Single neuron analysis of aging associated changes in learning reveals escalating impairments in transcriptional plasticity
Ontology highlight
ABSTRACT:
ORGANISM(S): Aplysia californica
PROVIDER: GSE234983 | GEO | 2024/06/14
REPOSITORIES: GEO
Similar Datasets
Project description:We used a custom-designed microarray and qPCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to repeated noxious shocks to one side of the body (4 ten-second shocks at 90mA, 30 min ISI), a procedure known to induce a transcription-dependent and long-lasting increase in reflex responsiveness that is restricted to the side of training. One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory. Â Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 102 transcripts. We used qPCR to test a subset of these transcripts and found that 86% were confirmed in the same samples, and 83% of these were again confirmed in an independent sample (n = 9 animals). Thus, our new microarray design shows very strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia. Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings. Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which encode a C/EBP gamma, a glycine transporter, and a vacuolar-protein-sorting-associated protein. Within-subjects comparison of trained (Cy5) to untrained (Cy3) pleural ganglia with 8 biological replicates. Each replicate is a trained sample from two animals (right and left trained) and each untrained sample is from the same two aniamls (right and left untrained)
2014-05-08 | E-GEOD-57458 | biostudies-arrayexpress
Project description:The complexity of events associated with age-related memory loss (ARML) cannot be overestimated. The problem is further complicated by the enormous diversity of neurons in the CNS and even synapses of one neuron within a neural circuit. Large-scale single-neuron analysis is not only challenging but mostly impractical for any model currently used in ARML. We simply do not know: do all neurons and synapses age differently or are some neurons (or synapses) more resistant to aging than others? What is happening in any given neuron while it undergoes “normal” aging? What are the genomic changes that make aging apparently irreversible? What would be the balance between neuron-specific vs global genome-wide changes in aging? In the proposed paper we address these questions and develop a new model to study the entire scope of genomic and epigenomic regulation in aging at the resolution of single functionally characterized cells and even cell compartments. In particular, the mollusc Aplysia californica has been implemented as a powerful paradigm in addressing fundamental questions of the neurobiology of aging. The proposed manuscript will consist of four parts. First, we will provide an introduction to Aplysia as a representative of the largest superclade of bilaterian animals (Lophotrochozoa). Aplysia has a short lifespan of 220-300 days with a well-characterized life cycle and characterized phenomenology of aging. Most importantly, Aplysia possess the largest nerve cells in the entire animal kingdom (only eggs are larger); these cells can be uniquely identified and mapped in terms of their well-defined interactions with other neurons forming relatively simpler neural circuits underlying several stereotypic and learned behaviors. Second, we have identified in Aplysia more that a hundred neurological- and age-related genes that were lost in other established invertebrate models (such as Drosophila and C. elegans). The proposed long-term regulatory age-related mechanisms include a high level of conservation among many epigenetic processes known to be lost in nematodes and flies with extremely short lifecycles and particularly derived genomes. We also identify and cloned more than 30 evolutionarily conserved homologs of genes involved in Alzheimer’s, Parkinson’s and Huntington’s diseases as well as age-related hormones. Third, we performed genome-wide analysis of expression patterns of more than 55,000 unique transcripts by comparing two different identified cholinergic neurons (R2 and LPl1) among young and aged animals. This direct single neuron genomic analysis indicates that there are significant cell-specific changes in gene-expression profiles as a function of aging. We estimated that only ~10-20% of genes that are differently expressed in the aging brain are common for all neuronal types - the remaining 80% are neuron-specific (i.e. found in aging neurons of one but not another type). The list of “common aging genes” includes components of insulin growth factor pathways, cell bioenergetics, telomerase-associated proteins, antioxidant enzymes, water channels and estrogen receptors. The rest were neuron-specific gene products (including apoptosis-related proteins, Alzheimer-related genes, growth factors and their receptors, ionic channels, transcription