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6. A Purkinje cell to parabrachial nucleus pathway enables broad cerebellar influence over the forebrain and emotional valence

Author

Chen, Christopher H., Leannah N. Newman, Stark, Amanda P., Bond, Katherine E., Dawei Zhang, Nardone, Stefano, Vanderberg, Charles, Nadaf, Naeem, Kefiloe Mutume, Zhiyi Yao, Flaquer, Isabella, Lowell, Bradford B., Macosko, Evan, and Regehr, Wade G.

Subjects
Parabrachial Nuclei, Cerebellum, Purkinje cell, Deep Cerebellar Nuclei
Abstract

OVERVIEW The following README contains: i) the raw count matrix relative to all nuclei of the dataset, called “filtered_feature_bc_matrix”; ii) the cell cycle genes lists (G2/M and S phase specific markers) named “cycle_gene”; iii) the markers gene lists used to generate the Dot Plots for the All_cells and Neuronal clustering (glial and neuronal markers); iv) the instruction to set up an R environment (R version 4.1.2) and to install R Studio on a Windows/macOS operative systems; iii) the instructions to install Seurat 3.2.3 along with all its dependencies; iv) the software code used to generate all the plots and figure as showed in the manuscript. SYSTEM REQUIREMENTS The following analysis can be performed on a standard computer with sufficient RAM to support the in-memory operation required by Seurat 3.2.3. The installation of Seurat 3.2.3 and all its dependencies have been tested on both Windows (version 10 64-bit ) and macOS (Big Sur version 11.6.1) operating systems. ALL PACKAGES and DEPENDENCIES R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.2.1 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] dplyr_1.0.8 scales_1.1.1 RColorBrewer_1.1-2 viridis_0.6.2 viridisLite_0.4.0 ggplot2_3.3.5 Matrix_1.3-4 [8] biomaRt_2.50.3 Seurat_3.2.3 loaded via a namespace (and not attached): [1] BiocFileCache_2.2.1 plyr_1.8.6 igraph_1.2.11 lazyeval_0.2.2 splines_4.1.2 [6] listenv_0.8.0 scattermore_0.8 GenomeInfoDb_1.30.1 digest_0.6.29 htmltools_0.5.2 [11] fansi_1.0.2 magrittr_2.0.3 memoise_2.0.1 tensor_1.5 cluster_2.1.2 [16] ROCR_1.0-11 limma_3.50.1 remotes_2.4.2 globals_0.14.0 Biostrings_2.62.0 [21] matrixStats_0.61.0 prettyunits_1.1.1 colorspace_2.0-3 blob_1.2.2 rappdirs_0.3.3 [26] ggrepel_0.9.1 crayon_1.5.0 RCurl_1.98-1.6 jsonlite_1.8.0 spatstat_1.64-1 [31] spatstat.data_2.1-2 survival_3.2-13 zoo_1.8-9 glue_1.6.2 polyclip_1.10-0 [36] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0 leiden_0.3.9 future.apply_1.8.1 [41] BiocGenerics_0.40.0 abind_1.4-5 DBI_1.1.2 miniUI_0.1.1.1 Rcpp_1.0.8 [46] xtable_1.8-4 progress_1.2.2 reticulate_1.24 bit_4.0.4 rsvd_1.0.5 [51] stats4_4.1.2 htmlwidgets_1.5.4 httr_1.4.2 ellipsis_0.3.2 ica_1.0-2 [56] pkgconfig_2.0.3 XML_3.99-0.9 farver_2.1.0 uwot_0.1.11 dbplyr_2.1.1 [61] deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 labeling_0.4.2 rlang_1.0.2 [66] reshape2_1.4.4 later_1.3.0 AnnotationDbi_1.56.2 munsell_0.5.0 tools_4.1.2 [71] cachem_1.0.6 cli_3.2.0 generics_0.1.2 RSQLite_2.2.10 pacman_0.5.1 [76] ggridges_0.5.3 stringr_1.4.0 fastmap_1.1.0 goftest_1.2-3 bit64_4.0.5 [81] fitdistrplus_1.1-6 purrr_0.3.4 RANN_2.6.1 KEGGREST_1.34.0 sceasy_0.0.6 [86] pbapply_1.5-0 future_1.24.0 nlme_3.1-153 mime_0.12 xml2_1.3.3 [91] compiler_4.1.2 rstudioapi_0.13 plotly_4.10.0 filelock_1.0.2 curl_4.3.2 [96] png_0.1-7 spatstat.utils_2.3-0 tibble_3.1.6 stringi_1.7.6 lattice_0.20-45 [101] vctrs_0.3.8 pillar_1.7.0 lifecycle_1.0.1 BiocManager_1.30.16 lmtest_0.9-39 [106] RcppAnnoy_0.0.19 data.table_1.14.2 cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5 [111] httpuv_1.6.5 patchwork_1.1.1 R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 [116] gridExtra_2.3 IRanges_2.28.0 parallelly_1.30.0 codetools_0.2-18 MASS_7.3-54 [121] assertthat_0.2.1 withr_2.5.0 sctransform_0.3.3 S4Vectors_0.32.3 GenomeInfoDbData_1.2.7 [126] mgcv_1.8-38 parallel_4.1.2 hms_1.1.1 grid_4.1.2 rpart_4.1-15 [131] tidyr_1.2.0 Rtsne_0.15 Biobase_2.54.0 shiny_1.7.1 SOFTWARE INSTALLATION GUIDE 1. R version 4.1.2 for Windows and for macOS can be downloaded at: https://cran.rstudio.com/. 2. All packages used can be installed running the following command install.packages() from R console. 3. Seurat 3.2.3 and all its dependencies can be installed running the following command line: remotes::install_version("Seurat", version = "3.2.3"). 4. A typical installation time on a “normal” desktop computer is around 15-20 minutes. INSTRUCTION FOR USE/EXPECTED OUTPUT/EXPECTED RUN TIME All the instructions to install and run the code on the data provided in this folder are in the document “SCRIPT.txt”. The expected outputs of the code are: 1) “NEURONS_markers.csv”; 2) Figure 5;3) Supplementary Figure12. Expected run time is about 10 min for all the analyses.

