Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Knockdown and overexpression of injury-responsive transcription factors in cultures of adult mouse dorsal root ganglia

ABSTRACT: The Activating Transcription Factor-4 (ATF4) contributes to pro-regenerative transcriptional responses following optic axon damage. Here we use an in vitro model of axon regeneration to investigate the contributions of ATF4 to the transcriptional injury response of adult mouse sensory neurons of the dorsal root ganglion (DRG). We find that, in contrast to optic axon injury, the upregulation of the pro-regenerative transcription factor ATF3 is not ATF4-dependent, and without that contribution, ATF4 instead limits adult DRG axon regrowth in collaboration with C/EBPgamma. Knockdown of ATF4 enhances axon regeneration in this model while regulating a collection of genes largely non-overlapping with those regulated by injury-activated pro-regenerative transcription factors, including ATF3 and c-Jun. We find that overexpression of ATF4 suppresses axon regeneration in a C/EBPgamma-dependent manner. This effect, however, is not a simple reciprocal of ATF4 knockdown, as it is also correlated with suppression of ATF3- and c-Jun-dependent transcription. Together these findings suggest that axon injury induces an ATF4-dependent transcriptional program that limits regeneration in parallel with pro-regenerative responses.

ORGANISM(S): Mus musculus

PROVIDER: GSE336380 | GEO | 2026/07/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Knockdown and knockout of the Integrated Stress Response (ISR) and ATF4 in cultures of adult mouse dorsal root ganglia

Project description:The Activating Transcription Factor-4 (ATF4) contributes to pro-regenerative transcriptional responses following optic axon damage. Here we use an in vitro model of axon regeneration to investigate the contributions of ATF4 to the transcriptional injury response of adult mouse sensory neurons of the dorsal root ganglion (DRG). We find that, in contrast to optic axon injury, the upregulation of the pro-regenerative transcription factor ATF3 is not ATF4-dependent, and without that contribution, ATF4 instead limits adult DRG axon regrowth in collaboration with C/EBPgamma. Knockout or knockdown of ATF4 enhances axon regeneration in this model while regulating a collection of genes strongly overlapping with those regulated by C/EBPgamma. We find that overexpression of ATF4 suppresses axon regeneration in a C/EBPgamma-dependent manner. This effect, however, is not a simple reciprocal of ATF4 knockout, as it is also correlated with suppression of ATF3- and c-Jun-dependent transcription. Together these findings suggest that axon injury induces an ATF4-dependent transcriptional program that limits regeneration in parallel with pro-regenerative responses.

2026-07-21 | GSE336472 | GEO

RNA-sequencing of injured cultured dorsal root ganglion neurons over time

Project description:Injured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured nervous system. Here, we used cultured dorsal root ganglia neurons to identify pro-regenerative transcription factors. Using RNA sequencing, we first characterized this neuronal culture and determined that embryonic day 13.5 DRG (eDRG) neurons cultured for 7 days are similar to e15.5 DRG neurons in vivo and that all neuronal subtypes are represented. This eDRG neuronal culture does not contain other non-neuronal cell types. Next, we performed RNA sequencing at different time points after in vitro axotomy. Analysis of differentially expressed genes revealed upregulation of know regeneration associated transcription factors, including Jun Atf3 and Rest, paralleling the axon injury response in vivo. Analysis of transcription factor binding sites in differentially expressed genes revealed other known transcription factors promoting axon regeneration, such as Myc, Hif1a, Pparg, Ascl1a, Srf, as well as other transcription factors not yet characterized in axon regeneration. We next tested if overexpression of known and novel candidate transcription factors alone or in combination promote axon regeneration in vitro. Our results demonstrate that expression of Ctcf with Yy1 or E2f2 enhances in vitro axon regeneration. Our analysis reveals that pairs of transcription factors can functionally synergize to promote axon regeneration and highlight that transcription factor interaction play an important role as a regulator of axon regeneration.

