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Examining Neuronal Subtype-Specific Genes Downregulated in Schizophrenia (SCZ) Using RNAscope in the Dorso-Lateral Prefrontal Cortex (DLPFC)
Biological Psychiatry
2021 May 01
Kim, D;Jambhale, A;Kim, P;Kim, B;Lipska, B;Auluck, P;Marenco, S;
| DOI: 10.1016/j.biopsych.2021.02.630
Background Bulk tissue RNA-sequencing studies in human post-mortem brains have reported differentially expressed genes between patients with Schizophrenia (SCZ) and controls. Single-nucleus RNA-sequencing data indicate that genes downregulated in SCZ were particularly enriched in a sub-population of excitatory neurons (Ex21) indexed by SMYD1 gene. POSTN and NR4A2 are two genes highly specific to Ex21 and significantly downregulated in SCZ. We hypothesized that either the number of Ex21 cells or the expression of POSTN and NR4A2 within them would be reduced in SCZ vs. controls. Methods We conducted a RNAscope in situ hybridization study in 20 SCZ and 20 controls. Three sections of the DLPFC per individual were stained for SMYD1 and NR4A2, and another three for SMYD1 and POSTN, using the colorimetric version of RNAscope (240 sections). Each RNAscope slide was counterstained using hematoxylin/eosin. Additional sections were stained with NeuN to assess neuronal numbers. Results ANCOVA revealed that there were no significant differences between SCZ and controls in the proportion of Ex21 (SMYD1+) cells (p = 0.40 for POSTN dataset, 0.36 for NR4A2 dataset), or the expression of marker and target genes within SMYD1+ cells in the DLPFC (p = 0.86 for POSTN dataset, p = 0.15 for NR4A2 dataset). Conclusions These results contradict prior conclusions that both POSTN and NR4A2 are downregulated in SCZ, but the modest sample size and several methodological issues suggest caution in interpreting these results.
EMBO reports
2022 Dec 16
Wang, B;Jiang, B;Li, GW;Dong, F;Luo, Z;Cai, B;Wei, M;Huang, J;Wang, K;Feng, X;Tong, F;Wang, S;Wang, Q;Han, Q;Li, C;Zhang, X;Yang, L;Bao, L;
PMID: 36524339 | DOI: 10.15252/embr.202154313
Somatosensory neurons are highly heterogeneous with distinct types of neural cells responding to specific stimuli. However, the distribution and roles of cell-type-specific long intergenic noncoding RNAs (lincRNAs) in somatosensory neurons remain largely unexplored. Here, by utilizing droplet-based single-cell RNA-seq (scRNA-seq) and full-length Smart-seq2, we show that lincRNAs, but not coding mRNAs, are enriched in specific types of mouse somatosensory neurons. Profiling of lincRNAs from single neurons located in dorsal root ganglia (DRG) identifies 200 lincRNAs localized in specific types or subtypes of somatosensory neurons. Among them, the conserved cell-type-specific lincRNA CLAP associates with pruritus and is abundantly expressed in somatostatin (SST)-positive neurons. CLAP knockdown reduces histamine-induced Ca2+ influx in cultured SST-positive neurons and in vivo reduces histamine-induced scratching in mice. In vivo knockdown of CLAP also decreases the expression of neuron-type-specific and itch-related genes in somatosensory neurons, and this partially depends on the RNA binding protein MSI2. Our data reveal a cell-type-specific landscape of lincRNAs and a function for CLAP in somatosensory neurons in sensory transmission.
