17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression.

To assess the role of rare copy number variations in Alzheimer's disease (AD), we conducted a case-control study using whole-exome sequencing data from 522 early-onset cases and 584 controls. The most recurrent rearrangement was a 17q21.31 microduplication, overlapping the CRHR1, MAPT, STH and KANSL1 genes that was found in four cases, including one de novo rearrangement, and was absent in controls. The increased MAPT gene dosage led to a 1.6-1.9-fold expression of the MAPT messenger RNA. Clinical signs, neuroimaging and cerebrospinal fluid biomarker profiles were consistent with an AD diagnosis in MAPT duplication carriers. However, amyloid positon emission tomography (PET) imaging, performed in three patients, was negative. Analysis of an additional case with neuropathological examination confirmed that the MAPT duplication causes a complex tauopathy, including prominent neurofibrillary tangle pathology in the medial temporal lobe without amyloid-ß deposits. 17q21.31 duplication is the genetic basis of a novel entity marked by prominent tauopathy, leading to early-onset dementia with an AD clinical phenotype. This entity could account for a proportion of probable AD cases with negative amyloid PET imaging recently identified in large clinical series.

SORL1 rare variants: a major risk factor for familial early-onset Alzheimer's disease.

The SORL1 protein plays a protective role against the secretion of the amyloid ß peptide, a key event in the pathogeny of Alzheimer's disease. We assessed the impact of SORL1 rare variants in early-onset Alzheimer's disease (EOAD) in a case-control setting. We conducted a whole exome analysis among 484 French EOAD patients and 498 ethnically matched controls. After collapsing rare variants (minor allele frequency ≤1%), we detected an enrichment of disruptive and predicted damaging missense SORL1 variants in cases (odds radio (OR)=5.03, 95% confidence interval (CI)=(2.02-14.99), P=7.49.10(-5)). This enrichment was even stronger when restricting the analysis to the 205 cases with a positive family history (OR=8.86, 95% CI=(3.35-27.31), P=3.82.10(-7)). We conclude that predicted damaging rare SORL1 variants are a strong risk factor for EOAD and that the association signal is mainly driven by cases with positive family history.

HLA-A*31:01 and different types of carbamazepine-induced severe cutaneous adverse reactions: an international study and meta-analysis.

HLA-A*31:01 was reported to be associated with carbamazepine (CBZ)-induced severe cutaneous adverse reactions (SCAR), including drug reaction with eosinophilia and systemic symptoms (DRESS), Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). We conducted an international study using consensus diagnosis criteria to enroll a total of 93 patients with CBZ-SCAR from Europe or Asia. We found that HLA-A*31:01 showed a significant association with CBZ-DRESS in Europeans (P<0.001; odds ratio (OR) (95% confidence interval (CI))=57.6 (11.0-340)), and the strong association was also found in Chinese (P<0.001; OR (95% CI)=23.0 (4.2-125)). However, HLA-A*31:01 had no association with CBZ-SJS/TEN in neither Chinese nor Europeans. By comparison, HLA-B*15:02 showed a strong association with CBZ-SJS/TEN in Chinese (P<0.001, OR (95% CI)=58.1 (17.6-192)). A meta-analysis of this and other published studies confirmed that in all populations, HLA-A*31:01 had an extremely strong association with CBZ-DRESS (P<0.001, a pooled OR (95% CI)=13.2 (8.4-20.8)), but a much weaker association with CBZ-SJS/TEN (P=0.01, OR (95% CI)=3.94 (1.4-11.5)). Our data revealed that HLA-A*31:01 is a specific predictor for CBZ-DRESS but not for CBZ-SJS/TEN. More studies are needed to investigate the genetic determinant of CBZ-SJS/TEN in Europeans. Considering the potential clinical utility, the cost-effectiveness of the combined HLA-A*31:01 and HLA-B*15:02 genetic test to prevent CBZ-SCAR in Chinese needs further investigation.

A homogenizing process of selection has maintained an "ultra-slow" acetylation NAT2 variant in humans.