2022-06-20 | GSE138480 | GEO

Transcriptional profiling of adult retinal ganglion cells during optic nerve regeneration

Project description:Objective: To identify genes that are differentially expressed in retinal ganglion cells undergoing axon regeneration after optic nerve injury. Adult mice that express cyan-fluorescent protein (CFP) in RGCs were treated with pro-regenerative treatment after optic nerve injury. The treated RGCs were selected by FACS (CFP+mcherry) and their RNA profiles were analyzed.

2020-12-29 | GSE142881 | GEO

Stimulation of neuronal stress signaling in optic nerve crush

Project description:Dual Leucine-zipper Kinase (DLK)-dependent stress signaling is a critical determinant of neuronal survival and regenerative potential following axon damage, but it remains uncertain whether injury-activated DLK is adequate to initiate and maintain a pro-regenerative transcriptional response in the CNS. Using a drug-activatable DLK construct, we stimulated stress signaling for comparison of the retinal transcriptional response to, and in addition to, the response stimulated by mouse optic nerve injury in wildtype mice and in the context of partial axon regeneration enabled by disruption of the tumor suppressor PTEN.

2024-09-29 | GSE278304 | GEO

MicroRNA-19a-PTEN axis is involved in the developmental decline of axon regenerative capacity in retinal ganglion cells

Project description:Irreversible blindness from glaucoma and optic neuropathies is attributed to retinal ganglion cells (RGCs) losing the ability to regenerate axons. While several transcription factors and proteins have demonstrated enhancement of axon regeneration after optic nerve injury, mechanisms contributing to the age-related decline in axon regenerative capacity remains elusive. Here, we show that microRNAs are differentially expressed during RGC development, and identify microRNA-19a (miR-19a) as a heterochronic marker; developmental decline of miR-19a relieves suppression of PTEN, a key regulator of axon regeneration, and serves as a temporal indicator of decreasing axon regenerative capacity. Intravitreal injection of miR-19a promotes axon regeneration after optic nerve crush in adult mice, and increases axon extension in RGCs isolated from aged human donors. This uncovers a previously unrecognized involvement of the miR-19a-PTEN axis in RGC axon regeneration, and demonstrates therapeutic potential of microRNA-mediated restoration of axon regenerative capacity via intravitreal injection in patients with optic neuropathies.

2020-07-04 | GSE102458 | GEO

The Peripheral Atf3+ Neuronal Population is Responsible for Nerve Regeneration at Early Stage of Nerve Injury Revealed by Single-Cell RNA Sequencing

Project description:Peripheral nerve injury (PNI) could transform primary somatosensory neurons into regenerative state. However, details of transcriptomic changes associated to nerve regeneration of somatosensory neurons maintain unclear. 10x single-cell RNA sequencing (scRNA-seq) was conducted on mice dorsal root ganglia (DRG) cells after early stage of nerve injury on day 3 post-constriction chronic injury (CCI). We observed that a novel CCI-induced neuronal population (CIP) emerged and expressed high levels of activating transcription factor (Atf3), a neuronal injury marker. CIP neurons highly expressed regenerative associated genes (RAGs) and were enriched in regeneration-related gene ontology (GO) terms, suggesting these neurons could be a pro-regenerative population. Moreover, intercellular communication networks showed that CIP neurons have a close communication to satellite glia cells (SGCs) and specifically transmitted strong Fgf3-Fgfr1 signaling to SGCs, which could initiate regeneration-associated transcriptional changes of SGCs. This study also confirmed that the regenerative progress occurred at the early stage of nerve injury because immunohistochemistry showed the expression of ATF3 significantly increased since day 3 post-CCI and decreased at 1 month. Our bioinformatics analysis at single-cell resolution advances the knowledge of regenerative dynamic transcriptional changes of DRG cells after injuries and their underlying molecular mechanisms.

