Decoding gene regulation in the fly brain
Jasper JanssensSara AibarIbrahim Ihsan TaskiranJoy N. IsmailAlicia Estacio‐GómezGabriel AugheyKatina I. SpanierFlorian De RopCarmen Bravo González‐BlasMarc DionneKrista GrimesXiao Jiang QuanDafni PapasokratiGert HulselmansSamira MakhzamiMaxime De WaegeneerValerie ChristiaensTony D. SouthallStein Aerts
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Keywords:
Cell type
Gene regulatory network
Reprogramming
Abstract Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. These networks reconfigure during dynamic processes such as cell fate specification to drive diverse cellular states. Single-cell transcriptomic technologies, such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine the transcriptional state of individual cells, allowing the study of cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific gene regulatory networks from these datasets are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the gene regulatory network for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated, published and newly collected single cell omic datasets, we show that scMTNI is able to accurately infer gene regulatory networks and captures meaningful network dynamics that identify GRN components associated with cell type transitions. Application of our method to mouse cellular reprogramming identified key regulators associated with cell populations that reprogram versus those that are stalled. Taken together, scMTNI is a powerful framework to infer cell type-specific gene regulatory networks and their dynamics from scRNA-seq and scATAC-seq datasets.
Gene regulatory network
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Cell fate determination
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Studies demonstrate that new cell birth occurs in adult brain,the rate of neurogenesis and the survival of new neurons are regulated by a number of environmental and pharmacological factors.The presence of neural progenitors in the adult mammalian brain raises the possibility that adult neurogenesis exists as a substrate for neural plasticity.Moreover,the continued production of neurons within the adult brain suggests that an understanding of adult neurogenesis may be of therapeutic relevance.In this review the factors influencing adult neurogenesis are discussed.
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Reprogramming of somatic cells to induced pluripotent stem cells, by overexpressing certain factors referred to as the reprogramming factors, can revolutionize regenerative medicine. To provide a coherent description of induced pluripotency from the gene regulation perspective, we use 35 microarray datasets to construct a reprogramming gene regulatory network. Comprising 276 nodes and 4471 links, the resulting network is, to the best of our knowledge, the largest gene regulatory network constructed for human fibroblast reprogramming and it is the only one built using a large number of experimental datasets. To build the network, a model that relates the expression profiles of the initial (fibroblast) and final (induced pluripotent stem cell) states is proposed and the model parameters (link strengths) are fitted using the experimental data. Twenty nine additional experimental datasets are collectively used to test the model/network, and good agreement between experimental and predicted gene expression profiles is found. We show that the model in conjunction with the constructed network can make useful predictions. For example, we demonstrate that our approach can incorporate the effect of reprogramming factor stoichiometry and that its predictions are consistent with the experimentally observed trends in reprogramming efficiency when the stoichiometric ratios vary. Using our model/network, we also suggest new (not used in training of the model) candidate sets of reprogramming factors, many of which have already been experimentally verified. These results suggest our model/network can potentially be used in devising new recipes for induced pluripotency with higher efficiencies. Additionally, we classify the links of the network into three classes of different importance, prioritizing them for experimental verification. We show that many of the links in the top ranked class are experimentally known to be important in reprogramming. Finally, comparing with other methods, we show that using our model is advantageous.
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Transdifferentiation
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Regenerative Medicine
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Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosis of the molecular changes in the differentiation of ESCs into specific organs. We describe a new approach to infer cell-type specific gene regulatory programs based on gene regulatory interactions in ESCs. Our method infers the molecular logic of gene regulatory mechanisms by mapping the position-specific combinatory patterns of numerous regulators in ESCs into cell-type specific gene regulations. We validate the proposed approach by recapitulating the RNA-seq and microarray data of neuronal progenitor cells, adult liver cells, and ESCs from the integrated patterns of diverse gene regulators in ESCs. We find that the collective functions of diverse gene regulators in ESCs represent distinct gene regulatory programs in specialized cell types. Our new approach expands our understanding of the differential gene regulatory information in developments encoded in regulatory networks of ESCs.
