Integrative transcriptome profiling of cognitive aging and its preservation through Ser/Thr protein phosphatase regulation

Environmental enrichment has been reported to delay or restore age-related cognitive deficits, however, a mechanism to account for the cause and progression of normal cognitive decline and its preservation by environmental enrichment is lacking. Using genome-wide SAGE-Seq, we provide a global assessment of differentially expressed genes altered with age and environmental enrichment in the hippocampus. Qualitative and quantitative proteomics in naïve young and aged mice was used to further identify phosphorylated proteins differentially expressed with age. We found that increased expression of endogenous protein phosphatase-1 inhibitors in aged mice may be characteristic of long-term environmental enrichment and improved cognitive status. As such, hippocampus-dependent performances in spatial, recognition, and associative memories, which are sensitive to aging, were preserved by environmental enrichment and accompanied by decreased protein phosphatase activity. Age-associated phosphorylated proteins were also found to correspond to the functional categories of age-associated genes identified through transcriptome analysis. Together, this study provides a comprehensive map of the transcriptome and proteome in the aging brain, and elucidates endogenous protein phosphatase-1 inhibition as a potential means through which environmental enrichment may ameliorate age-related cognitive deficits

Sleep pharmacogenetics: personalized sleep-wake therapy

Research spanning (genetically engineered) animal models, healthy volunteers, and sleep-disordered patients has identified the neurotransmitters and neuromodulators dopamine, serotonin, norepinephrine, histamine, hypocretin, melatonin, glutamate, acetylcholine, γ-amino-butyric acid, and adenosine as important players in the regulation and maintenance of wakefulness, rapid-eye-movement (REM) sleep, and non-rapid-eye-movement (NREM) sleep. Dysregulation of these neurochemical systems leads to sleep-wake disorders. Most currently available pharmacological treatments are symptomatic rather than causal, and their beneficial and adverse effects are often variable and in part genetically determined. To evaluate opportunities for evidence-based personalized medicine with present and future sleep-wake therapeutics, we review here the impact of known genetic variants affecting exposure of and sensitivity to drugs targeting the neurochemistry of sleep-wake regulation and the pathophysiology of sleep-wake disturbances. Many functional polymorphisms modify drug response phenotypes relevant for sleep. To corroborate the importance of these and newly identified variants for personalized sleep-wake therapy, human sleep pharmacogenetics should be complemented with pharmacogenomic investigations, research about sleep-wake-dependent pharmacological actions, and studies in mice lacking specific genes. These strategies, together with future knowledge about epigenetic mechanisms affecting sleep-wake physiology and treatment outcomes, may lead to potent and safe novel therapies for the increasing number of sleep-disordered patients (e.g., in aged populations). Expected final online publication date for the Annual Review of Pharmacology and Toxicology Volume 56 is January 06, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates

Assessment of aged and young mice after several weeks of undisturbed housing in EE or SH.

<p>(<b>A</b>) Fear conditioning in a novel context (FC2) and (<b>B</b>) memory test 24 hours later in the same context (n = 8, 6, 7, 7 for Aged EE (solid red), Aged SH (red stripes), Young EE (solid blue), Young SH (blue stripes), respectively; <i>F</i>_3,24 = 3.646). Escape latency to a hidden platform in an alternate Morris water maze and room (MWM2), different than that of MWM1, (<b>C</b>) by age and (<b>D</b>) separated by age and housing conditions (n = 11, 11, 11, 10 for Aged EE (red line), Aged SH (red dashes), Young EE (blue line), Young SH (blue dashes), respectively; days 1–5, <i>F</i>_3,39 = 5.524, p < 0.01; days 6–9, <i>F</i>_3,39 = 4.307, p < 0.05; days 1–9, <i>F</i>_3,39 = 4.652, p < 0.01; *<i>p</i> values shown with respect to aged (red) and young (blue); ^§<i>p</i> < 0.05 (Aged EE to Young SH); ^†<i>p</i> < 0.01 (Young EE to Aged SH); ^‡<i>p</i> < 0.05 (Young EE to Aged EE). Probe trial on day 10 with the hidden platform removed, (<b>E</b>) separated by age and housing conditions (O, opposite; R, right; L, left; T, target). *<i>p</i> < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001. Shown as mean ± s.e.m.</p

Recognition memory in aged and young mice following respective housing conditions.