factors and more than 120 identified proteins known to be involved in neurodevelopment and synaptogenesis). Surprisingly, even two different identified cholinergic motoneurons age differently and each of them has a unique subset of genes differentially expressed in older animals. Fourth, we showed that the activity of the entire genome and associated epigenomic modifications (e.g. DNA methylation, histone dynamics) can be efficiently monitored within a single Aplysia neuron and can be modified as a function of aging in a neuron-specific manner including selective histones and histone-modifying enzymes and DNA methylation-related enzymes. This genome-wide analysis of aging allows us to propose novel mechanisms of active DNA demethylation and cell-specific methylation as well as regional relocation of RNAs as three key processes underlying age-related memory loss. These mechanisms tune the dynamics of long-term chromatin remodeling, control weakening and the loss of synaptic connections in aging. At the same time, our genomic tests revealed evolutionarily conserved gene clusters in the Aplysia genome associated with senescence and regeneration (e.g. apoptosis- and redox- dependent processes, insulin signaling, etc.). This is a reference design experiment with all samples being compared to one CNS from Aplysia. Two cholinergic neurons (R2 and LPl1), two ages (young and old), two arrays (AAA and DAA), three biological replicates each sample type. Two direct comparison experiments were also performed. One with young and old abdominal ganglion and the other with young and old R2.
2010-05-20 | E-GEOD-18783 | biostudies-arrayexpress
Project description:We used a custom-designed microarray and qPCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to repeated noxious shocks to one side of the body (4 ten-second shocks at 90mA, 30 min ISI), a procedure known to induce a transcription-dependent and long-lasting increase in reflex responsiveness that is restricted to the side of training. One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory. Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 102 transcripts. We used qPCR to test a subset of these transcripts and found that 86% were confirmed in the same samples, and 83% of these were again confirmed in an independent sample (n = 9 animals). Thus, our new microarray design shows very strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia. Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings. Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which encode a C/EBP gamma, a glycine transporter, and a vacuolar-protein-sorting-associated protein.
2014-05-08 | GSE57458 | GEO
Project description:Despite the advances in our understanding of aging-associated behavioral decline, we know relatively little about how aging affect neural circuits that underlie specific behaviors. Specifically, we know little about how aging affect expression of genes in specific neural circuits. We have now addressed this problem by exploring a cholinergic neuron R15, an identified neuron of marine snail Aplysia. R15 is characterized by bursting action potentials and is implicated in reproduction, osmoregulation and locomotion. We examined changes in gene expression in R15 neurons during aging by microarray analyses of RNAs prepared from two different age groups, mature and old animals. Specifically we find that 1083 ESTs are differentially regulated in mature and old R15 neurons. Bioinformatics analyses of these genes have identified specific biological pathways and molecular processes that are up or down regulated in mature and old neurons. Comparison with human signaling networks using pathway analyses have identified three major networks that are altered in old R15 neurons. Furthermore, by single neuron qRTPCR we examined expression levels of candidate regulators involved in transcription (CREB1) and translation (S6 kinase) and find that aging is associated with a decrease in expression of these regulators. We next studied expression of CREB1 and S6 kinase in two different motor neurons (L7 and L11) and another cholinergic neuron R2 and find that these neurons have characteristic changes in gene expression during aging
2014-02-05 | E-GEOD-46618 | biostudies-arrayexpress
Project description:Aplysia pleural Ganglia 1 Hour After Long-Term Sensitization Training
| PRJNA246488 | ENA
Project description:Aplysia Pleural Ganglia 24 Hours After Long-Term Sensitization Training
| PRJNA377703 | ENA
Project description:Aplysia Pleural Ganglia 7 Days After Long-Term Sensitization Training
| PRJNA389603 | ENA
