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NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

ABSTRACT: NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

PROVIDER: PRJNA1090897 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28421161.fastq.gz	Fastqsanger.gz
	SRR28421162.fastq.gz	Fastqsanger.gz
	SRR28421163.fastq.gz	Fastqsanger.gz
	SRR28421164.fastq.gz	Fastqsanger.gz

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NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

Project description:Dysregulation of communication between cells mediates complex diseases such as cancer and diabetes. However, detecting cell-cell communication (CCC) at scale remains one of the greatest challenges in transcriptomics. While gene expression remains one of the greatest challenges in transcriptomics. While gene expression measured with single-cell RNA sequencing and spatial transcriptomics reinvigorated computational approaches to detecting CCC, most existing methods exhibit high false positive rates, do not integrate spatial proximity of ligand-receptor interactions, and cannot detect CCC between individual cells. We overcome these challenges by presenting NEST (NEural network on Spatial Transcriptomics), which uses a graph attention network paired with an unsupervised contrastive learning approach to decipher patterns of communication while retaining the strength of each signal. We introduce new synthetic benchmarking experiments which demonstrate how NEST outperforms existing tools and detects biologically-relevant CCC along with directionality and confidence across spot- and cell-based technologies measuring several different tissues and diseases. In our applications, NEST identifies T-cell homing signals in human lymph nodes, aggressive cancer CCC in lung adenocarcinoma, and discovers new patterns of communication in pancreatic cancer. Beyond two-dimensional data, we also highlight NEST's ability to detect CCC in three-dimensional spatial transcriptomic data.

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Spatially mapped single-cell chromatin accessibility

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Project description:During the nest-founding phase of the bumble bee colony cycle, queens undergo striking changes in maternal care behavior. Early in the founding phase, prior to the emergence of workers in the nest, queens are reproductive and also provision and feed their offspring. However, later in the founding phase, queens cease feeding offspring and become specialized on reproduction. This transition is synchronized with the emergence of workers in the colony, who assume the task of feeding their siblings. Using a social manipulation experiment, we tested the hypothesis that workers socially regulate the transition from feeding brood to specialization on reproduction in nest-founding bumble bee queens. Consistent with this hypothesis, we found that early-stage queens with workers prematurely added to their nests reduce their brood-feeding behavior and increase egg-laying, and likewise, late-stage queens increase their brood-feeding behavior and decrease egg-laying when workers are removed from their nests. Further, brood-feeding and egg-laying behavior were negatively correlated in these queens. We used an Agilent brain EST-based microarray to explore a second hypothesis, that workers alter brain gene expression in nest-founding queens. We found evidence that brain gene expression in nest-founding queens is altered by the presence of workers, with the effect much stronger in late-stage founding queens. Additionally, expression levels of some genes were correlated with quantitative differences in brood-feeding and egg-laying behavior. This study provides new insights into how the transition from feeding brood to specialization on reproduction in bumble bee queens is regulated during the nest initiation phase of the colony cycle.

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Stress regulation of sustained attention and the cholinergic attention system

Project description:Background: Stress exacerbates symptoms of schizophrenia and attention deficit hyperactivity disorder, which are characterized by impairments in sustained attention. Yet how stress regulates attention remains largely unexplored. Here we investigated whether a 6-day variable stressor (VS) altered sustained attention and the cholinergic attention system in male and female rats. Methods: Sustained attention was tested with the sustained attention task (SAT). Successful performance on SAT relies on the release of acetylcholine (ACh) into the cortex from cholinergic neurons in the nucleus basalis of Meynert (NBM). Thus, we evaluated whether VS altered the morphology of these neurons with a novel approach using Cre-dependent virus in genetically modified ChAT::Cre rats, a species used for this manipulation only. Next, electrochemical recordings measured cortical ACh following VS. Finally, we used RNAseq to identify VS-induced transcriptional changes in the NBM. Results: VS impaired attentional performance in SAT and increased the dendritic complexity of NBM cholinergic neurons in both sexes. NBM cholinergic neurons are mainly under inhibitory control, so this morphological change could increase inhibition on these neurons, reducing downstream ACh release to impair attention. Indeed, VS decreased ACh release in the prefrontal cortex of males. Quantification of global transcriptional changes revealed that, although VS induced many sex-specific changes in gene expression, it increased several signaling molecules in both sexes.

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