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Single-cell multiome sequencing clarifies enteric glial diversity and identifies an intraganglionic population poised for neurogenesis

Cell reports

2023 Feb 28

Guyer, RA;Stavely, R;Robertson, K;Bhave, S;Mueller, JL;Picard, NM;Hotta, R;Kaltschmidt, JA;Goldstein, AM;
PMID: 36857184 | DOI: 10.1016/j.celrep.2023.112194

The enteric nervous system (ENS) consists of glial cells (EGCs) and neurons derived from neural crest precursors. EGCs retain capacity for large-scale neurogenesis in culture, and in vivo lineage tracing has identified neurons derived from glial cells in response to inflammation. We thus hypothesize that EGCs possess a chromatin structure poised for neurogenesis. We use single-cell multiome sequencing to simultaneously assess transcription and chromatin accessibility in EGCs undergoing spontaneous neurogenesis in culture, as well as small intestine myenteric plexus EGCs. Cultured EGCs maintain open chromatin at genomic loci accessible in neurons, and neurogenesis from EGCs involves dynamic chromatin rearrangements with a net decrease in accessible chromatin. A subset of in vivo EGCs, highly enriched within the myenteric ganglia and that persist into adulthood, have a gene expression program and chromatin state consistent with neurogenic potential. These results clarify the mechanisms underlying EGC potential for neuronal fate transition.
Single-cell molecular and functional mapping of POMC neurons in obesity: a multi-modal approach

Endocrine Abstracts

2022 May 07

Leon, S;Simon, V;Lee, T;Clark, S;Dupuy, N;Le, F;Fioramonti, X;Cota, D;Quarta, C;
| DOI: 10.1530/endoabs.81.oc10.1

The brain plays a crucial role in maintaining the bodys energy needs, a process involving the activity of a group of hypothalamic neurons that express the neuropeptidergic marker pro-opiomelanocortin (POMC). POMC neuronal dysfunction can cause obesity and its associated metabolic sequelae. However, this population of neurons is highly diverse at a molecular and functional level, and whether or not such heterogeneity is implicated in disease establishment or progression has yet to be elucidated. Here, using a lineage-tracing approach in combination with histological and electrophysiological tools, we have characterized POMC neuronal cells at a single-cell resolution in control of lean and diet-induced obese (DIO) mice. Thanks to this genetic strategy, we traced with a reporter protein POMC neurons in adult mice, thus studying these neuronal cells independently from the expression of their main marker POMC. Different histological techniques, including immunohistochemistry, fluorescent in-situ hybridization, and RNAscope, have been used to cluster genetically traced POMC neuronal cells based on their expression of the main marker POMC. These different approaches consistently allowed the identification of a previously uncharacterized sub-population that expresses negligible POMC mRNA and protein levels, which we named Ghost-POMC neurons. We also observed that Ghost-POMC neurons are insensitive to acute nutritional cues (fasting and refeeding) relative to classic POMC positive neurons. Intriguingly, DIO mice presented an increased number of Ghost-POMC neurons relative to control animals. Furthermore, we developed an approach that combines whole-cell patch-clamp of traced POMC neurons with the subsequent molecular profiling of the patched cell by single-cell qPCR. Thanks to this approach, we observed that DIO leads to electrical alterations only in a fraction of POMC neurons expressing undetectable levels of POMC mRNA, which is reminiscent of the Ghost population previously identified by histological techniques. Thus, Ghost-POMC neurons might constitute a novel subpopulation of POMC neurons that undergo dysfunction in response to prolonged dietary cues, perhaps contributing to obesity establishment or progression.
The Orexigenic Force of Olfactory Palatable Food Cues in Rats

Nutrients

2021 Sep 03

Peris-Sampedro, F;Stoltenborg, I;Le May, MV;Sole-Navais, P;Adan, RAH;Dickson, SL;
PMID: 34578979 | DOI: 10.3390/nu13093101

