scholarly journals Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Nasna Nassir ◽  
Asma Bankapur ◽  
Bisan Samara ◽  
Abdulrahman Ali ◽  
Awab Ahmed ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
De Novo ◽  
Cell Types ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Loss Of Function ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Variant Genes

Abstract Background In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of ‘brain to behaviour’ pathogenic mechanisms, remains largely unknown. Methods We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single-cell transcriptomes (> million cells) and de novo loss-of-function (LOF) ASD variants (impacting 852 genes from 40,122 cases). Results We identified multiple single-cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high pLI genes. These clusters also showed significant enrichment with ASD loss-of-function variant genes (p < 5.23 × 10–11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF variant genes into large-scale human and mouse brain single-cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 × 10–11, oligodendrocyte, p < 1.31 × 10–09). Conclusion Among the ASD genes enriched with pathogenic de novo LOF variants (i.e. KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD and the need to explore other biological pathways for this disorder.

scholarly journals Single cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss of function mutation genes regulating glial cells

2021 ◽  
Author(s):  
Nasna Nassir ◽  
Asma Bankapur ◽  
Bisan Samara ◽  
Abdulrahman Ali ◽  
Awab Ahmed ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Single Cell ◽  
Large Scale ◽  
De Novo ◽  
Cell Types ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Loss Of Function ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of ‘brain to behaviour’ pathogenic mechanisms, remains largely unknown. Methods We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single cell transcriptomes (> million cells) and de novo loss of function (LOF) ASD mutations (impacting 852 genes from 40122 cases). Results We identified multiple single cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high PLi genes. These clusters also showed significant enrichment with ASD loss of function mutation genes (p < 5.23 x 10− 11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF mutated genes into large scale human and mouse brain single cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 x 10− 11; oligodendrocyte, p < 1.31 x 10− 09). Conclusion Among the ASD genes enriched with pathogenic de novo LOF mutations (i.e., KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD, and the need to explore other biological pathways for this disorder.

scholarly journals Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons

2017 ◽  
Author(s):  
Ping Wang ◽  
Dejian Zhao ◽  
Herbert M. Lachman ◽  
Deyou Zheng
Keyword(s):  
Single Cell ◽  
Gene Networks ◽  
Developmental Stages ◽  
Cell Types ◽  
Autism Spectrum ◽  
Inhibitory Neurons ◽  
Expression Of Genes ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Upregulated Genes

AbstractAutism spectrum disorder (ASD) is highly heritable but genetically heterogeneous. The affected neural circuits and cell types remain unclear and may vary at different developmental stages. By analyzing multiple sets of human single cell transcriptome profiles, we found that ASD candidates showed enriched gene expression in neurons, especially in inhibitory neurons. ASD candidates were also more likely to be the hubs of the co-expressed module that is highly expressed in inhibitory neurons, a feature not detected for excitatory neurons. In addition, we found that upregulated genes in multiple ASD cortex samples were also enriched with genes highly expressed in inhibitory neurons, suggesting a potential increase of inhibitory neurons and an imbalance in the ratio between excitatory and inhibitory neurons. Furthermore, the downstream targets of several ASD candidates, such as CHD8, EHMT1 and SATB2, also displayed enriched expression in inhibitory neurons. Taken together, our analysis of single cell transcriptomic data suggest that inhibitory neurons may be the major neuron subtype affected by the disruption of ASD gene networks, providing single cell functional evidence to support the excitatory/inhibitory (E/I) imbalance hypothesis.

scholarly journals High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports ◽  
2019 ◽  
Vol 27 (7) ◽  
pp. 2241-2247.e4 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Doina Ciobanu ◽  
Junyan Lin ◽  
Yuko Yoshinaga ◽  
...  
Keyword(s):  
Single Cell ◽  
Plant Cell ◽  
High Throughput ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yehuda Schlesinger ◽  
Oshri Yosefov-Levi ◽  
Dror Kolodkin-Gal ◽  
Roy Zvi Granit ◽  
Luriano Peters ◽  
...  
Keyword(s):  
Single Cell ◽  
Malignant Lesion ◽  
Tumor Development ◽  
Initial Step ◽  
Cell Types ◽  
Tumor Formation ◽  
Specific Cell ◽  
Preinvasive Lesions ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Acinar metaplasia is an initial step in a series of events that can lead to pancreatic cancer. Here we perform single-cell RNA-sequencing of mouse pancreas during the progression from preinvasive stages to tumor formation. Using a reporter gene, we identify metaplastic cells that originated from acinar cells and express two transcription factors, Onecut2 and Foxq1. Further analyses of metaplastic acinar cell heterogeneity define six acinar metaplastic cell types and states, including stomach-specific cell types. Localization of metaplastic cell types and mixture of different metaplastic cell types in the same pre-malignant lesion is shown. Finally, single-cell transcriptome analyses of tumor-associated stromal, immune, endothelial and fibroblast cells identify signals that may support tumor development, as well as the recruitment and education of immune cells. Our findings are consistent with the early, premalignant formation of an immunosuppressive environment mediated by interactions between acinar metaplastic cells and other cells in the microenvironment.

