Yang, Y;Wei, Z;Xiong, C;Qian, H;
PMID: 35752810 | DOI: 10.1186/s12985-022-01833-y
Myocardial injury induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is reportedly related to disease severity and mortality, attracting attention to exploring relevant pathogenic mechanisms. Limited by insufficient evidence, myocardial injury caused by direct viral invasion of cardiomyocytes (CMs) is not fully understood. Based on recent studies, endosomal dependence can compensate for S protein priming to mediate SARS-CoV-2 infection of CMs, damage the contractile function of CMs, trigger electrical dysfunction, and tip the balance of the renin-angiotensin-aldosterone system to exert a myocardial injury effect. In this review, we shed light on the direct injury caused by SARS-CoV-2 to provide a comprehensive understanding of the cardiac manifestations of coronavirus disease 2019 (COVID-19).
Bravo-Ferrer, I;Khakh, BS;Díaz-Castro, B;
PMID: 35620074 | DOI: 10.1016/j.xpro.2022.101397
Cell-specific RNA sequencing has revolutionized the study of cell biology. Here, we present a protocol to assess cell-specific translatomes of genetically targeted cell types. We focus on astrocytes and describe RNA purification using RiboTag tools. Unlike single-cell RNA sequencing, this approach allows high sequencing depth to detect low expression genes, and the exploration of RNAs translated in subcellular compartments. Furthermore, it avoids underestimation of transcripts from cells susceptible to cell isolation procedures. The protocol can be applied to a variety of cell types. For complete details on the use and execution of this protocol, please refer to Chai et al. (2017), Díaz-Castro et al. (2021), Díaz-Castro et al. (2019), Srinivasan et al. (2016), and Yu et al. (2018).
Erofeeva, T;Grigorenko, A;Gusev, F;Kosevich, I;Rogaev, E;
| DOI: 10.1134/S0006297922030075
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
GABA-receptive microglia selectively sculpt developing inhibitory circuits
Favuzzi, E;Huang, S;Saldi, GA;Binan, L;Ibrahim, LA;Fernández-Otero, M;Cao, Y;Zeine, A;Sefah, A;Zheng, K;Xu, Q;Khlestova, E;Farhi, SL;Bonneau, R;Datta, SR;Stevens, B;Fishell, G;
PMID: 34233165 | DOI: 10.1016/j.cell.2021.06.018
Microglia, the resident immune cells of the brain, have emerged as crucial regulators of synaptic refinement and brain wiring. However, whether the remodeling of distinct synapse types during development is mediated by specialized microglia is unknown. Here, we show that GABA-receptive microglia selectively interact with inhibitory cortical synapses during a critical window of mouse postnatal development. GABA initiates a transcriptional synapse remodeling program within these specialized microglia, which in turn sculpt inhibitory connectivity without impacting excitatory synapses. Ablation of GABAB receptors within microglia impairs this process and leads to behavioral abnormalities. These findings demonstrate that brain wiring relies on the selective communication between matched neuronal and glial cell types.
Embryo-scale, single-cell spatial transcriptomics
Srivatsan, SR;Regier, MC;Barkan, E;Franks, JM;Packer, JS;Grosjean, P;Duran, M;Saxton, S;Ladd, JJ;Spielmann, M;Lois, C;Lampe, PD;Shendure, J;Stevens, KR;Trapnell, C;
PMID: 34210887 | DOI: 10.1126/science.abb9536
Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However, current spatial transcriptomics methods either average local contexts or are restricted to limited fields of view. Here, we introduce sci-Space, which retains single-cell resolution while resolving spatial heterogeneity at larger scales. Applying sci-Space to developing mouse embryos, we captured approximate spatial coordinates and whole transcriptomes of about 120,000 nuclei. We identify thousands of genes exhibiting anatomically patterned expression, leverage spatial information to annotate cellular subtypes, show that cell types vary substantially in their extent of spatial patterning, and reveal correlations between pseudotime and the migratory patterns of differentiating neurons. Looking forward, we anticipate that sci-Space will facilitate the construction of spatially resolved single-cell atlases of mammalian development.