Environmental cues recalling palatable foods motivate eating beyond metabolic need, yet the timing of this response and whether it can develop towards a less palatable but readily available food remain elusive. Increasing evidence indicates that external stimuli in the olfactory modality communicate with the major hub in the feeding neurocircuitry, namely the hypothalamic arcuate nucleus (Arc), but the neural substrates involved have been only partially uncovered. By means of a home-cage hidden palatable food paradigm, aiming to mimic ubiquitous exposure to olfactory food cues in Western societies, we investigated whether the latter could drive the overeating of plain chow in non-food-deprived male rats and explored the neural mechanisms involved, including the possible engagement of the orexigenic ghrelin system. The olfactory detection of a familiar, palatable food impacted upon meal patterns, by increasing meal frequency, to cause the persistent overconsumption of chow. In line with the orexigenic response observed, sensing the palatable food in the environment stimulated food-seeking and risk-taking behavior, which are intrinsic components of food acquisition, and caused active ghrelin release. Our results suggest that olfactory food cues recruited intermingled populations of cells embedded within the feeding circuitry within the Arc, including, notably, those containing the ghrelin receptor. These data demonstrate the leverage of ubiquitous food cues, not only for palatable food searching, but also to powerfully drive food consumption in ways that resonate with heightened hunger, for which the orexigenic ghrelin system is implicated.
Antagonistic modulation of NPY/AgRP and POMC neurons in the arcuate nucleus by noradrenalin.

Elife.

2017 Jun 20

Paeger L, Karakasilioti I, Altmüller J, Frommolt P, Brüning J, Kloppenburg P.
PMID: 28632132 | DOI: 10.7554/eLife.25770

In the arcuate nucleus of the hypothalamus (ARH) satiety signaling (anorexigenic) pro-opiomelanocortin (POMC)-expressing and hunger signaling (orexigenic) agouti-related peptide (AgRP)-expressing neurons are key components of the neuronal circuits that control food intake and energy homeostasis. Here, we assessed whether the catecholamine noradrenalin directly modulates the activity of these neurons in mice. Perforated patch clamp recordings showed that noradrenalin changes the activity of these functionally antagonistic neurons in opposite ways, increasing the activity of the orexigenic NPY/AgRP neurons and decreasing the activity of the anorexigenic POMC neurons. Cell type-specific transcriptomics and pharmacological experiments revealed that the opposing effect on these neurons is mediated by the activation of excitatory α1A - and β- adrenergic receptors in NPY/AgRP neurons, while POMC neurons are inhibited via α2A - adrenergic receptors. Thus, the coordinated differential modulation of the key hypothalamic neurons in control of energy homeostasis assigns noradrenalin an important role to promote feeding.

Catabolic activity of osteoblast-lineage cells contributes to osteoclastic bone resorption in vitro.

J Cell Sci.

2019 Apr 11

Pirapaharan DC, Olesen JB, Andersen TL, Christensen SB, Kjærsgaard-Andersen P, Delaisse JM, Søe K.
PMID: 30975918 | DOI: 10.1242/jcs.229351

Osteoblast-lineage cells in bone human were recently shown to colonize eroded bone surfaces and to closely interact with osteoclasts. They proved identical with reversal cells and are believed to differentiate into bone forming osteoblasts thereby coupling resorption and formation. However, they also exert catabolic activity that contributes to osteoclastic bone resorption, but this has not received much attention. Herein, we used co-cultures of primary human osteoblast-lineage cells and human osteoclasts derived from peripheral blood monocytes to investigate whether a catabolic activity of osteoblast-lineage cells may impact on osteoclastic bone resorption. Through a combination of immunofluorescence, in-situ hybridization, and time-lapse we show that MMP-13 expressing osteoblast-lineage cells are attracted to and closely interact with bone resorbing osteoclasts. This close interaction results in a strong and significant increase in the bone resorptive activity of osteoclasts - especially those making trenches. Importantly, we show that osteoclastic bone resorption becomes sensitive to inhibition of matrix metalloproteinases in the presence, but not in the absence, of osteoblast-lineage cells. We propose that this may be due to the direct action of osteoblast-lineage-derived MMP-13 on bone resorption.

