Single-cell transcriptomic classification of rabies-infected cortical neurons

Decision letter: Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

Gradients of the Drosophila Chinmo BTB-Zinc Finger Protein Govern Neuronal Temporal Identity

The Neuron Identity Problem: Form Meets Function

Hippocampal Pyramidal Neurons Comprise Two Distinct Cell Types that Are Countermodulated by Metabotropic Receptors

GATA Factor-Mediated Gene Regulation in Human Erythropoiesis.

In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.

Genes regulated by neuronal activity are the focal point of plasticity-related brain functions, thereby providing the basis for behavioural adaptations such as memory. Cellular functions of activity-regulated genes are diverse; several genes encode transcription factors thus regulating a wide range of downstream processes. Pro-survival genes such as Bdnf rendering neurons more resistant against cellular stress and degeneration are another important class of activity regulated genes. Due to those crucial functions, it is essential to understand the regulation and relevance of activity-induced genes under physiological conditions, but also their response to pathological signals like glutamate mediated excitotoxicity. To examine neuronal activity-dependent gene regulation in physiological as well as pathological environments, this thesis was divided into two parts. The first part investigated whether activity-regulated gene expression is correlated with memory ability by comparing two inbred mouse strains, C57BL/6 and DBA/2. Robust spatial memory impairments were observed for DBA/2. However, the cognitive deficits in DBA/2 were not exclusive for this type of memory. Analysis of basic characteristics such as morphology and electrophysiological properties of CA1 pyramidal neurons, which are crucial for spatial memory formation, revealed no strain difference. Also, activity-dependent gene induction was mostly similar between the strains in cell culture and in vivo after a learning paradigm. Yet, two genes, Inhba and Npas4, showed significantly increased basal expression and increased induction in DBA/2 hippocampal regions, respectively. Since both genes are implicated in excitation/inhibition regulation, inhibitory neuronal input for CA1 neurons via mIPSC electrophysiological recordings was analysed and revealed decreased inhibition in DBA/2. Attenuated inhibition may underlie the DBA/2 learning impairment. Yet, dysregulation of single activity-regulated genes, in particular Inhba and Npas4, correlates with differences in memory ability and might be involved in dysfunction processes. The second part of this thesis analysed activity-dependent gene expression during the pathological condition of excitotoxicity. Intriguingly, differential response pattern of activity-dependent genes towards toxic NMDA stimuli were observed. Single genes like Inhba and Bdnf were intensely downregulated by NMDA-induced active deactivation processes, in contrast, rapid immediate early genes like Arc, Npas4 or Nr4a1 displayed no transcriptional shut-off during excitotoxicity. By analysing the activity of upstream kinases and transcription factors the mechanism underlying the differential regulation was investigated. Fast signalling kinases like ERK1/2 seem to depend predominantly on synaptic activity, transcription factors, however, were broadly dephosphorylated after NMDA application. Furthermore, additional experiments indicate that excitotoxicity-induced mitochondrial depolarization does not act as initiator of active transcriptional downregulation. Together, the presented data illustrate that dysregulation of single activity-dependent genes occurs in a physiological model of memory impairment, but also under the pathological condition of excitotoxicity. Inhba might play an important role in both processes and for memory formation in general since it was dysregulated in both models which are implicated in memory attenuation.

Calretinin gene promoter activity is differently regulated in neurons and cancer cells. Role of AP2-like cis element and zinc ions

Transcription changes in cells taken from bronchoalveolar fluid of COVID-19 patients indicate severe disruption of coagulation and fibrinolytic pathways in the lung and suggest similar processes in other organs.

Losing a spouse or life partner is a deeply traumatic event that can have long-term repercussions. Given enough time, however, most surviving partners are able to process their grief. The neural processes that enable people to adapt to their loss remain unknown. To explore this question, scientists often turn to animals that form long-term mating based pair bonds and can be raised in the laboratory. Monogamous prairie voles enter lifelong partnerships where the two individuals live together, prefer to cuddle with each other, and take care of their pups as a team. After having lost their mate, they show signs of distress that eventually subside with time. Sadino et al. examined the biological impact of partner loss in these animals by focusing on the nucleus accumbens, a brain region important for social connections. This involved tracking gene expression – which genes were switched on and off in this area – as the voles established their pair bonds, and then at different time points after one of the partners had been removed. The experiments revealed that establishing a relationship leads to a stable shift in nucleus accumbens gene expression, which may help maintain bonds over time. In particular, genes related to glia (the non-neuronal cells which assist neurons in their tasks) see their expression levels increase, indicating a previously undescribed role for this cell type in regulating pair bonding. Having their partner removed led to an erosion of the gene expression pattern that had emerged during pair bonding; this may help the remaining vole adapt to its loss and go on to form a new bond. In addition, Sadino et al. explored the gene expression of only neurons in the nucleus accumbens and uncovered biological processes distinct from those that occur in glia after partner separation. Together, these results shed light on the genetic and neuronal mechanisms which underlie adaptation to loss; this knowledge could one day inform how to better support individuals during this time.

