Probes for INS

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

Probes for INS (4638)
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Parahippocampal latrophilin-2 (ADGRL2) expression controls topographical presubiculum to entorhinal cortex circuit connectivity

Cell reports

2021 Nov 23

Donohue, JD;Amidon, RF;Murphy, TR;Wong, AJ;Liu, ED;Saab, L;King, AJ;Pae, H;Ajayi, MT;Anderson, GR;
PMID: 34818557 | DOI: 10.1016/j.celrep.2021.110031

Brain circuits are comprised of distinct interconnected neurons that are assembled by synaptic recognition molecules presented by defined pre- and post-synaptic neurons. This cell-cell recognition process is mediated by varying cellular adhesion molecules, including the latrophilin family of adhesion G-protein-coupled receptors. Focusing on parahippocampal circuitry, we find that latrophilin-2 (Lphn2; gene symbol ADGRL2) is specifically enriched in interconnected subregions of the medial entorhinal cortex (MEC), presubiculum (PrS), and parasubiculum (PaS). Retrograde viral tracing from the Lphn2-enriched region of the MEC reveals unique topographical patterning of inputs arising from the PrS and PaS that mirrors Lphn2 expression. Using a Lphn2 conditional knockout mouse model, we find that deletion of MEC Lphn2 expression selectively impairs retrograde viral labeling of inputs arising from the ipsilateral PrS. Combined with analysis of Lphn2 expression within the MEC, this study reveals Lphn2 to be selectively expressed by defined cell types and essential for MEC-PrS circuit connectivity.

Single-cell reconstruction with spatial context of migrating neural crest cells and their microenvironments during vertebrate head and neck formation

Development

2021 Nov 15

Morrison, J;McLennan, R;Teddy, J;Scott, A;Kasemeier-Kulesa, J;Gogol, M;Kulesa, P;
| DOI: 10.1242/dev.199468

The dynamics of multipotent neural crest cell differentiation and invasion as cells travel throughout the vertebrate embryo remain unclear. Here, we preserve spatial information to derive the transcriptional states of migrating neural crest cells and the cellular landscape of the first four chick cranial to cardiac branchial arches (BA1-4) using label-free, unsorted single-cell RNA sequencing. The faithful capture of branchial arch-specific genes led to identification of novel markers of migrating neural crest cells and 266 invasion genes common to all BA1-4 streams. Perturbation analysis of a small subset of invasion genes and time-lapse imaging identified their functional role to regulate neural crest cell behaviors. Comparison of the neural crest invasion signature to other cell invasion phenomena revealed a shared set of 45 genes, a subset of which showed direct relevance to human neuroblastoma cell lines analyzed after exposure to the in vivo chick embryonic neural crest microenvironment. Our data define an important spatio-temporal reference resource to address patterning of the vertebrate head and neck, and previously unidentified cell invasion genes with the potential for broad impact.

A proteogenomic portrait of lung squamous cell carcinoma

Cell

2021 Aug 05

Satpathy, S;Krug, K;Jean Beltran, PM;Savage, SR;Petralia, F;Kumar-Sinha, C;Dou, Y;Reva, B;Kane, MH;Avanessian, SC;Vasaikar, SV;Krek, A;Lei, JT;Jaehnig, EJ;Omelchenko, T;Geffen, Y;Bergstrom, EJ;Stathias, V;Christianson, KE;Heiman, DI;Cieslik, MP;Cao, S;Song, X;Ji, J;Liu, W;Li, K;Wen, B;Li, Y;Gümüş, ZH;Selvan, ME;Soundararajan, R;Visal, TH;Raso, MG;Parra, ER;Babur, Ö;Vats, P;Anand, S;Schraink, T;Cornwell, M;Rodrigues, FM;Zhu, H;Mo, CK;Zhang, Y;da Veiga Leprevost, F;Huang, C;Chinnaiyan, AM;Wyczalkowski, MA;Omenn, GS;Newton, CJ;Schurer, S;Ruggles, KV;Fenyö, D;Jewell, SD;Thiagarajan, M;Mesri, M;Rodriguez, H;Mani, SA;Udeshi, ND;Getz, G;Suh, J;Li, QK;Hostetter, G;Paik, PK;Dhanasekaran, SM;Govindan, R;Ding, L;Robles, AI;Clauser, KR;Nesvizhskii, AI;Wang, P;Carr, SA;Zhang, B;Mani, DR;Gillette, MA;Clinical Proteomic Tumor Analysis Consortium, ;
PMID: 34358469 | DOI: 10.1016/j.cell.2021.07.016

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.

