Brain-wide correspondence of neuronal epigenomics and distant projections

Single-cell analyses parse the brain's billions of neurons into thousands of 'cell-type' clusters residing in different brain structures1. Many cell types mediate their functions through targeted long-distance projections allowing interactions between specific cell types. Here we used epi-retro-seq2 to link single-cell epigenomes and cell types to long-distance projections for 33,034 neurons dissected from 32 different regions projecting to 24 different targets (225 source-to-target combinations) across the whole mouse brain. We highlight uses of these data for interrogating principles relating projection types to transcriptomics and epigenomics, and for addressing hypotheses about cell types and connections related to genetics. We provide an overall synthesis with 926 statistical comparisons of discriminability of neurons projecting to each target for every source. We integrate this dataset into the larger BRAIN Initiative Cell Census Network atlas, composed of millions of neurons, to link projection cell types to consensus clusters. Integration with spatial transcriptomics further assigns projection-enriched clusters to smaller source regions than the original dissections. We exemplify this by presenting in-depth analyses of projection neurons from the hypothalamus, thalamus, hindbrain, amygdala and midbrain to provide insights into properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription-factor-binding motifs, and neurotransmitter use.

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq)1 technologies to generate 301,626 methylomes and 176,003 chromatin conformation-methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 cross-modality-annotated subclasses. We identified 2.6 million differentially methylated regions across the genome that represent potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide spatial transcriptomics data validated the association of spatial epigenetic diversity with transcription and improved the anatomical mapping of our epigenetic datasets. Furthermore, chromatin conformation diversities occurred in important neuronal genes and were highly associated with DNA methylation and transcription changes. Brain-wide cell-type comparisons enabled the construction of regulatory networks that incorporate transcription factors, regulatory elements and their potential downstream gene targets. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a whole-brain SMART-seq2 dataset. Our study establishes a brain-wide, single-cell DNA methylome and 3D multi-omic atlas and provides a valuable resource for comprehending the cellular-spatial and regulatory genome diversity of the mouse brain.

A comparative atlas of single-cell chromatin accessibility in the human brain

Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer's disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.

Single-cell DNA methylation and 3D genome architecture in the human brain

Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.

Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

Cytosine DNA methylation is essential in brain development and has been implicated in various neurological disorders. A comprehensive understanding of DNA methylation diversity across the entire brain in the context of the brain's 3D spatial organization is essential for building a complete molecular atlas of brain cell types and understanding their gene regulatory landscapes. To this end, we employed optimized single-nucleus methylome (snmC-seq3) and multi-omic (snm3C-seq1) sequencing technologies to generate 301,626 methylomes and 176,003 chromatin conformation/methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell type taxonomy that contains 4,673 cell groups and 261 cross-modality-annotated subclasses. We identified millions of differentially methylated regions (DMRs) across the genome, representing potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide multiplexed error-robust fluorescence in situ hybridization (MERFISH2) data validated the association of this spatial epigenetic diversity with transcription and allowed the mapping of the DNA methylation and topology information into anatomical structures more precisely than our dissections. Furthermore, multi-scale chromatin conformation diversities occur in important neuronal genes, highly associated with DNA methylation and transcription changes. Brain-wide cell type comparison allowed us to build a regulatory model for each gene, linking transcription factors, DMRs, chromatin contacts, and downstream genes to establish regulatory networks. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a companion whole-brain SMART-seq3 dataset. Our study establishes the first brain-wide, single-cell resolution DNA methylome and 3D multi-omic atlas, providing an unparalleled resource for comprehending the mouse brain's cellular-spatial and regulatory genome diversity.

Vigilance behaviors and EEG activity in sustained attention may affect acute pain

During Sustained Attention to stimuli across many modalities neural activity often decreases over time on task, while Errors in task performance increase (Vigilance Decrement). Sustained Attention to pain has rarely been investigated experimentally despite its clinical significance. We have employed a Sustained Attention protocol (Continuous Performance Task, CPT) in which the subject counts painful laser stimuli (targets) when they occur randomly in a prolonged train of nonpainful nontargets. We hypothesize that the magnitude of the poststimulus oscillatory power divided by baseline power (Event-Related Spectral Perturbation, ERSP - scalp EEG) over Frontoparietal structures will decrease at all frequencies with time on task, while Beta ERSP (14-30Hz) will be correlated with Error Rates in performance of the CPT. During the CPT with a painful target ERSP was found in four separate Windows, as defined by both their frequency band and the time after the stimulus. A Vigilance Decrement was found which confirms that Sustained Attention to pain was produced by this CPT. In addition, Error Rates was correlated inversely with laser energy, and with ratings of pain unpleasantness and salience. Error Rates also were related directly to the Beta ERSP Window at scalp EEG electrodes over the central sulcus. Over time on task, the ERSP magnitude decreased in Alpha (8-14Hz) Window, was unchanged in early and late Delta/Theta Windows (0-8Hz), and increased in the Beta Window. The increase in Beta ERSP and a decrease in the Alpha ERSP occurred at the same EEG electrode over the parietal lobe to a significant degree across subjects. Overall, Beta activity increases with time on task, and with higher Error Rates as in the case of other modalities. In the case of pain increased Errors correspond to misidentification of painful and nonpainful stimuli and so modulate the sensation of pain under the influence of Sustained Attention.