Losing a spouse or life partner is a deeply traumatic event that can have long-term repercussions. Given enough time, however, most surviving partners are able to process their grief. The neural processes that enable people to adapt to their loss remain unknown. To explore this question, scientists often turn to animals that form long-term mating based pair bonds and can be raised in the laboratory. Monogamous prairie voles enter lifelong partnerships where the two individuals live together, prefer to cuddle with each other, and take care of their pups as a team. After having lost their mate, they show signs of distress that eventually subside with time. Sadino et al. examined the biological impact of partner loss in these animals by focusing on the nucleus accumbens, a brain region important for social connections. This involved tracking gene expression – which genes were switched on and off in this area – as the voles established their pair bonds, and then at different time points after one of the partners had been removed. The experiments revealed that establishing a relationship leads to a stable shift in nucleus accumbens gene expression, which may help maintain bonds over time. In particular, genes related to glia (the non-neuronal cells which assist neurons in their tasks) see their expression levels increase, indicating a previously undescribed role for this cell type in regulating pair bonding. Having their partner removed led to an erosion of the gene expression pattern that had emerged during pair bonding; this may help the remaining vole adapt to its loss and go on to form a new bond. In addition, Sadino et al. explored the gene expression of only neurons in the nucleus accumbens and uncovered biological processes distinct from those that occur in glia after partner separation. Together, these results shed light on the genetic and neuronal mechanisms which underlie adaptation to loss; this knowledge could one day inform how to better support individuals during this time.

Losing a spouse or life partner is a deeply traumatic event that can have long-term repercussions. Given enough time, however, most surviving partners are able to process their grief. The neural processes that enable people to adapt to their loss remain unknown. To explore this question, scientists often turn to animals that form long-term mating based pair bonds and can be raised in the laboratory. Monogamous prairie voles enter lifelong partnerships where the two individuals live together, prefer to cuddle with each other, and take care of their pups as a team. After having lost their mate, they show signs of distress that eventually subside with time. Sadino et al. examined the biological impact of partner loss in these animals by focusing on the nucleus accumbens, a brain region important for social connections. This involved tracking gene expression – which genes were switched on and off in this area – as the voles established their pair bonds, and then at different time points after one of the partners had been removed. The experiments revealed that establishing a relationship leads to a stable shift in nucleus accumbens gene expression, which may help maintain bonds over time. In particular, genes related to glia (the non-neuronal cells which assist neurons in their tasks) see their expression levels increase, indicating a previously undescribed role for this cell type in regulating pair bonding. Having their partner removed led to an erosion of the gene expression pattern that had emerged during pair bonding; this may help the remaining vole adapt to its loss and go on to form a new bond. In addition, Sadino et al. explored the gene expression of only neurons in the nucleus accumbens and uncovered biological processes distinct from those that occur in glia after partner separation. Together, these results shed light on the genetic and neuronal mechanisms which underlie adaptation to loss; this knowledge could one day inform how to better support individuals during this time.

Transcription factors that drive neuron type-specific terminal differentiation programs in the developing nervous system are often expressed in several distinct neuronal cell types, but to what extent they have similar or distinct activities in individual neuronal cell types is generally not well explored. We investigate this problem using, as a starting point, the C. elegans LIM homeodomain transcription factor ttx-3, which acts as a terminal selector to drive the terminal differentiation program of the cholinergic AIY interneuron class. Using a panel of different terminal differentiation markers, including neurotransmitter synthesizing enzymes, neurotransmitter receptors and neuropeptides, we show that ttx-3 also controls the terminal differentiation program of two additional, distinct neuron types, namely the cholinergic AIA interneurons and the serotonergic NSM neurons. We show that the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors. One of the collaborating transcription factors is the POU homeobox gene unc-86, which collaborates with ttx-3 to determine the identity of the serotonergic NSM neurons. unc-86 in turn operates independently of ttx-3 in the anterior ganglion where it collaborates with the ARID-type transcription factor cfi-1 to determine the cholinergic identity of the IL2 sensory and URA motor neurons. In conclusion, transcription factors operate as terminal selectors in distinct combinations in different neuron types, defining neuron type-specific identity features.

As a means to understand human neuropsychiatric disorders from human brain samples, we compared the transcription patterns and histological features of postmortem brain to fresh human neocortex isolated immediately following surgical removal. Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern. To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval. Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization. Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection. Predicted transcriptional changes were confirmed histologically on the same tissue demonstrating that while neurons were degenerating, glial cells underwent an outgrowth of their processes. The rapid loss of neuronal genes and reciprocal expression of glial genes highlights highly dynamic transcriptional and cellular changes that occur during the postmortem interval. Understanding these time-dependent changes in gene expression in post mortem brain samples is critical for the interpretation of research studies on human brain disorders.

LMO4 Controls the Balance between Excitatory and Inhibitory Spinal V2 Interneurons