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In JoVE (1)
Other Publications (9)
- Nature Reviews. Molecular Cell Biology
- The Journal of Comparative Neurology
- The Journal of Comparative Neurology
- PloS One
- The Journal of Comparative Neurology
- BMC Developmental Biology
- Development (Cambridge, England)
- Developmental Dynamics : an Official Publication of the American Association of Anatomists
- Proceedings of the National Academy of Sciences of the United States of America
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Articles by Jeffrey M. Trimarchi in JoVE
JoVE Neuroscience
Single-cell Profilering van het ontwikkelen en Jong netvlies Neuronen
Department of Genetics, Development and Cell Biology, Neuroscience Program, Iowa State University
Werkwijze voor het isoleren van een retinacellen en vervolgens amplificatie van de cDNA beschreven. Single-cell transcriptomics onthult de mate van cellulaire heterogeniteit aanwezig is in een tissue en onthult nieuwe marker-genen voor zeldzame celpopulaties. De bijbehorende protocol kan worden aangepast aan verschillende celtypen te passen.
Other articles by Jeffrey M. Trimarchi on PubMed
Sibling Rivalry in the E2F Family
The E2F transcription factor family determines whether or not a cell will divide by controlling the expression of key cell-cycle regulators. The individual E2Fs can be divided into distinct subgroups that act in direct opposition to one another to promote either cellular proliferation or cell-cycle exit and terminal differentiation. What is the underlying molecular basis of this 'push-me-pull-you' regulation, and what are its biological consequences?
Molecular Heterogeneity of Developing Retinal Ganglion and Amacrine Cells Revealed Through Single Cell Gene Expression Profiling
During development of the central nervous system (CNS), cycling uncommitted progenitor cells give rise to a variety of distinct neuronal and glial cell types. As these different cell types are born they progress from newly specified cells to fully differentiated neurons and glia. In order to define the developmental processes of individual cell types, single cell expression profiling was carried out on developing ganglion and amacrine cells of the murine retina. Individual cells from multiple developmental stages were isolated and profiled on Affymetrix oligonucleotide arrays. Two-color fluorescent in situ hybridization on dissociated retinas was used to verify and extend the microarray results by allowing quantitative measurements of a large number of cells coexpressing two genes. Together, these experiments have yielded an expanded view of the processes underway in developing retinal ganglion and amacrine cells, as well as several hundred new marker genes for these cell types. In addition, this study has allowed for the definition of some of the molecular heterogeneity both between developing ganglion and amacrine cells and among subclasses of each cell type.
Identification of Molecular Markers of Bipolar Cells in the Murine Retina
Retinal bipolar neurons serve as relay interneurons that connect rod and cone photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies essential for correct routing of photoreceptor cell signals to specific postsynaptic amacrine and ganglion cells. The development and physiology of these interneurons have not been completely defined molecularly. Despite previous identification of genes expressed in several bipolar cell subtypes, molecules that mark each bipolar cell type still await discovery. In this report, novel genetic markers of murine bipolar cells were found. Candidates were initially generated by using microarray analysis of single bipolar cells and mining of retinal serial analysis of gene expression (SAGE) data. These candidates were subsequently tested for expression in bipolar cells by RNA in situ hybridization. Ten new molecular markers were identified, five of which are highly enriched in their expression in bipolar cells within the adult retina. Double-labeling experiments using probes for previously characterized subsets of bipolar cells were performed to identify the subtypes of bipolar cells that express the novel markers. Additionally, the expression of bipolar cell genes was analyzed in Bhlhb4 knockout retinas, in which rod bipolar cells degenerate postnatally, to delineate further the identity of bipolar cells in which novel markers are found. From the analysis of Bhlhb4 mutant retinas, cone bipolar cell gene expression appears to be relatively unaffected by the degeneration of rod bipolar cells. Identification of molecular markers for the various subtypes of bipolar cells will lead to greater insights into the development and function of these diverse interneurons.
Individual Retinal Progenitor Cells Display Extensive Heterogeneity of Gene Expression
The development of complex tissues requires that mitotic progenitor cells integrate information from the environment. The highly varied outcomes of such integration processes undoubtedly depend at least in part upon variations among the gene expression programs of individual progenitor cells. To date, there has not been a comprehensive examination of these differences among progenitor cells of a particular tissue. Here, we used comprehensive gene expression profiling to define these differences among individual progenitor cells of the vertebrate retina. Retinal progenitor cells (RPCs) have been shown by lineage analysis to be multipotent throughout development and to produce distinct types of daughter cells in a temporal, conserved order. A total of 42 single RPCs were profiled on Affymetrix arrays. In situ hybridizations performed on both retinal sections and dissociated retinal cells were used to validate the results of the microarrays. An extensive amount of heterogeneity in gene expression among RPCs, even among cells isolated from the same developmental time point, was observed. While many classes of genes displayed heterogeneity of gene expression, the expression of transcription factors constituted a significant amount of the observed heterogeneity. In contrast to previous findings, individual RPCs were found to express multiple bHLH transcription factors, suggesting alternative models to those previously developed concerning how these factors may be coordinated. Additionally, the expression of cell cycle related transcripts showed differences among those associated with G2 and M, versus G1 and S phase, suggesting different levels of regulation for these genes. These data provide insights into the types of processes and genes that are fundamental to cell fate choices, proliferation decisions, and, for cells of the central nervous system, the underpinnings of the formation of complex circuitry.