The endoplasmic reticulum stress-autophagy pathway controls hypothalamic development and energy balance regulation in leptin-deficient neonates

Nat Commun

2020 Apr 20

Park S, Aintablian A, Coupe B, Bouret SG
PMID: 32313051 | DOI: 10.1038/s41467-020-15624-y

Obesity is associated with the activation of cellular responses, such as endoplasmic reticulum (ER) stress. Here, we show that leptin-deficient ob/ob mice display elevated hypothalamic ER stress as early as postnatal day 10, i.e., prior to the development of obesity in this mouse model. Neonatal treatment of ob/ob mice with the ER stress-relieving drug tauroursodeoxycholic acid (TUDCA) causes long-term amelioration of body weight, food intake, glucose homeostasis, and pro-opiomelanocortin (POMC) projections. Cells exposed to ER stress often activate autophagy. Accordingly, we report that in vitro induction of ER stress and neonatal leptin deficiency in vivo activate hypothalamic autophagy-related genes. Furthermore, genetic deletion of autophagy in pro-opiomelanocortin neurons of ob/ob mice worsens their glucose homeostasis, adiposity, hyperphagia, and POMC neuronal projections, all of which are ameliorated with neonatal TUDCA treatment. Together, our data highlight the importance of early life ER stress-autophagy pathway in influencing hypothalamic circuits and metabolic regulation
NF-κB drives epithelial-mesenchymal mechanisms of lung fibrosis in a translational lung cell model

JCI insight

2022 Dec 15

Sieber, P;Schäfer, A;Lieberherr, R;Caimi, SL;Lüthi, U;Ryge, J;Bergmann, JH;Le Goff, F;Stritt, M;Blattmann, P;Renault, B;Rammelt, P;Sempere, B;Freti, D;Studer, R;White, ES;Birker-Robaczewska, M;Boucher, M;Nayler, O;
PMID: 36520540 | DOI: 10.1172/jci.insight.154719

In the progression phase of idiopathic pulmonary fibrosis (IPF) the normal alveolar structure of the lung is lost and replaced by remodeled fibrotic tissue and by bronchiolized cystic airspaces. Although these are characteristic features of IPF, knowledge of specific interactions between these pathological processes is limited. Here, the interaction of lung epithelial and lung mesenchymal cells was investigated in a co-culture model of human primary airway epithelial cells (EC) and lung fibroblasts (FB). Single-cell RNA sequencing (sc-RNA-seq) revealed that the starting EC population was heterogenous and enriched for cells with a basal cell signature. Furthermore, fractions of the initial EC and FB cell populations adopted distinct pro-fibrotic cell differentiation states upon co-cultivation, resembling specific cell populations that were previously identified in lungs of IPF patients. Transcriptomic analysis revealed active nuclear factor NF-kappa-B (NF-κB) signaling early in the co-cultured EC and FB cells and the identified NF-κB expression signatures were also found in "HAS1 High FB" and "PLIN2+ FB" populations from IPF patient lungs. Pharmacological blockade of NF-κB signaling attenuated specific phenotypic changes of EC and prevented FB-mediated interleukin-6 (IL6), interleukin-8 (IL-8) and C-X-C motif chemokine ligand 6 (CXCL6) cytokine secretion, as well as collagen alpha-1(I) chain (COL1A1) and alpha-smooth muscle actin (α-SMA) accumulation. Thus, we identified NF-κB as a potential mediator, linking epithelial pathobiology with fibrogenesis.
Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice

