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Probes for LONG

ACD can configure probes for the various manual and automated assays for LONG for RNAscope Assay, or for Basescope Assay compatible for your species of interest.

ACD’s data images for Long gene.

  • RNA expression of long gene in Human Colorectal cancer sample using RNAscope™ 2.5 HD Assay Brown

  • RNA expression of long gene in Human Gastric cancer sample using RNAscope™ 2.5 HD Assay Brown

  • RNA expression of long gene in Human Glioma sample using RNAscope™ 2.5 HD Assay Brown

  • RNA expression of long gene in Human Lung cancer sample using RNAscope™ 2.5 HD Assay Brown

  • RNA expression of long gene in Human ovarian cancer sample using RNAscope™ 2.5 HD Assay Brown

  • Expression of long in Human Prostate cancer sample using RNAscope™ 2.5 HD Assay Brown

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Cholecystokinin neurons in mouse suprachiasmatic nucleus regulate the robustness of circadian clock

Neuron

2023 May 07

Xie, L;Xiong, Y;Ma, D;Shi, K;Chen, J;Yang, Q;Yan, J;
PMID: 37172583 | DOI: 10.1016/j.neuron.2023.04.016

The suprachiasmatic nucleus (SCN) can generate robust circadian behaviors in mammals under different environments, but the underlying neural mechanisms remained unclear. Here, we showed that the activities of cholecystokinin (CCK) neurons in the mouse SCN preceded the onset of behavioral activities under different photoperiods. CCK-neuron-deficient mice displayed shortened free-running periods, failed to compress their activities under a long photoperiod, and developed rapid splitting or became arrhythmic under constant light. Furthermore, unlike vasoactive intestinal polypeptide (VIP) neurons, CCK neurons are not directly light sensitive, but their activation can elicit phase advance and counter light-induced phase delay mediated by VIP neurons. Under long photoperiods, the impact of CCK neurons on SCN dominates over that of VIP neurons. Finally, we found that the slow-responding CCK neurons control the rate of recovery during jet lag. Together, our results demonstrated that SCN CCK neurons are crucial for the robustness and plasticity of the mammalian circadian clock.
Coding and long non-coding gene expression changes in the CNS traumatic injuries

Cellular and molecular life sciences : CMLS

2022 Feb 07

Wu, X;Wei, H;Wu, JQ;
PMID: 35129669 | DOI: 10.1007/s00018-021-04092-2

Traumatic brain injury (TBI) and spinal cord injury (SCI) are two main central nervous system (CNS) traumas, caused by external physical insults. Both injuries have devastating effects on the quality of life, and there is no effective therapy at present. Notably, gene expression profiling using bulk RNA sequencing (RNA-Seq) and single-cell RNA-Seq (scRNA-Seq) have revealed significant changes in many coding and non-coding genes, as well as important pathways in SCI and TBI. Particularly, recent studies have revealed that long non-coding RNAs (lncRNAs) with lengths greater than 200 nucleotides and without protein-coding potential have tissue- and cell type-specific expression pattern and play critical roles in CNS injury by gain- and loss-of-function approaches. LncRNAs have been shown to regulate protein-coding genes or microRNAs (miRNAs) directly or indirectly, participating in processes including inflammation, glial activation, cell apoptosis, and vasculature events. Therefore, lncRNAs could serve as potential targets for the diagnosis, treatment, and prognosis of SCI and TBI. In this review, we highlight the recent progress in transcriptome studies of SCI and TBI and insights into molecular mechanisms.
Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface

Cell Discovery

2017 Mar 28

Boulay AC, Saubaméa B, Adam N, Chasseigneaux S, Mazaré N, Gilbert A, Bahin M, Bastianelli L, Blugeon C, Perrin S, Pouch J, Ducos B, Le Crom S, Genovesio A, Chrétien F, Declèves X, Laplanche JL, Cohen-Salmon M.
PMID: 28377822 | DOI: 10.1038/celldisc.2017.5

Astrocytes send out long processes that are terminated by endfeet at the vascular surface and regulate vascular functions as well as homeostasis at the vascular interface. To date, the astroglial mechanisms underlying these functions have been poorly addressed. Here we demonstrate that a subset of messenger RNAs is distributed in astrocyte endfeet. We identified, among this transcriptome, a pool of messenger RNAs bound to ribosomes, the endfeetome, that primarily encodes for secreted and membrane proteins. We detected nascent protein synthesis in astrocyte endfeet. Finally, we determined the presence of smooth and rough endoplasmic reticulum and the Golgi apparatus in astrocyte perivascular processes and endfeet, suggesting for local maturation of membrane and secreted proteins. These results demonstrate for the first time that protein synthesis occurs in astrocyte perivascular distal processes that may sustain their structural and functional polarization at the vascular interface.