A constant pool of Lgr5+ intestinal stem cells is required for intestinal homeostasis
Tan, SH;Phuah, P;Tan, LT;Yada, S;Goh, J;Tomaz, LB;Chua, M;Wong, E;Lee, B;Barker, N;
PMID: 33503423 | DOI: 10.1016/j.celrep.2020.108633
Lgr5+ crypt base columnar cells, the operational intestinal stem cells (ISCs), are thought to be dispensable for small intestinal (SI) homeostasis. Using a Lgr5-2A-DTR (diphtheria toxin receptor) model, which ablates Lgr5+ cells with near-complete efficiency and retains endogenous levels of Lgr5 expression, we show that persistent depletion of Lgr5+ ISCs in fact compromises SI epithelial integrity and reduces epithelial turnover in vivo. In vitro, Lgr5-2A-DTR SI organoids are unable to establish or survive when Lgr5+ ISCs are continuously eliminated by adding DT to the media. However, transient exposure to DT at the start of culture allows organoids to form, and the rate of outgrowth reduces with the increasing length of DT presence. Our results indicate that intestinal homeostasis requires a constant pool of Lgr5+ ISCs, which is supplied by rapidly reprogrammed non-Lgr5+ crypt populations when preexisting Lgr5+ ISCs are ablated.
Clinical cancer research : an official journal of the American Association for Cancer Research
Frank, ML;Lu, K;Erdogan, C;Han, Y;Hu, J;Wang, T;Heymach, JV;Zhang, J;Reuben, A;
PMID: 36413126 | DOI: 10.1158/1078-0432.CCR-22-2469
T cells are integral components of the adaptive immune system, and their responses are mediated by unique T-cell receptors (TCR) that recognize specific antigens from a variety of biological contexts. As a result, analyzing the T-cell repertoire offers a better understanding of immune responses and of diseases like cancer. Next-generation sequencing technologies have greatly enabled the high-throughput analysis of the TCR repertoire. On the basis of our extensive experience in the field from the past decade, we provide an overview of TCR sequencing, from the initial library preparation steps to sequencing and analysis methods and finally to functional validation techniques. With regards to data analysis, we detail important TCR repertoire metrics and present several computational tools for predicting antigen specificity. Finally, we highlight important applications of TCR sequencing and repertoire analysis to understanding tumor biology and developing cancer immunotherapies.
Qiu, H;Miraucourt, LS;Petitjean, H;Theriault, C;
Spinal cord dorsal horn (DH) inhibition is critical to the processing of sensory inputs, and its impairment leads to mechanical allodynia. How this decreased inhibition occurs and whether its restoration alleviates allodynic pain is poorly understood. Here, we show that the calcium (Ca2+)-binding protein, parvalbumin (PV), controls the activity of inhibitory PV-expressing neurons (PVNs) by enabling them to sustain high-frequency tonic firing patterns. Upon nerve injury, PVNs transition to adaptive firing and decrease their PV expression. Interestingly, decreased PV is necessary and sufficient to the development of mechanical allodynia and the transition of PVNs to adaptive firing. This transition of firing pattern is due to the recruitment of calcium-activated potassium (SK) channels and blocking them during chronic pain restores normal tonic firing. Our findings indicate that PV is essential to the firing activity of PVNs and in preventing allodynia, these observations may lead to novel strategies for chronic pain relief.
Bi, R;Yin, Q;Li, H;Yang, X;Wang, Y;Li, Q;Fang, H;Li, P;Lyu, P;Fan, Y;Ying, B;Zhu, S;
PMID: 36788226 | DOI: 10.1038/s41467-023-36406-2
The biological characteristics of the temporomandibular joint disc involve complex cellular network in cell identity and extracellular matrix composition to modulate jaw function. The lack of a detailed characterization of the network severely limits the development of targeted therapies for temporomandibular joint-related diseases. Here we profiled single-cell transcriptomes of disc cells from mice at different postnatal stages, finding that the fibroblast population could be divided into chondrogenic and non-chondrogenic clusters. We also find that the resident mural cell population is the source of disc progenitors, characterized by ubiquitously active expression of the NOTCH3 and THY1 pathways. Lineage tracing reveals that Myh11+ mural cells coordinate angiogenesis during disc injury but lost their progenitor characteristics and ultimately become Sfrp2+ non-chondrogenic fibroblasts instead of Chad+ chondrogenic fibroblasts. Overall, we reveal multiple insights into the coordinated development of disc cells and are the first to describe the resident mural cell progenitor during disc injury.
