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Knit directory: Cinquina_2024/
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This repository contains code and output of the analysis of single-cell RNA sequencing data and experimental results for the article Cinquina V et al., 2024.
Please see file CITATION in the root of your Git repo
that contains the citation information.
To see the results of the analysis please visit the analysis website.
We aimed to investigate the role of astrocyte-derived factors in regulating neuronal morphogenesis during brain development. Specifically, we hypothesized that S100A6, a Ca²⁺-binding protein expressed by astrocytes, could act as a gliotransmitter to modulate neuronal development through its interaction with calcyclin-binding protein (CaCyBP) in neurons.
Our results describe a novel molecular axis of astrocyte-neuron communication, which is unique in limiting neuronal morphogenesis through the ER/UPS pathway. S100A6 acts as an astrocyte-specific gliotransmitter, which regulates neuronal proteostasis through CaCyBP. This signaling pathway is sensitive to environmental factors, particularly maternal nutrition during pregnancy.
Raw data were obtained from the Single Cell Portal (Tarhan et al., n.d.; Di Bella et al. 2021). All generated data are available in this repository.
The code for the analysis is available at https://github.com/harkany-lab/Cinquina_2024.
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] jsonlite_1.8.8 compiler_4.4.0 promises_1.3.0 Rcpp_1.0.12
[5] stringr_1.5.1 git2r_0.33.0 callr_3.7.6 later_1.3.2
[9] jquerylib_0.1.4 yaml_2.3.8 fastmap_1.2.0 here_1.0.1
[13] R6_2.5.1 knitr_1.47 tibble_3.2.1 rprojroot_2.0.4
[17] bslib_0.7.0 pillar_1.9.0 rlang_1.1.4 utf8_1.2.4
[21] cachem_1.1.0 stringi_1.8.4 httpuv_1.6.15 xfun_0.45
[25] getPass_0.2-4 fs_1.6.4 sass_0.4.9 cli_3.6.2
[29] magrittr_2.0.3 ps_1.7.6 digest_0.6.35 processx_3.8.4
[33] rstudioapi_0.16.0 lifecycle_1.0.4 vctrs_0.6.5 evaluate_0.24.0
[37] glue_1.7.0 whisker_0.4.1 fansi_1.0.6 rmarkdown_2.27
[41] httr_1.4.7 tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1