An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

The transcription factor Hypoxia-inducible factor 1 (HIF-1) plays a central role in the transcriptional response to oxygen flux. To gain insight into the molecular pathways regulated by HIF-1, it is essential to identify the downstream-target genes. We report here a strategy to identify HIF-1-target genes based on an integrative genomic approach combining computational strategies and experimental validation. To identify HIF-1-target genes microarrays data sets were used to rank genes based on their differential response to hypoxia. The proximal promoters of these genes were then analyzed for the presence of conserved HIF-1-binding sites. Genes were scored and ranked based on their response to hypoxia and their HIF-binding site score. Using this strategy we recovered 41% of the previously confirmed HIF-1-target genes that responded to hypoxia in the microarrays and provide a catalogue of predicted HIF-1 targets. We present experimental validation for ANKRD37 as a novel HIF-1-target gene. Together these analyses demonstrate the potential to recover novel HIF-1-target genes and the discovery of mammalian-regulatory elements operative in the context of microarray data sets

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases

The impact of PICALM genetic variations on reserve capacity of posterior cingulate in AD continuum

Phosphatidylinositolbinding clathrin assembly protein (PICALM) gene is one novel genetic player associated with late-onset Alzheimer’s disease (LOAD), based on recent genome wide association studies (GWAS). However, how it affects AD occurrence is still unknown. Brain reserve hypothesis highlights the tolerant capacities of brain as a passive means to fight against neurodegenerations. Here, we took the baseline volume and/or thickness of LOAD-associated brain regions as proxies of brain reserve capacities and investigated whether PICALM genetic variations can influence the baseline reserve capacities and the longitudinal atrophy rate of these specific regions using data from Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. In mixed population, we found that brain region significantly affected by PICALM genetic variations was majorly restricted to posterior cingulate. In sub-population analysis, we found that one PICALM variation (C allele of rs642949) was associated with larger baseline thickness of posterior cingulate in health. We found seven variations in health and two variations (rs543293 and rs592297) in individuals with mild cognitive impairment were associated with slower atrophy rate of posterior cingulate. Our study provided preliminary evidences supporting that PICALM variations render protections by facilitating reserve capacities of posterior cingulate in non-demented elderly

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Serotonergic agonists facilitate forelimb recovery in rats with cervical spinal cord injury

Serotonergic agents have been shown to improve the recovery of stepping ability in spinalized animals, but not yet of reaching and grasping ability. In the present study we tested whether buspirone, a serotonin 5-HT1A receptor agonist, or fluoxetine, a selective serotonin reuptake inhibitor, would facilitate forelimb motor function recovery after a C4 bilateral dorsal funiculi crush in adult female rats. Following injury, there was a significant decrease in single-pellet reaching and ladder-rung walking performance in all injured rats. From 1-6 weeks post-injury, 31 rats were tested on these tasks with and without Buspirone 1-2 mg/kg; or Fluoxetine 1-5 mg/kg. Buspirone reaching and grasping success rates improved rapidly within 2 weeks post-injury and plateaued over the next 4 weeks of testing. Forelimb performance after buspirone treatment returned to sham levels within 2 weeks of buspirone withdrawal. Fluoxetine treatment resulted in a progressive improvement in performance over 8 weeks, but performance on the ladder test did not change. The improved accuracy of reaching and grasping and the increase in spinal motor evoked potentials demonstrate improved supraspinal-spinal connectivity and within and among spinal sensory-motor networks. Combined these data suggest that buspirone or fluoxetine treatment has therapeutic potential for functional recovery after a cervical spinal cord injury

Serotonergic agonists facilitate forelimb recovery in rats with cervical spinal cord injury

Serotonergic agents have been shown to improve the recovery of stepping ability in spinalized animals, but not yet of reaching and grasping ability. In the present study we tested whether buspirone, a serotonin 5-HT1A receptor agonist, or fluoxetine, a selective serotonin reuptake inhibitor, would facilitate forelimb motor function recovery after a C4 bilateral dorsal funiculi crush in adult female rats. Following injury, there was a significant decrease in single-pellet reaching and ladder-rung walking performance in all injured rats. From 1-6 weeks post-injury, 31 rats were tested on these tasks with and without Buspirone 1-2 mg/kg; or Fluoxetine 1-5 mg/kg. Buspirone reaching and grasping success rates improved rapidly within 2 weeks post-injury and plateaued over the next 4 weeks of testing. Forelimb performance after buspirone treatment returned to sham levels within 2 weeks of buspirone withdrawal. Fluoxetine treatment resulted in a progressive improvement in performance over 8 weeks, but performance on the ladder test did not change. The improved accuracy of reaching and grasping and the increase in spinal motor evoked potentials demonstrate improved supraspinal-spinal connectivity and within and among spinal sensory-motor networks. Combined these data suggest that buspirone or fluoxetine treatment has therapeutic potential for functional recovery after a cervical spinal cord injury