N-Acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity, which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of whole-genome sequence data available from the 1000 Genomes project to investigate the global patterns of population genetic differentiation at NAT2 and determine whether they are atypical compared with the remaining variation of the genome. The nonsynonymous substitution c.590G>A (rs1799930) defining the slow NAT2*6 haplotype cluster exhibited an unusually low FST value compared with the genome average (FST = 0.006, P = 0.016). It was indicated as the most likely target of a homogenizing process of selection promoting the same allelic variant in globally distributed populations. The rs1799930 A allele has been associated with the slowest acetylation capacity in vivo, and its substantial correlation with the subsistence strategy adopted by past human populations suggests that it may have conferred a selective advantage in populations shifting from foraging to agricultural and pastoral activities in the Neolithic period. Results of neutrality tests further supported an adaptive evolution of the NAT2 gene through either balancing selection or directional selection acting on multiple standing slow acetylation variants.

Sub-nanoradiant beam pointing monitoring and stabilization system for controlling input beam jitter in gravitational wave interferometers.

In this paper, a simple and effective control system to monitor and suppress the beam jitter noise at the input of an optical system, called a beam pointing control (BPC) system, will be described, showing the theoretical principle and an experimental demonstration for the application of large-scale gravitational wave (GW) interferometers (ITFs), in particular for the Advanced Virgo detector. For this purpose, the requirements for the control accuracy and the sensing noise will be computed by taking into account the Advanced Virgo optical configuration, and the outcomes will be compared with the experimental measurement obtained in the laboratory. The system has shown unprecedented performance in terms of control accuracy and sensing noise. The BPC system has achieved a control accuracy of ~10⁻8 rad for the tilt and ~10⁻7 m for the shift and a sensing noise of less than 1 n rad/√Hz, which is compliant with the Advanced Virgo GW ITF requirements.

Displacement noise from back scattering and specular reflection of input optics in advanced gravitational wave detectors.

The second generation of ground-based interferometric gravitational wave detectors are currently being built and installed. They are designed to be better in strain sensitivity by about a factor 10 with respect to the first generation. Light originating from the laser and following unintended paths, called stray light, has been a major problem during the commissioning of all of the first generation detectors. Indeed, stray light carries information about the phase of the emitting object. Therefore, in the next generation all the optics will be suspended in the vacuum in order to mitigate their associated stray light displacement noise. Despite this additional precaution, the challenging target sensitivity at low frequency which is partially limited by quantum radiation pressure combined with up-conversion effects, requires more detailed investigation. In this paper, we turn our attention to stray light originating from auxiliary optical benches. We use a dedicated formalism to compute the re-coupling of back-reflected and back-scattered light. We show, in particular, how much care should be taken in designing and setting requirements for the input bench optics.

APOE and Alzheimer disease: a major gene with semi-dominant inheritance.

Apolipoprotein E (APOE) dependent lifetime risks (LTRs) for Alzheimer Disease (AD) are currently not accurately known and odds ratios alone are insufficient to assess these risks. We calculated AD LTR in 7351 cases and 10 132 controls from Caucasian ancestry using Rochester (USA) incidence data. At the age of 85 the LTR of AD without reference to APOE genotype was 11% in males and 14% in females. At the same age, this risk ranged from 51% for APOE44 male carriers to 60% for APOE44 female carriers, and from 23% for APOE34 male carriers to 30% for APOE34 female carriers, consistent with semi-dominant inheritance of a moderately penetrant gene. Using PAQUID (France) incidence data, estimates were globally similar except that at age 85 the LTRs reached 68 and 35% for APOE 44 and APOE 34 female carriers, respectively. These risks are more similar to those of major genes in Mendelian diseases, such as BRCA1 in breast cancer, than those of low-risk common alleles identified by recent GWAS in complex diseases. In addition, stratification of our data by age groups clearly demonstrates that APOE4 is a risk factor not only for late-onset but for early-onset AD as well. Together, these results urge a reappraisal of the impact of APOE in Alzheimer disease.