Nature communications

2021 May 13

Hunt, C;Hartford, SA;White, D;Pefanis, E;Hanna, T;Herman, C;Wiley, J;Brown, H;Su, Q;Xin, Y;Voronin, D;Nguyen, H;Altarejos, J;Crosby, K;Haines, J;Cancelarich, S;Drummond, M;Moller-Tank, S;Malpass, R;Buckley, J;Del Pilar Molina-Portela, M;Droguett, G;Frendewey, D;Chiao, E;Zambrowicz, B;Gong, G;
PMID: 33986266 | DOI: 10.1038/s41467-021-22932-4

CRISPR-based transcriptional activation is a powerful tool for functional gene interrogation; however, delivery difficulties have limited its applications in vivo. Here, we created a mouse model expressing all components of the CRISPR-Cas9 guide RNA-directed Synergistic Activation Mediator (SAM) from a single transcript that is capable of activating target genes in a tissue-specific manner. We optimized Lipid Nanoparticles and Adeno-Associated Virus guide RNA delivery approaches to achieve expression modulation of one or more genes in vivo. We utilized the SAM mouse model to generate a hypercholesteremia disease state that we could bidirectionally modulate with various guide RNAs. Additionally, we applied SAM to optimize gene expression in a humanized Transthyretin mouse model to recapitulate human expression levels. These results demonstrate that the SAM gene activation platform can facilitate in vivo research and drug discovery.
Long Acting Neurotensin Synergizes with Liraglutide to Reverse Obesity Through a Melanocortin-Dependent Pathway.

Diabetes

2019 Apr 01

Ratner C, He Z, Grunddal KV, Skov LJ, Hartmann B, Zhang F, Feuchtinger A, Bjerregaard A, Christoffersen C, Tschöp MH, Finan B, DiMarchi RD, Leinninger GM, Williams KW, Clemmensen C, Holst B.
PMID: 30936142 | DOI: 10.2337/db18-1009

Neurotensin, a gut hormone and neuropeptide, increases in circulation after bariatric surgery in rodents and humans and inhibits food intake in mice. However, its potential to treat obesity and the subsequent metabolic dysfunctions have been difficult to assess owing to its short half-life in vivo Here, we demonstrate that a long acting, pegylated analogue of the neurotensin peptide (P-NT) reduces food intake, body weight and adiposity in diet-induced obese (DIO) mice when administered once daily for 6 days. Strikingly, when P-NT was combined with the GLP-1 mimetic liraglutide the two peptides synergized to reduce food intake and body weight relative to each mono-therapy, without inducing a taste aversion. Further, P-NT and liraglutide co-administration improved glycemia and reduced steatohepatitis. Finally, we show that the melanocortin pathway is central for P-NT-induced anorexia and necessary for the full synergistic effect of P-NT and liraglutide combination-therapy. Overall, our data suggest that P-NT and liraglutide combination-therapy could be an enhanced treatment for obesity with improved tolerability compared to liraglutide mono-therapy.

Diet-induced adaptive thermogenesis requires neuropeptide FF receptor-2 signalling

Nat Commun.

2018 Nov 09

Zhang L, Ip CK, Lee ICJ, Qi Y, Reed F, Karl T, Low JK, Enriquez RF, Lee NJ, Baldock PA, Herzog H.
PMID: 30413707 | DOI: 10.1038/s41467-018-06462-0

Excess caloric intake results in increased fat accumulation and an increase in energy expenditure via diet-induced adaptive thermogenesis; however, the underlying mechanisms controlling these processes are unclear. Here we identify the neuropeptide FF receptor-2 (NPFFR2) as a critical regulator of diet-induced thermogenesis and bone homoeostasis. Npffr2-/- mice exhibit a stronger bone phenotype and when fed a HFD display exacerbated obesity associated with a failure in activating brown adipose tissue (BAT) thermogenic response to energy excess, whereas the activation of cold-induced BAT thermogenesis is unaffected. NPFFR2 signalling is required to maintain basal arcuate nucleus NPY mRNA expression. Lack of NPFFR2 signalling leads to a decrease in BAT thermogenesis under HFD conditions with significantly lower UCP-1 and PGC-1α levels in the BAT. Together, these data demonstrate that NPFFR2 signalling promotes diet-induced thermogenesis via a novel hypothalamic NPY-dependent circuitry thereby coupling energy homoeostasis with energy partitioning to adipose and bone tissue.

