An evolutionary analysis of cAMP-specific Phosphodiesterase 4 alternative splicing

<p>Abstract</p> <p>Background</p> <p>Cyclic nucleotide phosphodiesterases (PDEs) hydrolyze the intracellular second messengers: cyclic adenosine monophosphate (cAMP) and cyclic guanine monophosphate (cGMP). The cAMP-specific PDE family 4 (PDE4) is widely expressed in vertebrates. Each of the four PDE4 gene isoforms (PDE4 A-D) undergo extensive alternative splicing via alternative transcription initiation sites, producing unique amino termini and yielding multiple splice variant forms from each gene isoform termed long, short, super-short and truncated super-short. Many species across the vertebrate lineage contain multiple splice variants of each gene type, which are characterized by length and amino termini.</p> <p>Results</p> <p>A phylogenetic approach was used to visualize splice variant form genesis and identify conserved splice variants (genome conservation with EST support) across the vertebrate taxa. Bayesian and maximum likelihood phylogenetic inference indicated PDE4 gene duplication occurred at the base of the vertebrate lineage and reveals additional gene duplications specific to the teleost lineage. Phylogenetic inference and PDE4 splice variant presence, or absence as determined by EST screens, were further supported by the genomic analysis of select vertebrate taxa. Two conserved PDE4 long form splice variants were found in each of the PDE4A, PDE4B, and PDE4C genes, and eight conserved long forms from the PDE4 D gene. Conserved short and super-short splice variants were found from each of the PDE4A, PDE4B, and PDE4 D genes, while truncated super-short variants were found from the PDE4C and PDE4 D genes. PDE4 long form splice variants were found in all taxa sampled (invertebrate through mammals); short, super-short, and truncated super-short are detected primarily in tetrapods and mammals, indicating an increasing complexity in both alternative splicing and cAMP metabolism through vertebrate evolution.</p> <p>Conclusions</p> <p>There was a progressive independent incorporation of multiple PDE4 splice variant forms and amino termini, increasing PDE4 proteome complexity from primitive vertebrates to humans. While PDE4 gene isoform duplicates with limited alternative splicing were found in teleosts, an expansion of both PDE4 splice variant forms, and alternatively spliced amino termini predominantly occurs in mammals. Since amino termini have been linked to intracellular targeting of the PDE4 enzymes, the conservation of amino termini in PDE4 splice variants in evolution highlights the importance of compartmentalization of PDE4-mediated cAMP hydrolysis.</p

Cross-Sectional Exploration of Plasma Biomarkers of Alzheimer's Disease in Down Syndrome: Early Data from the Longitudinal Investigation for Enhancing Down Syndrome Research (LIFE-DSR) Study

With improved healthcare, the Down syndrome (DS) population is both growing and aging rapidly. However, with longevity comes a very high risk of Alzheimer's disease (AD). The LIFE-DSR study (NCT04149197) is a longitudinal natural history study recruiting 270 adults with DS over the age of 25. The study is designed to characterize trajectories of change in DS-associated AD (DS-AD). The current study reports its cross-sectional analysis of the first 90 subjects enrolled. Plasma biomarkers phosphorylated tau protein (p-tau), neurofilament light chain (NfL), amyloid β peptides (Aβ1-40, Aβ1-42), and glial fibrillary acidic protein (GFAP) were undertaken with previously published methods. The clinical data from the baseline visit include demographics as well as the cognitive measures under the Severe Impairment Battery (SIB) and Down Syndrome Mental Status Examination (DS-MSE). Biomarker distributions are described with strong statistical associations observed with participant age. The biomarker data contributes to understanding DS-AD across the spectrum of disease. Collectively, the biomarker data show evidence of DS-AD progression beginning at approximately 40 years of age. Exploring these data across the full LIFE-DSR longitudinal study population will be an important resource in understanding the onset, progression, and clinical profiles of DS-AD pathophysiology

Analysis of the antifreeze glycoprotein containing genomic locus in the Antarctic notothenioid fish dissostichus mawsoni

