Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage

Abstract

Owing to its pronounced regenerative capacity in many tissues and organs, the zebrafish brain represents an ideal platform to understand the endogenous regeneration mechanisms that restore tissue integrity and function upon injury or disease. Although radial glial and neuronal cell populations have been characterized with respect to specific marker genes, comprehensive transcriptomic profiling of the regenerating telencephalon has not been conducted so far. Here, by processing the lesioned and unlesioned hemispheres of the telencephalon separately, we reveal the differentially expressed genes (DEGs) at the early wound healing and early proliferative stages of regeneration, i.e., 20 h post-lesion (hpl) and 3 days post-lesion (dpl), respectively. At 20 hpl, we detect a far higher number of DEGs in the lesioned hemisphere than in the unlesioned half and only 7% of all DEGs in both halves. However, this difference disappears at 3 dpl, where the lesioned and unlesioned hemispheres share 40% of all DEGs. By performing an extensive comparison of the gene expression profiles in these stages, we unravel that the lesioned hemispheres at 20 hpl and 3 dpl exhibit distinct transcriptional profiles. We further unveil a prominent activation of Wnt/β-catenin signaling at 20 hpl, returning to control level in the lesioned site at 3 dpl. Wnt/β-catenin signaling indeed appears to control a large number of genes associated primarily with the p53, apoptosis, forkhead box O (FoxO), mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) signaling pathways specifically at 20 hpl. Based on these results, we propose that the lesioned and unlesioned hemispheres react to injury dynamically during telencephalon regeneration and that the activation of Wnt/β-catenin signaling at the early wound healing stage plays a key role in the regulation of cellular and molecular events.

Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury

“…Our findings on mRNA expression profiles are complementary to a recently published transcriptome study focusing on the immediate early changes in response to injury of the telencephalon (Demirci et al, 2020). Interestingly, this study reported activation of gene expression programs in both the injured and the uninjured hemispheres, even though the response was less pronounced and delayed in the injured hemisphere.…”

Multi-dimensional transcriptome analysis reveals modulation of cholesterol metabolism as highly integrated response to brain injury

“…The analysis of our sequencing data [14] with more than 600,000,000 Our findings on mRNA expression profiles are complementary to a recently published transcriptome study focusing on the immediate early changes in response to injury of the telencephalon [95]. Interestingly, this study reported activation of gene expression programs in both the injured and the uninjured hemispheres, even though the response was less pronounced and delayed in the injured hemisphere.…”

“…We systematically analysed hundreds of transcription regulators for their expression in the injured telencephalon by in situ hybridisation on sections. We did not observe gene activation in the uninjured hemisphere [14,13,95]. Demirci et al [95] inflicted lesions by inserting a needle into the nostril.…”

“…We did not observe gene activation in the uninjured hemisphere [14,13,95]. Demirci et al [95] inflicted lesions by inserting a needle into the nostril. In contrast, our protocol of injuring the telencephalon [96] involves the opening of the skull and inserting the needle directly into one hemisphere of the telencephalon.…”

“…In contrast, our protocol of injuring the telencephalon [96] involves the opening of the skull and inserting the needle directly into one hemisphere of the telencephalon. Most likely the protocol used by Demirci et al [95] causes damage of the second hemisphere or some of the extending nerves thereby causing activation of regenerative programs also in the seemingly uninjured hemisphere.…”