The very low penetrance of cystic fibrosis for the R117H mutation: a reappraisal for genetic counselling and newborn screening.

BACKGROUND: Cystic fibrosis (CF) is caused by compound heterozygosity or homozygosity of CF transmembrane conductance regulator gene (CFTR) mutations. Phenotypic variability associated with certain mutations makes genetic counselling difficult, notably for R117H, whose disease phenotype varies from asymptomatic to classical CF. The high frequency of R117H observed in CF newborn screening has also introduced diagnostic dilemmas. The aim of this study was to evaluate the disease penetrance for R117H in order to improve clinical practice. METHODS: The phenotypes in all individuals identified in France as compound heterozygous for R117H and F508del, the most frequent CF mutation, were described. The allelic prevalences of R117H (p(R117H)), on either intron 8 T5 or T7 background, and F508del (p(F508del)) were determined in the French population, to permit an evaluation of the penetrance of CF for the [R117H]+[F508del] genotype. RESULTS: Clinical details were documented for 184 [R117H]+[F508del] individuals, including 72 newborns. The disease phenotype was predominantly mild; one child had classical CF, and three adults' severe pulmonary symptoms. In 5245 healthy adults, p(F508del) was 1.06%, p(R117H;T7) 0.27% and p(R117H;T5)<0.01%. The theoretical number of [R117H;T7]+[F508del] individuals in the French population was estimated at 3650, whereas only 112 were known with CF related symptoms (3.1%). The penetrance of classical CF for [R117H;T7]+[F508del] was estimated at 0.03% and that of severe CF in adulthood at 0.06%. CONCLUSIONS: These results suggest that R117H should be withdrawn from CF mutation panels used for screening programmes. The real impact of so-called disease mutations should be assessed before including them in newborn or preconceptional carrier screening programmes.

Rapid progression to AIDS in HIV+ individuals with a structural variant of the chemokine receptor CX3CR1.

Human immunodeficiency virus (HIV) enters cells in vitro via CD4 and a coreceptor. Which of 15 known coreceptors are important in vivo is poorly defined but may be inferred from disease-modifying mutations, as for CCR5. Here two single nucleotide polymorphisms are described in Caucasians in CX3CR1, an HIV coreceptor and leukocyte chemotactic/adhesion receptor for the chemokine fractalkine. HIV-infected patients homozygous for CX3CR1-I249 M280, a variant haplotype affecting two amino acids (isoleucine-249 and methionine-280), progressed to AIDS more rapidly than those with other haplotypes. Functional CX3CR1 analysis showed that fractalkine binding is reduced among patients homozygous for this particular haplotype. Thus, CX3CR1-I249 M280 is a recessive genetic risk factor in HIV/AIDS.

Functionalisation of TiO2 nanoparticles with a fluorescent organosilane: A synergy enabling their visualisation in biological cells and an enhanced photocatalytic activity.

Nanoparticles, such as TiO2 particles, have a great potential for biomedical applications due to their ultra-small size and large specific surface area. However, their detection within cells is to date more than challenging. Thus, implementing fluorescence properties to nanoparticles via their controlled functionalisation with an organic chromophore is an original and efficient strategy to enable their visualization. In this work, a silylated coupling agent bearing a luminescent rhodamine B group was synthesised and grafted on the surface of anatase nanoparticles. The successful functionalisation was demonstrated via zeta potential, dynamic light scattering and diffuse reflectance infrared Fourier transform analyses. Remarkably, the obtained luminescent TiO2 particles showed an improved photocatalytic activity compared to the pristine nanoparticles. Both, as-synthesised and functionalised TiO2 nanoparticles samples appear to be non-toxic towards malignant and non-malignant cells. Moreover, the detection of the functionalised particles within cultured cells was proven to be easy and efficient via confocal fluorescence microscopy.

HLA-DRB1*15 allele influences the later course of relapsing remitting multiple sclerosis.