Development of the Antarctic Circumpolar Current (ACC) circa 25 mya resulted in cooling of the high latitude waters of the Southern Ocean to a chilly -1.86 ??C (near the freezing point of seawater) and extinction of most of the late Eocene temperate fish fauna. A notothenioid ancestral stock survived and went through an adaptive radiation that gave rise to a variety of ecotypes that filled the empty niches. The notothenioid fishes now account for 95% of the fish biomass that inhabits the continental shelf of Antarctica and islands of the Scotia Arc. The adaptive radiation was linked to the evolution of antifreeze glycoproteins (AFGPs). High blood levels of AFGPs (25 to 35 mg/ml) lower their freezing point a few tenths of a degree below that of seawater (-1.86oC) and are a vital part of their freeze avoidance strategy. The AFGP gene evolved from a trypsinogen-like protease (TLP) gene, and presumably through an ancestral intermediate, a chimeric AFGP/TLP gene. All three types of genes (TLP, AFGP, and chimeric AFGP/TLP) are found in Antarctic notothenioid genomes, but it is not known whether the chimeric gene is transcribed and translated into a protein that would provide both AFGP and TLP molecules. The AFGP/TLP genomic locus of an Antarctic notothenioid, Dissostichus mawsoni was characterized in order to determine the mechanism of gene family expansion that would provide the high blood AFGP concentrations. The AFGP/TLP locus was isolated by screening a bacterial artificial chromosome (BAC) library for AFGP/TLP positive clones. Seven BAC clones representing two haplotypes encompassed the AFGP/TLP locus. Assembly of the AFGP/TLP locus was complicated by its highly repetitive nature. Thus, an assembly protocol was developed which entailed construction of subclone libraries of two insert size ranges (1-5 kbp and 5-30 kbp) for some of the positive BAC clones. BAC clone shotgun subclone libraries were then sequenced and subjected to automated and manual sequence reconstruction. Matching of paired-end sequences of some of the 1-5 kbp and all of the 5-30 kbp shotgun subclones to the locus sequence assembly was carried out to establish the linear order of genes. The AFGP/TLP locus assembly and analysis showed a high AFGP gene dosage (14 AFGP polyprotein genes in haplotype 1 and 8 AFGP polyprotein genes in haplotype 2) that very likely resulted from segmental duplications of the AFGP gene and its flanking regions, as seen in the >95 % sequence identity between AFGP gene modules. Thus it is clear that extensive AFGP gene duplication resulting in high gene dosage is the molecular basis for the high serum AFGP concentrations observed in the Antarctic notothenioids. Besides the AFGP genes, the locus contains three AFGP/TLP chimeric genes and two TLP genes. Bayesian and Maximum Likelihood phylogenetic reconstructions of the AFGP, TLP, and AFGP/TLP chimeric coding regions indicated that the AFGP gene family arose from an ancestral chimeric gene related to a specific chimeric gene in the locus. Analysis of this extant paralog of the chimeric gene ancestor of AFGP gene revealed that the first stand-alone AFGP gene was most likely formed by slipped misalignment on the template strand during DNA replication in the chimeric ancestor, resulting in the removal of the bulk of the TLP coding regions. We hypothesize that extensive AFGP gene duplication may have been propagated by a recombination hotspot located downstream of all AFGP genes. Double stranded DNA breakage at this recombination hotspot may have resulted in AFGP gene duplication via non-homologous segmental duplication by unequal crossing-over. Increased AFGP gene dosage conceivably was selected for upon advent of icy Antarctic marine conditions, increasing survival fitness in Antarctic notothenioids in the form of increased serum AFGP concentrations. Examination of the AFGP polypeptide coding regions of AFGP and AFGP/TLP chimeric genes (exon 2) showed that the AFGP genes encode predominantly the smaller AFGP molecules, consistent with their high abundance observed in the serum. The larger AFGP molecules are predominantly encoded in the AFGP/TLP chimeric genes. The chimeric genes are transcribed, and the tissue distribution of the chimeric gene transcript expression is similar to that of AFGP genes, suggesting that the chimeric gene may be functional in present day Antarctic notothenioids as an AFGP, providing the larger serum AFGP molecules. Three types of trypsinogen genes are also associated with the AFGP/TLP genomic locus. Bayesian and Maximum Likelihood phylogenetic reconstructions using spliced D. mawsoni trypsinogen coding sequences, and a large sampling of vertebrate trypsinogen sequences from the NCBI EST and nucleotide databases, indicate D. mawsoni trypsinogens belonged to two of the three previously classified teleost trypsinogen gene types, group I (digestive) trypsinogen and group III (cold active) trypsinogen. Group I and group III trypsinogens are located within clade I and clade III respectively identified in our analysis. Phylogenetic analysis and intron-exon structure mapping revealed that clade III trypsinogens consists of two distinct subclades (clade IIIA and IIIB), encompassing the previously classified cold-active group III trypsinogens. BLAST searches of NCBI ESTs from different teleosts revealed clade III trypsinogens to be present in more basal warm-water teleosts (catfish, Siluriformes), suggesting they evolved in a time of warm climate, and thus were not of cold adaptive origin thus the cold active capability of some extant paralogs may be a subsequent evolutionary acquisition. Antarctic notothenioid clade I and III trypsinogen transcript abundance were determined by relative qPCR. Both clade III trypsinogens transcripts were higher than that of clade I in the Antarctic notothenioid D. mawsoni. Tissue expression distributions of Antarctic notothenioid clade III trypsinogens, determined by PCR, were also broader than those of temperate O. mykiss clade III paralogs. Absolute qPCR quantification of transcript expression showed that in a warm-acclimated Antarctic notothenioid fish, clade III trypsinogen transcripts decreased while clade I trypsinogen transcripts increased. These analyses suggest clade III trypsins, which are expressed at very low levels in warm water teleosts, were recruited in Antarctic notothenioids for potential cold-active capabilities, and evolved into the primarily expressed trypsinogen type in these fishes. The clade III trypsinogens that persist at low transcript levels in warm-water teleosts may perform other proteolytic functions unrelated to digestion or their potential cold-active capabilities

Gender and Age Stratified Analyses of Nutrient and Dietary Pattern Associations with Circulating Lipid Levels Identify Novel Gender and Age-Specific Correlations

Dyslipidemia is a precursor to a myriad of cardiovascular diseases in the modern world. Age, gender, and diet are known modifiers of lipid levels, however they are not frequently investigated in subset analyses. Food and nutrient intakes from National Health and Nutrition Examination Study 2001&#8315;2013 were used to assess the correlation between lipid levels (high-density lipoprotein (HDL) cholesterol, triglycerides (TG), low-density lipoprotein (LDL) cholesterol, and total cholesterol (TC):HDL cholesterol ratio) and nutritional intake using linear regression. Associations were initially stratified by gender and significant gender correlations were further stratified by age. Analyses were performed at both the dietary pattern and nutrient level. Dietary pattern and fat intake correlations agreed with the literature in direction and did not demonstrate gender or age effects; however, we observed gender and age interactions among other dietary patterns and individual nutrients. These effects were independent of ethnicity, caloric intake, socioeconomic status, and physical activity. Elevated HDL cholesterol levels correlated with increasing vitamin and mineral intake in females of child bearing age but not males or older females (&#8805;65 years). Moreover, increases in magnesium and retinol intake correlated with HDL cholesterol improvement only in females (all age groups) and males (35&#8315;64), respectively. Finally, a large amount of gender-specific variation was associated with TG levels. Females demonstrated positive associations with sugar and carbohydrate while males show inverse associations with polyunsaturated fatty acid (PUFA) intake. The female-specific association increased with the ratio of carbohydrate: saturated fatty acid (SFA) intake, suggesting that gender specific dietary habits may underlie the observed TG-nutrient correlations. Our study provides evidence that a subset of previously established nutrient-lipid associations may be gender or age-specific. Such discoveries provide potential new avenues for further research into personalized nutritional approaches to treat dyslipidemia

Correction: Nicodemus-Johnson, J.; et al. Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways. Nutrients 2017, 9, 752

We would like to submit the following correction to our recently published paper [1] due to the error in illustration of the abbreviation eFORGE. The details are as follows:[...

Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways

Epidemiological evidence strongly suggests that fruit consumption promotes many health benefits. Despite the general consensus that fruit and juice are nutritionally similar, epidemiological results for juice consumption are conflicting. Our objective was to use DNA methylation marks to characterize fruit and juice epigenetic signatures within PBMCs and identify shared and independent signatures associated with these groups. Genome-wide DNA methylation marks (Illumina Human Methylation 450k chip) for 2,148 individuals that participated in the Framingham Offspring exam 8 were analyzed for correlations between fruit or juice consumption using standard linear regression. CpG sites with low P-values (P &lt; 0.01) were characterized using Gene Set Enrichment Analysis (GSEA), Ingenuity Pathway Analysis (IPA), and experimentally derived Functional element Overlap analysis of ReGions from EWAS (eFORGE). Fruit and juice-specific low P-value epigenetic signatures were largely independent. Genes near the fruit-specific epigenetic signature were enriched among pathways associated with antigen presentation and chromosome or telomere maintenance, while the juice-specific epigenetic signature was enriched for proinflammatory pathways. IPA and eFORGE analyses implicate fruit and juice-specific epigenetic signatures in the modulation of macrophage (fruit) and B or T cell (juice) activities. These data suggest a role for epigenetic regulation in fruit and juice-specific health benefits and demonstrate independent associations with distinct immune functions and cell types, suggesting that these groups may not confer the same health benefits. Identification of such differences between foods is the first step toward personalized nutrition and ultimately the improvement of human health and longevity

Genome-Wide Gene Expression Analysis Shows AKAP13-Mediated PKD1 Signaling Regulates the Transcriptional Response to Cardiac Hypertrophy

In the heart, scaffolding proteins such as A-Kinase Anchoring Proteins (AKAPs) play a crucial role in normal cellular function by serving as a signaling hub for multiple protein kinases including protein kinase D1 (PKD1). Under cardiac hypertrophic conditions AKAP13 anchored PKD1 activates the transcription factor MEF2 leading to subsequent fetal gene activation and hypertrophic response. We used an expression microarray to identify the global transcriptional response in the hearts of wild-type mice expressing the native form of AKAP13 compared to a gene-trap mouse model expressing a truncated form of AKAP13 that is unable to bind PKD1 (AKAP13-ΔPKD1). Microarray analysis showed that AKAP13-ΔPKD1 mice broadly failed to exhibit the transcriptional profile normally associated with compensatory cardiac hypertrophy following trans-aortic constriction (TAC). The identified differentially expressed genes in WT and AKAP13-ΔPKD1 hearts are vital for the compensatory hypertrophic response to pressure-overload and include myofilament, apoptotic, and cell growth/differentiation genes in addition to genes not previously identified as affected by AKAP13-anchored PKD1. Our results show that AKAP13-PKD1 signaling is critical for transcriptional regulation of key contractile, cell death, and metabolic pathways during the development of compensatory hypertrophy in vivo

Molecular evolution of a-kinase anchoring protein (AKAP)-7: implications in comparative PKA compartmentalization

