Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses

Scientists performed the largest single-cell transcriptomic study of human iPSC-derived dopaminergic neurons to elucidate gene expression dynamics in response to cytotoxic and genetic stressors.
[Cell Reports]
Fernandes, H. J. R., Patikas, N., Foskolou, S., Field, S. F., Park, J.-E., Byrne, M. L., Bassett, A. R., & Metzakopian, E. (2020). Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses. Cell Reports, 33(2). https://doi.org/10.1016/j.celrep.2020.108263 Cite
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tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis

Investigators introduced a low-input tagmentation-based Hi-C (tagHi-C) method to capture the chromatin structures of hundreds of cells. Using tagHi-C, they were able to map the spatiotemporal dynamics of chromatin structure in ten primary hematopoietic stem, progenitor, and differentiated cell populations from mouse bone marrow.
[Cell Reports]
Zhang, C., Xu, Z., Yang, S., Sun, G., Jia, L., Zheng, Z., Gu, Q., Tao, W., Cheng, T., Li, C., & Cheng, H. (2020). tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis. Cell Reports, 32(13). https://doi.org/10.1016/j.celrep.2020.108206 Cite
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Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T Cells Reveal Long-Range Dysregulation of Key Inflammatory Pathways Mediated by Disease-Associated Susceptibility Loci

[Genome Medicine]
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci | Genome Medicine | Full Text. (n.d.). Retrieved September 29, 2020, from https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00779-6 Cite
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Genetic Variant Effects on Gene Expression in Human Pancreatic Islets and Their Implications for T2D

The authors explored the relationship between genetic variants influencing predisposition to type 2 diabetes and related glycemic traits, and human pancreatic islet transcription using data from 420 donors.
[Nature Communications]
Viñuela, A., Varshney, A., van de Bunt, M., Prasad, R. B., Asplund, O., Bennett, A., Boehnke, M., Brown, A. A., Erdos, M. R., Fadista, J., Hansson, O., Hatem, G., Howald, C., Iyengar, A. K., Johnson, P., Krus, U., MacDonald, P. E., Mahajan, A., Manning Fox, J. E., … McCarthy, M. I. (2020). Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. Nature Communications, 11(1), 4912. https://doi.org/10.1038/s41467-020-18581-8 Cite
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Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T Cells Reveal Long-Range Dysregulation of Key Inflammatory Pathways Mediated by Disease-Associated Susceptibility Loci

[Genome Medicine]
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci | Genome Medicine | Full Text. (n.d.). Retrieved September 29, 2020, from https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00779-6 Cite
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Single-Cell Genomics Reveals a Novel Cell State during Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human

To reveal the trajectories of smooth muscle cell (SMC) transdifferentiation during atherosclerosis and to identify molecular targets for disease therapy, researchers combined SMC fate mapping and single-cell RNA sequencing of both mouse and human atherosclerotic plaques.
[Circulation]
Pan Huize, Xue Chenyi, Auerbach Benjamin J., Fan Jiaxin, Bashore Alexander C., Cui Jian, Yang Dina Y., Trignano Sarah B., Liu Wen, Shi Jianting, Ihuegbu Chinyere O., Bush Erin C., Worley Jeremy, Vlahos Lukas, Laise Pasquale, Solomon Robert A., Connolly Edward S., Califano Andrea, Sims Peter A., … Reilly Muredach P. (n.d.). Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human. Circulation, 0(0). https://doi.org/10.1161/CIRCULATIONAHA.120.048378 Cite
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Pharmacologically Reversible Zonation-Dependent Endothelial Cell Transcriptomic Changes with Neurodegenerative Disease Associations in the Aged Brain

Researchers report zonation-dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which prominently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier and glucose/energy metabolism especially in capillary ECs.
[Nature Communications]
Zhao, L., Li, Z., Vong, J. S. L., Chen, X., Lai, H.-M., Yan, L. Y. C., Huang, J., Sy, S. K. H., Tian, X., Huang, Y., Chan, H. Y. E., So, H.-C., Ng, W.-L., Tang, Y., Lin, W.-J., Mok, V. C. T., & Ko, H. (2020). Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain. Nature Communications, 11(1), 4413. https://doi.org/10.1038/s41467-020-18249-3 Cite
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Massively Parallel Reporter Assays of Melanoma Risk Variants Identify MX2 as a Gene Promoting Melanoma

Researchers showed that melanocyte-specific expression of human MX2 in a zebrafish model demonstrated accelerated melanoma formation in a BRAFV600E background.
[Nature Communications]
Choi, J., Zhang, T., Vu, A., Ablain, J., Makowski, M. M., Colli, L. M., Xu, M., Hennessey, R. C., Yin, J., Rothschild, H., Gräwe, C., Kovacs, M. A., Funderburk, K. M., Brossard, M., Taylor, J., Pasaniuc, B., Chari, R., Chanock, S. J., Hoggart, C. J., … Brown, K. M. (2020). Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nature Communications, 11(1), 2718. https://doi.org/10.1038/s41467-020-16590-1 Cite
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