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High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler

Methods in molecular biology (Clifton, N.J.)

2023 May 16

Wang, N;Li, X;Ding, Z;
PMID: 37191791 | DOI: 10.1007/978-1-0716-3163-8_6

The rapid emergence of spatial multi-omics technologies in recent years has revolutionized biomedical research. Among these, the Digital Spatial Profiler (DSP, commercialized by nanoString) has become one of the dominant technologies in spatial transcriptomics and proteomics and has assisted in deconvoluting complex biological questions. Based on our practical experience in the past 3 years with DSP, we share here a detailed hands-on protocol and key handling notes that will allow the broader community to optimize their work procedure.
Peripheral CCL2-CCR2 signalling contributes to chronic headache-related sensitization

Brain : a journal of neurology

2023 Jun 07

Ryu, S;Liu, X;Guo, T;Guo, Z;Zhang, J;Cao, YQ;
PMID: 37284790 | DOI: 10.1093/brain/awad191

Migraine, especially chronic migraine, is highly debilitating and still lacks effective treatment. The persistent headache arises from activation and sensitization of primary afferent neurons in the trigeminovascular pathway, but the underlying mechanisms remain incompletely understood. Animal studies indicate that signaling through chemokine C-C motif ligand 2 (CCL2) and C-C motif chemokine receptor 2 (CCR2) mediates the development of chronic pain after tissue or nerve injury. Some migraine patients had elevated CCL2 levels in CSF or cranial periosteum. However, whether the CCL2-CCR2 signaling pathway contributes to chronic migraine is not clear. Here, we modeled chronic headache with repeated administration of nitroglycerin (NTG, a reliable migraine trigger in migraineurs) and found that both Ccl2 and Ccr2 mRNA were upregulated in dura and trigeminal ganglion (TG) tissues that are implicated in migraine pathophysiology. In Ccl2 and Ccr2 global knockout mice, repeated NTG administration did not evoke acute or persistent facial skin hypersensitivity as in wild-type mice. Intraperitoneal injection of CCL2 neutralizing antibodies inhibited chronic headache-related behaviors induced by repeated NTG administration and repetitive restraint stress, suggesting that the peripheral CCL2-CCR2 signaling mediates headache chronification. We found that CCL2 was mainly expressed in TG neurons and cells associated with dura blood vessels, whereas CCR2 was expressed in subsets of macrophages and T cells in TG and dura but not in TG neurons under both control and disease states. Deletion of Ccr2 gene in primary afferent neurons did not alter NTG-induced sensitization, but eliminating CCR2 expression in either T cells or myeloid cells abolished NTG-induced behaviors, indicating that both CCL2-CCR2 signaling in T cells and macrophages are required to establish chronic headache-related sensitization. At cellular level, repeated NTG administration increased the number of TG neurons that responded to calcitonin-gene-related peptide (CGRP) and pituitary adenylate cyclase-activating polypeptide (PACAP) as well as the production of CGRP in wild-type but not Ccr2 global knockout mice. Lastly, co-administration of CCL2 and CGRP neutralizing antibodies was more effective in reversing NTG-induced behaviors than individual antibodies. Taken together, these results suggest that migraine triggers activate CCL2-CCR2 signaling in macrophages and T cells. This consequently enhances both CGRP and PACAP signaling in TG neurons, ultimately leading to persistent neuronal sensitization underlying chronic headache. Our work not only identifies the peripheral CCL2 and CCR2 as potential targets for chronic migraine therapy, but also provides proof-of-concept that inhibition of both peripheral CGRP and CCL2-CCR2 signaling is more effective than targeting either pathway alone.
Distinct immune modulatory roles of regulatory T cells in gut versus joint inflammation in TNF-driven spondyloarthritis

Annals of the rheumatic diseases

2023 May 17

Venken, K;Jarlborg, M;Decruy, T;Mortier, C;Vlieghe, C;Gilis, E;De Craemer, AS;Coudenys, J;Cambré, I;Fleury, D;Klimowicz, A;Van den Bosch, F;Hoorens, A;Lobaton, T;de Roock, S;Sparwasser, T;Nabozny, G;Jacques, P;Elewaut, D;
PMID: 37197892 | DOI: 10.1136/ard-2022-223757

