The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Drokhlyansky, Eugene; Smillie, Christopher; Wittenberghe, Nicholas Van; Ericsson, Maria; Griffin, Gabriel K.; Eraslan, Gökçen; Dionne, Danielle; Cuoco, Michael S.; Goder-Reiser, Max N.; Sharova, Tatyana; Kuksenko, Olena; Aguirre, Andrew J.; Boland, Genevieve M.; Graham, Daniel B.; Rozenblatt-Rosen, Orit; Xavier, Ramnik J.; Regev, Aviv

doi:10.1016/j.cell.2020.08.003

Cited by 367 publications

(563 citation statements)

References 89 publications

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“…We generated single-cell/single-nucleus atlases of the lung ( n =16 individuals, k =106,792 cells/nuclei), heart ( n =15, k =36,662), liver ( n =16, k =47,001) and kidney ( n =11, k =29,568). We initially tested both scRNA-Seq and snRNA-Seq on tissue samples collected from COVID-19 autopsies through methods we recently established for analyzing human tumor biopsies and resections 29, 30 ( Methods ). In these pilots, snRNA-Seq, which is well-suited for processing hard-to-dissociate or damaged tissues, performed better in systematically capturing the complex tissue cellular ecosystem (Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

“…5a). Moreover, as we rely on an snRNA-Seq procedure (albeit with associated ribosomes 30 ), we may under-represent viral RNA. Spatial analysis of COVID-19 lung tissue supports the observation that high viral levels are mainly found at the earlier stages of infection 64 , as we observed upregulation of the immediate early genes ( EGR1 , JUN , FOS , IER2 , and NR4A1 ) only in SARS-CoV-2 high epithelial regions of the lung (Supplemental Fig.…”

Section: Discussionmentioning

confidence: 99%

“…To overcome these challenges, we leveraged ongoing clinical COVID-19 autopsy efforts across three major Boston area hospitals to orchestrate a concerted study and assemble a comprehensive biobank of approximately 420 autopsy specimens spanning 11 organs from 17 donors who succumbed to COVID-19. We then utilized recently developed methods for single-nucleus RNA-Seq (snRNA-Seq) from frozen specimens 29, 30 and for spatial RNA profiling from formalin fixed paraffin embedded (FFPE) tissues 31 , and developed and applied analytical strategies to overcome ambient RNA in autopsy specimens and relate annotations across datasets. Together, this enabled us to generate comprehensive single-cell/single-nucleus tissue atlases of lung, kidney, liver and heart tissues from COVID-19 donors, and to further analyze several distinct lung regions with spatial RNA profiling methods.…”

Section: Introductionmentioning

confidence: 99%

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A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Delorey¹,

Ziegler²,

Heimberg³

et al. 2021

Preprint

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The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Delorey¹,

Ziegler²,

Heimberg³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

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“…While both molecules are thought to be mediators that can signal to IPANs, our data does not support the involvement of mucosal release of GLP-1 or CCK-8 in the activation of enteric sensory nerve endings. Further examination of the activation of enteric IPANs by mucosal mediators will be informed by single cell RNA-sequencing (scRNA-seq) data on EECsubtype enriched genes encoding for key signaling molecules (Haber et al, 2017), together with data on the gene expression of corresponding receptors in putative IPANs (Zeisel et al, 2018, Drokhlyansky et al, 2020.…”

Section: -Ht Mediates Communication Between Eecs and Enteric Nerves mentioning

confidence: 99%

“…Until recently, the presence of conventional IPANs in the submucosal plexus has been elusive (Mao et al, 2006, Wong et al, 2008, Mongardi Fantaguzzi et al, 2009, Foong et al, 2014. Latest work shows that there are IPANs present in the mouse SMP based on neuronal morphology, projection patterns, and advillin expression (Melo et al, 2020), as well as scRNA-seq data (Drokhlyansky et al, 2020). Hence, submucosal neurons can receive luminal information directly and/or secondarily via neurons residing in the myenteric plexus.…”

Section: Some Submucosal Neurons Receive Luminal Information Via Myenmentioning

confidence: 99%

Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine

Fung

Hao

Obata

et al. 2021

Preprint

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Nutrient signals sensed by enteroendocrine cells are conveyed to the enteric nervous system (ENS) to initiate intestinal reflexes. We addressed whether there are specific enteric pathways dedicated to detecting different luminal nutrients. Calcium imaging was performed on intact jejunal preparations from Wnt1-cre;R26R-GCaMP3 and Villin-cre;R26R-GCaMP3 mice which express a fluorescent calcium indicator in their ENS or intestinal epithelium, respectively. Glucose, acetate, and L-phenylalanine were perfused onto the mucosa whilst imaging underlying enteric neurons. Nutrient transport or diffusion across the mucosa was mimicked by applying nutrients onto sensory nerve endings in a villus, or onto myenteric ganglia. The nutrients perfused onto the mucosa each elicited Ca2+ transients in submucosal neurons and in distinct patterns of myenteric neurons. Notably, the neurochemical subtypes of myenteric neurons that responded differed between the nutrients, while submucosal responders were predominantly cholinergic. Nutrients applied into villi or onto ganglia did not elicit specific neuronal responses but did stimulate Ca2+ signaling in the mucosal epithelium. These data suggest that nutrients are first detected at the level of the epithelium and that the ENS is capable of discriminating between different compositions of luminal content. Furthermore, our data show that responses to mucosal stimulation are primarily in the myenteric plexus and submucosal neurons respond secondarily.

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Stem Cell‐Based Models for Studying the Effects of Cancer and Cancer Therapies on the Peripheral Nervous System

Richter

Fattahi

2022

Advanced Biology

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despite these advancements, these traditional models have failed to deliver any therapies approved to target these interactions. For example, despite many neurotoxic chemotherapeutics being on the market for decades, there are no treatments available that prevent or ameliorate their effects on the nervous system. Similarly, there are no therapies approved that leverage cancer-PNS interactions as an antineoplastic mechanism. These clinical failings are largely due to the technical and translational limitations of the experimental models routinely used for studying PNS disorders. To make research in the evolving area of cancer neuroscience more translational and compatible with drug discovery an interdisciplinary approach utilizing tools that span cancer biology, developmental biology, functional genomics, neuroscience, and pharmacology must be employed. Here, human stem cell-derived cultures are discussed as exciting model systems that may help incorporate novel methodologies into cancer and cancer therapy PNS research.

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The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Cited by 367 publications

References 89 publications

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine

Stem Cell‐Based Models for Studying the Effects of Cancer and Cancer Therapies on the Peripheral Nervous System

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