A sub-micron depletion-type photonic modulator in Silicon On Insulator

We provide detailed analysis of a four terminal p+pnn+ optical modulator integrated into a silicon-on-insulator (SOI) rib waveguide. The proposed depletion device has been designed to approach birefringence free operation. The modulation mechanism is the carrier depletion effect in a pn junction; carrier losses induced are minimised in our design and because we use a depletion device, the device is insensitive to carrier lifetime. The rise time and fall time of the proposed device have both been calculated to be 7 ps for a reverse bias of only 5 volts. A maximum excess loss of 2 dB is predicted for TE and TM due to the presence of p type and n type carriers in the waveguide.

Dimethylsulfoxide enhances CNS neuronal plasma membrane resealing after injury in low temperature or low calcium

The inability to repair the damaged membrane may be one of the key mechanisms underlying the severe neuronal degeneration and overall functional loss seen in in vivo spinal cord injury and traumatic axonal injury in blunt head trauma. Promoting membrane resealing following damage may therefore constitute a potential effective therapeutic intervention in treating head trauma and spinal cord injuries. In our previous studies, we have shown that the axolemma failed to reseal following transection in clinically related situations, such as low extracellular calcium and low temperature. Our current studies indicate that DMSO is capable of rendering significant improvement in guinea pig axonal membrane resealing following transection in both 0.5 mM [Ca(2+)](0) and 25 degrees C situations. This was demonstrated physiologically by monitoring membrane potential recovery and anatomically by conducting HRP-exclusion assays 60 minutes after injury. Further, we have shown that the addition of DMSO in normal Krebs' solution (2 mM [Ca(2+)](0) and 37 degrees C) resulted in a decrease in membrane repair following injury. This indicates that DMSO-mediated membrane repair is sensitive to temperature and calcium. This study suggests the role of DMSO in axonal membrane resealing in clinically relevant conditions and raises the possibility of using DMSO in combination with other more established therapies in spinal cord injury treatment.

Identification and disruption of lisRK, a genetic locus encoding a two-component signal transduction system involved in stress tolerance and virulence in Listeria monocytogenes

lisRK encodes a two-component regulatory system in the food pathogen Listeria monocytogenes LO28. Following identification of the operon in an acid-tolerant Tn917 mutant, a deletion in the histidine kinase component was shown to result in a growth phase variation in acid tolerance, an ability to grow in high ethanol concentrations, and a significant reduction in virulence.

Ventilatory effects of the nonimmobilizer 1,2-dichlorohexafluorocyclobutane (2N) in swine

Nonimmobilizers (inhaled compounds that do not suppress movement in response to a noxious stimulus) resemble anesthetics in their capacity to suppress memory, but unlike anesthetics, they can cause convulsions. Higher concentrations of nonimmobilizers may cause death, even with apparent suppression of convulsions by the concurrent administration of conventional inhaled anesthetics. We hypothesized that nonimmobilizers can depress ventilation and can cause death by adding to the depression of ventilation produced by conventional anesthetics. To test these hypotheses, we administered 1,2-dichlorohexafluorocyclobutane (2N) to four pigs anesthetized with desflurane. The addition of 2N decreased PaCO2 and tended to increase the slope of the ventilatory response to imposed increases in PETCO2. Limited results from study of two other nonimmobilizers (2,3-dichlorooctafluorobutane and perfluoropentane), in two pigs each, were consistent with the findings for 2N. However, experimental limitations (e.g., toxicity of 2,3-dichlorooctafluorobutane, and hypoxia from perfluoropentane) confound interpretation of these latter results. Our findings do not support our hypotheses--2N (and presumably all nonimmobilizers) seems to be a respiratory stimulant, not a depressant.

IMPLICATIONS

A new class of inhaled compounds, nonimmobilizers, allow tests of how inhaled anesthetics act. Nonimmobilizers may act like anesthetics (e.g., impair learning) or may not (e.g., do not prevent movement in response to a noxious stimulus). The present work shows that, unlike anesthetics,nonimmobilizers do not depress breathing.

A mutant of Listeria monocytogenes LO28 unable to induce an acid tolerance response displays diminished virulence in a murine model

Exposing Listeria monocytogenes LO28 to sublethal pH induces protection against normally lethal pH conditions, a phenomenon known as the acid tolerance response. We identified a mutant, L. monocytogenes ATR1, which is incapable of inducing such tolerance, either against low pH or against any other stress tested. The virulence of this mutant was considerably decreased, suggesting that the acid tolerance response contributes to in vivo survival of L. monocytogenes.