Biology subjects

Kagan, S.

Publications and source records attributed to Kagan, S..

5 recordsLinked to original sources

bioRxiv2026

The 3D Ultrastructure of C. elegans Gut Granules

We identify an endoderm-restricted organelle in published volume electron microscopy datasets of C. elegans embryos. The organelle consists of a tubular ring surrounding a membrane-bound compartment harboring a prominent dense particle and exhibits a basal polarity and size concordant with canonical gut granules. This finding offers ultrastructural detail to recent evidence that gut granules are bi-lobed organelles with two distinct compartments.

cell biology↗

bioRxiv2025

Dynamic Functional Pathway Development in Type 1 Spinal Interneurons: Stage-specific roles of retinoic acid activity

BackgrounddI1 spinal interneuron development requires precise coordination of proliferation, differentiation, and migration, yet the molecular and cellular properties underlying the temporal coupling of these processes remain unresolved. ResultsSingle-cell RNA sequencing of the E4 quail neural tube under control and retinoic acid (RA)-deprived conditions generated a high-resolution atlas spanning a continuous trajectory from dorsal progenitors to differentiated neurons. Pseudotime and RNA velocity analyses revealed transitions consistent with medial-to-lateral displacement in vivo. Early progenitors expressed cell cycle and BMP-associated programs, followed by induction of cytoskeletal and extracellular matrix remodelling genes and later activation of pan-neuronal and synaptic pathways. BMP signaling declined during differentiation through upregulation of BMP antagonists, whereas apoptosis-related genes were poised during specification without overt cell death. Autophagy-associated genes peaked during differentiation. Disruption of RA signaling by dominant-negative RAR403 uncovered stage-specific functions of RA. In progenitors, RA inhibition increased proliferation. In differentiating neurons, it upregulated BARHL1/2 and enhanced ion channel, synaptic, cytoskeletal, and extracellular matrix gene programs. RA inhibition also impaired ventral displacement of BarHL2-positive dI1 neurons, causing abnormal positioning. ConclusionsThese findings define a dI1-centered single-cell atlas of the progenitor-to-neuron transition and identify stage-specific roles for RA in dorsal hinterneuron maturation. Key findingsO_LIWe provide a high-resolution single-cell atlas of dI1 spinal interneuron development in the E4 quail neural tube, analysis of this single stage reveals a continuous trajectory from proliferative dorsal progenitors to differentiated neurons. C_LIO_LIDevelopment along this trajectory is tightly staged: early cells are dominated by cell-cycle and progenitor-maintenance programs, while later cells progressively activate cytoskeletal, extracellular matrix, axon-guidance, synaptic, and mature neuronal pathways. C_LIO_LIBMP signaling is strongest in early dI1 progenitors and is progressively attenuated during differentiation through the induction of BMP inhibitors, supporting a stage-specific role for BMP in early specification rather than late maturation. C_LIO_LIRetinoic acid acts in a stage-dependent manner: RA inhibition increases progenitor proliferation, alters differentiation-associated gene programs, and upregulates neuronal maturation, ion-channel, and synaptic genes in differentiating neurons. C_LIO_LIRepressing RA signaling causes BarHL2-positive dI1 neurons to fail their normal ventral migration. Instead, they accumulate near their dorsal origin and show ectopic localization, indicating that RA is required for proper migration. C_LI

developmental biology↗

bioRxiv2024

Retinoic acid, an essential component of the RP organizer, promotes the spatio-temporal segregation of dorsal neural fates

Dorsal neural tube-derived retinoic acid promotes the end of neural crest production and transition into a definitive roof plate. Here we analyze how this impacts the segregation of central and peripheral lineages, a process essential for tissue patterning and function. Localized in-ovo inhibition of retinoic acid activity followed by single cell transcriptomics unraveled a comprehensive list of differentially expressed genes relevant to these processes. Importantly, progenitors co-expressed neural crest, roof plate and dI1 interneuron markers indicating a failure in proper lineage segregation. Furthermore, we found that separation between roof plate and dI1 interneurons is mediated by Notch activity downstream of retinoic acid, highlighting their critical role in establishing the roof plate-dI1 boundary. Within the peripheral branch, where absence of retinoic acid resulted in neural crest production and emigration extending into the roof plate stage, sensory progenitors failed to separate from melanocytes leading to formation of a common glia-melanocyte cell with aberrant migratory patterns. Together, we uncover and characterize a molecular mechanism responsible for segregation of dorsal neural fates during development.

developmental biology↗

bioRxiv2021

Targeting neurons in the tumor microenvironment with bupivacaine nanoparticles reduces breast cancer progression and metastases

Neurons within the tumor microenvironment promote cancer progression, thus their local targeting has potential clinical benefits. We designed PEGylated lipid nanoparticles loaded with a non-opioid analgesic, bupivacaine, to target neurons within breast cancer tumors and suppress nerve-to-cancer crosstalk. In vitro, 100-nm nanoparticles were taken up readily by primary neurons, trafficking from the neuronal body and along the axons. We demonstrate that signaling between triple-negative breast cancer cells (4T1) and neurons involves secretion of cytokines stimulating neurite outgrowth. Reciprocally, neurons stimulated 4T1 proliferation, migration and survival through secretion of neurotransmitters. Bupivacaine curbs neurite growth and signaling with cancer cells, inhibiting cancer-cell viability. In vivo, bupivacaine-loaded nanoparticles administered intravenously, suppressed neurons in orthotopic triple-negative breast cancer tumors, inhibiting tumor growth and metastatic dissemination. Overall, our findings suggest that reducing nerve involvement in tumors is important for treating cancer.

cancer biology↗

bioRxiv2020

Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube

The factors underlying establishment of the definitive roof plate (RP) and its segregation from neural crest (NC) and interneurons are unknown. We performed transcriptome analysis at trunk levels of quail embryos comparing the dorsal neural tube at premigratory NC and RP stages. This unraveled molecular heterogeneity between NC and RP stages, and within the RP itself. By implementing these genes, we asked whether Notch signaling is involved in RP development. First, we observed that Notch is active at the RP-interneuron interface. Furthermore, gain and loss of Notch function in quail and mouse embryos, respectively, revealed no effect on early NC behavior. Constitutive Notch activation caused a local downregulation of RP markers with a concomitant development of dI1 interneurons, as well as an ectopic upregulation of RP markers in the interneuron domain. Reciprocally, in mice lacking Notch activity both the RP and dI1 interneurons failed to form and this was associated with expansion of the dI2 population. Collectively, our results offer a new resource for defining specific cell types, and provide evidence that Notch is required to establish the definitive RP, and to determine the choice between RP and interneuron fates, but not the segregation of RP from NC. Summary statementA new set of genes involved in Notch-dependent roof plate formation is unraveled by transcriptome analysis.

developmental biology↗