Far from home: the role of glial mRNA localization in synaptic plasticity

RNA (New York, N.Y.)

2022 Nov 28

Gala, DS;Titlow, JS;Teodoro, RO;Davis, I;
PMID: 36442969 | DOI: 10.1261/rna.079422.122

Neurons and glia are highly polarized cells, whose distal cytoplasmic functional subdomains require specific proteins. Neurons have axonal and dendritic cytoplasmic extensions containing synapses requiring mRNA transport and localized translation to regulate synaptic plasticity efficiently. The principles behind these mechanisms are equally attractive for explaining rapid local regulation of distal glial cytoplasmic projections, independent of their cell nucleus. However, in contrast to neurons, this topic has received little experimental attention in glia. Nevertheless, there are many functionally diverse glial sub-types, containing extensive networks of long cytoplasmic projections with likely localized regulation that influence neurons and their synapses. Moreover, glia have many other neuron-like properties, including electrical activity, secretion of gliotransmitters and calcium signaling, influencing for example synaptic transmission, plasticity and axon pruning. Here, we review previous studies concerning glial transcripts with important roles in influencing synaptic plasticity, focusing on a few cases involving localized translation. We discuss a variety of important questions about mRNA transport and localized translation in glia that remain to be addressed using cutting-edge tools already available for neurons.
Leptin Receptor Expression in Mouse Intracranial Perivascular Cells

Front. Neuroanat.

2018 Jan 23

Yuan X, Caron A, Wu H, Gautron L.
PMID: - | DOI: 10.3389/fnana.2018.00004

Past studies have suggested that non-neuronal brain cells express the leptin receptor. However, the identity and distribution of these leptin receptor-expressing non-neuronal brain cells remain debated. This study assessed the distribution of the long form of the leptin receptor (LepRb) in non-neuronal brain cells using a reporter mouse model in which LepRb-expressing cells are permanently marked by tdTomato fluorescent protein (LepRb-CretdTomato). Double immunohistochemistry revealed that, in agreement with the literature, the vast majority of tdTomato-tagged cells across the mouse brain were neurons (i.e., based on immunoreactivity for NeuN). Non-neuronal structures also contained tdTomato-positive cells, including the choroid plexus and the perivascular space of the meninges and, to a lesser extent, the brain. Based on morphological criteria and immunohistochemistry, perivascular cells were deduced to be mainly pericytes. Notably, tdTomato-positive cells were immunoreactive for vitronectin and platelet derived growth factor receptor beta (PDGFBR). In situ hybridization studies confirmed that most tdTomato-tagged perivascular cells were enriched in leptin receptor mRNA (all isoforms). Using qPCR studies, we confirmed that the mouse meninges were enriched in Leprb and, to a greater extent, the short isoforms of the leptin receptor. Interestingly, qPCR studies further demonstrated significantly altered expression for Vtn and Pdgfrb in the meninges and hypothalamus of LepRb-deficient mice. Collectively, our data demonstrate that the only intracranial non-neuronal cells that express LepRb in the adult mouse are cells that form the blood-brain barrier, including, most notably, meningeal perivascular cells. Our data suggest that pericytic leptin signaling plays a role in the integrity of the intracranial perivascular space and, consequently, may provide a link between obesity and numerous brain diseases.

Interactions between β‐endorphin and kisspeptin neurons of the ewe arcuate nucleus are modulated by photoperiod.

Journal of Neuroendocrinology

2023 Feb 10

Hellier, V;Dardente, H;Lomet, D;Cognié, J;Dufourny, L;
| DOI: 10.1111/jne.13242

Opioid peptides are well-known modulators of the central control of reproduction. Among them, dynorphin coexpressed in kisspeptin (KP) neurons of the arcuate nucleus (ARC) has been thoroughly studied for its autocrine effect on KP release through κ opioid receptors. Other studies have suggested a role for β-endorphin (BEND), a peptide cleaved from the pro-opiomelanocortin precursor, on food intake and central control of reproduction. Similar to KP, BEND content in the ARC of sheep is modulated by day length and BEND modulates food intake in a dose-dependent manner. Because KP levels in the ARC vary with photoperiodic and metabolic status, a photoperiod-driven influence of BEND neurons on neighboring KP neurons is plausible. The present study aimed to investigate a possible modulatory action of BEND on KP neurons located in the ovine ARC. Using confocal microscopy, numerous KP appositions on BEND neurons were found but there was no photoperiodic variation of the number of these interactions in ovariectomized, estradiol-replaced ewes. By contrast, BEND terminals on KP neurons were twice as numerous under short days, in ewes having an activated gonadotropic axis, compared to anestrus ewes under long days. Injection of 5 μg BEND into the third ventricle of short-day ewes induced a significant and specific increase of activated KP neurons (16% vs. 9% in controls), whereas the percentage of overall activated (c-Fos positive) neurons, was similar between both groups. These data suggest a photoperiod-dependent influence of BEND on KP neurons of the ARC, which may influence gonadotropin-releasing hormone pulsatile secretion and inform KP neurons about metabolic status.
Retinal ganglion cell expression of cytokine enhances occupancy of NG2 cell-derived astrocytes at the nerve injury site: Implication for axon regeneration

