Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes

[Background] The rise of the primate lineage is accompanied by an outstanding emergence of microRNAs, small non-coding RNAs with a prominent role in gene regulation. In spite of their biological importance little is known about the way in which natural selection has influenced microRNAs in the human lineage. To study the recent evolutionary history of human microRNAs and to analyze the signatures of natural selection in genomic regions harbouring microRNAs we have investigated the nucleotide substitution rates of 1,872 human microRNAs in the human and chimpanzee lineages.[Results] We produced a depurated set of microRNA alignments of human, chimpanzee and orang-utan orthologs combining BLAT and liftOver and selected 1,214 microRNA precursors presenting optimal secondary structures. We classified microRNAs in categories depending on their genomic organization, duplication status and conservation along evolution. We compared substitution rates of the aligned microRNAs between human and chimpanzee using Tajima’s Relative Rate Test taking orang-utan as out-group and found several microRNAs with particularly high substitution rates in either the human or chimpanzee branches. We fitted different models of natural selection on these orthologous microRNA alignments and compared them using a likelihood ratio test that uses ancestral repeats and microRNA flanking regions as neutral sequences. We found that although a large fraction of human microRNAs is highly conserved among the three species studied, significant differences in rates of molecular evolution exist among microRNA categories. Particularly, primate-specific microRNAs, which are enriched in isolated and single copy microRNAs, more than doubled substitution rates of those belonging to older, non primate-specific microRNA families.[Conclusions] Our results corroborate the remarkable conservation of microRNAs, a proxy of their functional relevance, and indicate that a subset of human microRNAs undergo nucleotide substitutions at higher rates, which may be suggestive of the action of positive selection.This work was supported by the Ministerio de Ciencia e Innovación, España (BFU2012-38236, BFU2010-18477, BFU2009-06974, and CGL2009-09013), Direcció General de Recerca de la Generalitat de Catalunya” (2009SGR-1101, 2014SGR-866 and SGR2014-1311) and European Union Seventh Framework Programme (PIOF-GA-2009-236836 and PIRSES-GA-2013-612583). This publication has been cofinanced by FEDER —European Regional Development Fund “A way to build Europe.” MLV is funded by a Beca per a la Formació de Personal Investigador (FI) fellowship from the Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya.Peer reviewe

Lipid alterations in lipid rafts from alzheimer's disease human brain cortex

Lipid rafts are membrane microdomains intimately associated with cell signaling. These biochemical microstructures are characterized by their high contents of sphingolipids, cholesterol and saturated fatty acids and a reduced content of polyunsaturated fatty acids (PUFA). Here, we have purified lipid rafts of human frontal brain cortex from normal and Alzheimer's disease (AD) and characterized their biochemical lipid composition. The results revealed that lipid rafts from AD brains exhibit aberrant lipid profiles compared to healthy brains. In particular, lipid rafts from AD brains displayed abnormally low levels of n-3 long chain polyunsaturated fatty acids (LCPUFA, mainly 22:6n-3, docosahexaenoic acid) and monoenes (mainly 18:1n-9, oleic acid), as well as reduced unsaturation and peroxidability indexes. Also, multiple relationships between phospholipids and fatty acids were altered in AD lipid rafts. Importantly, no changes were observed in the mole percentage of lipid classes and fatty acids in rafts from normal brains throughout the lifespan (24-85 years). These indications point to the existence of homeostatic mechanisms preserving lipid raft status in normal frontal cortex. The disruption of such mechanisms in AD brains leads to a considerable increase in lipid raft order and viscosity, which may explain the alterations in lipid raft signaling observed in AD

Gene expression profile in frontal córtex in sporadic frontotemporal lobar degeneration-TDP

Molecular alterations compromising key metabolic pathways are poorly understood in sporadic frontotemporal lobar degeneration with TDP-43 pathology (sFTLD-TDP). Whole-transcriptome array, RT-qPCR validation, gel electrophoresis, and Western blotting, and mitochondrial electron transport chain (ETC) activity were comparatively examined in frontal cortex (area 8) of 16 sFTLD-TDP cases and 14 controls. Assessment of 111 genes by RT-qPCR showed deregulation of 81 genes linked to neurotransmission and synapses, neuronal architecture, cytoskeleton of axons and dendrites, vesicle trafficking, purines, mitochondria, and energy metabolism in sFTLD-TDP. Western blotting studies disclosed downregulation of several mitochondrial subunits encoded by genomic DNA and MTCO1 encoded by the mitochondrial DNA. Mitochondrial ETC activity of complexes I, IV, and V was decreased in sFTLD-TDP. These findings provide robust information about downregulation of genes involved in vital biochemical pathways and in synaptic neurotransmission which may help to increase understanding about the biochemical substrates of clinical manifestations in sFTLD-TDP. Key Words: Energy metabolism, Frontotemporal lobar degeneration, Mitochondria, Neurotransmission, Purines, Synapses, TDP43

Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders

Neurodegenerative and neuropsychiatric disorders (ND-NPs) are multifactorial, polygenic and complex behavioral phenotypes caused by brain abnormalities. Large-scale collaborative efforts have tried to identify the genetic architecture of these conditions. However, the specific and shared underlying molecular pathobiology of brain illnesses is not clear. Here, we examine transcriptome-wide characterization of eight conditions, using a total of 2,633 post-mortem brain samples from patients with Alzheimer’s disease (AD), Parkinson’s disease (PD), Progressive Supranuclear Palsy (PSP), Pathological Aging (PA), Autism Spectrum Disorder (ASD), Schizophrenia (Scz), Major Depressive Disorder (MDD), and Bipolar Disorder (BP)–in comparison with 2,078 brain samples from matched control subjects. Similar transcriptome alterations were observed between NDs and NPs with the top correlations obtained between Scz-BP, ASD-PD, AD-PD, and Scz-ASD. Region-specific comparisons also revealed shared transcriptome alterations in frontal and temporal lobes across NPs and NDs. Co-expression network analysis identified coordinated dysregulations of cell-type-specific modules across NDs and NPs. This study provides a transcriptomic framework to understand the molecular alterations of NPs and NDs through their shared- and specific gene expression in the brain

Altered distribution of RhoA in alzheimer's disease and AβPP overexpressing mice

RhoGTPases control cytoskeleton dynamics thereby modulating synaptic plasticity. Because Alzheimer's disease (AD) is characterized by synaptic dysfunction, we sought to determine whether the expression, activity, or localization of the GTPases RhoA, Rac1 and Cdc42, as well as p21-PAK, a downstream target of Rac1/Cdc42, were altered in 18-month-old AbetaPP Tg2576 mice (Swedish mutation) or in brains from patients with AD and, for comparison in the case of RhoA, Pick's disease (PiD), a neurodegenerative disorder characterized by hyper-phosphorylated tau accumulation. Immunohistochemical analyses revealed a distinct localization of each RhoGTPase in synapses, dendrite shafts, neuronal bodies, or astrocytes. The association of RhoA with synapses and dendritic microtubules was confirmed by electron microscopy. In AbetaPP mice, RhoA expression decreased in synapses and increased in dystrophic neurites, suggesting altered subcellular targeting of RhoA. In AD, RhoA immunostaining decreased in the neuropil and markedly increased in neurons, co-localizing with hyperphosphorylated tau inclusions, as though RhoA were sequestered by neurofibrillary tangles. Additionally, total RhoA protein was lower in the AD brain hippocampus, reflecting loss of the membrane bound, presumably active, GTPase. RhoA colocalized with hyperphosphorylated tau in PiD, again suggesting that altered subcellular targeting of RhoA is related to neurodegeneration. No major immunohistochemical changes were observed for Rac1, Cdc42, or p21-PAK, thus identifying RhoA among RhoGTPases as a possible therapeutic target in AD

Transcriptional network analysis in frontal cortex in Lewy body diseases with focus on dementia with Lewy bodies

The present study investigates global transcriptional changes in frontal cortex area 8 in incidental Lewy Body disease (iLBD), Parkinson disease (PD) and Dementia with Lewy bodies (DLB). We identified different co-expressed gene sets associated with disease stages, and gene ontology categories enriched in gene modules and differentially expressed genes including modules or gene clusters correlated to iLBD comprising upregulated dynein genes and taste receptors, and down-regulated innate inflammation. Focusing on DLB, we found modules with genes significantly enriched in functions related to RNA and DNA production, mitochondria and energy metabolism, purine metabolism, chaperone and protein folding system, and synapses and neurotransmission (particularly the GABAergic system). The expression of more than fifty selected genes was assessed with RT-qPCR. Our findings provide, for the first time, evidence of molecular cortical alterations in iLBD and involvement of several key metabolic pathways and gene hubs in DLB which may underlie cognitive impairment and dementia. Key words: Lewy body diseases, dementia with Lewy bodies, cerebral cortex, transcriptome, mitochondria, synapses, neurotransmission, GABA, purine metabolism, chaperones, dynein, axonema, taste receptors

Study of the human African genome landscape through the analysis of complete genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding the genetic diversity in humans within the African continent is pivotal to have a full picture of the demographic history of the human species. Here, we study complete genome sequeces of a diverse panel of African individuals in terms of geographical location, linguistic context and lifestyle. Most African diversity studies have mainly focused on uniparental markers or selected autosomal markers, which introduce an ascertainment bias in the analysis. The analysis of complete genomes has been poorly developed in the study of African human genomics and internal population diversity. The main goals of this study are: 1. Characterisation of the internal human diversity in Africa overcoming ascertainment bias-related problems by using complete genomes. 2. Characterization of the deepest splits in the human lineage and the processes (such as migrations and admixtures) that have shaped the current genetic map.Funded by: MINECO CGL 2013-44351-P.N

Demographic inferences from a diverse panel of African human genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding genetic variation across ethnically and geographically diverse extant African populations is of great importance for reconstructing human complex demographic history. Here, we study the recent history and relationships among 15 different African populations, by analyzing the whole-genome sequence data of 21 individuals sequenced at deep coverage covering all major contine ntal linguistic groups, ecosystems and life-styles within Africa. We detected 12 million single nucleotide substitutions, providing a rich picture of the genome diversity and population history in Africa. We observe a remarkable correlation among genetic diversity and geographic origins and recent demographic history of the individuals studied. While different hunter-gatherer groups show more differentiation compared with the rest of samples, Bantu individuals are genetically more homogeneous and present evidence of admixture with neighboring hunter-gatherer groups, depending on the geographic area. Northern African individuals are closely related to non-African populations, in agreement with a recent split of both groups and continuous gene flow. To gain in sight into the deepest split of our species, we explore if recent admixture of Pygmies and Khoesan with other populations may cover up their real diversity, becoming the human most diverse groups.N

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

BackgroundPopulation demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.ResultsHere, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.Peer reviewe