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1. Cell alignment modulated by surface nano-topography – Roles of cell-matrix and cell-cell interactions

   https://doi.org/10.1016/j.actbio.2022.01.057  

   Coyle, Stephen; Doss, Bryant; Huo, Yucheng; Singh, Hemang Raj; Quinn, David; Jimmy Hsia, K.; LeDuc, Philip R. (April 2022, Acta Biomaterialia)
2. Inference and analysis of cell-cell communication using CellChat

   https://doi.org/10.1038/s41467-021-21246-9  

   Jin, Suoqin; Guerrero-Juarez, Christian_F; Zhang, Lihua; Chang, Ivan; Ramos, Raul; Kuan, Chen-Hsiang; Myung, Peggy; Plikus, Maksim_V; Nie, Qing (February 2021, Nature Communications)

   Abstract Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues. 

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3. Rap1 coordinates cell-cell adhesion and cytoskeletal reorganization to drive collective cell migration in vivo

   https://doi.org/10.1016/j.cub.2023.05.009  

   Rothenberg, Katheryn E.; Chen, Yujun; McDonald, Jocelyn A.; Fernandez-Gonzalez, Rodrigo (July 2023, Current Biology)
4. Molecular basis of sidekick-mediated cell-cell adhesion and specificity

   https://doi.org/10.7554/eLife.19058  

   Goodman, Kerry M; Yamagata, Masahito; Jin, Xiangshu; Mannepalli, Seetha; Katsamba, Phinikoula S; Ahlsén, Göran; Sergeeva, Alina P; Honig, Barry; Sanes, Joshua R; Shapiro, Lawrence (September 2016, eLife)

   Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1–4), arranged in a horseshoe conformation. These Ig1–4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (via trans interactions) and Sdk clustering in isolated cells (via cis interactions). Sdk1/Sdk2 recognition specificity is encoded across Ig1–4, with Ig1–2 conferring the majority of binding affinity and differential specificity. We suggest that competition between cis and trans interactions provides a novel mechanism to sharpen the specificity of cell-cell interactions. 

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5. Plant stem-cell organization and differentiation at single-cell resolution

   https://doi.org/10.1073/pnas.2018788117  

   Satterlee, James W.; Strable, Josh; Scanlon, Michael J. (December 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 ( KN1 ) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level. 

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