Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability

Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder.     

Differential gene expression in ovaries of pregnant pigs with high and low prolificacy levels and identification of candidate genes for litter size

Previous results from a genome scan in an F(2) Iberian × Meishan pig intercross showed several chromosome regions associated with litter size traits in this species. In order to identify candidate genes underlying these quantitative trait loci (QTL), we performed an ovary gene expression analysis during the sow's pregnancy. F(2) sows were ranked by their estimated breeding values for prolificacy: six sows with the highest estimated breeding value (EBV) (i.e., high prolificacy) and six sows with the lowest EBV (low prolificacy) were selected. Samples were hybridized using an Affymetrix GeneChip porcine genome array. Statistical analysis with a mixed model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify genetic pathways overrepresented in this list. Among the functional groups most represented was, in first position, immune system response activation against external stimulus. The second group consisted of integrated genes that regulate maternal homeostasis by complement and coagulation cascades. A third group was involved in lipid and fatty acid enzymes of metabolic processes, which participate in the steroidogenesis pathway. In order to identify powerful candidate genes for prolificacy, the second approach of this study was to merge microarray data with the QTL positional information affecting litter size, previously detected in the same experimental cross. As a result, we have identified 27 differentially expressed genes colocalizing with QTL for litter size traits, which fulfill the biological, positional, and functional criteria.     

Microhomology-mediated deletion and gene conversion in African trypanosomes

Antigenic variation in African trypanosomes is induced by DNA double-strand breaks (DSBs). In these protozoan parasites, DSB repair (DSBR) is dominated by homologous recombination (HR) and microhomology-mediated end joining (MMEJ), while non-homologous end joining (NHEJ) has not been reported. To facilitate the analysis of chromosomal end-joining, we established a system whereby inter-allelic repair by HR is lethal due to loss of an essential gene. Analysis of intrachromosomal end joining in individual DSBR survivors exclusively revealed MMEJ-based deletions but no NHEJ. A survey of microhomologies typically revealed sequences of between 5 and 20 bp in length with several mismatches tolerated in longer stretches. Mean deletions were of 54 bp on the side closest to the break and 284 bp in total. Break proximity, microhomology length and GC-content all favored repair and the pattern of MMEJ described above was similar at several different loci across the genome. We also identified interchromosomal gene conversion involving HR and MMEJ at different ends of a duplicated sequence. While MMEJ-based deletions were RAD51-independent, one-sided MMEJ was RAD51 dependent. Thus, we describe the features of MMEJ in Trypanosoma brucei, which is analogous to micro single-strand annealing; and RAD51 dependent, one-sided MMEJ. We discuss the contribution of MMEJ pathways to genome evolution, subtelomere recombination and antigenic variation.     

Resultados de la endarterectomía carotídea en pacientes ancianos

Introduction

Forty-five per cent of stoke patients have a surgically accessible stenosis. The objective of our study is to describe the response to carotid endarterectomy (EA) in patients of advanced age compared to younger ones.

Material and method

Retrospective evaluation of the clinical history of all patients who underwent an endarterectomy in a tertiary hospital between January 1995 and December 2006. The patients were grouped into those 75 years or older and those less than this age. The incidence of peri-operative complications in the first month after surgery, and the long-term mortality was evaluated using a survival analysis.

Results

Data were collected on 147 EA in 134 patients of 75 years or more, and on 201 EA in 177 patients less than 75 years-old. The incidence of peri-operative complications was similar in both groups, with a mortality of 2% in the older age group and a stroke incidence of 2.6% (half transient ischaemic accidents). The older patients had a mean follow-up of 4.1 years, with a survival of 86% at one year and 54% at 5 years and with the main cause of death being heart disease.

Conclusions

Carotid EA is a safe and effective technique for the treatment of extracranial carotid stenosis in the elderly, having the same peri-operative morbidity and mortality as younger ones. Age must not affect our therapeutic attitude, although an exhaustive cardiology study must be made in the elderly prior to the operation.     

Endotoxin tolerance represents a distinctive state of alternative polarization (M2) in human mononuclear cells

Classical (M1) and alternative (M2) polarization of mononuclear cells (MNCs) such as monocyte and macrophages is known to occur in response to challenges within a microenvironment, like the encounter of a pathogen. LPS, also known as endotoxin, is a potent inducer of inflammation and M1 polarization. LPS can also generate an effect in MNCs known as endotoxin tolerance, defined as the reduced capacity of a cell to respond to LPS activation after an initial exposure to this stimulus. Using systems biology approaches in PBMCs, monocytes, and monocyte-derived macrophages involving microarrays and advanced bioinformatic analysis, we determined that gene responses during endotoxin tolerance were similar to those found during M2 polarization, featuring gene and protein expression critical for the development of key M2 MNC functions, including reduced production of proinflammatory mediators, expression of genes involved in phagocytosis, as well as tissue remodeling. Moreover, expression of different metallothionein gene isoforms, known for their role in the control of oxidative stress and in immunomodulation, were also found to be consistently upregulated during endotoxin tolerance. These results demonstrate that after an initial inflammatory stimulus, human MNCs undergo an M2 polarization probably to control hyperinflammation and heal the affected tissue.     

A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants

Background

The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even in model organisms, little is known about how the genetic determinants of lipid traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) for cholesterol (CHOL), triglyceride (TRIG) and low (LDL) and high (HDL) density lipoprotein concentrations measured in Duroc pigs at two time points (45 and 190 days).