The Transcriptome of Retinal Müller Glial Cells
Müller glial cells are the major type of glia in the mammalian retina. To identify the molecular machinery that defines Müller glial cell identity and function, single cell gene expression profiling was performed on Affymetrix microarrays. Identification of a cluster of genes expressed at high levels suggests a Müller glia core transcriptome, which likely underlies many of the functions of Müller glia. Expression of components of the cell cycle machinery and the Notch pathway, as well as of growth factors, chemokines, and lipoproteins might allow communication between Müller glial cells and the neurons that they support, including modulation of neuronal activity. This approach revealed a set of transcripts that were not previously characterized in (Müller) glia; validation of the expression of some of these genes was performed by in situ hybridization. Genes expressed exclusively by Müller glia were identified as novel markers. In addition, a novel BAC transgenic mouse that expresses Cre in Müller glia cells was generated. The molecular fingerprint of Müller glia provides a foundation for further studies of Müller glia development and function in normal and diseased states.
Thyroid Hormone Components Are Expressed in Three Sequential Waves During Development of the Chick Retina
Thyroid hormone (TH) is an important developmental regulator in many tissues, including the retina. TH is activated locally via deiodinase 2 (Dio2), and it is destroyed by deiodinase 3 (Dio3). The TH receptors, TRa and TRb, mediate TH activity through hormone and DNA binding, and interactions with transcription regulators.
Temporal Requirement of the Alternative-splicing Factor Sfrs1 for the Survival of Retinal Neurons
Alternative splicing is the primary mechanism by which a limited number of protein-coding genes can generate proteome diversity. We have investigated the role of the alternative-splicing factor Sfrs1, an arginine/serine-rich (SR) protein family member, during mouse retinal development. Loss of Sfrs1 function during embryonic retinal development had a profound effect, leading to a small retina at birth. In addition, the retina underwent further degeneration in the postnatal period. Loss of Sfrs1 function resulted in the death of retinal neurons that were born during early to mid-embryonic development. Ganglion cells, cone photoreceptors, horizontal cells and amacrine cells were produced and initiated differentiation. However, these neurons subsequently underwent cell death through apoptosis. By contrast, Sfrs1 was not required for the survival of the neurons generated later, including later-born amacrine cells, rod photoreceptors, bipolar cells and Müller glia. Our results highlight the requirement of Sfrs1-mediated alternative splicing for the survival of retinal neurons, with sensitivity defined by the window of time in which the neuron was generated.
Identification of Genes Expressed Preferentially in the Developing Peripheral Margin of the Optic Cup
Specification of the peripheral optic cup by Wnt signaling is critical for formation of the ciliary body/iris. Identification of marker genes for this region during development provides a starting point for functional analyses. During transcriptional profiling of single cells from the developing eye, two cells were identified that expressed genes not found in most other single cell profiles. In situ hybridizations demonstrated that many of these genes were expressed in the peripheral optic cup in both early mouse and chicken development, and in the ciliary body/iris at subsequent developmental stages. These analyses indicate that the two cells probably originated from the developing ciliary body/iris. Changes in expression of these genes were assayed in embryonic chicken retinas when canonical Wnt signaling was ectopically activated by CA-beta-catenin. Twelve ciliary body/iris genes were identified as upregulated following induction, suggesting they are excellent candidates for downstream effectors of Wnt signaling in the optic cup.
Development and Diversification of Retinal Amacrine Interneurons at Single Cell Resolution
The vertebrate retina uses diverse neuronal cell types arrayed into complex neural circuits to extract, process, and relay information from the visual scene to the higher order processing centers of the brain. Amacrine cells, a class of interneurons, are thought to mediate much of the processing of the visual signal that occurs within the retina. Although amacrine cells display extensive morphological diversity, the molecular nature of this diversity is largely unknown. Furthermore, it is not known how this diversity arises during development. Here, we have combined in vivo genetic labeling, single cell genome-wide expression profiling, and classical birthdating to (i) identify specific molecular types of amacrine cells, (ii) demonstrate the molecular diversity of the amacrine cell class, and (iii) show that amacrine cell diversity arises at least in part through temporal patterning.
