chains and that removal of fibrinopeptides A and B upon fibrin assembly results in dissociation of the alphaC regions and their switch to intermolecular interactions. To test this hypothesis, we studied the interactions of the recombinant alphaC region (Aalpha221-610 fragment) and its subfragments, alphaC-connector (Aalpha221-391) and alphaC-domain (Aalpha392-610), between each other and with the recombinant (Bbeta1-66)2 and (beta15-66)2 fragments and NDSK corresponding to the fibrin(ogen) central E region, using laser tweezers-based force spectroscopy. The alphaC-domain, but not the alphaC-connector, bound to NDSK, which contains fibrinopeptides A and B, and less frequently to desA-NDSK and (Bbeta1-66)2 containing only fibrinopeptides B; it was poorly reactive with desAB-NDSK and (beta15-66)2 both lacking fibrinopeptide B. The interactions of the alphaC-domains with each other and with the alphaC-connector were also observed, although they were weaker and heterogeneous in strength. These results provide the first direct evidence for the interaction between the alphaC-domains and the central E region through fibrinopeptide B, in agreement with the hypothesis given above, and indicate that fibrinopeptide A is also involved. They also confirm the hypothesized homomeric interactions between the alphaC-domains and display their interaction with the alphaC-connectors, which may contribute to covalent cross-linking of alpha polymers in fibrin.     

Intrinsic fluctuations, robustness, and tunability in signaling cycles

Covalent modification cycles (e.g., phosphorylation-dephosphorylation) underlie most cellular signaling and control processes. Low molecular copy number, arising from compartmental segregation and slow diffusion between compartments, potentially renders these cycles vulnerable to intrinsic chemical fluctuations. How can a cell operate reliably in the presence of this inherent stochasticity? How do changes in extrinsic parameters lead to variability of response? Can cells exploit these parameters to tune cycles to different ranges of stimuli? We study the dynamics of an isolated phosphorylation cycle. Our model shows that the cycle transmits information reliably if it is tuned to an optimal parameter range, despite intrinsic fluctuations and even for small input signal amplitudes. At the same time, the cycle is sensitive to changes in the concentration and activity of kinases and phosphatases. This sensitivity can lead to significant cell-to-cell response variability. It also provides a mechanism to tune the cycle to transmit signals in various amplitude ranges. Our results show that signaling cycles possess a surprising combination of robustness and tunability. This combination makes them ubiquitous in eukaryotic signaling, optimizing signaling in the presence of fluctuations using their inherent flexibility. On the other hand, cycles tuned to suppress intrinsic fluctuations can be vulnerable to changes in the number and activity of kinases and phosphatases. Such trade-offs in robustness to intrinsic and extrinsic fluctuations can influence the evolution of signaling cascades, making them the weakest links in cellular circuits.     

E-wave deceleration time may not provide an accurate determination of LV chamber stiffness if LV relaxation/viscoelasticity is unknown

Average left ventricular (LV) chamber stiffness (Delta P(avg)/Delta V(avg)) is an important diastolic function index. An E-wave-based determination of Delta P(avg)/Delta V(avg) (Little WC, Ohno M, Kitzman DW, Thomas JD, Cheng CP. Circulation 92: 1933-1939, 1995) predicted that deceleration time (DT) determines stiffness as follows: Delta P(avg)/Delta V(avg) = N(pi/DT)(2) (where N is constant), which implies that if the DTs of two LVs are indistinguishable, their stiffness is indistinguishable as well. We observed that LVs with indistinguishable DTs may have markedly different Delta P(avg)/Delta V(avg) values determined by simultaneous echocardiography-catheterization. To elucidate the mechanism by which LVs with indistinguishable DTs manifest distinguishable chamber stiffness, we use a validated, kinematic E-wave model (Kovács SJ, Barzilai B, Perez JE. Am J Physiol Heart Circ Physiol 252: H178-H187, 1987) with stiffness (k) and relaxation/viscoelasticity (c) parameters. Because the predicted linear relation between k and Delta P(avg)/Delta V(avg) has been validated, we reexpress the DT-stiffness (Delta P(avg)/Delta V(avg)) relation of Little et al. as follows: DT(k) approximately pi/(2k). Using the kinematic model, we derive the general DT-chamber stiffness/viscoelasticity relation as follows: DT(k,c) = pi/(2skrt[k])+c/(2k)(where c and k are determined directly from the E-wave), which reduces to DT(k) when c < k. Validation involved analysis of 400 E-waves by determination of five-beat averaged k and c from 80 subjects undergoing simultaneous echocardiography-catheterization. Clinical E-wave DTs were compared with model-predicted DT(k) and DT(k,c). Clinical DT was better predicted by stiffness and relaxation/viscoelasticity (r(2) = 0.84, DT vs. DT(k,c)) jointly rather than by stiffness alone (r(2) = 0.60, DT vs. DT(k)). Thus LVs can have indistinguishable DTs but significantly different Delta P(avg)/Delta V(avg) if chamber relaxation/viscoelasticity differs. We conclude that DT is a function of both chamber stiffness and chamber relaxation viscoelasticity. Quantitative diastolic function assessment warrants consideration of simultaneous stiffness and relaxation/viscoelastic effects.