Review Basal Ganglion papers for cell types missing from CL

[dosumis]

The main aim of BICAN this year is to build a taxonomy of cell types for the Basal Ganglion

The following papers are being used as sources for defining basal ganglion cell types. Please review them for missing CL terms - adding term requests to the CL tracker for each:

• He, Jing, Michael Kleyman, Jianjiao Chen, Aydin Alikaya, Kathryn M. Rothenhoefer, Bilge Esin Ozturk, Morgan Wirthlin, et al. 2021. “Transcriptional and Anatomical Diversity of Medium Spiny Neurons in the Primate Striatum.” Current Biology: CB 31 (24): 5473–86.e6. https://doi.org/10.1016/j.cub.2021.10.015.

• Krienen, Fenna M., Melissa Goldman, Qiangge Zhang, Ricardo C H Del Rosario, Marta Florio, Robert Machold, Arpiar Saunders, et al. 2020. “Innovations Present in the Primate Interneuron Repertoire.” Nature 586 (7828): 262–69. https://doi.org/10.1038/s41586-020-2781-z

I think it's also worth funding some good general reviews of BG cell types to curate. We can also review names in the current draft of the taxonomy.

@jeremymiller ; @UCDNJJ - can you suggest other papers?

[AvolaAmg]

From He et al., 2021 9 cell types in the striatum are mentioned in the main text, 8 of these are all already present in the CL database under the medium spiny neuron type:

• matrix D1 medium spiny neuron

• striosomal D1 medium spiny neuron

• matrix D2 medium spiny neuron

• striosomal D2 medium spiny neuron

• nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron

• nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron

• RXFP1-positive interface island D1-medium spiny neuron

• eccentric medium spiny neuron This cell comes from a different resource

There is two novel term:

• TAC3-positive interneuron in the striatum
• TAC3-positive medium spiny neurons

The TAC3-positive interneuron in the striatum is observed in He et al., 2021 and Krienen et al., 2020.

I will raise a ticket for both these cells to be added as a novel Cell type on CL.

I will also check that the description of the medium spiny neuron is complete in CL

For potential papers to review for the Basal Ganglia cell types to curate I will have a look at the following:

• Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells, GigaScience, Volume 12, 2023, giad095, https://doi.org/10.1093/gigascience/giad095

• Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain. Neuron. 2021 Oct 6 https://doi.org/10.1016/j.neuron.2021.09.001

• Transcriptomic diversity of cell types across the adult human brain Kimberly Siletti https://doi.org/10.1101/2022.10.12.511898

this is on mouse, I will have a quick look to find some leads as well

• Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq. Cell Rep. 2018 Aug 21;24(8):2179-2190.e7. doi: 10.1016/j.celrep.2018.07.053. PMID: 30134177; PMCID: PMC6117871.

if you have any other papers in mind feel free to tag me in the comments.

[dosumis]

DOne or still in progress?