Circulation
2022 Jan 01
Kawai, K;Sakamoto, A;Mokry, M;Ghosh, S;Xu, W;
| DOI: 10.1161/circ.146.suppl_1.15249
Background: Studies using techniques that relied on expression of an X-linked gene suggested predominant clones of smooth muscle cells (SMC) may exist in human atherosclerosis. These studies were limited by spatial resolution and nature of plaque types studied. We investigated whether clones of SMCs exist in unstable human atheroma. Methods and Results: We used a 25 nucleotide deletion in the 3’ UTR of the BGN gene, highly expressed by SMC and prevalent in 30% of females, to study clonal proliferation. Three different types of plaques (erosion, rupture, and adaptive intimal thickening) were selected from females heterozygous for the deletion mutant. Hybridization of target RNA-specific BaseScope probes was conducted to visualize the distribution of mutants and images displayed as a bubble plots. Clonality index was calculated as the percentage of each probe in each ROI. A clonality index equal to or exceeding the three times the standard deviation above the mean of the clonality index of the media in all plaques was considered clonal. In comparing clonality between media and intima, the mean percent ROI with clonality was significantly higher in the intima than in the media (42.3±18.2 vs 18.3±9.6%, P=0.003) and this was consistent for both eroded (27.0±9.8 vs 9.0±3.8%, P=0.04) and ruptured plaques (41.3±10.7 vs 20.0±3.5%, P=0.03). The relationship of dominant clone in the intima and media shows significant concordance in the majority of plaques studied (R=0.72, P
Experimental neurology
2022 Oct 07
Fang, YP;Qin, ZH;Zhang, Y;Ning, B;
PMID: 36216123 | DOI: 10.1016/j.expneurol.2022.114239
Microglia are widely distributed in the central nervous system (CNS), where they aid in the maintenance of neuronal function and perform key auxiliary roles in phagocytosis, neural repair, immunological control, and nutrition delivery. Microglia in the undamaged spinal cord is in a stable state and serve as immune monitors. In the event of spinal cord injury (SCI), severe changes in the microenvironment and glial scar formation lead to axonal regeneration failure. Microglia participates in a series of pathophysiological processes and behave both positive and negative consequences during this period. A deep understanding of the characteristics and functions of microglia can better identify therapeutic targets for SCI. Technological innovations such as single-cell RNA sequencing (Sc-RNAseq) have led to new advances in the study of microglia heterogeneity throughout the lifespan. Here,We review the updated studies searching for heterogeneity of microglia from the developmental and pathological state, survey the activity and function of microglia in SCI and explore the recent therapeutic strategies targeting microglia in the CNS injury.
Science advances
2022 Sep 02
Porcu, A;Nilsson, A;Booreddy, S;Barnes, SA;Welsh, DK;Dulcis, D;
PMID: 36054362 | DOI: 10.1126/sciadv.abn9867
Seasonal changes in day length (photoperiod) affect numerous physiological functions. The suprachiasmatic nucleus (SCN)-paraventricular nucleus (PVN) axis plays a key role in processing photoperiod-related information. Seasonal variations in SCN and PVN neurotransmitter expression have been observed in humans and animal models. However, the molecular mechanisms by which the SCN-PVN network responds to altered photoperiod is unknown. Here, we show in mice that neuromedin S (NMS) and vasoactive intestinal polypeptide (VIP) neurons in the SCN display photoperiod-induced neurotransmitter plasticity. In vivo recording of calcium dynamics revealed that NMS neurons alter PVN network activity in response to winter-like photoperiod. Chronic manipulation of NMS neurons is sufficient to induce neurotransmitter switching in PVN neurons and affects locomotor activity. Our findings reveal previously unidentified molecular adaptations of the SCN-PVN network in response to seasonality and the role for NMS neurons in adjusting hypothalamic function to day length via a coordinated multisynaptic neurotransmitter switching affecting behavior.
Science translational medicine
2022 Feb 09
Liu, J;Trefry, JC;Babka, AM;Schellhase, CW;Coffin, KM;Williams, JA;Raymond, JLW;Facemire, PR;Chance, TB;Davis, NM;Scruggs, JL;Rossi, FD;Haddow, AD;Zelko, JM;Bixler, SL;Crozier, I;Iversen, PL;Pitt, ML;Kuhn, JH;Palacios, G;Zeng, X;
PMID: 35138912 | DOI: 10.1126/scitranslmed.abi5229
Effective therapeutics have been developed against acute Ebola virus disease (EVD) in both humans and experimentally infected nonhuman primates. However, the risk of viral persistence and associated disease recrudescence in survivors receiving these therapeutics remains unclear. In contrast to rhesus macaques that survived Ebola virus (EBOV) exposure in the absence of treatment, we discovered that EBOV, despite being cleared from all other organs, persisted in the brain ventricular system of rhesus macaque survivors that had received monoclonal antibody (mAb) treatment. In mAb-treated macaque survivors, EBOV persisted in macrophages infiltrating the brain ventricular system, including the choroid plexuses. This macrophage infiltration was accompanied by severe tissue damage, including ventriculitis, choroid plexitis, and meningoencephalitis. Specifically, choroid plexus endothelium-derived EBOV infection led to viral persistence in the macaque brain ventricular system. This resulted in apoptosis of ependymal cells, which constitute the blood-cerebrospinal fluid barrier of the choroid plexuses. Fatal brain-confined recrudescence of EBOV infection manifested as severe inflammation, local pathology, and widespread infection of the ventricular system and adjacent neuropil in some of the mAb-treated macaque survivors. This study highlights organ-specific EBOV persistence and fatal recrudescent disease in rhesus macaque survivors after therapeutic treatment and has implications for the long-term follow-up of human survivors of EVD.
