The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis

Nigel S Michki; Ye Li; Kayvon Sanjasaz; Yimeng Zhao; Fred Y Shen; Logan A Walker; Wenjia Cao; Cheng-Yu Lee; Dawen Cai

doi:10.1016/j.celrep.2021.109039

The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis

Cell Rep. 2021 Apr 27;35(4):109039. doi: 10.1016/j.celrep.2021.109039.

Authors

Nigel S Michki¹, Ye Li², Kayvon Sanjasaz³, Yimeng Zhao², Fred Y Shen⁴, Logan A Walker¹, Wenjia Cao⁵, Cheng-Yu Lee⁶, Dawen Cai⁷

Affiliations

¹ Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA.
² Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
³ Molecular, Cellular, and Developmental Biology LS&A, University of Michigan, Ann Arbor, MI, USA.
⁴ Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.
⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
⁶ Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
⁷ Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address: [email protected].

Abstract

The Drosophila type II neuroblast lineages present an attractive model to investigate the neurogenesis and differentiation process as they adapt to a process similar to that in the human outer subventricular zone. We perform targeted single-cell mRNA sequencing in third instar larval brains to study this process of the type II NB lineage. Combining prior knowledge, in silico analyses, and in situ validation, our multi-informatic investigation describes the molecular landscape from a single developmental snapshot. 17 markers are identified to differentiate distinct maturation stages. 30 markers are identified to specify the stem cell origin and/or cell division numbers of INPs, and at least 12 neuronal subtypes are identified. To foster future discoveries, we provide annotated tables of pairwise gene-gene correlation in single cells and MiCV, a web tool for interactively analyzing scRNA-seq datasets. Taken together, these resources advance our understanding of the neural differentiation process at the molecular level.

Keywords: Drosophila; MiCV; developmental brain; multi-informatic analysis; targeted scRNA-seq; type-II neuroblast.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brain
Cell Differentiation
Cell Proliferation
Drosophila
Drosophila Proteins / metabolism*
Informatics / methods*
Single-Cell Analysis / methods*

Substances

Drosophila Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding