Transcriptome-wide genotype-phenotype associations in Daphnia in a predation risk environment.

Phenotypic variation plays an important role in how species cope with environmental challenges. Pinpointing which genes and genomic regions are underlying phenotypic variability thus helps to understand the processes of acclimation and adaptation. We used Daphnia as a system to identify candidates playing a role in phenotypic variation related to a predation risk environment with a genome-wide association approach. Furthermore, a gene co-expression network analysis allowed identifying clusters of co-expressed genes which correlated to life history traits. To enhance the understanding of the functional roles of the transcripts, we identified orthologs and paralogs from related species and used ontologies to annotate the candidates of interest. Our study revealed that only one life history trait and two morphometric traits have a genetic association in the presence of predation risk (fish kairomones), whereas most genotype-phenotype associations were detected in a genotype-environment interaction analysis for reproduction-related phenotypic traits. The gene co-expression network analysis identified a total of 44 modules, of which one module correlated to another life history trait namely the 'total number of broods'. The combined use of gene co-expression network and transcriptome-wide association analysis allowed the identification of 131 candidate transcripts associated with life history traits in Daphnia galeata. These results lay the ground for targeted studies to further understand phenotypic variability in this species.

Population transcriptomics in Daphnia: The role of thermal selection.

The complex interplay of forces influencing genetic divergence among populations complicates the discovery of the genetic basis underlying local adaptation. Here, we utilized for the first time a combined reverse ecology and population transcriptomic approach to assess the contribution of thermal selection to population differentiation, thereby considering transcriptome-wide variation in both gene expression profiles and DNA sequences. We compared transcriptomes among four Daphnia galeata populations and identified transcripts potentially responding to local thermal selection based on an extensive literature search for candidate genes possibly under thermal selection in arthropods. Over-representation of temperature-relevant candidate genes among transcripts strongly contributing to sequence divergence among two populations indicates that local thermal selection acted on the coding sequence level. We identified a large number of transcripts, which may contribute to local thermal adaptation based on outlier tests and distinctive expression profiles. However, among these, temperature-relevant candidate genes were not over-represented compared to the global gene set, suggesting that thermal selection played a minor role in divergence among Daphnia populations. Interestingly, although the majority of genes contributing strongly to sequence divergence did not contribute strongly to divergence at the expression level and vice versa, the affected gene functions were largely consistent between the two data sets. This suggests that genetic and regulatory variation constitutes alternative routes for responses to natural selection. Our combined utilization of a population transcriptomics approach and literature-based identification of ecologically informative candidate genes represents a useful and powerful methodology with a wide range of applications in evolutionary biology.

Proteomic analysis of Alzheimer's disease cerebrospinal fluid reveals alterations associated with APOE ε4 and atomoxetine treatment.

Alzheimer's disease (AD) is currently defined by the aggregation of amyloid-ß (Aß) and tau proteins in the brain. Although biofluid biomarkers are available to measure Aß and tau pathology, few markers are available to measure the complex pathophysiology that is associated with these two cardinal neuropathologies. Here, we characterized the proteomic landscape of cerebrospinal fluid (CSF) changes associated with Aß and tau pathology in 300 individuals using two different proteomic technologies-tandem mass tag mass spectrometry and SomaScan. Integration of both data types allowed for generation of a robust protein coexpression network consisting of 34 modules derived from 5242 protein measurements, including disease-relevant modules associated with autophagy, ubiquitination, endocytosis, and glycolysis. Three modules strongly associated with the apolipoprotein E ε4 (APOE ε4) AD risk genotype mapped to oxidant detoxification, mitogen-associated protein kinase signaling, neddylation, and mitochondrial biology and overlapped with a previously described lipoprotein module in serum. Alterations of all three modules in blood were associated with dementia more than 20 years before diagnosis. Analysis of CSF samples from an AD phase 2 clinical trial of atomoxetine (ATX) demonstrated that abnormal elevations in the glycolysis CSF module-the network module most strongly correlated to cognitive function-were reduced by ATX treatment. Clustering of individuals based on their CSF proteomic profiles revealed heterogeneity of pathological changes not fully reflected by Aß and tau.

Proteomic Network Analysis of Alzheimer's Disease Cerebrospinal Fluid Reveals Alterations Associated with APOE ε4 Genotype and Atomoxetine Treatment.

Alzheimer's disease (AD) is currently defined at the research level by the aggregation of amyloid-ß (Aß) and tau proteins in brain. While biofluid biomarkers are available to measure Aß and tau pathology, few biomarkers are available to measure the complex pathophysiology that is associated with these two cardinal neuropathologies. Here we describe the proteomic landscape of cerebrospinal fluid (CSF) changes associated with Aß and tau pathology in 300 individuals as assessed by two different proteomic technologies-tandem mass tag (TMT) mass spectrometry and SomaScan. Harmonization and integration of both data types allowed for generation of a robust protein co-expression network consisting of 34 modules derived from 5242 protein measurements, including disease-relevant modules associated with autophagy, ubiquitination, endocytosis, and glycolysis. Three modules strongly associated with the apolipoprotein E ε4 (APOE ε4) AD risk genotype mapped to oxidant detoxification, mitogen associated protein kinase (MAPK) signaling, neddylation, and mitochondrial biology, and overlapped with a previously described lipoprotein module in serum. Neddylation and oxidant detoxification/MAPK signaling modules had a negative association with APOE ε4 whereas the mitochondrion module had a positive association with APOE ε4. The directions of association were consistent between CSF and blood in two independent longitudinal cohorts, and altered levels of all three modules in blood were associated with dementia over 20 years prior to diagnosis. Dual-proteomic platform analysis of CSF samples from an AD phase 2 clinical trial of atomoxetine (ATX) demonstrated that abnormal elevations in the glycolysis CSF module-the network module most strongly correlated to cognitive function-were reduced by ATX treatment. Individuals who had more severe glycolytic changes at baseline responded better to ATX. Clustering of individuals based on their CSF proteomic network profiles revealed ten groups that did not cleanly stratify by Aß and tau status, underscoring the heterogeneity of pathological changes not fully reflected by Aß and tau. AD biofluid proteomics holds promise for the development of biomarkers that reflect diverse pathologies for use in clinical trials and precision medicine.

Author Correction: Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations.

Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.

Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation.

Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or "hypothetical" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for "hypothetical proteins" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnia's genetic and phenotypic variability.

Functional annotation of introns in mitochondrial genome--a brief review.

The present study is to decipher the non-coding regions present in mitochondrial genomes that cause diseases in humans and predict their functional roles through comparative genomics approach followed by functional annotation of these segments.