Progress in retinal and eye research
2021 Dec 28
Lewandowski, D;Sander, CL;Tworak, A;Gao, F;Xu, Q;Skowronska-Krawczyk, D;
PMID: 34971765 | DOI: 10.1016/j.preteyeres.2021.101037
The retinal pigment epithelium-photoreceptor interphase is renewed each day in a stunning display of cellular interdependence. While photoreceptors use photosensitive pigments to convert light into electrical signals, the RPE supports photoreceptors in their function by phagocytizing shed photoreceptor tips, regulating the blood retina barrier, and modulating inflammatory responses, as well as regenerating the 11-cis-retinal chromophore via the classical visual cycle. These processes involve multiple protein complexes, tightly regulated ligand-receptors interactions, and a plethora of lipids and protein-lipids interactions. The role of lipids in maintaining a healthy interplay between the RPE and photoreceptors has not been fully delineated. In recent years, novel technologies have resulted in major advancements in understanding several facets of this interplay, including the involvement of lipids in phagocytosis and phagolysosome function, nutrient recycling, and the metabolic dependence between the two cell types. In this review, we aim to integrate the complex role of lipids in photoreceptor and RPE function, emphasizing the dynamic exchange between the cells as well as discuss how these processes are affected in aging and retinal diseases.
Acta neuropathologica
2021 Dec 03
Seeker, LA;Williams, A;
PMID: 34860266 | DOI: 10.1007/s00401-021-02390-4
It is the centenary of the discovery of oligodendrocytes and we are increasingly aware of their importance in the functioning of the brain in development, adult learning, normal ageing and in disease across the life course, even in those diseases classically thought of as neuronal. This has sparked more interest in oligodendroglia for potential therapeutics for many neurodegenerative/neurodevelopmental diseases due to their more tractable nature as a renewable cell in the central nervous system. However, oligodendroglia are not all the same. Even from the first description, differences in morphology were described between the cells. With advancing techniques to describe these differences in human tissue, the complexity of oligodendroglia is being discovered, indicating apparent functional differences which may be of critical importance in determining vulnerability and response to disease, and targeting of potential therapeutics. It is timely to review the progress we have made in discovering and understanding oligodendroglial heterogeneity in health and neuropathology.
The role of endoplasmic reticulum stress in astrocytes
Glia
2021 Aug 31
Sims, SG;Cisney, RN;Lipscomb, MM;Meares, GP;
PMID: 34462963 | DOI: 10.1002/glia.24082
Astrocytes are glial cells that support neurological function in the central nervous system (CNS), in part, by providing structural support for neuronal synapses and blood vessels, participating in electrical and chemical transmission, and providing trophic support via soluble factors. Dysregulation of astrocyte function contributes to neurological decline in CNS diseases. Neurological diseases are highly heterogeneous but share common features of cellular stress including the accumulation of misfolded proteins. Endoplasmic reticulum (ER) stress has been reported in nearly all neurological and neurodegenerative diseases. ER stress occurs when there is an accumulation of misfolded proteins in the ER lumen and the protein folding demand of the ER is overwhelmed. ER stress initiates the unfolded protein response (UPR) to restore homeostasis by abating protein translation and, if the cell is irreparably damaged, initiating apoptosis. Although protein aggregation and misfolding in neurological disease has been well described, cell-specific contributions of ER stress and the UPR in physiological and disease states are poorly understood. Recent work has revealed a role for active UPR signaling that may drive astrocytes toward a maladaptive phenotype in various model systems. In response to ER stress, astrocytes produce inflammatory mediators, have reduced trophic support, and can transmit ER stress to other cells. This review will discuss the current known contributions and consequences of activated UPR signaling in astrocytes.
Myomixer is expressed during embryonic and post-larval hyperplasia, muscle regeneration and differentiation of myoblats in rainbow trout (Oncorhynchus mykiss)
Gene
2021 Jul 20
Perello-Amoros, M;Rallière, C;Gutiérrez, J;Gabillard, JC;
PMID: 33961974 | DOI: 10.1016/j.gene.2021.145688
In contrast to mice or zebrafish, trout exhibits post-larval muscle growth through hypertrophy and formation of new myofibers (hyperplasia). The muscle fibers are formed by the fusion of mononucleated cells (myoblasts) regulated by several muscle-specific proteins such as Myomaker or Myomixer. In this work, we identified a unique gene encoding a Myomixer protein of 77 amino acids (aa) in the trout genome. Sequence analysis and phylogenetic tree showed moderate conservation of the overall protein sequence across teleost fish (61% of aa identity between trout and zebrafish Myomixer sequences). Nevertheless, the functionally essential motif, AxLyCxL is perfectly conserved in all studied sequences of vertebrates. Using in situ hybridization, we observed that myomixer was highly expressed in the embryonic myotome, particularly in the hyperplasic area. Moreover, myomixer remained readily expressed in white muscle of juvenile (1 and 20 g) although its expression decreased in mature fish. We also showed that myomixer is up-regulated during muscle regeneration and in vitro myoblasts differentiation. Together, these data indicate that myomixer expression is consistently associated with the formation of new myofibers during somitogenesis, post-larval growth and muscle regeneration in trout.