Project description:The complexity of events associated with age-related memory loss (ARML) cannot be overestimated. The problem is further complicated by the enormous diversity of neurons in the CNS and even synapses of one neuron within a neural circuit. Large-scale single-neuron analysis is not only challenging but mostly impractical for any model currently used in ARML. We simply do not know: do all neurons and synapses age differently or are some neurons (or synapses) more resistant to aging than others? What is happening in any given neuron while it undergoes “normal” aging? What are the genomic changes that make aging apparently irreversible? What would be the balance between neuron-specific vs global genome-wide changes in aging? In the proposed paper we address these questions and develop a new model to study the entire scope of genomic and epigenomic regulation in aging at the resolution of single functionally characterized cells and even cell compartments. In particular, the mollusc Aplysia californica has been implemented as a powerful paradigm in addressing fundamental questions of the neurobiology of aging. The proposed manuscript will consist of four parts. First, we will provide an introduction to Aplysia as a representative of the largest superclade of bilaterian animals (Lophotrochozoa). Aplysia has a short lifespan of 220-300 days with a well-characterized life cycle and characterized phenomenology of aging. Most importantly, Aplysia possess the largest nerve cells in the entire animal kingdom (only eggs are larger); these cells can be uniquely identified and mapped in terms of their well-defined interactions with other neurons forming relatively simpler neural circuits underlying several stereotypic and learned behaviors. Second, we have identified in Aplysia more that a hundred neurological- and age-related genes that were lost in other established invertebrate models (such as Drosophila and C. elegans). The proposed long-term regulatory age-related mechanisms include a high level of conservation among many epigenetic processes known to be lost in nematodes and flies with extremely short lifecycles and particularly derived genomes. We also identify and cloned more than 30 evolutionarily conserved homologs of genes involved in Alzheimer’s, Parkinson’s and Huntington’s diseases as well as age-related hormones. Third, we performed genome-wide analysis of expression patterns of more than 55,000 unique transcripts by comparing two different identified cholinergic neurons (R2 and LPl1) among young and aged animals. This direct single neuron genomic analysis indicates that there are significant cell-specific changes in gene-expression profiles as a function of aging. We estimated that only ~10-20% of genes that are differently expressed in the aging brain are common for all neuronal types - the remaining 80% are neuron-specific (i.e. found in aging neurons of one but not another type). The list of “common aging genes” includes components of insulin growth factor pathways, cell bioenergetics, telomerase-associated proteins, antioxidant enzymes, water channels and estrogen receptors. The rest were neuron-specific gene products (including apoptosis-related proteins, Alzheimer-related genes, growth factors and their receptors, ionic channels, transcription factors and more than 120 identified proteins known to be involved in neurodevelopment and synaptogenesis). Surprisingly, even two different identified cholinergic motoneurons age differently and each of them has a unique subset of genes differentially expressed in older animals. Fourth, we showed that the activity of the entire genome and associated epigenomic modifications (e.g. DNA methylation, histone dynamics) can be efficiently monitored within a single Aplysia neuron and can be modified as a function of aging in a neuron-specific manner including selective histones and histone-modifying enzymes and DNA methylation-related enzymes. This genome-wide analysis of aging allows us to propose novel mechanisms of active DNA demethylation and cell-specific methylation as well as regional relocation of RNAs as three key processes underlying age-related memory loss. These mechanisms tune the dynamics of long-term chromatin remodeling, control weakening and the loss of synaptic connections in aging. At the same time, our genomic tests revealed evolutionarily conserved gene clusters in the Aplysia genome associated with senescence and regeneration (e.g. apoptosis- and redox- dependent processes, insulin signaling, etc.).
2010-05-20 | GSE18783 | GEO
Project description:We used a custom-designed microarray and qPCR to characterize the persistent transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock). Training produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training). Immediately after 24h post-tests, pleural ganglia was harvested. Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression. The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.
2017-03-03 | GSE95596 | GEO
Project description:New, Forgotten, and Savings Memory for Long-Term Sensitization in Aplysia Pleural Ganglia
| PRJNA638149 | ENA