Gut and joint inflammation commonly co-occur in spondyloarthritis (SpA) which strongly restricts therapeutic modalities. The immunobiology underlying differences between gut and joint immune regulation, however, is poorly understood. We therefore assessed the immunoregulatory role of CD4+FOXP3+ regulatory T (Treg) cells in a model of Crohn's-like ileitis and concomitant arthritis.RNA-sequencing and flow cytometry was performed on inflamed gut and joint samples and tissue-derived Tregs from tumour necrosis factor (TNF)∆ARE mice. In situ hybridisation of TNF and its receptors (TNFR) was applied to human SpA gut biopsies. Soluble TNFR (sTNFR) levels were measured in serum of mice and patients with SpA and controls. Treg function was explored by in vitro cocultures and in vivo by conditional Treg depletion.Chronic TNF exposure induced several TNF superfamily (TNFSF) members (4-1BBL, TWEAK and TRAIL) in synovium and ileum in a site-specific manner. Elevated TNFR2 messenger RNA levels were noted in TNF∆ARE/+ mice leading to increased sTNFR2 release. Likewise, sTNFR2 levels were higher in patients with SpA with gut inflammation and distinct from inflammatory and healthy controls. Tregs accumulated at both gut and joints of TNF∆ARE mice, yet their TNFR2 expression and suppressive function was significantly lower in synovium versus ileum. In line herewith, synovial and intestinal Tregs displayed a distinct transcriptional profile with tissue-restricted TNFSF receptor and p38MAPK gene expression.These data point to profound differences in immune-regulation between Crohn's ileitis and peripheral arthritis. Whereas Tregs control ileitis they fail to dampen joint inflammation. Synovial resident Tregs are particularly maladapted to chronic TNF exposure.
Expression of Cav-1, MCT1, and MCT4 in Ductal Carcinoma In Situ of the Breast and Their Associations With Clinicopathologic Features

Applied immunohistochemistry & molecular morphology : AIMM

2023 Feb 24

Kim, NI;Park, MH;Lee, JS;
PMID: 36867736 | DOI: 10.1097/PAI.0000000000001106

Loss of caveolin-1 (Cav-1) and upregulation of monocarboxylate transporters (MCTs, especially MCT1 and MCT4) in respectively tumor-associated stromal cells and malignant epithelial cells of invasive carcinoma have been found to play an important role in the metabolic coupling. However, this phenomenon has only been scarcely described in pure ductal carcinoma in situ (DCIS) of the breast. mRNA and protein expression levels of Cav-1, MCT1, and MCT4 in nine pairs of DCIS tissues and matched normal tissues were examined by quantitative real-time polymerase chain reaction, RNAscope in situ hybridization, and immunohistochemistry. Immunohistochemical staining of Cav-1, MCT1, and MCT4 in 79 DCIS samples was also done using tissue microarray. Cav-1 mRNA expression was significantly lower in DCIS tissues than in their corresponding normal tissues. In contrast, MCT1 and MCT4 mRNA expression levels were higher in DCIS tissues than in corresponding normal tissues. Low stromal Cav-1 expression was significantly associated with high nuclear grade. High epithelial MCT4 expression was associated with larger tumor size and human epidermal growth factor 2 positivity. At a mean follow-up of 10 years, patients with high epithelial MCT1/high epithelial MCT4 expression showed shorter disease-free survival than those with other expressions. No significant association was observed between stromal Cav-1 expression and epithelial MCT 1 or MCT4 expression. Changes in Cav-1, MCT1, and MCT4 are associated with carcinogenesis of DCIS. A high epithelial MCT1/high epithelial MCT4 expression might be associated with a more aggressive phenotype.
Enhanced AMPAR-dependent synaptic transmission by S-nitrosylation in the vmPFC contributes to chronic inflammatory pain-induced persistent anxiety in mice

Acta pharmacologica Sinica

2022 Dec 02

Chen, ZJ;Su, CW;Xiong, S;Li, T;Liang, HY;Lin, YH;Chang, L;Wu, HY;Li, F;Zhu, DY;Luo, CX;
PMID: 36460834 | DOI: 10.1038/s41401-022-01024-z