<p>Abstract</p> <p>Background</p> <p>A-Kinase Anchoring Proteins (AKAPs) are molecular scaffolding proteins mediating the assembly of multi-protein complexes containing cAMP-dependent protein kinase A (PKA), directing the kinase in discrete subcellular locations. Splice variants from the AKAP7 gene (AKAP15/18) are vital components of neuronal and cardiac phosphatase complexes, ion channels, cardiac Ca²⁺ handling and renal water transport.</p> <p>Results</p> <p>Shown in evolutionary analyses, the formation of the AKAP7-RI/RII binding domain (required for AKAP/PKA-R interaction) corresponds to vertebrate-specific gene duplication events in the PKA-RI/RII subunits. Species analyses of AKAP7 splice variants shows the ancestral AKAP7 splice variant is AKAP7α, while the ancestral long form AKAP7 splice variant is AKAP7γ. Multi-species AKAP7 gene alignments, show the recent formation of AKAP7δ occurs with the loss of native AKAP7γ in rats and basal primates. AKAP7 gene alignments and two dimensional Western analyses indicate that AKAP7γ is produced from an internal translation-start site that is present in the AKAP7δ cDNA of mice and humans but absent in rats. Immunofluorescence analysis of AKAP7 protein localization in both rat and mouse heart suggests AKAP7γ replaces AKAP7δ at the cardiac sarcoplasmic reticulum in species other than rat. DNA sequencing identified Human AKAP7δ insertion-deletions (indels) that promote the production of AKAP7γ instead of AKAP7δ.</p> <p>Conclusions</p> <p>This AKAP7 molecular evolution study shows that these vital scaffolding proteins developed in ancestral vertebrates and that independent mutations in the AKAP7 genes of rodents and early primates has resulted in the recent formation of AKAP7δ, a splice variant of likely lesser importance in humans than currently described.</p

Avoiding future controversies in the Alzheimer’s disease space through understanding the aducanumab data and FDA review

Abstract Key points of disagreement between the aducanumab FDA statistical review, which had primarily negative conclusions, and the clinical review, which had primarily positive conclusions, were investigated. Results from secondary endpoints in positive Study 302 were significant and these endpoints provided meaningful additional information. Findings indicate the statistical review of the aducanumab data was incorrect in a number of key areas. Greater placebo decline was not responsible for the significant results in Study 302. Correlations did exist between reduction in β-amyloid and clinical outcomes. Missing data and functional unblinding did not likely bias results. In contrast, the clinical review went too far in saying the negative results in Study 301 did not detract from the positive results in Study 302, as all clinical data should be considered in the evaluation, and the clinical review accepted the company’s explanation for divergence of the results between the studies although much of the divergence remained unexplained. Interestingly, both the statistical review and the clinical review considered the available efficacy evidence despite both studies being terminated early. Implications of these findings include that the divergence in results seen in the two phase 3 aducanumab studies can be expected in other studies with similar design and analysis. Therefore, further research is needed to determine if analysis methods other than MMRM and/or optimized outcomes will provide more consistent results across studies

Genome-Wide Gene Expression Analysis Shows AKAP13-Mediated PKD1 Signaling Regulates the Transcriptional Response to Cardiac Hypertrophy

<div><p>In the heart, scaffolding proteins such as A-Kinase Anchoring Proteins (AKAPs) play a crucial role in normal cellular function by serving as a signaling hub for multiple protein kinases including protein kinase D1 (PKD1). Under cardiac hypertrophic conditions AKAP13 anchored PKD1 activates the transcription factor MEF2 leading to subsequent fetal gene activation and hypertrophic response. We used an expression microarray to identify the global transcriptional response in the hearts of wild-type mice expressing the native form of AKAP13 compared to a gene-trap mouse model expressing a truncated form of AKAP13 that is unable to bind PKD1 (AKAP13-ΔPKD1). Microarray analysis showed that AKAP13-ΔPKD1 mice broadly failed to exhibit the transcriptional profile normally associated with compensatory cardiac hypertrophy following trans-aortic constriction (TAC). The identified differentially expressed genes in WT and AKAP13-ΔPKD1 hearts are vital for the compensatory hypertrophic response to pressure-overload and include myofilament, apoptotic, and cell growth/differentiation genes in addition to genes not previously identified as affected by AKAP13-anchored PKD1. Our results show that AKAP13-PKD1 signaling is critical for transcriptional regulation of key contractile, cell death, and metabolic pathways during the development of compensatory hypertrophy <i>in vivo</i>.</p></div