Experimental neurology

2022 Jun 20

Ribeiro, M;Ayupe, AC;Beckedorff, FC;Levay, K;Rodriguez, S;Tsoulfas, P;Lee, JK;Nascimento-Dos-Santos, G;Park, KK;
PMID: 35738417 | DOI: 10.1016/j.expneurol.2022.114147

Following injury in the central nervous system, a population of astrocytes occupy the lesion site, form glial bridges and facilitate axon regeneration. These astrocytes originate primarily from resident astrocytes or NG2+ oligodendrocyte progenitor cells. However, the extent to which these cell types give rise to the lesion-filling astrocytes, and whether the astrocytes derived from different cell types contribute similarly to optic nerve regeneration remain unclear. Here we examine the distribution of astrocytes and NG2+ cells in an optic nerve crush model. We show that optic nerve astrocytes partially fill the injury site over time after a crush injury. Viral mediated expression of a growth-promoting factor, ciliary neurotrophic factor (CNTF), in retinal ganglion cells (RGCs) promotes axon regeneration without altering the lesion size or the degree of lesion-filling GFAP+ cells. Strikingly, using inducible NG2CreER driver mice, we found that CNTF overexpression in RGCs increases the occupancy of NG2+ cell-derived astrocytes in the optic nerve lesion. An EdU pulse-chase experiment shows that the increase in NG2 cell-derived astrocytes is not due to an increase in cell proliferation. Lastly, we performed RNA-sequencing on the injured optic nerve and reveal that CNTF overexpression in RGCs results in significant changes in the expression of distinct genes, including those that encode chemokines, growth factor receptors, and immune cell modulators. Even though CNTF-induced axon regeneration has long been recognized, this is the first evidence of this procedure affecting glial cell fate at the optic nerve crush site. We discuss possible implication of these results for axon regeneration.
Median raphe non-serotonergic neurons modulate hippocampal theta oscillations

The Journal of neuroscience : the official journal of the Society for Neuroscience

2022 Jan 18

Huang, WQ;Ikemoto, S;Wang, DV;
PMID: 35064000 | DOI: 10.1523/JNEUROSCI.1536-21.2022

Hippocampal theta oscillations (HTO) during rapid eye movement (REM) sleep play an important role in mnemonic processes by coordinating hippocampal and cortical activities. However, it is not fully understood how HTO are modulated by subcortical regions, including the median raphe nucleus (MnR). The MnR is thought to suppress HTO through its serotonergic outputs. Here, our study on male mice revealed a more complex framework indicating roles of non-serotonergic MnR outputs in regulating HTO. We found that non-selective optogenetic activation of MnR neurons at theta frequency increased HTO amplitude. Granger causality analysis indicated that MnR theta oscillations during REM sleep influence HTO. By utilizing three transgenic mouse lines, we found that MnR serotonergic neurons exhibited little or no theta-correlated activity during HTO. Instead, most MnR GABAergic neurons and Vglut3 neurons respectively increased and decreased activities during HTO and exhibited hippocampal theta phase-locked activities. Although MnR GABAergic neurons do not directly project to the hippocampus, they could modulate HTO through local Vglut3 and serotonergic neurons, since we found that MnR GABAergic neurons monosynaptically targeted Vglut3 and serotonergic neuronal activities. Additionally, MnR P-wave activity at about 1 Hz during REM sleep accompanied non-serotonergic activity increase and HTO acceleration. These results suggest that MnR non-serotonergic neurons modulate hippocampal theta activity during REM sleep, which regulates memory processes.Significance Statement:The median raphe nucleus (MnR) is the major source of serotonergic inputs to multiple brain regions including the hippocampus and medial septal area. It has long been thought that those serotonergic outputs suppress hippocampal theta oscillations (HTO). However, our results revealed that MnR serotoninergic neurons displayed little firing changes during HTO. Instead, MnR Vglut3 neurons were largely silent during HTO associated with REM sleep. Additionally, many MnR GABAergic neurons fired rhythmically phase-locked to HTO. These results indicate an important role of MnR non-serotonergic neurons in modulating HTO.
A thyroid hormone-independent role for transthyretin in neural stem cells of the postnatal mouse subventricular zone?