Published
2022
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8. A Purkinje cell to parabrachial nucleus pathway enables broad cerebellar influence over the forebrain

Author

Chen, Christopher H., primary, Newman, Leannah N., additional, Stark, Amanda P., additional, Bond, Katherine E., additional, Zhang, Dawei, additional, Nardone, Stefano, additional, Vanderburg, Charles R., additional, Nadaf, Naeem M., additional, Yao, Zhiyi, additional, Mutume, Kefiloe, additional, Flaquer, Isabella, additional, Lowell, Bradford B., additional, Macosko, Evan Z., additional, and Regehr, Wade G., additional

Published
2021
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12. Cerebellar Purkinje cell activity modulates aggressive behavior

Author

Jackman, Skyler L., primary, Chen, Christopher H., additional, Offermann, Heather L., additional, Drew, Iain R., additional, Harrison, Bailey M., additional, Bowman, Anna M., additional, Flick, Katelyn M., additional, Flaquer, Isabella, additional, and Regehr, Wade G., additional

Published
2020
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13. Cerebellum-specific deletion of the GABAAreceptor δ subunit alters anxiety-like, social and maternal behaviors without affecting motor performance

Author

Rudolph, Stephanie, primary, Guo, Chong, additional, Pashkovski, Stan, additional, Osorno, Tomas, additional, Gillis, Winthrop, additional, Krauss, Jeremy, additional, Nyitrai, Hajnalka, additional, Flaquer, Isabella, additional, El-Rifai, Mahmoud, additional, Datta, Robert Sandeep, additional, and Regehr, Wade, additional

Published
2019
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14. Silk Fibroin Films Facilitate Single-Step Targeted Expression of Optogenetic Proteins

Author

Jackman, Skyler L., primary, Chen, Christopher H., additional, Chettih, Selmaan N., additional, Neufeld, Shay Q., additional, Drew, Iain R., additional, Agba, Chimuanya K., additional, Flaquer, Isabella, additional, Stefano, Alexis N., additional, Kennedy, Thomas J., additional, Belinsky, Justine E., additional, Roberston, Keiramarie, additional, Beron, Celia C., additional, Sabatini, Bernardo L., additional, Harvey, Christopher D., additional, and Regehr, Wade G., additional

Published
2018
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15. Silk Fibroin Films Facilitate Single-Step Targeted Expression of Optogenetic Proteins

Author

Jackman, Skyler L., Chen, Christopher H., Chettih, Selmaan N., Neufeld, Shay Q., Drew, Iain R., Agba, Chimuanya K., Flaquer, Isabella, Stefano, Alexis N., Kennedy, Thomas J., Belinsky, Justine E., Roberston, Keiramarie, Beron, Celia C., Sabatini, Bernardo L., Harvey, Christopher D., and Regehr, Wade G.

