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  • Airway basal cells show regionallydistinct potential to undergo metaplastic differentiation. eLife Zhou, Y., Yang, Y., Guo, L., Qian, J., Ge, J., Sinner, D., Ding, H., Califano, A., Cardoso, W. V. 2022; 11


    Basal cells are multipotent stem cells of a variety of organs, including the respiratory tract, where they are major components of the airway epithelium. However, it remains unclear how diverse basal cells are, and how distinct subpopulations respond to airway challenges. Using single cell RNA-sequencing and functional approaches, we report a significant and previously underappreciated degree of heterogeneity in the basal cell pool, leading to identification of six subpopulations in the adult murine trachea. Among these, we found two major subpopulations collectively comprising the most uncommitted of all the pool, but with distinct gene expression signatures. Notably, these occupy distinct ventral and dorsal tracheal niches and differ in their ability to self-renew and initiate a program of differentiation in response to environmental perturbations in primary cultures and in mouse injury models in vivo. We found that such heterogeneity is acquired prenatally, when the basal cell pool and local niches are still being established, and depends on the integrity of these niches, as supported by the altered basal cell phenotype of tracheal cartilage-deficient mouse mutants. Lastly, we show that features that distinguish these progenitor subpopulations in murine airways are conserved in humans. Together, the data provide novel insights into the origin and impact of basal cell heterogeneity on the establishment of regionally distinct responses of the airway epithelium during injury-repair and in disease conditions.

    View details for DOI 10.7554/eLife.80083

    View details for PubMedID 36178196

  • Contribution of Trp63CreERT2 labeled cells to alveolar regeneration is independent of tuft cells. eLife Huang, H., Fang, Y., Jiang, M., Zhang, Y., Biermann, J., Melms, J. C., Danielsson, J. A., Yang, Y., Qiang, L., Liu, J., Zhou, Y., Wang, M., Hu, Z., Wang, T. C., Saqi, A., Sun, J., Matsumoto, I., Cardoso, W. V., Emala, C. W., Zhu, J., Izar, B., Mou, H., Que, J. 2022; 11


    Viral infection often causes severe damage to the lungs, leading to the appearance of ectopic basal cells (EBCs) and tuft cells in the lung parenchyma. Thus far the roles of these ectopic epithelial cells in alveolar regeneration remain controversial. Here, we confirm that the ectopic tuft cells are originated from EBCs in mouse models and COVID-19 lungs. The differentiation of tuft cells from EBCs is promoted by Wnt inhibition while suppressed by Notch inhibition. Although progenitor functions have been suggested in other organs, pulmonary tuft cells don't proliferate or give rise to other cell lineages. Consistent with previous reports, Trp63CreERT2 and KRT5-CreERT2 labeled ectopic EBCs do not exhibit alveolar regeneration potential. Intriguingly, when tamoxifen was administrated post viral infection, Trp63CreERT2 but not KRT5-CreERT2 labels islands of alveolar epithelial cells that are negative for EBC biomarkers. Furthermore, germline deletion of Trpm5 significantly increases the contribution of Trp63CreERT2 labeled cells to the alveolar epithelium. Although Trpm5 is known to regulate tuft cell development, complete ablation of tuft cell production fails to improve alveolar regeneration in Pou2f3-/- mice, implying that Trpm5 promotes alveolar epithelial regeneration through a mechanism independent of tuft cells.

    View details for DOI 10.7554/eLife.78217

    View details for PubMedID 36129169

  • Prioritizing transcriptional factors in gene regulatory networks with PageRank. iScience Ding, H., Yang, Y., Xue, Y., Seninge, L., Gong, H., Safavi, R., Califano, A., Stuart, J. M. 2021; 24 (1): 102017


    Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating gene regulatory networks reverse engineered from multi-omics profiles, e.g. gene expression, chromatin accessibility, and chromosome conformation assays, using multiplex PageRank.

    View details for DOI 10.1016/j.isci.2020.102017

    View details for PubMedID 33490923