Cell-specific regulation of gene expression using splicing-dependent frameshifting

AAV, RNA splicing,

Ling, J. P., Bygrave, A. M., Santiago, C. P., Carmen-Orozco, R. P., Trinh, V. T., Yu, M., Li, Y., Liu, Y., Bowden, K. D., Duncan, L. H., Han, J., Taneja, K., Dongmo, R., Babola, T. A., Parker, P., Jiang, L., Leavey, P. J., Smith, J. J., Vistein, R., Gimmen, M. Y., … Blackshaw, S. (2022). Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature communications, 13(1), 5773. https://doi.org/10.1038/s41467-022-33523-2

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LRLoop: A method to predict feedback loops in cell-cell communication

Cell fate, Development, Neural development, Neurogenesis, Retina, scRNA-Seq, , , , ,

Xin, Y., Lyu, P., Jiang, J., Zhou, F., Wang, J., Blackshaw, S., & Qian, J. (2022). LRLoop: A method to predict feedback loops in cell-cell communication. Bioinformatics (Oxford, England), 38(17), 4117–4126. Advance online publication. https://doi.org/10.1093/bioinformatics/btac447

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Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy

Muller glia, Neurodegeneration, Neurogenesis, Notch/Delta, Photoreceptor, Retina, scRNA-Seq, , , , , ,

Fogerty, J., Song, P., Boyd, P., Grabinski, S. E., Hoang, T., Reich, A., Cianciolo, L. T., Blackshaw, S., Mumm, J. S., Hyde, D. R., & Perkins, B. D. (2022). Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy. The Journal of neuroscience : the official journal of the Society for Neuroscience, 42(26), 5144–5158. https://doi.org/10.1523/JNEUROSCI.0244-22.2022

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Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina

Cell lineage analysis, Muller glia, Neurogenesis, Retina, RNA binding proteins, , , ,

Hoang, T., Kim, D. W., Appel, H., Pannullo, N. A., Leavey, P., Ozawa, M., Zheng, S., Yu, M., Peachey, N. S., & Blackshaw, S. (2022). Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina. Cell reports, 39(11), 110849. https://doi.org/10.1016/j.celrep.2022.110849

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Loss of Function of the Neural Cell Adhesion Molecule NrCAM Regulates Differentiation, Proliferation and Neurogenesis in Early Postnatal Hypothalamic Tanycytes

Development, Hypothalamus, Neural development, Neurogenesis, scRNA-Seq, Tanycytes, , , , ,

Moore, A., Chinnaiya, K., Kim, D. W., Brown, S., Stewart, I., Robins, S., Dowsett, G., Muir, C., Travaglio, M., Lewis, J. E., Ebling, F., Blackshaw, S., Furley, A., & Placzek, M. (2022). Loss of Function of the Neural Cell Adhesion Molecule NrCAM Regulates Differentiation, Proliferation and Neurogenesis in Early Postnatal Hypothalamic Tanycytes. Frontiers in neuroscience, 16, 832961. https://doi.org/10.3389/fnins.2022.832961

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In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration

Neurodegeneration, Photoreceptor, Retina, scRNA-Seq, , ,

Choi, E. H., Suh, S., Foik, A. T., Leinonen, H., Newby, G. A., Gao, X. D., Banskota, S., Hoang, T., Du, S. W., Dong, Z., Raguram, A., Kohli, S., Blackshaw, S., Lyon, D. C., Liu, D. R., & Palczewski, K. (2022). In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration. Nature communications, 13(1), 1830. https://doi.org/10.1038/s41467-022-29490-3

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Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids

Retina, scRNA-Seq,

Thomas, E. D., Timms, A. E., Giles, S., Harkins-Perry, S., Lyu, P., Hoang, T., Qian, J., Jackson, V. E., Bahlo, M., Blackshaw, S., Friedlander, M., Eade, K., & Cherry, T. J. (2022). Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids. Developmental cell, 57(6), 820–836.e6. https://doi.org/10.1016/j.devcel.2022.02.018

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Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration

Neurodegeneration, Retina,

Shah, S. H., Schiapparelli, L. M., Ma, Y., Yokota, S., Atkins, M., Xia, X., Cameron, E. G., Huang, T., Saturday, S., Sun, C. B., Knasel, C., Blackshaw, S., Yates, J. R., Cline, H. T., & Goldberg, J. L. (2022). Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. eLife, 11, e68148. https://doi.org/10.7554/eLife.68148

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