Most of the published works so far have aimed at finding genes associated with multiple sclerosis (MS) susceptibility. Very few studies have attempted to correlate disease features with DNA variants. In a well-characterized sample (651 patients) representative of multiple sclerosis natural history, we engaged a comprehensive study of the role of human leukocyte antigen (HLA) in the course of the disease. We investigated the role of HLA-DRB1*15 allele in samples stratified according to severity evaluated by the Multiple Sclerosis Severity Score (MSSS), time to reach EDSS 6.0 and disease type. We found that HLA-DRB1*15 genotype does not influence MS severity even among patients presenting with a given type of the disease. However, we show for the first time that HLA-DRB1*15 allele modulates the course of MS for relapsing-remitting (RR) onset patients likely by precipitating the secondary progressive (SP) phase.

Molecular basis of variant pseudo-hurler polydystrophy (mucolipidosis IIIC)

Mucolipidosis IIIC, or variant pseudo-Hurler polydystrophy, is an autosomal recessive disease of lysosomal hydrolase trafficking. Unlike the related diseases, mucolipidosis II and IIIA, the enzyme affected in mucolipidosis IIIC (N-Acetylglucosamine-1-phosphotransferase [GlcNAc-phosphotransferase]) retains full transferase activity on synthetic substrates but lacks activity on lysosomal hydrolases. Bovine GlcNAc-phosphotransferase has recently been isolated as a multisubunit enzyme with the subunit structure alpha(2)beta(2)gamma(2). We cloned the cDNA for the human gamma-subunit and localized its gene to chromosome 16p. We also showed, in a large multiplex Druze family that exhibits this disorder, that MLIIIC also maps to this chromosomal region. Sequence analysis of the gamma-subunit cDNA in patients from 3 families identified a frameshift mutation, in codon 167 of the gamma subunit, that segregated with the disease, indicating MLIIIC results from mutations in the phosphotransferase gamma-subunit gene. This is to our knowledge the first description of the molecular basis for a human mucolipidosis and suggests that the gamma subunit functions in lysosomal hydrolase recognition.

Exclusion of the adrenocorticotropin (ACTH) receptor (MC2R) locus in some families with ACTH resistance but no mutations of the MC2R coding sequence (familial glucocorticoid deficiency type 2).

Several mutations in the coding exon of the ACTH receptor (MC2R) gene have been reported in cases of familial glucocorticoid deficiency or FGD. However, many patients with a similar syndrome do not present any mutation in the coding region of this gene. This is the case in 11 families we have investigated. Patients in these families present the typical clinical features of FGD, but no mutation was found in the coding exon of the ACTH receptor. To determine whether mutations on MC2R gene, but outside the coding region, may be involved in FGD in these families, we have performed a linkage analysis. Using three markers flanking MC2R gene on chromosome 18, we were able to exclude linkage in a region of 12 centimorgans around the gene. This result clearly indicates that FGD is genetically heterogeneous. Defects in gene(s) different from MC2R gene are implicated in this syndrome.

A robust test for assortative mating.

Testing for random mating in human populations is difficult due to confounding factors such as ethnic preference and population stratification. With HLA, the high level of polymorphism is an additional problem since it is rare for couples to share the same haplotype. Focus on an ethnically homogeneous population, where levels of polymorphism at HLA loci are more limited, may provide the best situation in which to detect non-random mating. However, such populations are often genetic isolates where there may be inbreeding to an extent that is difficult to quantify and account for. We have developed a test for random mating at a multiallelic locus that is robust to stratification and inbreeding. This test relies on the availability of genotypic information from the parents of both spouses. The focus of the test is on families where there is allele sharing between the parents of both spouses, so that potential spouses could share an allele. Denoting the shared allele at the locus of interest by A, then under the assumption of random mating, heterozygous parents AX should transmit allele A equally as frequently as allele X to their offspring. When there is positive (negative) assortative mating, A will be transmitted more (less) often than X. The power of the test has been computed in a number of situations. Data on high resolution HLA haplotypes from the Hutterite population were reinvestigated by the proposed test. The test detects significant negative assortative mating when the parental origin of the shared haplotype is taken into account.