SALM4 negatively regulates NMDA receptor function and fear memory consolidation

Communications biology

2021 Sep 29

Lie, E;Yeo, Y;Lee, EJ;Shin, W;Kim, K;Han, KA;Yang, E;Choi, TY;Bae, M;Lee, S;Um, SM;Choi, SY;Kim, H;Ko, J;Kim, E;
PMID: 34588597 | DOI: 10.1038/s42003-021-02656-3

Many synaptic adhesion molecules positively regulate synapse development and function, but relatively little is known about negative regulation. SALM4/Lrfn3 (synaptic adhesion-like molecule 4/leucine rich repeat and fibronectin type III domain containing 3) inhibits synapse development by suppressing other SALM family proteins, but whether SALM4 also inhibits synaptic function and specific behaviors remains unclear. Here we show that SALM4-knockout (Lrfn3-/-) male mice display enhanced contextual fear memory consolidation (7-day post-training) but not acquisition or 1-day retention, and exhibit normal cued fear, spatial, and object-recognition memory. The Lrfn3-/- hippocampus show increased currents of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors (GluN2B-NMDARs), but not α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors (AMPARs), which requires the presynaptic receptor tyrosine phosphatase PTPσ. Chronic treatment of Lrfn3-/- mice with fluoxetine, a selective serotonin reuptake inhibitor used to treat excessive fear memory that directly inhibits GluN2B-NMDARs, normalizes NMDAR function and contextual fear memory consolidation in Lrfn3-/- mice, although the GluN2B-specific NMDAR antagonist ifenprodil was not sufficient to reverse the enhanced fear memory consolidation. These results suggest that SALM4 suppresses excessive GluN2B-NMDAR (not AMPAR) function and fear memory consolidation (not acquisition).

Spiny mice activate unique transcriptional programs after severe kidney injury regenerating organ function without fibrosis

iScience

2021 Nov 01

Okamura, D;Brewer, C;Wakenight, P;Bahrami, N;Bernardi, K;Tran, A;Olson, J;Shi, X;Yeh, S;Piliponsky, A;Collins, S;Nguyen, E;Timms, A;MacDonald, J;Bammler, T;Nelson, B;Millen, K;Beier, D;Majesky, M;
| DOI: 10.1016/j.isci.2021.103269

Fibrosis-driven solid organ failure is an enormous burden on global health. Spiny mice (Acomys) are terrestrial mammals that can regenerate severe skin wounds without scars to avoid predation. Whether spiny mice also regenerate internal organ injuries is unknown. Here, we show that despite equivalent acute obstructive or ischemic kidney injury, spiny mice fully regenerate nephron structure and organ function without fibrosis, whereas C57Bl/6 or CD1 mice progress to complete organ failure with extensive renal fibrosis. Two mechanisms for vertebrate regeneration have been proposed that emphasize either extrinsic (pro-regenerative macrophages) or intrinsic (surviving cells of the organ itself) controls. Comparative transcriptome analysis revealed that the Acomys genome appears poised at the time of injury to initiate regeneration by surviving kidney cells, whereas macrophage accumulation was not detected until about day 7. Thus, we provide evidence for rapid activation of a gene expression signature for regenerative wound healing in the spiny mouse kidney.

Glucokinase neurons of the paraventricular nucleus of the thalamus sense glucose and decrease food consumption

iScience

2021 Oct 01

Kessler, S;Labouèbe, G;Croizier, S;Gaspari, S;Tarussio, D;Thorens, B;
| DOI: 10.1016/j.isci.2021.103122

The paraventricular nucleus of the thalamus (PVT) controls goal-oriented behavior through its connections to the nucleus accumbens (NAc). We previously characterized Glut2aPVT neurons that are activated by hypoglycemia, and which increase sucrose seeking behavior through their glutamatergic projections to the NAc. Here, we identified glucokinase (Gck)-expressing neurons of the PVT (GckaPVT) and generated a mouse line expressing the Cre recombinase from the glucokinase locus (GckCre/+ mice). Ex vivo calcium imaging and whole-cell patch clamp recordings revealed that GckaPVT neurons that project to the NAc were mostly activated by hyperglycemia. Their chemogenetic inhibition or optogenetic stimulation, respectively, enhanced food intake or decreased sucrose-seeking behavior. Collectively, our results describe a neuronal population of Gck-expressing neurons in the PVT, which has opposite glucose sensing properties and control over feeding behavior than the previously characterized Glut2aPVT neurons. This study allows a better understanding of the complex regulation of feeding behavior by the PVT.