Chronic pain patients often have anxiety disorders, and some of them suffer from anxiety even after analgesic administration. In this study, we investigated the role of AMPAR-mediated synaptic transmission in the ventromedial prefrontal cortex (vmPFC) in chronic pain-induced persistent anxiety in mice and explored potential drug targets. Chronic inflammatory pain was induced in mice by bilateral injection of complete Freund's adjuvant (CFA) into the planta of the hind paws; anxiety-like behaviours were assessed with behavioural tests; S-nitrosylation and AMPAR-mediated synaptic transmission were examined using biochemical assays and electrophysiological recordings, respectively. We found that CFA induced persistent upregulation of AMPAR membrane expression and function in the vmPFC of anxious mice but not in the vmPFC of non-anxious mice. The anxious mice exhibited higher S-nitrosylation of stargazin (an AMPAR-interacting protein) in the vmPFC. Inhibition of S-nitrosylation by bilaterally infusing an exogenous stargazin (C302S) mutant into the vmPFC rescued the surface expression of GluA1 and AMPAR-mediated synaptic transmission as well as the anxiety-like behaviours in CFA-injected mice, even after ibuprofen treatment. Moreover, administration of ZL006, a small molecular inhibitor disrupting the interaction of nNOS and PSD-95 (20 mg·kg-1·d-1, for 5 days, i.p.), significantly reduced nitric oxide production and S-nitrosylation of AMPAR-interacting proteins in the vmPFC, resulting in anxiolytic-like effects in anxious mice after ibuprofen treatment. We conclude that S-nitrosylation is necessary for AMPAR trafficking and function in the vmPFC under chronic inflammatory pain-induced persistent anxiety conditions, and nNOS-PSD-95 inhibitors could be potential anxiolytics specific for chronic inflammatory pain-induced persistent anxiety after analgesic treatment.
The Edinger-Westphal nucleus: sex differences in midbrain neuropeptide control of binge drinking

Alcohol

2023 Jun 01

Walker, L;Shesham, A;Maddern, X;Ch’ng, S;Reed, F;Giardino, W;Lawrence, A;
| DOI: 10.1016/j.alcohol.2023.03.045

The circuitry mediating excessive alcohol consumption includes the understudied central projecting Edinger-Westphal (EWcp); a structure dense in neuropeptide expression, including cocaine and amphetamine regulated transcript (CART). While studies have shown a critical role for this nucleus in alcohol consumption, few studies have interrogated the contributions of distinct EW populations. To examine a functional role of these cells in binge drinking we used chemogenetics to inhibit EWcpCART cells in male or female CART-Cre mice. Chemogenetic inhibition of EWcpCART cells had no effect on binge drinking, anxiety behaviour or other consummatory behaviours in male mice; however, a specific reduction in alcohol binge drinking was observed in female mice. Using RNAscope we examined the neurochemistry of EWCART cells observing strong overlap with the ghrelin receptor (GHSR). Given the dense expression of GHSR on EWCART cells we examined whether CART-GHSR interactions within the EWcp mediate binge drinking in female mice. Ghrelin administration increased binge drinking in female mice, which was reduced by chemogenetic inhibition of EWcpCART cells. Finally, we knocked down GHSR expression non-specifically in the EW of male and female mice using a shRNA and specifically from CART (CART-Cre) and glutamatergic (vGlut2-Cre) populations using Cre-dependent Ghsr-shRNA. Non-specific EW Ghsr-shRNA knockdown reduced binge drinking specifically in female, but not male mice compared to scram-ShRNA controls. Further in female mice, Ghsr-shRNA localised to EWCART, but not EWvGlut2 cells reduced binge drinking. Together, our results suggest the EWcp is a region mediating excessive alcohol bingeing through GHSR and CART interactions in female mice. Given the recent clinical success of GHSR1a inverse agonists to treat AUD, understanding the neural mechanism(s) underpinning how the ghrelin system mediates alcohol consumption are critical.
Cannabinoid CB2 receptors modulate alcohol induced behavior, and neuro-immune dysregulation in mice

Behavioural brain research

2023 Apr 14

Kibret, BG;Roberts, A;Kneebone, A;Embaby, S;Fernandez, J;Liu, QR;Onaivi, ES;
PMID: 37061199 | DOI: 10.1016/j.bbr.2023.114439