Determination of polychlorodibenzo-p-dioxins and polychlorodibenzofurans by gas chromatography/tandem mass spectrometry and gas chromatography/triple mass spectrometry in a quadrupole ion trap.

The determination of tetra- to octachlorodibenzo-p-dioxins and tetra- to octachlorodibenzofurans (PCCD/Fs) by high-resolution gas chromatography/tandem mass spectrometry (HRGC/MS/MS) and high-resolution gas chromatography/triple mass spectrometry (HRGC/MS(3)) in a quadrupole ion trap, equipped with an external ion source, is presented. MS/MS involves a typical four-step process, namely ionization, parent ion isolation, collision-induced dissociation (CID) and mass analysis of the daughter ions. For the MS(3) experiment, the MS/MS scan function is used with the addition of selected daughter ion isolation, their CID and the mass analysis of second-generation product ions called 'grand-daughter ions.' For both methods, the energies necessary for the CID of the 17 PCDD/Fs were determined and optimized using multiple scan functions with different CID amplitudes. The CID efficiency, defined as the signal ratio of fragment ions detected from the major dissociation channels to molecular ions isolated, was 1.15-2.40 V for parent ion dissociation (MS/MS) and 1.05-1.50 V for daughter ion dissociation (MS(3)) and for all the chloro congeners. The same sensitivity (1 pg microl(-1)) can be reached with both the MS/MS and MS(3) methods and linear responses were obtained between 1 and 100 pg microl(-1) injected.

Genetic studies of polymorphisms in ten non-insulin-dependent diabetes mellitus candidate genes in Tamil Indians from Pondichery.

We report a study of 10 candidate genes presumably involved in diabetes or insulin resistance or obesity among Pondicherian Tamil Indians, an isolated population with a high prevalence of diabetes. Forty-nine families with at least two affected patients in the sibship (567 individuals) were selected and tested by PCR-RFLP techniques for reported mutations in 10 diabetes or obesity candidate genes: glucagon receptor, insulin receptor substrate 1, insulin receptor, human beta 3 adrenergic receptor, fatty acid binding protein 2, mitochondrial tRNA(Leu(UUR)), sulphonylurea receptor, human uncoupling protein and the glycogen-associated regulatory subunit of protein phosphatase-1. Glucokinase gene was also screened for mutations. No mutations were found in glucokinase, glucagon receptor and mitochondrial genes in any of the 49 probands. Frequencies of polymorphisms at other loci were similar to those reported in Caucasian populations, except for 4 of the loci at which a higher frequency of variants was observed: human beta 3 adrenergic receptor, human uncoupling type 1 protein, fatty acid binding protein 2 and the glycogen-associated regulatory subunit of protein phosphatase-1. However, no evidence of association between any of these gene variants and non-insulin-dependent diabetes mellitus (NIDDM) or quantitative traits related to NIDDM (including body mass index, waist/hip ratio, insulinaemia, glycaemia, triglycerides and total cholesterol) was found in our sample. These results suggest that none of these gene variants commonly found in the Pondicherian Tamil population of South India is a major NIDDM predisposing locus, although it cannot be excluded that they may contribute to the polygenic background of the metabolic syndrome in Pondichery.

Application of liquid chromatography with mass spectrometry combined with photodiode array detection and tandem mass spectrometry for monitoring pesticides in surface waters.

