Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development

Immunity

2022 Dec 13

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.

In mice and humans, brain microvascular contractility matures postnatally

Brain structure & function

2022 Nov 16

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.

Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation

The Journal of experimental medicine

2022 Apr 04

Snyder, ME;Moghbeli, K;Bondonese, A;Craig, A;Popescu, I;Fan, L;Tabib, T;Lafyatis, R;Chen, K;Trejo Bittar, HE;Lendermon, E;Pilewski, J;Johnson, B;Kilaru, S;Zhang, Y;Sanchez, PG;Alder, JK;Sims, PA;McDyer, JF;
PMID: 35285873 | DOI: 10.1084/jem.20212059

Acute cellular rejection is common after lung transplantation and is associated with an increased risk of early chronic rejection. We present combined single-cell RNA and TCR sequencing on recipient-derived T cells obtained from the bronchoalveolar lavage of three lung transplant recipients with rejection and compare them with T cells obtained from the same patients after treatment of rejection with high-dose systemic glucocorticoids. At the time of rejection, we found an oligoclonal expansion of cytotoxic CD8+ T cells that all persisted as tissue resident memory T cells after successful treatment. Persisting CD8+ allograft-resident T cells have reduced gene expression for cytotoxic mediators after therapy with glucocorticoids but accumulate around airways. This clonal expansion is discordant with circulating T cell clonal expansion at the time of rejection, suggesting in situ expansion. We thus highlight the accumulation of cytotoxic, recipient-derived tissue resident memory T cells within the lung allograft that persist despite the administration of high-dose systemic glucocorticoids. The long-term clinical consequences of this persistence have yet to be characterized.

Epidermal growth factor-like domain protein 6 recombinant protein facilitates osteogenic differentiation in adipose stem cells via bone morphogenetic protein 2/recombinant mothers against decapentaplegic homolog 4 signaling pathway

Bioengineered

2022 Mar 01

Liu, H;Wang, X;
PMID: 35220882 | DOI: 10.1080/21655979.2022.2037380

Adipose-derived mesenchymal stem cells (ADSCs) are a class of pluripotent stem cells isolated from the adipose tissue; they can differentiate into osteoblasts after induction and play an important role in bone repair. EGFL6 protein is secreted by adipocytes and osteoblasts and can promote endothelial cell migration and angiogenesis. This study aimed to explore the effect of recombinant EGFL6 protein on the osteogenic differentiation of ADSCs. The cells were incubated with fluorescein isothiocyanate-conjugated antibodies and analyzed by flow cytometry. Alizarin red staining and alkaline phosphatase staining were used to detect the osteogenic differentiation ability. mRNA expression was analyzed by real-time quantitative polymerase chain reaction (RT-qPCR). Protein expression was determined using Western blotting. The osteogenic differentiation ability of ADSCs isolated from the adipose tissue was significantly weakened after EGFL6 knockdown; this ability was restored upon the addition of EGFL6 recombinant protein. BMP2 knockdown inhibited the effect of EGFL6 recombinant protein on osteogenic differentiation. EGFL6 recombinant protein promoted osteogenic differentiation of ADSCs through the BMP2/SMAD4 signaling pathway. This may provide a potential target for the osteogenic differentiation of ADSCs.

Antiviral Activities of Carbazole Derivatives against Porcine Epidemic Diarrhea Virus In Vitro

Viruses

2021 Dec 16

Chen, Z;Chen, J;Wei, X;Hua, H;Hu, R;Ding, N;Zhang, J;Song, D;Ye, Y;Tang, Y;Ding, Z;Ke, S;
PMID: 34960796 | DOI: 10.3390/v13122527

Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, causes neonatal pig acute gastrointestinal infection with a characterization of severe diarrhea, vomiting, high morbidity, and high mortality, resulting in tremendous damages to the swine industry. Neither specific antiviral drugs nor effective vaccines are available, posing a high priority to screen antiviral drugs. The aim of this study is to investigate anti-PEDV effects of carbazole alkaloid derivatives. Eighteen carbazole derivatives (No.1 to No.18) were synthesized, and No.5, No.7, and No.18 were identified to markedly reduce the replication of enhanced green fluorescent protein (EGFP) inserted-PEDV, and the mRNA level of PEDV N. Flow cytometry assay, coupled with CCK8 assay, confirmed No.7 and No.18 carbazole derivatives displayed high inhibition effects with low cell toxicity. Furthermore, time course analysis indicated No.7 and No.18 carbazole derivatives exerted inhibition at the early stage of the viral life cycle. Collectively, the analysis underlines the benefit of carbazole derivatives as potential inhibitors of PEDV, and provides candidates for the development of novel therapeutic agents.