Abstract

SUMMARY Optical methods of interrogating neural circuits have emerged as powerful tools for understanding how the brain drives behaviors. Optogenetic proteins are widely used to control neuronal activity, while genetically encoded fluorescent reporters are used to monitor activity. These proteins are often expressed by injecting viruses, which frequently leads to inconsistent experiments due to misalignment of expression and optical components. Here, we describe how silk fibroin films simplify optogenetic experiments by providing targeted delivery of viruses. Films composed of silk fibroin and virus are applied to the surface of implantable optical components. After surgery, silk releases the virus to transduce nearby cells and provide localized expression around optical fibers and endoscopes. Silk films can also be used to express genetically encoded sensors in large cortical regions by using cranial windows coated with a silk/virus mixture. The ease of use and improved performance provided by silk make this a promising approach for optogenetic studies.

Published
2018
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16. Cerebellum-Specific Deletion of the GABAAReceptor δ Subunit Leads to Sex-Specific Disruption of Behavior

Author

Rudolph, Stephanie, Guo, Chong, Pashkovski, Stan L., Osorno, Tomas, Gillis, Winthrop F., Krauss, Jeremy M., Nyitrai, Hajnalka, Flaquer, Isabella, El-Rifai, Mahmoud, Datta, Sandeep Robert, and Regehr, Wade G.

Abstract

Granule cells (GCs) of the cerebellar input layer express high-affinity δ GABAAsubunit-containing GABAAreceptors (δGABAARs) that respond to ambient GABA levels and context-dependent neuromodulators like steroids. We find that GC-specific deletion of δGABAA(cerebellar [cb] δ knockout [KO]) decreases tonic inhibition, makes GCs hyperexcitable, and in turn, leads to differential activation of cb output regions as well as many cortical and subcortical brain areas involved in cognition, anxiety-like behaviors, and the stress response. Cb δ KO mice display deficits in many behaviors, but motor function is normal. Strikingly, δGABAAdeletion alters maternal behavior as well as spontaneous, stress-related, and social behaviors specifically in females. Our findings establish that δGABAARs enable the cerebellum to control diverse behaviors not previously associated with the cerebellum in a sex-dependent manner. These insights may contribute to a better understanding of the mechanisms that underlie behavioral abnormalities in psychiatric and neurodevelopmental disorders that display a gender bias.

Published
2020
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17. Cerebellum-Specific Deletion of the GABA A Receptor δ Subunit Leads to Sex-Specific Disruption of Behavior.

Author

Rudolph S, Guo C, Pashkovski SL, Osorno T, Gillis WF, Krauss JM, Nyitrai H, Flaquer I, El-Rifai M, Datta SR, and Regehr WG

Subjects
Animals, Anxiety pathology, Behavior, Animal, Female, Learning, Male, Maternal Behavior, Mice, Inbred C57BL, Mice, Knockout, Motor Activity, Organ Specificity, Stress, Psychological, Cerebellum metabolism, Gene Deletion, Protein Subunits metabolism, Receptors, GABA-A metabolism, Sex Characteristics
Abstract

Granule cells (GCs) of the cerebellar input layer express high-affinity δ GABA A subunit-containing GABA A receptors (δGABA A Rs) that respond to ambient GABA levels and context-dependent neuromodulators like steroids. We find that GC-specific deletion of δGABA A (cerebellar [cb] δ knockout [KO]) decreases tonic inhibition, makes GCs hyperexcitable, and in turn, leads to differential activation of cb output regions as well as many cortical and subcortical brain areas involved in cognition, anxiety-like behaviors, and the stress response. Cb δ KO mice display deficits in many behaviors, but motor function is normal. Strikingly, δGABA A deletion alters maternal behavior as well as spontaneous, stress-related, and social behaviors specifically in females. Our findings establish that δGABA A Rs enable the cerebellum to control diverse behaviors not previously associated with the cerebellum in a sex-dependent manner. These insights may contribute to a better understanding of the mechanisms that underlie behavioral abnormalities in psychiatric and neurodevelopmental disorders that display a gender bias., Competing Interests: Declaration of Interests S.R.D. is on the scientific advisory board of RBNC Inc., which has licensed the MoSeq technology, and holds patents related to the use of MoSeq to characterize behavior for drug development., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2020
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