Endocrine Abstracts

2022 Sep 02

Vancamp, P;Le, B;Demeneix, B;Remaud, S;
| DOI: 10.1530/endoabs.84.op-04-19

Transthyretin (TTR) distributes thyroxine in the cerebrospinal fluid of mammals. Choroid plexus epithelial cells produce and secrete TTR, and were long recognized as the only CNS source of TTR. However, research over the last years has reported neuronal-specific expression as well, but without a clear function. Recently, we found Ttr transcripts in cells of the adult mouse subventricular zone (SVZ), the largest neural stem cell (NSC) region, but the protein was undetectable. We therefore investigated in more detail what role TTR might play in the SVZ, and when. We mapped temporal-spatial Ttr expression by re-analysing publicly available single-cell RNA-Seq data obtained from dissected mouse SVZs at E14-E17-P2-P7-P20-P61. We observed a peak in Ttr expression in NSCs, neural progenitors and differentiating cells at postnatal day 7 (P7). That is one week prior to when thyroxine serum levels peak and T3 activates SVZ-NSCs that start generating neurons and glia at a constant rate. RNAscope on P7 brain sections confirmed that few Ttr transcripts are present in a many SVZ-progenitors, oligodendrocyte precursors and neuroblasts. Unexpectedly though, no protein was detectable using commercially available antibodies, signal amplification and appropriate controls. This might suggest TTR is rapidly secreted to affect nearby cells. To test this hypothesis, we prepared neurospheres from dissected SVZ-progenitors at P7. After 7 days of proliferation, cells were dissociated, and allowed to differentiate for 1 or 5 days. In parallel with controls, we treated them once at day 0 of differentiation with a low (2.5 µg/ml) or a high dose (25 µg/ml) of human recombinant TTR, or with 5 nM T3. Low TTR doses reduced cell mitosis at day 1, as did T3. After 5 days, we counted a 30% lower proportion of differentiated neuroblasts with the highest TTR dose. That proportion had dropped 3-fold in the presence of T3. Proportions of oligodendroglia after 5 days of differentiation were only significantly higher in T3 conditions. As a result, the neuron/glia balance shifted in favour of oligodendrogenesis under T3, and borderline-significantly following high TTR doses. Altogether, the murine SVZ represents a novel region containing cells that express Ttr, with a peak at P7, despite seeming absence of the protein itself, precluding deducing its exact role. Single-cell RNA-Seq on treated neurospheres could reveal how exogenous TTR affects intracellular pathways, and whether its action is TH-dependent or not. This can help unravelling the pathophysiology of familial amyloid polyneuropathy, in which misfolded TTR proteins cause neurodegeneration.
Post-surgical latent pain sensitization is driven by descending serotonergic facilitation and masked by µ-opioid receptor constitutive activity (MORCA) in the rostral ventromedial medulla

The Journal of neuroscience : the official journal of the Society for Neuroscience

2022 Jun 13

Cooper, AH;Hedden, NS;Prasoon, P;Qi, Y;Taylor, BK;
PMID: 35701159 | DOI: 10.1523/JNEUROSCI.2038-21.2022

