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1. Defining mammary basal cell transcriptional states using single-cell RNA-sequencing

   https://doi.org/10.1038/s41598-022-08870-1  

   Gutierrez, Guadalupe ; Sun, Peng ; Han, Yingying ; Dai, Xing ( December 2022 , Scientific Reports)

   Abstract Breast cancer is a heterogenous disease that can be classified into multiple subtypes including the most aggressive basal-like and triple-negative subtypes. Understanding the heterogeneity within the normal mammary basal epithelial cells holds the key to inform us about basal-like cancer cell differentiation dynamics as well as potential cells of origin. Although it is known that the mammary basal compartment contains small pools of stem cells that fuel normal tissue morphogenesis and regeneration, a comprehensive yet focused analysis of the transcriptional makeup of the basal cells is lacking. We used single-cell RNA-sequencing and multiplexed RNA in-situ hybridization to characterize mammary basal cell heterogeneity. We used bioinformatic and computational pipelines to characterize the molecular features as well as predict differentiation dynamics and cell–cell communications of the newly identified basal cell states. We used genetic cell labeling to map the in vivo fates of cells in one of these states. We identified four major distinct transcriptional states within the mammary basal cells that exhibit gene expression signatures suggestive of different functional activity and metabolic preference. Our in vivo labeling and ex vivo organoid culture data suggest that one of these states, marked by Egr2 expression, represents a dynamic transcriptional state that allmore »basal cells transit through during pubertal mammary morphogenesis. Our study provides a systematic approach to understanding the molecular heterogeneity of mammary basal cells and identifies previously unknown dynamics of basal cell transcriptional states.« less
2. Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR

   https://doi.org/10.1038/s41467-022-34363-w  

   Sempou, Emily ; Kostiuk, Valentyna ; Zhu, Jie ; Cecilia Guerra, M. ; Tyan, Leonid ; Hwang, Woong ; Camacho-Aguilar, Elena ; Caplan, Michael J. ; Zenisek, David ; Warmflash, Aryeh ; et al ( November 2022 , Nature Communications)

   Transitioning from pluripotency to differentiated cell fates is fundamental to both embryonic development and adult tissue homeostasis. Improving our understanding of this transition would facilitate our ability to manipulate pluripotent cells into tissues for therapeutic use. Here, we show that membrane voltage (V_m) regulates the exit from pluripotency and the onset of germ layer differentiation in the embryo, a process that affects both gastrulation and left-right patterning. By examining candidate genes of congenital heart disease and heterotaxy, we identifyKCNH6, a member of the ether-a-go-go class of potassium channels that hyperpolarizes the V_mand thus limits the activation of voltage gated calcium channels, lowering intracellular calcium. In pluripotent embryonic cells, depletion ofkcnh6leads to membrane depolarization, elevation of intracellular calcium levels, and the maintenance of a pluripotent state at the expense of differentiation into ectodermal and myogenic lineages. Using high-resolution temporal transcriptome analysis, we identify the gene regulatory networks downstream of membrane depolarization and calcium signaling and discover that inhibition of the mTOR pathway transitions the pluripotent cell to a differentiated fate. By manipulating V_musing a suite of tools, we establish a bioelectric pathway that regulates pluripotency in vertebrates, including human embryonic stem cells.
3. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

   https://doi.org/10.1038/s41467-021-25548-w  

   Zhou, Peijie ; Wang, Shuxiong ; Li, Tiejun ; Nie, Qing ( September 2021 , Nature Communications)

   Advances in single-cell technologies allow scrutinizing of heterogeneous cell states, however, detecting cell-state transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique to identify the underlying stochastic dynamics that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transitions, and distinguishes stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. The method is consistent with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.
4. Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt

   https://doi.org/10.1038/s42003-020-01181-z  

   Habowski, Amber N. ; Flesher, Jessica L. ; Bates, Jennifer M. ; Tsai, Chia-Feng ; Martin, Kendall ; Zhao, Rui ; Ganesan, Anand K. ; Edwards, Robert A. ; Shi, Tujin ; Wiley, H. Steven ; et al ( August 2020 , Communications Biology)

   Intestinal stem cells are non-quiescent, dividing epithelial cells that rapidly differentiate into progenitor cells of the absorptive and secretory cell lineages. The kinetics of this process is rapid such that the epithelium is replaced weekly. To determine how the transcriptome and proteome keep pace with rapid differentiation, we developed a new cell sorting method to purify mouse colon epithelial cells. Here we show that alternative mRNA splicing and polyadenylation dominate changes in the transcriptome as stem cells differentiate into progenitors. In contrast, as progenitors differentiate into mature cell types, changes in mRNA levels dominate the transcriptome. RNA processing targets regulators of cell cycle, RNA, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.
5. Single-cell transcriptional diversity is a hallmark of developmental potential

   https://doi.org/10.1126/science.aax0249  

   Gulati, Gunsagar S. ; Sikandar, Shaheen S. ; Wesche, Daniel J. ; Manjunath, Anoop ; Bharadwaj, Anjan ; Berger, Mark J. ; Ilagan, Francisco ; Kuo, Angera H. ; Hsieh, Robert W. ; Cai, Shang ; et al ( January 2020 , Science)

   Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential—the number of expressed genes per cell—and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.