Biology subjects

Trakhtenberg, E. F.

Publications and source records attributed to Trakhtenberg, E. F..

3 recordsLinked to original sources

bioRxiv2023

Transcriptomic profiling of retinal cells reveals a subpopulation of microglia/macrophages expressing Rbpms and Spp1 markers of retinal ganglion cells (RGCs) that confound identification of RGCs

Analysis of retinal ganglion cells (RGCs) by scRNA-seq is emerging as a state-of-the-art method for studying RGC biology and subtypes, as well as for studying the mechanisms of neuroprotection and axon regeneration in the central nervous system (CNS). Rbpms has been established as a pan-RGC marker, and Spp1 has been established as an RGC type marker. Here, we analyzed by scRNA-seq retinal microglia and macrophages, and found Rbpms+ and Spp1+ subpopulations of retinal microglia/macrophages, which pose a potential pitfall in scRNA-seq studies involving RGCs. We performed comparative analysis of cellular identity of the presumed RGC cells isolated in recent scRNA-seq studies, and found that Rbpms+ and Spp1+ microglia/macrophages confounded identification of RGCs. We also provide solutions for circumventing this potential pitfall in scRNA-seq studies, by including in RGC and RGC selection criteria other pan-RGC and RGC markers.

neuroscience↗

bioRxiv2021

Retroactive analysis of single cell transcriptome profiles using next-generation algorithms revised the identification of several resilient retinal ganglion cell types

The clustering of single cell RNA-sequencing (scRNA-seq) data enables the classification of cell types, and the development of integration mapping algorithms has enabled the tracing of altered-from-baseline transcriptomes to their respective cell type origins. Here, we developed an algorithm that removes sources of noise from scRNA-seq reference dataset, and in the next step optimizes weight-assignment to anchors, cumulatively improving the accuracy of query cells mapping to reference dataset. The denoising step of our algorithm also improved the performance of other mapping algorithms. To further demonstrate biological relevance, using our algorithm we determined the type-origin of the 17% of injured retinal ganglion cells (RGCs) that a prior algorithm did not identify. As we found that most of the originally unassigned cells belonged to only some RGC types, a consequent change in the proportions of the surviving types resulted in an amended ranking of resiliency to injury. We also identified new cluster-markers for RGC types, validated two novel markers by immunostaining in retinas, and developed a website for cluster-by-cluster comparison of gene expression between uninjured and injured RGC types. Additional bioinformatic analyses contributed new insights into the global characteristics of RGC types and how axonal injury affects them, showing how dissimilarity between transcriptomes of RGC types increases during maturation and after injury. We further characterized the correspondence between the neonatal and adult RGC types, and showed which cluster markers change expression developmentally or after injury. We also show, for the first time, that global properties of the transcriptome can predict the resilience to injury of at least some cell types. The R-package, CellTools, for the algorithms we developed, will assist scRNA-seq studies across biological fields.

neuroscience↗

bioRxiv2021

Post-injury born oligodendrocytes integrate into the glial scar and inhibit growth of regenerating axons by premature myelination

Pathologies of the central nervous system (CNS) white matter often result in permanent functional deficits because mature mammalian projection neurons fail to regenerate long-distance axons after injury. A major barrier to axonal regenerative research is that the CNS axons that regenerate in response to experimental treatments stall growth before reaching their post-synaptic targets. Here, we test the hypothesis that premature, de novo, myelination of regenerating axons stalls their growth, even after bypassing the glial scar. To test this hypothesis, first, we used single cell RNA-seq (scRNA-seq) and immunohistological analysis to investigate whether post-injury born oligodendrocytes integrate into the glial scar after optic nerve injury. Then, we used a multiple sclerosis model of demyelination concurrently with the stimulation of axon regeneration by Pten knockdown (KD) in projection neurons after optic nerve injury. We found that post-injury born oligodendrocytes integrate into the glial scar, where they are susceptible to the demyelination treatment, which prevented premature myelination, and thereby enhanced Pten KD-stimulated axon regeneration. We also present a website for comparing the gene expression of scRNA-seq-profiled optic nerve oligodendrocytes under physiological and pathophysiological conditions. SIGNIFICANCE STATEMENTMyelin debris from degenerating axons along with reactive astrocytes in the glial scar inhibit CNS axon regeneration. However, even with the recently developed experimental approaches which activate axons to regenerate passed the glial scar, almost all axons still stall growth before reaching their post-synaptic targets. Here, we show that post-injury born oligodendrocytes integrate into the glial scar, and that other than myelin debris, live oligodendrocytes prematurely myelinating the regenerating axons inhibit growth, even if the axons have already regenerated passed the glial scar.

neuroscience↗