Results

Analysis of data with mixed-model methods (EMMAX, GEMMA, GenABEL) and PLINK showed a low positional concordance between trait-associated regions (TARs) for serum lipids at 45 and 190 days. Besides, the proportion of phenotypic variance explained by SNPs at these two time points was also substantially different. The four analyses consistently detected two regions on SSC3 (124 Mb, CHOL and LDL at 190 days) and SSC6 (135 Mb, CHOL and TRIG at 190 days) with highly significant effects on the porcine blood lipid profile. Moreover, we have found that SNP variation within SSC3, SSC6, SSC10, SSC13 and SSC16 TARs is associated with the expression of several genes mapping to other chromosomes and related to lipid metabolism.

Conclusions

Our data demonstrate that the effects of genomic determinants influencing lipid concentrations in pigs, as well as the amount of phenotypic variance they explain, are influenced by age-related factors.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-758) contains supplementary material, which is available to authorized users.     

A Retained Secretory Signal Peptide Mediates High Density Lipoprotein (HDL) Assembly and Function of Haptoglobin-related Protein

Haptoglobin-related protein (Hpr) is a component of a minor subspecies of high density lipoproteins (HDL) that function in innate immunity. Here we show that assembly of Hpr into HDL is mediated by its retained N-terminal signal peptide, an unusual feature for a secreted protein and the major difference between Hpr and the soluble acute phase protein haptoglobin (Hp). The 18-amino acid signal peptide is necessary for binding to HDL and interacts directly with the hydrocarbon region of lipids. Utilizing model liposomes, we show that the rate of assembly and steady-state distribution of Hpr in lipid particles is mediated by the physical property of lipid fluidity. Dye release assays reveal that Hpr interacts more rapidly with fluid liposomes. Conversely, steady-state binding assays indicate that more rigid lipid compositions stabilize Hpr association. Lipid association also plays a role in facilitating hemoglobin binding by Hpr. Our data may offer an explanation for the distinct distribution of Hpr among HDL subspecies. Rather than protein-protein interactions mediating localization, direct interaction with phospholipids and sensitivity to lipid fluidity may be sufficient for localization of Hpr and may represent a mechanism of HDL subspeciation.     

Divergent Human Y-Chromosome Microsatellite Evolution Rates

In this work, we analyze several characteristics influencing the low variability of the microsatellite DYS19 in the major founder Amerindian Y chromosome lineage containing the point mutation DYS199-T. Variation of DYS19 was compared with that of five other Y-linked tetranucleotide repeat loci (DYS389A, DYS389B, DYS390, DYS391, and DYS393) in the DYS199-T lineage. All the other microsatellites showed significantly higher levels of variability than DYS19 as measured by gene diversity and repeat number variance. Moreover, we had previously shown that DYS19 had high diversity in Brazilians and in several other populations worldwide. Thus, the slow DYS19 evolution in the DYS199-T lineage seems to be both locus and allele specific. To understand the slow DYS19 evolutionary rate, the microsatellite loci were compared according to their mapping on the Y chromosome and also on the basis of structural aspects such as the base composition of the repeat motif and flanking regions and the degree of perfection and size (repeat number) of the variable blocks. The only observed difference that might be related to the low DYS19 variability is its small average number of repeats, a value expected to be closer to the founder DYS19 allele in the DYS199-T lineage. These data were also compared to other derived Y lineages. The Tat-C lineage displayed a lower DYS19 variability correlated to a small average repeat number, while in the DYS234-G lineage, a high DYS19 variability was found associated to a larger average repeat number. This approach reveals that evolution of Y microsatellites in lineages defined by slowly evolving markers, such as point mutations, can be greatly influenced by the size (number of repeats of the variable block) of the founder allele in each microsatellite locus. Thus lineage-dating methods using microsatellite variation should be practiced with great care. Received: 7 November 1998 / Accepted: 9 April 1999     

Acute effect of an amino acid mixture in the rat glycemic profile

Amino acid mixtures (AAM) are protein substitutes used for phenylketonuria treatment, but their metabolic effects have not been well characterized. The objective of this study was to compare the acute glycemic response to free amino acids (free AA) from AAM with the response to intact protein (iProtein). Male Wistar rats (n = 14) were administered by gavage a bolus of free AA (n = 7) or iProtein as albumin (n = 7) containing equivalent amounts of nitrogen. Blood glucose and insulin levels were measured at baseline and 15, 30, 60 and 120 minutes later, when gut GLP-1 content and pancreatic insulin, GLP-1 receptor and Ki67 expression were quantified at 120 minutes time point. After AAM, glucose area under the curve (free AA vs iProtein; P < 0.01), serum insulin levels at 120 minutes (free AA vs iProtein; P < 0.05), colon GLP-1 content (free AA vs iProtein; P < 0.01), pancreatic GLP-1 receptor (free AA vs iProtein; P < 0.01) and insulin expression (free AA vs iProtein; p < 0.01) were significantly lower as compared with iProtein. AAM increased Ki67 expression in pancreatic islets (free AA vs iProtein; P < 0.05). In conclusion, this study demonstrated that acute response to AAM differs from iProtein and is characterized by a lower glucose excursion, along with a decrease in gut GLP-1 and pancreatic GLP-1 receptor and insulin. This data suggests the modulation of glycemia by free AA is mediated by the incretin axis.