Nutrient-sensing AgRP neurons relay control of liver autophagy during energy deprivation

Cell metabolism

2023 May 02

Chen, W;Mehlkop, O;Scharn, A;Nolte, H;Klemm, P;Henschke, S;Steuernagel, L;Sotelo-Hitschfeld, T;Kaya, E;Wunderlich, CM;Langer, T;Kononenko, NL;Giavalisco, P;Brüning, JC;
PMID: 37075752 | DOI: 10.1016/j.cmet.2023.03.019

Autophagy represents a key regulator of aging and metabolism in sensing energy deprivation. We find that fasting in mice activates autophagy in the liver paralleled by activation of hypothalamic AgRP neurons. Optogenetic and chemogenetic activation of AgRP neurons induces autophagy, alters phosphorylation of autophagy regulators, and promotes ketogenesis. AgRP neuron-dependent induction of liver autophagy relies on NPY release in the paraventricular nucleus of the hypothalamus (PVH) via presynaptic inhibition of NPY1R-expressing neurons to activate PVHCRH neurons. Conversely, inhibiting AgRP neurons during energy deprivation abrogates induction of hepatic autophagy and rewiring of metabolism. AgRP neuron activation increases circulating corticosterone concentrations, and reduction of hepatic glucocorticoid receptor expression attenuates AgRP neuron-dependent activation of hepatic autophagy. Collectively, our study reveals a fundamental regulatory principle of liver autophagy in control of metabolic adaptation during nutrient deprivation.
CircRNA circCOL1A1 Acts as a Sponge of miR-30a-5p to Promote Vascular Smooth Cell Phenotype Switch through Regulation of Smad1 Expression

Thrombosis and haemostasis

2022 Dec 03

Ye, M;Ni, Q;Wang, H;Wang, Y;Yao, Y;Li, Y;Wang, W;Yang, S;Chen, J;Lv, L;Zhao, Y;Xue, G;Guo, X;Zhang, L;
PMID: 36462769 | DOI: 10.1055/s-0042-1757875

Phenotypic switch of vascular smooth muscle cells (VSMCs) plays an important role in the pathogenesis of atherosclerosis. The mRNA expression of the synthetic biomarker Collagen Type I Alpha 1 Chain (COL1A1) gene is upregulated during the switch of VSMCs from the contractile to the synthetic phenotype. The association of noncoding circular RNAs transcribed by the COL1A1 gene with VSMC phenotype alteration and atherogenesis remains unclear. Here we reported a COL1A1 circular RNA (circCOL1A1) which is specifically expressed in VSMCs and is upregulated during phenotype alteration of VSMCs. CircCOL1A1 is also detectable in the serum or plasma. Healthy vascular tissues have a low expression of CircCOL1A1, while it is upregulated in atherosclerosis patients. Through ex vivo and in vitro assays, we found that circCOL1A1 can promote VSMC phenotype switch. Mechanistic analysis showed that circCOL1A1 may exert its function as a competing endogenous RNA of miR-30a-5p. Upregulation of circCOL1A1 ameliorates the inhibitory effect of miR-30a-5p on its target SMAD1, which leads to suppression of transforming growth factor-β (TGF-β) signaling. Our findings demonstrate that circCOL1A1 promotes the phenotype switch of VSMCs through the miR-30a-5p/SMAD1/TGF-β axis and it may serve as a novel marker of atherogenesis or as a therapeutic target for atherosclerosis.Thieme. All rights reserved.

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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
EnEmProbe targets exons n and m
En-EmProbe 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

Enabling research, drug development (CDx) and diagnostics

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