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New neurons are continuously born in the hippocampus of several mammalian species throughout adulthood. Adult neurogenesis represents a natural model for understanding how to grow and incorporate new nerve cells into preexisting circuits in the brain. Finding molecules or biological pathways that increase neurogenesis has broad potential for regenerative medicine. One strategy is to identify mouse strains that display large vs. small increases in neurogenesis in response to wheel running so that the strains can be contrasted to find common genes or biological pathways associated with enhanced neuron formation. Therefore, mice from 12 different isogenic strains were housed with or without running wheels for 43 days to measure the genetic regulation of exercise-induced neurogenesis. During the first 10 days mice received daily injections of 5-bromo-2'-deoxyuridine (BrdU) to label dividing cells. Neurogenesis was measured as the total number of BrdU cells co-expressing NeuN mature neuronal marker in the hippocampal granule cell layer by immunohistochemistry. Exercise increased neurogenesis in all strains, but the magnitude significantly depended on genotype. Strain means for distance run on wheels, but not distance traveled in cages without wheels, were significantly correlated with strain mean level of neurogenesis. Furthermore, certain strains displayed greater neurogenesis than others for a fixed level of running. Strain means for neurogenesis under sedentary conditions were not correlated with neurogenesis under runner conditions suggesting that different genes influence baseline vs. exercise-induced neurogenesis. Genetic contributions to exercise-induced hippocampal neurogenesis suggest that it may be possible to identify genes and pathways associated with enhanced neuroplastic responses to exercise.
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Neural stem cells are multipotent stem cells that generate functional newborn neurons through a process called neurogenesis. Neurogenesis in the adult brain is tightly regulated and plays a pivotal role in the maintenance of brain function. Disruption of adult neurogenesis impairs cognitive function and is correlated with numerous neurologic disorders. Deciphering the mechanisms underlying adult neurogenesis not only advances our understanding of how the brain functions, but also offers new insight into neurologic diseases and potentially contributes to the development of effective treatments. The field of adult neurogenesis is experiencing significant growth in China. Chinese researchers have demonstrated a multitude of factors governing adult neurogenesis and revealed the underlying mechanisms of and correlations between adult neurogenesis and neurologic disorders. Here, we provide an overview of recent advancements in the field of adult neurogenesis due to Chinese scientists.
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The dentate gyrus (DG) is one of only two brain structures known to retain the ability to produce new neurons in adulthood. The functional significance of adult neurogenesis in the DG is not yet well understood, but recent evidence has implicated adult neurogenesis in the etiology and treatment of depression. Elevated stress hormone levels, which are present in some depressed patients and can precipitate the onset of depression, reduce neurogenesis in animal models. Conversely, virtually all antidepressant treatments studied to date, including drugs of various classes, electroconvulsive therapy, and behavioral treatments, increase neurogenesis in the DG. We critically review this literature linking DG neurogenesis with depression, looking to both animal and human studies. We conclude that a reduction in neurogenesis by itself is not likely to produce depression. However, at least some therapeutic effects of antidepressant treatments appear to be neurogenesis-dependent. We review the cellular pathways through which antidepressant drugs boost neurogenesis and present several hypotheses about how DG neurogenesis may be instrumental in the therapeutic effects of these drugs.
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Neurons and glias are produced from neural stem cells. These phenomena are called "Neurogenesis." Neurogenesis largely occurs in developmental stages. However, it is now known that active neurogenesis continues throughout life in discrete regions such as the hippocampus of the adult brain of all mammals, including humans. Neurogenesis can be affected by various genetic or environmental factors. Neurogenesis is related to learning and memory and may also have a function in the vulnerability to the onset of mental illness (Neurogenesis theory). We have studied this theory by using rodents and tried to improve psychotic behavior by enhancing postnatal neurogenesis. Our results showed that administration of polyunsaturated fatty acids or breeding the animals in exciting environments improved psychotic behavior, suggesting their usefulness in preventing or curing mental illness which follows declining neurogenesis.
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Uncovering gene regulatory mechanisms in individual cells can provide insight into cell heterogeneity and function. Recent accumulated Single-Cell RNA-Seq data have made it possible to analyze gene regulation at single-cell resolution. Understanding cell-type-specific gene regulation can assist in more accurate cell type and state identification. Computational approaches utilizing such relationships are under development. Methods pioneering in integrating gene regulatory mechanism discovery with cell-type classification encounter challenges such as determine gene regulatory relationships and incorporate gene regulatory network structure. To fill this gap, we developed INSISTC, a computational method to incorporate gene regulatory network structure information for single-cell type classification. INSISTC is capable of identifying cell-type-specific gene regulatory mechanisms while performing single-cell type classification. INSISTC demonstrated its accuracy in cell type classification and its potential for providing insight into molecular mechanisms specific to individual cells. In comparison with the alternative methods, INSISTC demonstrated its complementary performance for gene regulation interpretation.
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Identification
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