<p>(<b>A</b>) Experimental design of the displaced and novel object recognition memory (DNOR) tasks over two days in 5 min blocks with 5 min ITI (n = 9, 8, 9, 8 for Aged EE (solid red), Aged SH (red stripes), Young EE (solid blue), Young SH (blue stripes), respectively). Recognition test of a displaced object 24 hours after training (<b>B</b>), shown as a ratio of time spent with the displaced object over all objects, show no difference in group preferences for the displaced object (<i>F</i>_3,30 = 2.216). Test for recognition of a novel object shows differing group preferences for the novel object relative to the pre-existing objects (<b>C</b>), shown as a discrimination ratio for the novel object (<i>F</i>_3,30 = 3.316). *<i>p</i> < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001. Shown as mean ± s.e.m.</p

Hippocampal genes associated with EE in aged and young mice using SAGE-Seq.

<p>(<b>A</b>) Unbiased clustering of transcripts differentially expressed in young EE (EY) compared to young SH (SY). Clusters 2 and 5 are associated with EY and clusters 1, 3, 4, and 6 are associated with SY. Counts are cutoff at 2000 for visualization. (<b>B</b>) Clustering of transcripts differentially expressed in aged EE (EA) compared to aged SH (SA). Clusters 1, 5, and 6 are associated with EA and clusters 2, 3, and 4 are associated with SA. (<b>C</b>) Heatmap of the 27,581 genes shown as absolute expression levels greater than 250 transcripts (yellow), less than 100 transcripts (blue), and counts inbetween are in shades of green. Transcript levels range from 0–76,000, and EA average of 513 and median of 37, EY average of 484 and median of 42, SA average of 285 and median of 21, and SY average of 455 and median of 40. Distribution of GO categories in (<b>D</b>) EE, (<b>E</b>) SH, (<b>F</b>) young (YG), and (<b>G</b>) aged (AG). GO terms were classified into ten functional groups including, clockwise from DNA maintenance (blue), protein dynamics (green), transcriptional activity (orange), biosynthesis (red), morphogenesis and developmental processes (violet), receptor and channel function (grey), cellular signaling pathways (cornflower blue), intracellular components (pale green), extracellular components (pale orange), and metabolic and homeostatic functions (pale red). The broader categories of binding, cell, and metabolism were excluded.</p

Measure of protein phosphatases’ activity following 6 weeks of respective housing conditions.

<p>(<b>A</b>) Absolute quantitation of free phosphates released in whole hippocampal fractions due to PP1 and PP2A activities (n = 6, 6, 6, 6 for Aged EE (solid red), Aged SH (red stripes), Young EE (solid blue), Young SH (blue stripes), respectively; <i>F</i>_3,20 = 6.591; ^§<i>p</i> < 0.05 relative to both aged EE and young EE). (<b>B</b>) Free phosphates released due to calcineurin activity (<i>F</i>_3,20 = 4.274; ^†<i>p</i> < 0.05 relative to aged EE). *<i>p</i> < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001. Shown as mean ± s.e.m.</p

Assessment of middle-aged and young mice before separation into EE and SH.

<p>The schedule of contextual fear conditioning (<b>A</b>; 18 aged and 16 young mice) and Morris water maze tests (<b>B</b>; 22 aged and 21 young mice) before and after separation into respective housing conditions. Hab: habituation period, OF: Open field, FC: Fear conditioning, MWM: Morris water maze. (<b>C</b>) Fear conditioning in the first context and (<b>D</b>) accompanying memory test 24 hours later in the original context. (<b>E</b>) Escape latency to find the hidden platform in the Morris water maze test across 10 days of training and (<b>F</b>) probe trial on day 11 with the hidden platform removed (T, target; R, right; L, left; O, opposite). *<i>p</i> < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001. Shown as mean ± s.e.m.</p