The identification of additional lipid mediators, enzymes, and receptors revealed an expanded endocannabinoid system (ECS) called the endocannabinoidome (eCBome). Furthermore, eCBome research using wild type and genetically modified mice indicate the involvement of this system in modulating alcohol induced neuroinflammatory alterations associated with behavioral impairments and the release of proinflammatory cytokines. We investigated the role of cannabinoid type 2 receptors (CB2Rs) in modulating behavioral and neuro-immune changes induced by alcohol using conditional knockout (cKO) mice with selective deletion of CB2Rs in dopamine neurons (DAT-Cnr2) and in microglia (Cx3Cr1-Cnr2) cKO mice. We used a battery of behavioral tests including locomotor and wheel running activity, rotarod performance test, and alcohol preference tests to evaluate behavioral changes induced by alcohol. ELISA assay was used, to detect alterations in IL-6, IL-1α, and IL-1β in the prefrontal cortex, striatum, and hippocampal regions of mice to investigate the role of CB2Rs in neuroinflammation induced by alcohol in the brain. The involvement of cannabinoid receptors in alcohol-induced behavior was also evaluated using the non-selective cannabinoid receptor mixed agonist WIN 55,212-2. The results showed that cell-type specific deletion of CB2Rs in dopamine neurons and microglia significantly and differentially altered locomotor activity and rotarod performance activities. The result also revealed that cell-type specific deletion of CB2Rs enhanced alcohol-induced inflammation, and WIN significantly reduced alcohol preference in all genotypes compared to the vehicle controls. These findings suggest that the involvement of CB2Rs in modulating behavioral and neuroinflammatory alterations induced by alcohol may be potential therapeutic targets in the treatment of alcohol use disorder.
NCI-41356, a promising small inhibitor of HSPB5 in idiopathic pulmonary fibrosis?

Revue des Maladies Respiratoires

2023 Feb 01

Tanguy, J;Boutanquoi, P;Dondaine, L;Burgy, O;Bellaye, P;Beltramo, G;Garrido, C;Bonniaud, P;Goirand, F;
| DOI: 10.1016/j.rmr.2022.11.068

Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive and lethal disease of unknown aetiology. In France, it ranks among the most frequent interstitial pathologies and affects 6 out of 8 people per 100,000 each year. IPF is characterized by dysregulated healing mechanisms that leads to the accumulation of large amounts of collagen in the lung tissue that disrupts the alveolar architecture. Nintedanib and Pirfenidone are the only currently available treatments even though they are only able to slow down the disease without being curative. In this context, inhibiting HSPB5, a low molecular weight heat shock protein known to be involved in the development of fibrosis, could constitute a potential therapeutic target. Our aim consist to explore how NCI-41356 (a chemical inhibitor of HSPB5) can limit the development of pulmonary fibrosis. Methods In vivo, fibrosis was assessed in mice injected intratracheally (i.t.) with Bleomycin (BLM) and treated with NaCl or NCI-41356 (3 times i.t. or 3 times a week i.v.). Fibrosis was evaluated by collagen quantification (Sircol, Sirius Red staining), Immunofluorescence, TGF-β gene expression (RNAscope). In vitro, TGF-β1 signaling was evaluated in epithelial cells treated by TGF-β1 with or without NCI-41356 (Western Blot, Immunofluorescence, Proximity ligation assay). Results In vivo, NCI-41356 reduced the accumulation of collagen, the expression of TGF-β1 and several pro-fibrotic markers (PAI-1, α-SMA). In vitro, NCI-41356 decreased the interaction between HSPB5 and SMAD4 explaining NCI-41356 anti-fibrotic properties. Conclusion In this study, we determined that inhibition of HSPB5/SMAD4 could limit IPF in mice. NCI-41356 modulates SMAD4 nuclear translocation thus limiting TGF-β1 signaling and synthesis of collagen and pro-fibrotic markers. Further investigations with human fibrotic lung tissues are needed to determine if these results can be transposed in human.
The Epidemiology of Invasive, Multipleantibiotic-resistant Klebsiella pneumoniae Infection in a Breeding Colony of Immunocompromised NSG Mice

Comparative medicine

2022 Aug 01

Stair, MI;Carrasco, SE;Annamalai, D;Jordan, EB;Mannion, A;Feng, Y;Fabian, N;Ge, Z;Muthupalani, S;Dzink-Fox, J;Krzisch, MA;Fox, JG;
PMID: 35882504 | DOI: 10.30802/AALAS-CM-21-000088

