Single-cell RNA sequencing

A five-day practical course for experimentalists and computational biologists analysing single-cell RNA sequencing. Lectures and exercises follow data from sequencing files to expression matrices, quality control, normalisation, batch correction, dimensionality reduction, clustering, annotation and differential expression. Later sessions cover trajectory and pseudotime inference, RNA velocity, single-cell multi-omics integration and functional analysis. Participants finish with an independent dataset analysis and presentation. Bash and R/Bioconductor support reproducible workflows and interpre

…Whole-genome sequencing revealed homozygosity for an Apolipoprotein E mutation (Christchurch, APOECh). As the ApoECh mutation is found within the heparan sulfate proteoglycan (HSPG) binding domain, we hypothes

…Using single-cell RNA-sequencing, we identified interferon (IFN)-responsive oligodendrocytes, which localize in proximity to CD8+ T cells in aging white matter. Absence of functional lymphocytes decreased the number of IFN-responsive oligodendrocytes and rescued oligodendr

Octopuses are an emerging model organism in neurobiology due to their unique nervous system and capacity for intelligence. However, due to this novelty, nothing is currently known about many of their receptors, including those involved in neuromodulation. Given the historical significance of dopamine action in the brain and our recent findings implicating it as one of the three main neurotransmitters used in the optic lobe, we have chosen to explore dopaminergic GPCRs in Octopus vulgaris. We have identified approximately twenty candidate octopus monoamine GPCRs, utilising protein sequence simi

Cytoplasmic FMR1-interacting protein family contains two members, CYFIP1 and CYFIP2, evolutionarily conserved multifunctional proteins. Despite their high sequence homology, varied evidence indicates that CYFIP1 and CYFIP2 have distinct functions in vivo and are linked to different brain disorders. However, the underlying mechanisms remain largely unknown.We conducted reciprocal immunoprecipitation experiments to explore the underlying mechanisms using CYFIP1-2×Myc and CYFIP2-3×Flag knock-in mice. The results revealed that CYFIP1 and CYFIP2 are not significantly co-immunoprecipitated with each

…from 180 to over 1000 days using single-cell RNA-sequencing, electron microscopy and functional assays.Our analysis revealed various neuronal populations with specific subclusters that gradually decreased in complexity over time, while astrocyte populations became more prominent. We hy

Our research focuses on the elucidation of the PRPF31 gene mutation's impact on retinal cells, specifically within the context of Retinitis Pigmentosa (RP), employing human-induced pluripotent stem cells (hiPSCs). These hiPSCs, sourced from a patient with severe RP harboring the PRPF31 mutation and a healthy control, were differentiated into retinal organoids (ROs) using a refined protocol. The study's methodology encompassed a range of techniques including flow cytometry for assessing pluripotency, immunofluorescence and qPCR for progenitor and photoreceptor-specific markers, microelectrode a

Animals exhibit a stunning array of natural behaviors, many of which are innate and controlled by intricate neural circuits genetically specified. In the fruit fly, connectomics work has revealed precise patterns of neuronal connectivity and their computational potential. However, we lack a molecular understanding of how such circuit connectivity is established with synaptic specificity, in part because it remains challenging to define the molecular landscape and interactions at subcellular resolution in intact tissue. Taking advantage of the well-defined and accessible Drosophila motion visio

…Maternal immune activation (MIA) during gestation can disturb this delicate balance and increase the offsprings risk for neurodevelopmental disorders like schizophrenia and autism later in life.This study investigates the differential impact of MIA on neuronal progenitor cells at E10.5 (polyI:C administration at E9.5) by using single-cell RNA sequencing. Additionally, we examined the role of microglia in mediating the effects of MIA at different developmental stages.

The hippocampus plays an important role in memory formation. Hippocampal sharp wave ripples (SWRs) are critical for memory consolidation, during which a large number of hippocampal pyramidal neurons fire synchronously. Recent studies indicate that the participation of hippocampal pyramidal neurons in SWRs is variable. The variability may be explained by gene expression pattterns. However, there are no adequate methods to comprehensively analyze these molecular properties of a single neuron in the context of its electrophysiological spike patterns. Here, we developed an experimental technique t

…of these cells, we conducted single-cell RNA sequencing (scRNA-seq) on the cells in the lateral ventricle of E10.5 embryos. The scRNA-seq data were analyzed alongside transcript data from other brain-derived cells, enabling the identif

