L1CAM Is a Marker for Enriching Corticospinal Motor Neurons in the Developing Brain

Samata, Bumpei; Takaichi, Rika; Ishii, Yuko; Fukushima, Kaori; Nakagawa, Harumi; Ono, Yūichi; Takahashi, Jun

doi:10.3389/fncel.2020.00031

Cited by 8 publications

(4 citation statements)

References 43 publications

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“…We have previously reported that mouse embryonic stem cell-derived cortical neurons express L1CAM ( Samata et al., 2020 ). In that study, L1CAM + cells sorted from the cortical tissue of E14.5 mice contained a higher number of CTIP2 + cells, namely, cerebral projection neurons, and extended longer axons in the mouse brain than L1CAM cells.…”

Section: Discussionmentioning

confidence: 99%

Viral delivery of L1CAM promotes axonal extensions by embryonic cerebral grafts in mouse brain

et al. 2023

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Section: Discussionmentioning

confidence: 99%

Viral delivery of L1CAM promotes axonal extensions by embryonic cerebral grafts in mouse brain

et al. 2023

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“…We have shown that early-stage organoids extend more axons but cause graft overgrowth. Elimination of the proliferating cells by sorting may solve this problem ( Samata et al., 2020 ). In parallel, the clarification and administration of supportive factors may enhance graft survival and axonal extensions.…”

Section: Discussionmentioning

confidence: 99%

Axonal Extensions along Corticospinal Tracts from Transplanted Human Cerebral Organoids

et al. 2020

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Summary The reconstruction of lost neural circuits by cell replacement is a possible treatment for neurological deficits after cerebral cortex injury. Cerebral organoids can be a novel source for cell transplantation, but because the cellular composition of the organoids changes along the time course of the development, it remains unclear which developmental stage of the organoids is most suitable for reconstructing the corticospinal tract. Here, we transplanted human embryonic stem cell-derived cerebral organoids at 6 or 10 weeks after differentiation (6w- or 10w-organoids) into mouse cerebral cortices. 6w-organoids extended more axons along the corticospinal tract but caused graft overgrowth with a higher percentage of proliferative cells. Axonal extensions from 10w-organoids were smaller in number but were enhanced when the organoids were grafted 1 week after brain injury. Finally, 10w-organoids extended axons in cynomolgus monkey brains. These results contribute to the development of a cell-replacement therapy for brain injury and stroke.

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“…For gross cell type identification (i.e., GABA/Glutamatergic neurons vs. non-neuronal cell types) we used a combination of scRNA-seq integration, cross-checking with ArchR's GeneScoreModule function, which scores clusters based on aggregate marker gene accessibility. The scRNA-seq was sourced from the Allen mouse brain atlas, with gene lists were primarily based on the Allen Brain Atlas for mouse, as well as the Linnarsson Adolescent mouse brain atlas, (Zeisel et al 2018;Tiklová et al 2019;Arlotta et al 2005;Samata et al 2020) (http://hippocampome.org/php/markers.php). Due to the size of the datasets, we randomly downsampled the scRNA-seq to 10,000 cell profiles to prevent ArchR from crashing during integration.…”

Section: Cell Type Identification With Archrmentioning

confidence: 99%

Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

et al. 2023

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Here we present advancements in single-cell combinatorial indexed ATAC-seq (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>105) at low cost. The platform leverages the core of the sciATAC workflow where multiple indexed tagmentation reactions are performed, followed by pooling and distribution to a second set of reaction wells for PCR-based indexing. In this work, we instead leverage a chip containing 5,184 nanowells as the PCR stage of indexing, enabling a 52-fold improvement in scale and reduction in per-cell preparation costs. We detail three variants that balance cell throughput and depth of coverage and apply these methods to banked mouse brain tissue, producing maps of cell types as well as neuronal subtypes that includes integration with exiting scATAC and scRNA-seq datasets. Our optimized workflow achieves a high fraction of reads that fall within called peaks (>80%) and low cell doublet rates. The high cell coverage technique produces high unique reads per cell, while retaining high enrichment for open chromatin regions, enabling the assessment of >70,000 unique accessible on average for each cell profiled. When compared to current methods in the field, our technique provides similar or superior per-cell information with very low levels of cell-to-cell crosstalk, and achieves this at a cost point much lower than existing assays.

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L1CAM Is a Marker for Enriching Corticospinal Motor Neurons in the Developing Brain

Cited by 8 publications

References 43 publications

Viral delivery of L1CAM promotes axonal extensions by embryonic cerebral grafts in mouse brain

Viral delivery of L1CAM promotes axonal extensions by embryonic cerebral grafts in mouse brain

Axonal Extensions along Corticospinal Tracts from Transplanted Human Cerebral Organoids

Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

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