Epithelial STAT6 O-GlcNAcylation Drives Anti-Helminth Immunity via a Concerted Alarmin Response

SSRN Electronic Journal

2021 Sep 08

Zhao, M;Ren, K;Xiong, X;Xin, Y;Kim, A;Maynard, J;Zou, Y;Battist, A;Koneripalli, N;Huang, Z;Zhang, Z;Yu, J;Wang, H;Salgado, O;Hogquist, K;Revelo, X;Burlingame, A;Gao, X;Lin, Z;von Moltke, J;Ruan, H;
| DOI: 10.2139/ssrn.3917158

The epithelium is an integral component of mucosal barrier and host immunity. Following helminth parasite infection, the intestinal epithelial cells secrete "alarmin” cytokines, such as interleukin (IL)-25 and IL-33, to initiate the type 2 immune responses for helminth expulsion and tolerance. However, it is unknown how helminth infection and the resulting type 2 cytokine milieu drive epithelial remodeling and orchestrate alarmin secretion. Here we report that, intestinal epithelial O-linked N-Acetylglucosamine (O-GlcNAc) protein modification is induced upon helminth infections. By modifying and activating STAT6, O-GlcNAc transferase (OGT) promotes the transcription of lineage-defining transcription factor _Pou2f3_ in tuft cell differentiation and IL-25 production. Meanwhile, STAT6 O-GlcNAcylation activates the expression of _Gsdmc_ family genes. The resulting membrane pore formed by GSDMC facilitates the unconventional secretion of IL-33 from goblet cells. GSDMC-mediated IL-33 secretion is indispensable for the host to mount effective antihelminth immunity and support intestinal homeostasis. Protein O-GlcNAcylation can be harnessed for the future treatment of type 2 inflammation-associated human diseases.

Avances en citometría de masas y aplicabilidad en patología digital para estudios clínico-traslacionales en oncología

Advances in Laboratory Medicine / Avances en Medicina de Laboratorio

2021 Aug 25

Cereceda, K;Jorquera, R;Villarroel-Espíndola, F;
| DOI: 10.1515/almed-2021-0051

Resumen El desarrollo de la citometría de masas y posteriormente su adaptación para el análisis de secciones histológicas ha revolucionado la forma de caracterizar a nivel espacial múltiples componentes de manera simultánea, permitiendo la correlación genotípica y fenotípica de la célula y su entorno durante estudios clínicos-traslaciones. En este trabajo, hemos revisado los hitos más relevantes en el desarrollo, implementación y aplicabilidad del análisis de imágenes de componentes múltiples para el estudio de cáncer y otras dolencias, y enfocado nuestro interés que aquellos autores que utilizan imágenes obtenidas mediante citometría de masas o bien haz de iones. Esta revisión tiene como objetivo que el lector se familiarice con las estrategias técnicas de verificación de la herramienta y las múltiples posibilidades de uso abordadas por diferentes autores, y además, poder proyectar sus propias investigaciones hacia la utilización de imágenes obtenidas por citometría de masas (IMC), o imágenes por haz de iones multiplexados (MIBI) en cualquiera de los campos de investigación biomédica.

TRESK channel contributes to depolarization-induced shunting inhibition and modulates epileptic seizures

Cell reports

2021 Jul 20

Huang, W;Ke, Y;Zhu, J;Liu, S;Cong, J;Ye, H;Guo, Y;Wang, K;Zhang, Z;Meng, W;Gao, TM;Luhmann, HJ;Kilb, W;Chen, R;
PMID: 34289346 | DOI: 10.1016/j.celrep.2021.109404

Glutamatergic and GABAergic synaptic transmission controls excitation and inhibition of postsynaptic neurons, whereas activity of ion channels modulates neuronal intrinsic excitability. However, it is unclear how excessive neuronal excitation affects intrinsic inhibition to regain homeostatic stability under physiological or pathophysiological conditions. Here, we report that a seizure-like sustained depolarization can induce short-term inhibition of hippocampal CA3 neurons via a mechanism of membrane shunting. This depolarization-induced shunting inhibition (DShI) mediates a non-synaptic, but neuronal intrinsic, short-term plasticity that is able to suppress action potential generation and postsynaptic responses by activated ionotropic receptors. We demonstrate that the TRESK channel significantly contributes to DShI. Disruption of DShI by genetic knockout of TRESK exacerbates the sensitivity and severity of epileptic seizures of mice, whereas overexpression of TRESK attenuates seizures. In summary, these results uncover a type of homeostatic intrinsic plasticity and its underlying mechanism. TRESK might represent a therapeutic target for antiepileptic drugs.