Tissue architecture delineates field cancerization in BRAFV600E-induced tumor development

Disease models & mechanisms

2021 Jun 04

Schoultz, E;Johansson, E;Moccia, C;Jakubikova, I;Ravi, N;Liang, S;Carlsson, T;Montelius, M;Patyra, K;Kero, J;Paulsson, K;Fagman, H;Bergo, MO;Nilsson, M;
PMID: 34085700 | DOI: 10.1242/dmm.048887

Cancer cells hijack developmental growth mechanisms but whether tissue morphogenesis and architecture modify tumorigenesis is unknown. Here, we characterized a new mouse model of sporadic thyroid carcinogenesis based on inducible expression of BRAFV600E from the thyroglobulin promoter (TgCreERT2). Spontaneous activation of this Braf-mutant allele due to leaky CRE activity revealed that intrinsic properties of thyroid follicles determined BRAF-mutant cell fate. Papillary thyroid carcinomas developed multicentrically within a normal microenvironment. Each tumor originated from a single follicle that provided a confined space for growth of a distinct tumor type. Lineage tracing revealed oligoclonal tumor development in infancy and early selection of BRAFV600E kinase inhibitor-resistant clones. Somatic mutations were few, non-recurrent, and limited to advanced tumors. Female mice developed larger tumors than males, reproducing the gender difference of human thyroid cancer. These data indicate that BRAFV600E-induced tumorigenesis is spatiotemporally regulated depending on the maturity and heterogeneity of follicles. Moreover, thyroid tissue organization seems to determine whether a BRAF-mutant lineage becomes a cancerized lineage. The sporadic thyroid cancer model provides a new tool to evaluate drug therapy at different stages of tumor evolution.

A Procedure for Mouse Dorsal Root Ganglion Cryosectioning

jove.com

2023 Jan 01

He, L;Zhao, W;Zhang, L;Ilango, M;Zhao, N;Yang, L;Guan, Z;

High-quality mouse dorsal root ganglion (DRG) cryostat sections are crucial for proper immunochemistry staining and RNAscope studies in the research of inflammatory and neuropathic pain, itch, as well as other peripheral neurological conditions. However, it remains a challenge to consistently obtain high-quality, intact, and flat cryostat sections onto glass slides because of the tiny sample size of the DRG tissue. So far, there is no article describing an optimal protocol for DRG cryosectioning. This protocol presents a step-by-step method to resolve the frequently encountered difficulties associated with DRG cryosectioning. The presented article explains how to remove the surrounding liquid from the DRG tissue samples, place the DRG sections on the slide facing the same orientation, and flatten the sections on the glass slide without curving up. Although this protocol has been developed for cryosectioning the DRG samples, it can be applied for the cryosectioning of many other tissues with a small sample size.

Dual blockages of a broad and potent neutralizing IgM antibody targeting GH loop of EV-As

Immunology

2023 Feb 01

Zhu, W;Li, J;Wu, Z;Li, H;Zhang, Z;Zhu, X;Sun, M;Dong, S;
PMID: 36726218 | DOI: 10.1111/imm.13629

The reported enterovirus A 71 (EVA71) vaccines and immunoglobin G (IgG) antibodies have no cross-antiviral efficacy against other enterovirus A (EV-A) which caused hand, foot and mouth disease (HFMD). Here we constructed an IgM antibody (20-IgM) based on our previous discovery to address the resistance encountered by IgG-based immunotherapy. Although binding to the same conserved neutralizing epitope within the GH loop of EV-As VP1, the antiviral breath and potency of 20-IgM are still higher than its parental 20-IgG1. The 20-IgM blocks the interaction between the EV-As and its receptors, scavenger receptor class B, member 2 (SCARB2) and Kringle-containing transmembrane protein 1(KREMEN1) of the host cell. The 20-IgM also neutralizes the EV-As at the post-attachment stages, including postattachment neutralization, uncoating and RNA release inhibition after internalization. Mechanistically, the dual blockage effect of 20-IgM is dependent on both a conserved site targeting and high affinity binding. Meanwhile, 20-IgM provides cross-antiviral efficacy in EV-As orally infected neonatal ICR mice. Collectively, 20-IgM and its property exhibit excellent antiviral activity with a dual-blockage inhibitory effect at both the pre- and post-attachment stages. The finding enhances our understanding of IgM-mediated immunity and highlights the potential of IgM subtype antibodies against enterovirus infections.