scholarly journals Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants

2021 ◽  
Author(s):  
Zhouhuan Xi ◽  
Bilge E. Ozturk ◽  
Molly E. Johnson ◽  
Leah C. Byrne
Keyword(s):  
Single Cell ◽  
Viral Vector ◽  
Cell Types ◽  
Adeno Associated Virus ◽  
Altered Expression ◽  
Gene Therapies ◽  
Retinal Tissue ◽  
Retinal Explants ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Gene therapy is a rapidly developing field, and adeno-associated virus (AAV) is a leading viral vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models, due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue, and are thus important for the validation of candidate AAV vectors. In this study, we evaluated 18 wildtype and engineered AAV capsids in human retinal explants using a recently developed single-cell RNA-Seq AAV engineering pipeline (scAAVengr). Human retinal explants retained the same major cell types as fresh retina, with similar expression of cell-specific markers, except for a cone population with altered expression of cone-specific genes. The efficiency and tropism of AAVs in human explants were quantified, with single-cell resolution. The top performing serotypes, K91, K912, and 7m8, were further validated in non-human primate and human retinal explants. Together, this study provides detailed information about the transcriptome profiles of retinal explants, and quantifies the infectivity of leading AAV serotypes in human retina, accelerating the translation of retinal gene therapies to the clinic.

scholarly journals A Single-Cell Transcriptome Atlas for Zebrafish Development

2019 ◽  
Author(s):  
Dylan R. Farnsworth ◽  
Lauren Saunders ◽  
Adam C. Miller
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Types ◽  
Developmental Time ◽  
Cell Type ◽  
Specific Expression ◽  
Transcriptional Profiles ◽  
Larval Stages ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

ABSTRACTThe ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome Atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic (mutant) or functional analysis, to launch an effort to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.

scholarly journals A single cell transcriptome atlas of the developing zebrafish hindbrain

2019 ◽  
Author(s):  
Monica Tambalo ◽  
Richard Mitter ◽  
David G. Wilkinson
Keyword(s):  
Single Cell ◽  
Neuronal Differentiation ◽  
Cell Types ◽  
Spatial Patterning ◽  
Rna Seq ◽  
Valuable Resource ◽  
Dorsoventral Axis ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSegmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at bounderies and segment centres, in part mediated by Fgf20 signaling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

scholarly journals Single-Cell RNA-Seq Reveals Novel Mitochondria-related Musculoskeletal Cell Populations during Adult Axolotl Limb Regeneration Process

2019 ◽  
Author(s):  
Tian Qin ◽  
Chun-mei Fan ◽  
Ting-zhang Wang ◽  
Long Yang ◽  
Wei-liang Shen ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Limb Regeneration ◽  
Regenerative Process ◽  
Regeneration Process ◽  
The Novel ◽  
Cell Subpopulations ◽  
Cell Transcriptome ◽  
Human Limb ◽  
Single Cell Transcriptome

ABSTRACTWhile the capacity to regenerate tissues or limbs is limited in mammals including humans, unlike us, axolotls are able to regrow entire limbs and major organs. The wound blastema have been extensively studied in limb regeneration. However, due to the inadequate characterization and coordination of cell subpopulations involved in the regeneration process, it hinders the discovery of the key clue for human limb regeneration. In this study, we applied unbiased large-scale single-cell RNA sequencing to classify cells throughout the adult axolotl limb regeneration process. We computationally identified 7 clusters in regenerating limbs, including the novel regeneration-specific mitochondria-related cluster supporting regeneration through energy providing and the COL2+ cluster contributing to regeneration through cell-cell interactions signals. We also discovered the dedifferentiation and re-differentiation of the COL1+/COL2+ cellular subpopulation and uncovered a COL2-mitochondria sub-cluster supporting the musculoskeletal system regeneration. On the basis of these findings, we reconstructed the dynamic single-cell transcriptome atlas of adult axolotl limb regenerative process, and identified the novel regenerative mitochondria-related musculoskeletal populations, which yielded deeper insights into the crucial interactions between cell clusters within the regenerative microenvironment.

scholarly journals scAAVengr: Single-cell transcriptome-based quantification of engineered AAVs in non-human primate retina

2020 ◽  
Author(s):  
Bilge E. Öztürk ◽  
Molly E. Johnson ◽  
Michael Kleyman ◽  
Serhan Turunç ◽  
Jing He ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Types ◽  
Adeno Associated Virus ◽  
Gene Therapies ◽  
Naturally Occurring ◽  
Cell Transcriptome ◽  
Large Animals ◽  
Single Cell Transcriptome ◽  
Human Primate

AbstractAdeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging. Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to quantify efficiency of AAV-mediated gene expression across all cell types. scAAVengr allows for definitive, head-to-head comparison of vectors in the same animal. To demonstrate proof-of-concept for the scAAVengr workflow, we quantified – with cell-type resolution – the abilities of naturally occurring and newly engineered AAVs to mediate gene expression in primate retina following intravitreal injection. A top performing variant, K912, was used to deliver SaCas9 and edit the rhodopsin gene in macaque retina, resulting in editing efficiency similar to infection rates detected by the scAAVengr workflow. These results validate scAAVengr as a powerful method for development of AAV vectors.

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