Spatiotemporal dynamics of inner ear sensory and non-sensory cells revealed by single-cell transcriptomics

Cell reports

2021 Jul 13

Jan, TA;Eltawil, Y;Ling, AH;Chen, L;Ellwanger, DC;Heller, S;Cheng, AG;
PMID: 34260939 | DOI: 10.1016/j.celrep.2021.109358

The utricle is a vestibular sensory organ that requires mechanosensitive hair cells to detect linear acceleration. In neonatal mice, new hair cells are derived from non-sensory supporting cells, yet cell type diversity and mechanisms of cell addition remain poorly characterized. Here, we perform computational analyses on single-cell transcriptomes to categorize cell types and resolve 14 individual sensory and non-sensory subtypes. Along the periphery of the sensory epithelium, we uncover distinct groups of transitional epithelial cells, marked by Islr, Cnmd, and Enpep expression. By reconstructing de novo trajectories and gene dynamics, we show that as the utricle expands, Islr+ transitional epithelial cells exhibit a dynamic and proliferative phase to generate new supporting cells, followed by coordinated differentiation into hair cells. Taken together, our study reveals a sequential and coordinated process by which non-sensory epithelial cells contribute to growth of the postnatal mouse sensory epithelium.

Specialized endothelial tip cells guide neuroretina vascularization and blood-retina-barrier formation

Developmental cell

2021 Jul 12

Zarkada, G;Howard, JP;Xiao, X;Park, H;Bizou, M;Leclerc, S;Künzel, SE;Boisseau, B;Li, J;Cagnone, G;Joyal, JS;Andelfinger, G;Eichmann, A;Dubrac, A;
PMID: 34273276 | DOI: 10.1016/j.devcel.2021.06.021

Endothelial tip cells guiding tissue vascularization are primary targets for angiogenic therapies. Whether tip cells require differential signals to develop their complex branching patterns remained unknown. Here, we show that diving tip cells invading the mouse neuroretina (D-tip cells) are distinct from tip cells guiding the superficial retinal vascular plexus (S-tip cells). D-tip cells have a unique transcriptional signature, including high TGF-β signaling, and they begin to acquire blood-retina barrier properties. Endothelial deletion of TGF-β receptor I (Alk5) inhibits D-tip cell identity acquisition and deep vascular plexus formation. Loss of endothelial ALK5, but not of the canonical SMAD effectors, leads to aberrant contractile pericyte differentiation and hemorrhagic vascular malformations. Oxygen-induced retinopathy vasculature exhibits S-like tip cells, and Alk5 deletion impedes retina revascularization. Our data reveal stage-specific tip cell heterogeneity as a requirement for retinal vascular development and suggest that non-canonical-TGF-β signaling could improve retinal revascularization and neural function in ischemic retinopathy.

Spatial and cell type transcriptional landscape of human cerebellar development

Nature neuroscience

2021 Jun 17

Aldinger, KA;Thomson, Z;Phelps, IG;Haldipur, P;Deng, M;Timms, AE;Hirano, M;Santpere, G;Roco, C;Rosenberg, AB;Lorente-Galdos, B;Gulden, FO;O'Day, D;Overman, LM;Lisgo, SN;Alexandre, P;Sestan, N;Doherty, D;Dobyns, WB;Seelig, G;Glass, IA;Millen, KJ;
PMID: 34140698 | DOI: 10.1038/s41593-021-00872-y

The human neonatal cerebellum is one-fourth of its adult size yet contains the blueprint required to integrate environmental cues with developing motor, cognitive and emotional skills into adulthood. Although mature cerebellar neuroanatomy is well studied, understanding of its developmental origins is limited. In this study, we systematically mapped the molecular, cellular and spatial composition of human fetal cerebellum by combining laser capture microscopy and SPLiT-seq single-nucleus transcriptomics. We profiled functionally distinct regions and gene expression dynamics within cell types and across development. The resulting cell atlas demonstrates that the molecular organization of the cerebellar anlage recapitulates cytoarchitecturally distinct regions and developmentally transient cell types that are distinct from the mouse cerebellum. By mapping genes dominant for pediatric and adult neurological disorders onto our dataset, we identify relevant cell types underlying disease mechanisms. These data provide a resource for probing the cellular basis of human cerebellar development and disease.

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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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