Following tissue injury, latent sensitization (LS) of nociceptive signaling can persist indefinitely, kept in remission by compensatory µ-opioid receptor constitutive activity (MORCA) in the dorsal horn of the spinal cord. To demonstrate LS, we conducted plantar incision in mice and then waited 3-4 weeks for hypersensitivity to resolve. At this time (remission), systemic administration of the opioid receptor antagonist/inverse agonist naltrexone reinstated mechanical and heat hypersensitivity. We first tested the hypothesis that LS extends to serotonergic neurons in the rostral ventral medulla (RVM) that convey pronociceptive input to the spinal cord. We report that in male and female mice, hypersensitivity was accompanied by increased Fos expression in serotonergic neurons of the RVM, abolished upon chemogenetic inhibition of RVM 5-HT neurons, and blocked by intrathecal injection of the 5-HT3R antagonist ondansetron; the 5-HT2AR antagonist MDL-11,939 had no effect. Second, to test for MORCA, we microinjected the MOR inverse agonist CTAP and/or neutral opioid receptor antagonist 6β-naltrexol. Intra-RVM CTAP produced mechanical hypersensitivity at both hindpaws. 6β-naltrexol had no effect by itself, but blocked CTAP-induced hypersensitivity. This indicates that MORCA, rather than an opioid ligand-dependent mechanism, maintains LS in remission. We conclude that incision establishes LS in descending RVM 5-HT neurons that drives pronociceptive 5-HT3R signaling in the dorsal horn, and this LS is tonically opposed by MORCA in the RVM. The 5-HT3 receptor is a promising therapeutic target for the development of drugs to prevent the transition from acute to chronic post-surgical pain.Significance statementSurgery leads to latent pain sensitization and a compensatory state of endogenous pain control that is maintained long after tissue healing. Here we show that either chemogenetic inhibition of serotonergic neuron activity in the rostral ventromedial medulla (RVM), or pharmacological inhibition of 5-HT3 receptor signaling at the spinal cord blocks behavioral signs of post-surgical latent sensitization. We conclude that µ-opioid receptor constitutive activity (MORCA) in the RVM opposes descending serotonergic facilitation of LS, and that the 5-HT3 receptor is a promising therapeutic target for the development of drugs to prevent the transition from acute to chronic post-surgical pain.
A230 THE ROLE OF THE MICROBIOTA IN NOCICEPTOR DEVELOPMENT AND PAIN SENSITIVITY

Journal of the Canadian Association of Gastroenterology

2022 Feb 21

Abdullah, N;Defaye, M;Hassan, A;Cumenal, M;Iftinca, M;Young, D;Ohland, C;Dufour, A;McCoy, K;Altier, C;
| DOI: 10.1093/jcag/gwab049.229

Background Pain is the most common cause of disability in IBD. What causes inter-individual variability in chronic pain after successful treatment of inflammation remains elusive. We have shown that activation of TRPV1+ colonic nociceptors is essential for the establishment of persistent pain in DSS colitis. Nociceptor development coincides with microbial colonization, while early life dysbiosis can lead to visceral hypersensitivity in adulthood. Whether the microbiota dictates nociceptor development and pain susceptibility remains unknown. Here we test the hypothesis that the microbiota programs nociceptor specification during early development, rendering them more susceptible to sensitization later in life. We have identified the aryl hydrocarbon receptor (AHR) that senses bacterial-derived metabolites as a candidate target that orchestrates transcriptional regulation in nociceptors. Aims We investigated the developmental regulation of nociceptors by the microbiome and how it influences pain sensitivity. We will determine the effects of AHR activation on nociceptor lineage and function as well as the long term impact of AHR signaling on pain sensitivity. Methods We have developed a germ-free (GF) TRPV1-GFP reporter mouse that was used to phenotype and visualise TRPV1+ nociceptors in the absence of a microbiota. We will isolate TRPV1+ neurons by FACS to identify genes that are under the control of the microbiota and to characterise the phosphoproteome of TRPV1+ nociceptors in GF conditions. Finally, we will investigate the role of AHR signaling in nociceptors both acutely and during development. Results We showed a reduction in thermal pain threshold and a reduction in capsaicin test responses in GF mice. The number and size of DRG neurons was unchanged in GF mice. Examination of molecular markers for peptidergic (CGRP) and non-peptidergic (IB4) neurons did not show a difference. Finally, there was no difference in the expression of TRPV1, suggesting post-translational modification of the channel. In cultured DRG neurons, we found a decrease in capsaicin induced action potentials and a decrease in the amplitude of the capsaicin response in GF mice. Using RNAscope, we showed that TRPV1+ neurons express AHR. Conclusions Our results highlight the importance of bacterial composition in regulating the development of nociceptors and pain sensitivity in adulthood. Furthermore, we are the first to demonstrate the expression of AHR in sensory neurons. These findings point to a role of the microbiota in programming nociceptors during development. My work will advance our understanding of the role of commensal bacteria in regulating pain and could lead to recommendations for the treatment of neonates in early life to reduce their risk of developing chronic pain later in life. Funding Agencies CAG, CIHR
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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
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A mixture of multiple probe sets targeting multiple genes or transcripts
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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
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Example: Hs-LEPR-tv1
Designed to target transcript variant n
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Example: Hs-ACVRL1-ORF
Probe targets open reading frame
UTR
Example: Hs-HTT-UTR-C3
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Example: Hs-GNRHR-5UTR
Probe targets the 5' untranslated region only
3UTR
Example: Rn-Npy1r-3UTR
Probe targets the 3' untranslated region only
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Example: Pool
A mixture of multiple probe sets targeting multiple genes or transcripts

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