Wu, CT;Lidsky, PV;Xiao, Y;Cheng, R;Lee, IT;Nakayama, T;Jiang, S;He, W;Demeter, J;Knight, MG;Turn, RE;Rojas-Hernandez, LS;Ye, C;Chiem, K;Shon, J;Martinez-Sobrido, L;Bertozzi, CR;Nolan, GP;Nayak, JV;Milla, C;Andino, R;Jackson, PK;
PMID: 36580912 | DOI: 10.1016/j.cell.2022.11.030
How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger formation of apically extended and highly branched microvilli that organize viral egress from the microvilli back into the mucus layer, supporting a model of virus dispersion throughout airway tissue via mucociliary transport. Phosphoproteomics and kinase inhibition reveal that microvillar remodeling is regulated by p21-activated kinases (PAK). Importantly, Omicron variants bind with higher affinity to motile cilia and show accelerated viral entry. Our work suggests that motile cilia, microvilli, and mucociliary-dependent mucus flow are critical for efficient virus replication in nasal epithelia.
Kim, JE;Li, B;Fei, L;Horne, R;Lee, D;Loe, AK;Miyake, H;Ayar, E;Kim, DK;Surette, MG;Philpott, DJ;Sherman, P;Guo, G;Pierro, A;Kim, TH;
PMID: 36473468 | DOI: 10.1016/j.immuni.2022.11.003
Intestinal stem cell maturation and development coincide with gut microbiota exposure after birth. Here, we investigated how early life microbial exposure, and disruption of this process, impacts the intestinal stem cell niche and development. Single-cell transcriptional analysis revealed impaired stem cell differentiation into Paneth cells and macrophage specification upon antibiotic treatment in early life. Mouse genetic and organoid co-culture experiments demonstrated that a CD206+ subset of intestinal macrophages secreted Wnt ligands, which maintained the mesenchymal niche cells important for Paneth cell differentiation. Antibiotics and reduced numbers of Paneth cells are associated with the deadly infant disease, necrotizing enterocolitis (NEC). We showed that colonization with Lactobacillus or transfer of CD206+ macrophages promoted Paneth cell differentiation and reduced NEC severity. Together, our work defines the gut microbiota-mediated regulation of stem cell niches during early postnatal development.
Brain structure & function
Slaoui, L;Gilbert, A;Rancillac, A;Delaunay-Piednoir, B;Chagnot, A;Gerard, Q;Letort, G;Mailly, P;Robil, N;Gelot, A;Lefebvre, M;Favier, M;Dias, K;Jourdren, L;Federici, L;Auvity, S;Cisternino, S;Vivien, D;Cohen-Salmon, M;Boulay, AC;
PMID: 36380034 | DOI: 10.1007/s00429-022-02592-w
Although great efforts to characterize the embryonic phase of brain microvascular system development have been made, its postnatal maturation has barely been described. Here, we compared the molecular and functional properties of brain vascular cells on postnatal day (P)5 vs. P15, via a transcriptomic analysis of purified mouse cortical microvessels (MVs) and the identification of vascular-cell-type-specific or -preferentially expressed transcripts. We found that endothelial cells (EC), vascular smooth muscle cells (VSMC) and fibroblasts (FB) follow specific molecular maturation programs over this time period. Focusing on VSMCs, we showed that the arteriolar VSMC network expands and becomes contractile resulting in a greater cerebral blood flow (CBF), with heterogenous developmental trajectories within cortical regions. Samples of the human brain cortex showed the same postnatal maturation process. Thus, the postnatal phase is a critical period during which arteriolar VSMC contractility required for vessel tone and brain perfusion is acquired and mature.