Klebsiella pneumoniae (Kp) is a gram-negative opportunistic pathogen that causes severe pneumonia, pyelonephritis, and sepsis in immunocompromised hosts. During a 4-mo interval, several NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) breeders and pups in our facilities were diagnosed with Kp infections. An initial 6 adult and 1 juvenile NSG mice were submitted for necropsy and histologic examination because of acute onset of diarrhea and death. The evaluation revealed typhlocolitis in 2 of the mice and tritrichomoniasis in all 7. Escherichia coli positive for polyketide synthase (pks+) and Kp were isolated from the intestines. Given a history of sepsis due to pks+ E. coli in NSG mice in our facilities and determination of its antimicrobial susceptibility, trimethoprim-sulfamethoxazole (TMP-SMX) was administered to the colony in the drinking water for 4 wk. After this intervention, an additional 21 mice became ill or died; 11 of these mice had suppurative pneumonia, meningoencephalitis, hepatitis, metritis, pyelonephritis, or sepsis. Kp was cultured from pulmonary abscesses or blood of 10 of the mice. Whole-genome sequencing (WGS) indicated that the Kp isolates contained genes associated with phenotypes found in pore-forming Kp isolates cultured from humans with ulcerative colitis and primary sclerosing cholangitis. None of the Kp isolates exhibited a hyperviscous phenotype, but 13 of 14 were resistant to TMP-SMX. Antimicrobial susceptibility testing indicated sensitivity of the Kp to enrofloxacin, which was administered in the drinking water. Antibiotic sensitivity profiles were confirmed by WGS of the Kp strains; key virulence and resistance genes to quaternary ammonia compounds were also identified. Enrofloxacin treatment resulted in a marked reduction in mortality, and the study using the NSG mice was completed successfully. Our findings implicate intestinal translocation of Kp as the cause of pneumonia and systemic infections in NSG mice and highlight the importance of identification of enteric microbial pathogens and targeted antibiotic selection when treating bacterial infections in immunocompromised mice.
BS19 Histone deacetylase 6 inhibition induces dna damage accumulation in aortic smooth muscle cells

Basic science

2022 Jun 01

Solanki, R;Warren, D;Johnson, R;
| DOI: 10.1136/heartjnl-2022-bcs.199

Rationale DNA damage accumulation is a hallmark of vascular smooth muscle cell (VSMC) ageing. Importantly, VSMC DNA damage accumulation and ageing has been implicated in the progression of cardiovascular disease (CVD), including atherosclerosis and vascular calcification. Chemotherapy drugs used in the treatment of many cancers are known to induce DNA damage in cardiovascular cells and accelerate CVD. Histone deacetylase (HDAC) inhibitors are drugs being investigated for novel treatments of many cancers. HDACs perform many vital functions in cells; HDAC6 is known to deacetylate alpha-tubulin to regulate microtubule stability and flexibility. We have recently shown that microtubule stability regulates both VSMC morphology and contractility. Therefore, in this study we investigate the impact of HDAC6 inhibition upon VSMC function. Methodology We use polyacrylamide hydrogels (PAHs) of physiological aortic stiffness to investigate the impact of HDAC6 inhibition on the contractile response of angiotensin II stimulated quiescent VSMC function. In this study, we utilise HDAC6 inhibitor BRD 9757 and Tubastatin a HDAC6 inhibitor inducing tubulin hyperacetylation. Results Our data shows that HDAC6 inhibition resulted in increased alpha-tubulin acetylation and decreased VSMC area. Further analysis revealed that although VSMC volume was unaltered, nuclear volume was decreased. Immunofluorescence microscopy revealed that HDAC6 inhibitor treatment resulted in DNA damage accumulation in VSMCs. We hypothesised that altered microtubule stability participated in this phenotype. To test this possibility, we performed a cold-stable microtubule stability assay, which revealed that HDAC6 inhibitor treated VSMCs possessed decreased microtubule stability. To test whether changes in microtubule stability induced DNA damage accumulation, we used the microtubule destabilising agents colchicine and demecholcine, and the microtubule stabilising agent paclitaxel. Importantly, either colchicine or demecholcine treatment increased DNA damage accumulation in VSMCs. In contrast, paclitaxel treatment had no effect on DNA damage levels.
Relationship between impaired BMP signalling and clinical risk factors at early-stage vascular injury in the preterm infant