GPR151 in nociceptors modulates neuropathic pain via regulating P2X3 function and microglial activation
Brain : a journal of neurology
2021 Jul 09
Xia, LP;Luo, H;Ma, Q;Xie, YK;Li, W;Hu, H;Xu, ZZ;
PMID: 34244727 | DOI: 10.1093/brain/awab245
Neuropathic pain is a major health problem that affects up to 7-10% of the population worldwide. Currently, neuropathic pain is difficult to treat due to its elusive mechanisms. Here we report that orphan G protein-coupled receptor 151 (GPR151) in nociceptive sensory neurons controls neuropathic pain induced by nerve injury. GPR151 was mainly expressed in nonpeptidergic C-fiber dorsal root ganglion (DRG) neurons and highly upregulated after nerve injury. Importantly, conditional knockout of Gpr151 in adult nociceptive sensory neurons significantly alleviated chronic constriction injury (CCI)-induced neuropathic pain-like behavior but did not affect basal nociception. Moreover, GPR151 in DRG neurons was required for CCI-induced neuronal hyperexcitability and upregulation of colony-stimulating factor 1 (CSF1), which is necessary for microglial activation in the spinal cord after nerve injury. Mechanistically, GPR151 coupled with P2X3 ion channels and promoted their functional activities in neuropathic pain-like hypersensitivity. Knockout of Gpr151 suppressed P2X3-mediated calcium elevation and spontaneous pain behavior in CCI mice. Conversely, overexpression of Gpr151 significantly enhanced P2X3-mediated calcium elevation and DRG neuronal excitability. Furthermore, knockdown of P2X3 in DRGs reversed CCI-induced CSF1 upregulation, spinal microglial activation, and neuropathic pain-like behavior. Finally, the co-expression of GPR151 and P2X3 was confirmed in small-diameter human DRG neurons, indicating the clinical relevance of our findings. Together, our results suggest that GPR151 in nociceptive DRG neurons plays a key role in the pathogenesis of neuropathic pain and could be a potential target for treating neuropathic pain.
Targeting netrin-3 in small cell lung cancer and neuroblastoma
EMBO molecular medicine
2021 Mar 15
Jiang, S;Richaud, M;Vieugué, P;Rama, N;Delcros, JG;Siouda, M;Sanada, M;Redavid, AR;Ducarouge, B;Hervieu, M;Breusa, S;Manceau, A;Gattolliat, CH;Gadot, N;Combaret, V;Neves, D;Ortiz-Cuaran, S;Saintigny, P;Meurette, O;Walter, T;Janoueix-Lerosey, I;Hofman, P;Mulligan, P;Goldshneider, D;Mehlen, P;Gibert, B;
PMID: 33719214 | DOI: 10.15252/emmm.202012878
The navigation cue netrin-1 is well-documented for its key role in cancer development and represents a promising therapeutic target currently under clinical investigation. Phase 1 and 2 clinical trials are ongoing with NP137, a humanized monoclonal antibody against netrin-1. Interestingly, the epitope recognized by NP137 in netrin-1 shares 90% homology with its counterpart in netrin-3, the closest member to netrin-1 in humans, for which little is known in the field of cancer. Here, we unveiled that netrin-3 appears to be expressed specifically in human neuroblastoma (NB) and small cell lung cancer (SCLC), two subtypes of neuroectodermal/neuroendocrine lineages. Netrin-3 and netrin-1 expression are mutually exclusive, and the former is driven by the MYCN oncogene in NB, and the ASCL-1 or NeuroD1 transcription factors in SCLC. Netrin-3 expression is correlated with disease stage, aggressiveness, and overall survival in NB. Mechanistically, we confirmed the high affinity of netrin-3 for netrin-1 receptors and we demonstrated that netrin-3 genetic silencing or interference using NP137, delayed tumor engraftment, and reduced tumor growth in animal models. Altogether, these data support the targeting of netrin-3 in NB and SCLC.
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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 | |
| 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 | |
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