OME-Zarr: a cloud-optimized bioimaging file format with international community support

bioRxiv : the preprint server for biology

2023 Feb 25

Moore, J;Basurto-Lozada, D;Besson, S;Bogovic, J;Brown, EM;Burel, JM;de Medeiros, G;Diel, EE;Gault, D;Ghosh, SS;Gold, I;Halchenko, YO;Hartley, M;Horsfall, D;Keller, MS;Kittisopikul, M;Kovacs, G;Küpcü Yoldaş, A;de la Villegeorges, ALT;Li, T;Liberali, P;Linkert, M;Lindner, D;Lüthi, J;Maitin-Shepard, J;Manz, T;McCormick, M;Mohamed, K;Moore, W;Özdemir, B;Pape, C;Pelkmans, L;Prete, M;Pietzsch, T;Preibisch, S;Rzepka, N;Stirling, DR;Striebel, J;Tischer, C;Toloudis, D;Walczysko, P;Watson, AM;Wong, F;Yamauchi, KA;Bayraktar, O;Haniffa, M;Saalfeld, S;Swedlow, JR;
PMID: 36865282 | DOI: 10.1101/2023.02.17.528834

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself - OME-Zarr - along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain - the file format that underlies so many personal, institutional, and global data management and analysis tasks.

Anatomical contacts between sensory neurons and epidermal cells: an unrecognized anatomical network for neuro-immuno-cutaneous crosstalk

British Journal of Dermatology

2022 Jan 01

Talagas, M;
| DOI: 10.1093/bjd/ljac066/6788796

Sensory neurons innervating the skin are conventionally thought to be the sole transducers of 3 touch, temperature, pain, and itch. However, recent studies have shown that keratinocytes - like 4 Merkel cells - act as sensory transducers, whether for innocuous or noxious mechanical, thermal, 5 or chemical stimuli and communicate with intra-epidermal free nerve endings via chemical 6 synaptic contacts. This paradigm shift leads to the consideration of the whole epidermis as a 7 sensory epithelium. Sensory neurons additionally function as an efferent system. Through the 8 release of neuropeptides in intimate neuro-epidermal contact areas, they contribute to epidermal 9 homeostasis and to the pathogenesis of inflammatory skin diseases. To counteract the dogma 10 regarding neuro-cutaneous interactions, seen exclusively from the perspective of soluble and 11 spreading mediators, this review highlights the essential contribution of the unrecognized 12 anatomical contacts between the sensory neurons and the epidermal cells (keratinocytes, 13 melanocytes, Langerhans cells, and Merkel cells) which serve the reciprocal dialogue between 14 the skin, nervous system, and immune system.

Extracellular mechanical forces drive endocardial cell volume decrease during zebrafish cardiac valve morphogenesis

Developmental cell

2022 Mar 14

Vignes, H;Vagena-Pantoula, C;Prakash, M;Fukui, H;Norden, C;Mochizuki, N;Jug, F;Vermot, J;
PMID: 35245444 | DOI: 10.1016/j.devcel.2022.02.011

Organ morphogenesis involves dynamic changes of tissue properties while cells adapt to their mechanical environment through mechanosensitive pathways. How mechanical cues influence cell behaviors during morphogenesis remains unclear. Here, we studied the formation of the zebrafish atrioventricular canal (AVC) where cardiac valves develop. We show that the AVC forms within a zone of tissue convergence associated with the increased activation of the actomyosin meshwork and cell-orientation changes. We demonstrate that tissue convergence occurs with a reduction of cell volume triggered by mechanical forces and the mechanosensitive channel TRPP2/TRPV4. Finally, we show that the extracellular matrix component hyaluronic acid controls cell volume changes. Together, our data suggest that multiple force-sensitive signaling pathways converge to modulate cell volume. We conclude that cell volume reduction is a key cellular feature activated by mechanotransduction during cardiovascular morphogenesis. This work further identifies how mechanical forces and extracellular matrix influence tissue remodeling in developing organs.

SCAMPR: Single-Cell Automated Multiplex Pipeline for RNA Quantification and Spatial Mapping

SSRN Electronic Journal

2022 Mar 24

Ali Marandi Ghoddousi, R;Magalong, V;Kamitakahara, A;Levitt, P;
| DOI: 10.2139/ssrn.4064105

Spatial gene expression, achieved classically through _in situ_ hybridization, is a fundamental tool for topographic phenotyping of cell types in the nervous system. Newly developed techniques allow for the visualization of multiple mRNAs at single-cell resolution, greatly expanding the ability to link gene expression to tissue topography. Yet, methods for efficient and accurate quantification and analysis of high dimensional _in situ_- hybridization are limited. To this end, the Single-Cell Automated Multiplex Pipeline for RNA (SCAMPR) was developed, facilitating rapid and accurate segmentation of neuronal cell bodies using a dual immunohistochemistry-RNAscope protocol and quantification of low and high abundance mRNA signals using open-source image processing and automated segmentation tools. Proof of principle using SCAMPR focused on spatial mapping of gene expression by peripheral (vagal nodose) and central (visual cortex) neurons. The analytical effectiveness of SCAMPR is demonstrated by identifying the impact of early life stress on differential gene expression by vagal neuron subtypes.

Pages

	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

Search form

Probes for INS

Content for comparison

Gene

Product

Research area

Category

Pages

Advanced Cell Diagnostics

Bio-Techne

Advanced Cell Diagnostics China