Brain-wide mapping of fear memory circuits during development identifies a role for retrosplenial cortex in the emergence of persistent memory

Memories made early in life are rapidly forgotten, but those made later in life can last a lifetime. Recent work shows that early-formed memories leave a lasting trace in the brain, but why they fail to be retrieved remains poorly understood. Here, we performed a brain-wide screen to identify developmental changes in fear memory networks that align with the emergence of persistent memory. We used TRAP2 mice (Targeted Recombination in Active Populations) in combination with brain clearing and light sheet fluorescence microscopy to compare neuronal populations and networks activated by recent (1 day) fear memory retrieval at infant (P17), juvenile (P25) or adult (P60) stages. While adults had more functional connectivity with the thalamus and hypothalamus, infants had more functional connectivity within the cortex and olfactory areas at 1 day memory retrieval. Network analyses revealed that the functional organization of memory networks was also developmentally regulated. Infant memory network was highly interconnected across the entire brain, while the juvenile network was sparser. The adult fear memory network was sparse and more clustered, with most connections between cortical regions, hippocampal formation, amygdala, and striatum. Of these regions, the retrosplenial cortex (RSP), a key memory center, had activation patterns highly corresponding to successful memory retrieval at all ages. To further examine how RSP memory functions change with age, we examined the extent to which neurons activated during recent memory retrieval (1d) are reactivated during later memory retrieval (7d) at different ages. Adults had higher reactivation rates in RSP compared to younger groups, suggesting ensemble stability contributes to memory persistence. We next tested whether chemogenetic reactivation of tagged RSP ensembles could enhance memory. Chemogenetic RSP reactivation a week after learning enhanced memory retrieval in adults, but not in infants. In contrast, reactivating infant-tagged RSP ensembles a month later recovered forgotten memories. Together these data reveal specific changes in the activity and functional connectivity of brain regions and circuits that coincide with the developmental transition from amnesic to persistent memories. Particularly the RSP, which stores latent infant memories and continues to functionally mature with age, may contribute to the developmental emergence of persistent memories

Serotonergic Facilitation of Forelimb Functional Recovery in Rats with Cervical Spinal Cord Injury

Serotonergic agents can improve the recovery of motor ability after a spinal cord injury. Herein, we compare the effects of buspirone, a 5-HT1A receptor partial agonist, to fluoxetine, a selective serotonin reuptake inhibitor, on forelimb motor function recovery after a C4 bilateral dorsal funiculi crush in adult female rats. After injury, single pellet reaching performance and forelimb muscle activity decreased in all rats. From 1 to 6&nbsp;weeks after injury, rats were tested on these tasks with and without buspirone (1-2&nbsp;mg/kg) or fluoxetine (1-5&nbsp;mg/kg). Reaching and grasping success rates of buspirone-treated rats improved rapidly within 2&nbsp;weeks after injury and plateaued over the next 4&nbsp;weeks of testing. Electromyography (EMG) from selected muscles in the dominant forelimb showed that buspirone-treated animals used new reaching strategies to achieve success after the injury. However, forelimb performance dramatically decreased within 2&nbsp;weeks of buspirone withdrawal. In contrast, fluoxetine treatment resulted in a more progressive rate of improvement in forelimb performance over 8&nbsp;weeks after injury. Neither buspirone nor fluoxetine significantly improved quadrupedal locomotion on the horizontal ladder test. The improved accuracy of reaching and grasping, patterns of muscle activity, and increased excitability of spinal motor-evoked potentials after buspirone administration reflect extensive reorganization of connectivity within and between supraspinal and spinal sensory-motor netxcopy works. Thus, both serotonergic drugs, buspirone and fluoxetine, neuromodulated these networks to physiological states that enabled markedly improved forelimb function after cervical spinal cord injury