Thorax

2022 May 17

Heydarian, M;Oak, P;Zhang, X;Kamgari, N;Kindt, A;Koschlig, M;Pritzke, T;Gonzalez-Rodriguez, E;Förster, K;Morty, RE;Häfner, F;Hübener, C;Flemmer, AW;Yildirim, AO;Sudheendra, D;Tian, X;Petrera, A;Kirsten, H;Ahnert, P;Morrell, N;Desai, TJ;Sucre, J;Spiekerkoetter, E;Hilgendorff, A;
PMID: 35580897 | DOI: 10.1136/thoraxjnl-2021-218083

Chronic lung disease, that is, bronchopulmonary dysplasia (BPD) is the most common complication in preterm infants and develops as a consequence of the misguided formation of the gas-exchange area undergoing prenatal and postnatal injury. Subsequent vascular disease and its progression into pulmonary arterial hypertension critically determines long-term outcome in the BPD infant but lacks identification of early, disease-defining changes.We link impaired bone morphogenetic protein (BMP) signalling to the earliest onset of vascular pathology in the human preterm lung and delineate the specific effects of the most prevalent prenatal and postnatal clinical risk factors for lung injury mimicking clinically relevant conditions in a multilayered animal model using wild-type and transgenic neonatal mice.We demonstrate (1) the significant reduction in BMP receptor 2 (BMPR2) expression at the onset of vascular pathology in the lung of preterm infants, later mirrored by reduced plasma BMP protein levels in infants with developing BPD, (2) the rapid impairment (and persistent change) of BMPR2 signalling on postnatal exposure to hyperoxia and mechanical ventilation, aggravated by prenatal cigarette smoke in a preclinical mouse model and (3) a link to defective alveolar septation and matrix remodelling through platelet derived growth factor-receptor alpha deficiency. In a treatment approach, we partially reversed vascular pathology by BMPR2-targeted treatment with FK506 in vitro and in vivo.We identified impaired BMP signalling as a hallmark of early vascular disease in the injured neonatal lung while outlining its promising potential as a future biomarker or therapeutic target in this growing, high-risk patient population.
Sickle Cell Disease Associated Changes in the Gut Microbiome Contribute to Persistent Pain

The Journal of Pain

2022 May 01

Sadler, K;Ehlers, V;Brandow, A;Stucky, C;
| DOI: 10.1016/j.jpain.2022.03.027

Many patients with sickle cell disease (SCD) suffer from chronic pain, the underlying causes of which are unclear. Recent 16s ribosomal RNA sequencing studies revealed differences in the number and types of bacteria in the gastrointestinal tract of patients and mouse models of SCD relative to controls, but it is unclear if or how these changes contribute to symptomology. In these experiments, we used transgenic SCD mice to determine the extent to which disease related gut dysbiosis contributes to persistent pain. Reflexive pain behaviors were first measured in SCD mice following longitudinal probiotic or antibiotic treatment. Vehicle-treated SCD mice displayed significant mechanical allodynia relative to vehicle-treated wildtype mice, and antibiotic treatment further exacerbated mechanical allodynia in both genotypes. In contrast, probiotic treatment completely reversed persistent touch hypersensitivity in SCD mice. Persistent touch pain was also transiently reversed in SCD mice following fecal material transplant from healthy mice. In complementary experiments, wildtype recipient mice developed cold and touch hypersensitivity that persisted for several weeks after fecal material transplant from SCD donors. Using whole-cell patch clamp recordings, we further determined that these behavioral observations were accompanied by altered intrinsic plasticity in a select class of nodose ganglia sensory neurons, the peripheral terminals of which are well positioned to detect sensory information in the gut. Nodose ganglia neurons isolated from animals that received sickle cell fecal material transplants were hyperexcitable relative to those isolated from animals that received control fecal material transplants. These data are the first to suggest that disease-related gut dysbiosis induces pain through changes in vagal nerve activity. Ongoing studies are examining specific bacterial populations and/or metabolites responsible for these functional changes in order to develop novel therapeutics for chronic SCD pain management. Grant support from National Institutes of Health grants K99HL155791 and R01NS070711.

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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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