Maternal diet is a key determinant of later child’s metabolic and mental health outcomes. Human and/or animals consuming a western diet (WD), as compared to a healthy diet (HD), exhibit microbiota dysbiosis, low-grade inflammation, behavioral alterations and defects in the central reward circuit. Accordingly, epidemiological studies show that WD consumption during pregnancy is associated with adverse metabolic and mental health outcomes in offspring. We have developed a mouse model to study the impact of maternal WD on the offspring and challenged hypotheses related to dysbiosis, inflammation

…pattern elucidated by bulk and single-cell RNA sequencing performed on wt and HD isolated mouse striatal primordia at differ

CDKL5 deficiency disorder (CDD) is an X-linked neurodevelopmental disorder caused by mutations in the CDKL5 gene. CDD is characterized by early-onset epilepsy, global developmental delay, intellectual disability, autistic features, visual impairment, and motor impairment. The CDKL5 gene is located on the X-chromosome and is highly expressed in the forebrain. Despite some molecular and cellular functions of CDKL5 being revealed, gaps and controversies still exist between different studies. The molecular actions of CDKL5 in human-derived neurons and the effects of CDKL5 disruption remain unclear

…Here we combine single-cell RNA-sequencing of cortical microglia and brain bulk RNA-sequencing, together with 3D brain imaging in experimental cuprizone demyelination to provide a longitudinal characterization of brain transcriptome and microglia signatures during disease progression and remyelination. First, brain RNA-sequencing of healthy, demyelination and remyelination states revealed upregulation of microglia genes involved in inflammation,

General anesthesia (GA) is an unconscious state produced by anesthetic drugs, which act on neurons to cause overall suppression of neuronal activity in the brain. Recent studies have revealed that GA also substantially enhances the dynamics of microglia, the primary brain immune cells, with increased process motility and territory surveillance. However, whether microglia are actively involved in GAmodulation remains unknown. Here, we report a previously unrecognized role for microglia engaging in multiple GA processes. We found that microglial ablation reduced the sensitivity of mice to anesth

…We first generated a comprehensive single-cell RNA sequencing dataset of the telencephalon of adult zebrafish and mapped the diversity of neuronal cell types to anatomical brain areas. Gene expression data of G-protein coupled receptors were mined to embed individual cell types in neuromodulatory networks, allowing inference about which modu

Elucidating the factors that facilitate or impede the extinction of remote memories is imperative for the advancement of targeted therapeutic interventions aimed at addressing maladaptive memory persistence. Despite the extensive body of research on memory processes, there is a notable paucity of studies focusing on the diminution of long-standing memory traces . Recently, our lab has identified a hippocampal remote recall engram that is a key player in remote memory attenuation (Khalaf et al., 2018, Science), yet its molecular underpinnings remain elusive. In this study, we seek to delineate

Astrocytes are rapidly gaining ground as important regulators and potential therapeutic targets in neurodegeneration. Here, we used the cuprizone model of multiple sclerosis to explore the phenotypic signature of astrocytes in the cortex of mice during early demyelination at week 3 (CPZ3), a timepoint of initial demyelination and glia cell activation. Confocal imaging combined with detailed cell-morphometric analysis of cortical astrocytes after 3-dimensional cell reconstruction revealed the morphological phenotype of astrocytes in early demyelination, characterized by thick and long processes

The entorhinal cortex (EC) is a brain region playing an important role in memory and navigational processes. This is driven by its unique cellular organization as well as its extrinsic connectivity. Specific neuronal cell types have been associated with the specific navigation-related functions of the EC such as grid cells, border cells, speed cells or head-direction cells. These cell types have been characterized based on their firing properties, however, still lack a molecular profile. Similarly, detailed anatomical cell types have been described within the different EC layers, including ste

Non-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed bulk and single-cell RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs in both neuronal and non-neuronal cells, potentially associated with

…Single-cell transcriptomics can provide insights into behavior-associated cell state changes. Here we present a detailed cell-type taxonomy of the adult mouse amygdala during fear learning and memory consolidation. We perform single-cell RNA sequencing on naïve and fear-conditioned mice, identify 130 neuronal cell types and validate their spatial distributions

Periventricular heterotopia (PH) is a cortical malformation characterized by misplaced neurons adjacent to the lateral ventricles, commonly associated with epilepsy. It is genetically diverse, and its underlying mechanisms are not fully understood. While recent research suggests that neuronal differentiation can also be affected, it has traditionally been considered a neuronal migration disorder, supported by the identification of mutations in neuronal-enriched cytoskeletal genes. Furthermore, it is still unclear why only some neurons are affected in this condition, while the majority of other

…publicly available single cell RNA-sequencing and proteomics databases and showed that oligodendrocytes express all the components required to produce Aβ. By employing RNAscope in situ hybridisation we revealed that the brains of AD patients ha