Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of Drosophila olfactory projection neurons

ABSTRACT: Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global downregulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. To compare the RNA and protein dynamics of PN surface molecules in the developing-to-mature transition, we also profiled the PN transcriptomes from 36hAPF pupae and 5d adults. We performed bulk RNA-sequencing of PNs with 3 samples for each stage and 2k cells for each sample.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE140093 | GEO | 2019/12/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers New Wiring Regulators

Project description:Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, Quake sR, Carr SA, Ting AY, Luo L. 2019. Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global down-regulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 new cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally-resolved in situ cell-surface proteomic profiling in discovering new regulators of brain wiring.

2019-11-06 | MSV000084543 | MassIVE

Transcription Factor Acj6 Controls Dendrite Targeting via Combinatorial Cell-Surface Codes

Project description:Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combinatorial expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

2022-04-21 | GSE200841 | GEO

Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-cell RNA Sequencing

Project description:How a neuronal cell type is defined and how this relates to its transcriptome are still open questions. The Drosophila olfactory projection neurons (PNs) are among the bestcharacterized neuronal types: Different PN classes target dendrites to distinct olfactory glomeruli and PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA-sequencing, we comprehensively characterized the transcriptomes of 40 PN classes and unequivocally identified transcriptomes for 6 classes. We found a new lineage-specific transcription factor that instructs PN dendrite targeting. Transcriptomes of closely-related PN classes exhibit the largest difference during circuit assembly, but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Genes encoding transcription factors and cell-surface molecules are the most differentially expressed, indicating their central roles in specifying neuronal identity. Finally, we show that PNs use highly redundant combinatorial molecular codes to distinguish subtypes, enabling robust specification of cell identity and circuit assembly.

2017-10-21 | GSE100058 | GEO

Transcription Factor Acj6 Specifies Distinct Dendrite Targets via Unique Cell-Surface Protein Combinations

Project description:Xie Q, Li J1, Li H, Udeshi ND, Svinkina T, Kohani S, Guajardo R, Mani DR, Xu C, Li T, Han S, Wei W, Shuster SA, Luginbuhl DJ, Ting AY, Carr SA, Luo L. 2022. Transcription factors specify the fate and connectivity of developing neurons. To understand how distal neurites execute commands from these nucleus-residing factors to specify their connectivity, we investigated how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs). Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and molecules previously not associated with wiring, such as the mechanosensitive ion channel Piezo. Ion channel activity is dispensable for Piezo's function in PN dendrite targeting. Combinatorial expression of Acj6 executors more strongly rescued specific acj6 mutant phenotypes than expression of individual executors. Together, our findings reveal that a key transcription factor controls wiring specificity of different neuron types by regulating expression of unique combinations of cell-surface executors.

2022-04-01 | MSV000089187 | MassIVE

Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons

Project description:Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological features. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of Drosophila olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage—neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

2020-11-11 | GSE161228 | GEO

Selumetinib in adults with NF1 and inoperable plexiform neurofibroma

Project description:The MEK inhibitor selumetinib induces objective responses and provides clinical benefit in children with neurofibromatosis type 1 (NF1) and inoperable plexiform neurofibromas (PNs). To evaluate whether similar outcomes were possible in adult patients, in whom PN growth is generally slower than in pediatric patients, an open-label phase 2 study of selumetinib in adults with NF1 PNs was conducted. Correlative analysis included extraction of RNA followed by sequencing. Samples include paired specimens collected before and on treatment.

2024-10-07 | GSE277520 | GEO

Profiling the transcriptome of layer 5 intratelencephalic-projection neurons (IT-PNs) in the mature mouse motor cortex

Project description:Low input RNA-seq analysis of fluorescently activated cell sorted IT-PNs from layer 5 of the mature mouse motor cortex. Comparison of two distinct IT-PN subtypes previously described by Tantirigama et al. (2014) identifies unique gene expression.

2018-12-06 | GSE107586 | GEO

Proprioception is governed by highly diverse and versatile sensory neuron types

Project description:Proprioceptive neurons (PNs) are essential for the proper execution of all our movements by providing muscle sensory feedback to the central motor network. Here, using deep single cell RNAseq of adult PNs coupled with advanced virus- and genetic tracings, we have molecularly identified the 3 main types of PNs (Ia, Ib and II) and unexpectedly found that they segregate into 8 subgroups. Our data further reveal a highly sophisticated organization of PNs into discrete sensory input channels with distinct spatial distribution, innervation patterns and molecular profiles, that together contribute to the sensory monitoring of complex motor behavior. Moreover, while Ib- and II-PN subtypes are specified around birth, Ia-PN subtypes diversify later along with increased motor activity and show versatility in the adult following exercise training, suggesting adaptive proprioceptive function.

2020-12-25 | GSE156180 | GEO

Changes in composition and levels of hemolymph proteins provide insights to their functions in pharate, early and late pupae and adults of Manduca sexta

Project description:The tobacco hornworm, Manduca sexta, is a lepidopteran model species widely used to study insect biochemical processes. While some of its larval hemolymph proteins are well understood, a detailed proteomic analysis was unavailable until 2016, revealing features such as correlation with transcriptome data, formation of immune complexes, and constitution of an immune signaling system. Yet, it is unclear how these may change in other developmental stages. In this paper, we report the proteomes of cell-free hemolymph from prepupae, pupae on days 4 and 13, and young adults. Of the 1,824 proteins identified, 907 have a signal peptide and 215 are related to immunity. Drastic changes in abundance of the storage proteins, for instance, reflect physiological disparities among prepupae, pupae, and adults. Considerably more proteins lacking signal peptide are present in the late pupae, suggesting that plasma acts as a temporary reservoir for intracellular components released from remodeling tissues during metamorphosis. In summary, the proteins and their levels revealed in this study are expected to stimulate focused explorations of humoral immunity in wandering larvae, pupae, and adults of M. sexta and shed light upon functional and comparative genomic research in other holometabolous insects.

2020-10-30 | PXD019392 | Pride

In situ cell-surface proteomic profiling in mice

Project description:Shuster SA, Li J, Chon U, Hu MC, Luginbuhl DJ, Udeshi ND, Carey DK, Takeo YH, Xu C, Mani D.R., Han S, Ting AY, Carr SA, Luo L. Cell-surface proteins mediate cell-cell interactions throughout the lifetime of multicellular organisms, yet there are no general methods for profiling them in vertebrate tissues. Here, we present in-situ cell-surface proteome extraction by extracellular labeling (iPEEL) in mice, which enables cell-type-specific profiling of cell-surface proteomes in native tissues. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed a differential enrichment in cell-surface proteins with post-translational processing and synaptic functions in the developing and mature proteomes, respectively. A proteome-instructed in vivo loss-of-function screen identified a critical role for Armadillo-like helical domain-containing protein 4 (Armh4) in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disruption of endocytosis. Our results highlight the utility of cell-surface proteomic profiling in native tissues in identifying regulators of cell-surface signaling events.

2021-12-03 | MSV000088506 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data