Liquid chromatography with photodiode array detection (LC-DAD) and liquid chromatography with mass spectrometry (LC-MS) are two techniques that have been widely used in monitoring pesticides and their degradation products in the environment. However, the application of liquid chromatography with tandem mass spectrometry (LC-MS-MS) for such purposes, once considered too costly, is now gaining considerable ground. In this study, we compare these methods for the multi-residue analysis of pesticides in surface waters collected from the central and southeastern regions of France, and from the St. Lawrence River in Canada. Forty-eight pesticides belonging to eight different classes (triazine, amide, phenylurea, triazole, triazinone, benzimidazole, morpholine, phenoxyalkanoic), along with some of their degradation products, were monitored on a regular basis in the surface waters. For LC-MS, we used the electrospray ionization (ESI) interface in the negative ionization mode on acidic pesticides (phenoxyalkanoic, sulfonylurea), and the atmospheric pressure chemical ionization (APCI) interface in the positive ionization mode on the remaining chemicals. Different extraction techniques were employed, including liquid-liquid extraction with dichloromethane, and solid-phase extraction using C18-bonded silica and graphitized carbon black cartridges. Eleven of the target chemicals (desethylatrazine, desisopropylatrazine, atrazine, simazine, terbuthylazine, metolachlor, carbendazime, bentazone, penconazole, diuron and isoproturon) were detected by LC-MS at concentrations ranging from 20 to 900 ng/l in the surface waters from France, and six pesticides (atrazine, desethylatrazine, desisopropylatrazine, cyanazine, simazine and metolachlor) were detected by LC-MS and LC-MS-MS at concentrations ranging from 3 to 52 ng/l in the samples drawn from the St. Lawrence River. There was good correlation between the LC-DAD and LC-MS techniques for 60 samples. The slope of the curves expressing the relationship between the results obtained with LC-DAD versus those obtained by LC-MS was near 1, with a correlation coefficient (r) of over 0.93. The identification potential of the LC-MS technique, however, was greater than that of the LC-DAD; its mass spectra, mainly reflecting the pseudomolecular ion resulting from a protonation or a deprotonation of the molecule, was rich in information. The LC-MS-MS technique with ion trap detectors, tested against the LC-MS on 10 surface water samples, gave results that correlated well with the LC-MS results, albeit generating mass spectra that yielded far more information about the structure of unknown substances. The sensitivity of the LC-MS-MS was equivalent to the selected ion monitoring (SIM) acquisition mode in LC-MS. The detection limits of the target pesticides ranged from 20 to 100 ng/l for the LC-MS technique (under full scan acquisition), and from 2 to 6 ng/l for LC-MS-MS. These limits were improved by a factor of almost 10 by increasing the sample volume to 10 l.

1,2,4-Oxadiazoles identified by virtual screening and their non-covalent inhibition of the human 20S proteasome.

Although several constitutive proteasome inhibitors have been reported these recent years, potent organic, noncovalent and readily available inhibitors are still poorly documented. Here we used a structure- and ligand-based in silico approach to identify commercially available 1,2,4-oxadiazole derivatives as non-covalent human 20S proteasome inhibitors. Their optimization led to the newly synthesized compound 4h that is a mixed proteasomal inhibitor of the chymotrypsin- like activity (K(i) of 26,1 nM and K'(i) of 7.5 nM) which is in addition selective versus the challenging cathepsin B and calpain proteases. Molecular modelling studies corroborated the mechanism of inhibition and suggest an unusual binding of the inhibitor within the S5 binding pocket (ß6 subunit). The cellular effects of our compounds validate their utility as potential pharmacological agents for anti-cancer pre-clinical studies.

Proteasome inhibitors: recent advances and new perspectives in medicinal chemistry.

The search for proteasome inhibitors began fifteen years ago. These inhibitors proved to be powerful tools for investigating many important cellular processes regulated by the ubiquitin-proteasome pathway. Targeting the proteasome pathway can also lead to new treatments for disorders like cancer, muscular dystrophies, inflammation and immune diseases. This is already true for cancer; the FDA approved bortezomib, a potent proteasome inhibitor, for treating multiple myeloma in 2003, and mantle cell lymphoma in 2006. The chemical structures identified in some of the early proteasome inhibitors have led to the development of new anti-cancer drugs (CEP-18770, Carfilzomib, NPI-0052). All these molecules are covalent bonding inhibitors that react with the catalytic Thr1-O(gamma) of the three types of active site. This review covers recent developments in medicinal chemistry of natural and synthetic proteasome inhibitors. Advances in non-covalent inhibitors that have no reactive group will be highlighted as they should minimize side-effects. New structures and new modes of action have been recently identified that open the door to new drug candidates for treating a range of diseases.