2024-02-09 | GSE255014 | GEO

Role of ATF3 in the transcription of GI-SINEs (growth inducing B2-SINEs) in DRG neurons in response to sciatic nerve crush

Project description:Injury of the sciatic nerve upregulates a specific subset of B2-SINE RNAs in Dorsal Root Ganglia (DRG) neurons that enhances axon regeneration, which we termed GI-SINEs (growth inducing SINEs). Based on ATAC-seq and transcription factor binding site analysis and in-culture perturbation of AP-1 TFs, we hypotheiszed that GI-SINEs specifically regulated by injury activated AP-1 TFs. Here we experimentally tested the role of ATF3, a CREB TF that belongs to the AP-1 TF superfamily, in the transcriptional upregulation of GI-SINEs. ATF3 was previously identified and characterized as a key activator of nerve-injury induced regeneration associated genes (RAGs) mRNA. Cre recombinase expressed under the Advillin promoter was used for ATF3-exon3 excision in a broad and specific manner in the DRG. Sciatic nerve injury was carried on on mice with a conditional knockout of ATF3 in sensory neurons and ATF3-wt mice and total RNAseq was carried on RNA extracred from on sciatic innervating DRGs (L4-L6) from the injured side ("Inj") and non-injured side (naive / "Na").

2025-05-16 | GSE279906 | GEO

Aryl hydrocarbon receptor restricts axon regeneration of DRG neurons in response to injury [DRG_AN00024583]

Project description:Injured neurons sense environmental cues to balance neural protection and axon regeneration, but the mechanisms are unclear. Here, we unveil aryl hydrocarbon receptor (AhR), a ligand-activated bHLH-PAS transcription factor, as a molecular sensor and key regulator of acute stress response at the expense of axon regeneration. We demonstrated responsiveness of DRG sensory neurons to AhR signaling, which functions to inhibit axon regeneration. Conditional neuronal Ahr deletion accelerated axon regeneration after sciatic nerve injury. Ahr deletion partially mimics the conditioning lesion in priming DRG to initiate axonogenesis gene programs; upon peripheral axotomy, Ahr ablation suppressed inflammation and stress signaling while augmenting pro-growth pathways. Moreover, comparative transcriptomics revealed signaling interactions between AhR and HIF-1α, two structurally related bHLH-PAS α units that share the dimerization partner Arnt/HIF-1β. Functional assays showed that the growth advantage of AhR-deficient DRG neurons requires HIF-1α; but in the absence of Arnt, DRG neurons can still mount a regenerative response. We further unveiled a link between bHLH-PAS transcription factors and DNA hydroxymethylation in response to peripheral axotomy, while RNA-seq of DRG neurons and neuronal single cell RNA-seq analysis revealed a link of AhR regulon to RNA regulation and integrated stress response (ISR), impacting global translation. Altogether, AhR activation favors stress coping and inflammation at the expense of axon regeneration; targeting AhR has the potential to enhance nerve repair.

2026-02-05 | GSE307639 | GEO

Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline [snRNA-seq]

Project description:Peripheral sensory neurons regenerate their axons after injury to regain function, but this ability declines with age. The mechanisms behind this decline are not fully understood. While excessive production of endothelin 1 (ET-1), a potent vasoconstrictor, is linked to many diseases that increase with age, the role of ET-1 and its receptors in axon regeneration is unknown. Using single cell RNA sequencing, we show that satellite glial cells (SGCs), which completely envelop the sensory neuron soma residing in the dorsal root ganglia (DRG), express the endothelin B receptor (ETBR), while ET-1 is expressed by endothelial cells. Inhibition of ETBR ex-vivo in DRG explant cultures improves axon growth in both adult and aged conditions. In vivo, treatment with the FDA-approved compound, Bosentan, improves axon regeneration and reverses the age-dependent decrease in axonal regenerative capacity. Single-nuclei RNA sequencing and electron microscopy analyses reveal a decreased abundance of SGCs in aged mice compared to adult mice. Additionally, the decreased expression of connexin 43 (Cx43) in SGCs in aged mice after nerve injury is partially rescued by Bosentan treatment. These results reveal that inhibiting ETBR function enhances axon regeneration and rescues the age-dependent decrease in axonal regenerative capacity, providing a potential avenue for future therapies.

2025-07-17 | GSE298413 | GEO

Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline [scRNA-seq]

2025-07-17 | GSE298412 | GEO