Biology subjects

Holguera, I.

Publications and source records attributed to Holguera, I..

5 recordsLinked to original sources

bioRxiv2025

Gene expression cartography of a developing neuronal structure

The brain is a complex structure comprising thousands to billions of neurons that belong to thousands to millions of different neuronal types. These neurons often come from different progenitor domains and have very diverse developmental histories, yet they need to find their precise location in the brain and integrate into appropriate circuits. Therefore, describing the neuronal parts list of the brain in the form of single-cell mRNA sequencing atlases, while invaluable, lacks the spatial information that is instrumental to brain structures. While a large number of brain single-cell mRNA sequencing atlases have become available over the last years, spatial transcriptomic studies have lagged behind for a variety of reasons. Here, we use a gene expression cartography algorithm, called Novosparc, to reconstruct the spatial distribution of gene expression and cell type localization in a complex, yet tractable, developing brain structure, the Drosophila optic lobe. We generate a three-dimensional atlas of this structure, which we made available through a dedicated website (https://larva3dnovosparc.ijm.fr). This allowed us to identify spatially compartmentalized cell types and spatially patterned genes, to predict hotspots of neuronal cell death and identify the expression of neuronal type-defining transcription factors. Importantly, we identify caveats in such algorithms that could allow for the development of refined versions. Altogether, this work provides an invaluable tool for brain researchers to formulate hypotheses and paves the way for the generation of three-dimensional atlases of more complex brain structures, which will enhance our understanding of how neurons with diverse developmental lineages can integrate to form a functional brain.

developmental biology↗

bioRxiv2025

Temporal and Notch identity determine layer targeting and synapse location of medulla neurons

How specification mechanisms that generate neural diversity translate into specific neuronal targeting, connectivity, and function in the adult brain is not understood. In the medulla region of the Drosophila optic lobe, neural progenitors generate different neurons in a fixed order by sequentially expressing a series of temporal transcription factors as they age. Then, Notch signaling in intermediate progenitors further diversifies neuronal progeny. Using the Electron Microscopy reconstruction of the adult fly brain, we matched the temporal and Notch identity of medulla neurons with their adult targeting features across the different optic lobe neuropils at synapse resolution, and found that these specification mechanisms are significantly associated with the depth of neuropil targeting in the adult brain, for both local interneurons and projection neurons. We show that this temporal identity-dependent targeting of projection neurons unfolds early in development and is genetically determined. Notably, synapse location in the adult brain of putative medulla neurons can be used to predict their temporal origin. Moreover, synapses of neuronal types from different connectome-predicted functional subsystems are compartmentalized in the different neuropils, suggesting a link between synaptic stratification and specific visual functions. Finally, we show that candidate terminal selector TFs are significantly associated with a specific depth bias in the optic lobe neuropils, providing putative molecular determinants of this targeting. Together, we show that temporal identity and Notch status of medulla neurons can predict their neuropil synapse location, linking their developmental patterning with adult circuit architecture.

developmental biology↗

bioRxiv2024

High-throughput identification of the spatial origins of Drosophila optic lobe neurons using single-cell mRNA-sequencing

The medulla is the part of the Drosophila optic lobe with the greatest neuronal diversity, in which the identity of each neuronal type is specified in progenitors and newborn neurons via the integration of temporal, spatial, and Notch-driven patterning mechanisms. This identity is maintained in differentiating and adult neurons by the expression of neuronal type-specific combinations of terminal selectors, which are transcription factors expressed continuously during development and in the adult that are thought to control all neuronal type-specific gene expression. However, how the patterning mechanisms establish terminal selector expression is unknown. We have previously characterized the temporal and Notch origin of medulla neurons. Here we have used single-cell mRNA-sequencing to characterize their spatial origins and identified two new spatial subdomains. Together, this makes the medulla the first complex brain structure for which the patterning mechanisms specifying the identity of each neuronal type are known. This knowledge allowed us to identify correlations between patterning information, terminal selector expression and neuronal features. Our results suggest that different subsets of the patterning information accessible to a given neuronal type control the expression of each of its terminal selectors and of modules of terminal features, including neurotransmitter identity. Therefore, the evolution of new neuronal types could rely on the acquisition of modules of neuronal features pre-determined by their developmental origin.

developmental biology↗

bioRxiv2022

Coordinated control of neuronal differentiation and wiring by a sustained code of transcription factors

The enormous diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of [~]10 transcription factors that are continuously expressed by them. We show that targeted modifications of this selector code induce predictable conversions of cell fates between neurons in vivo. These conversions appear morphologically and transcriptionally complete, arguing for a conserved gene regulatory program that jointly instructs both the type-specific development and the terminal features of neurons. Cis-regulatory sequence analysis of open chromatin links one of these selectors to an upstream patterning gene in stem cells that specifies neuronal fates. Experimentally validated network models show that selectors interact with ecdysone signaling to regulate downstream effectors controlling brain wiring. Our results provide a generalizable framework of how specific fates are initiated and maintained in postmitotic neurons.

neuroscience↗

bioRxiv2020

R7 photoreceptor axon targeting requires matching levels of the lost and found protein in R7 and its synaptic partners

As neural circuits form, growing processes select the correct synaptic partners through interactions between cell surface proteins. The presence of such proteins on two neuronal processes may lead to either adhesion or repulsion; however, the consequences of mismatched expression have rarely been explored. Here we show that the Drosophila CUB-LDL protein Lost and found (Loaf) is required in the UV-sensitive R7 photoreceptor for normal axon targeting only when Loaf is also present in its synaptic partners. Although targeting occurs normally in loaf mutant animals, removing loaf from photoreceptors or expressing it in their postsynaptic neurons Tm5a/b or Dm9 in a loaf mutant causes mistargeting of R7 axons. Loaf localizes primarily to intracellular vesicles including endosomes. We propose that Loaf regulates the trafficking or function of one or more cell surface proteins, and an excess of these proteins on the synaptic partners of R7 prevents the formation of stable connections.

developmental biology↗