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Probes for CMS

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

  • Probes for Cms (72)
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A Clinical Applicable Gene Expression Classifier Reveals Intrinsic and Extrinsic Contributions to Consensus Molecular Subtypes in Primary and Metastatic Colon Cancer.

Clin Cancer Res.

2019 Apr 19

Piskol R, Huw LY, Sergin I, Klijn C, Modrusan Z, Kim D, Kljavin NM, Tam R, Patel R, Burton J, Penuel E, Qu X, Koeppen H, Sumiyoshi T, de Sauvage FJ, Lackner MR, de Sousa E Melo F, Kabbarah O.
PMID: 31004000 | DOI: 10.1158/1078-0432.CCR-18-3032

Abstract

PURPOSE:

Four consensus molecular subtypes (CMS1-4) of colorectal cancer (CRC) were identified in primary tumors and found to be associated with distinctive biological features and clinical outcomes. Given that distant metastasis largely accounts for CRC-related mortality, we examined the molecular and clinical attributes of CMS in metastatic CRC (mCRC).

EXPERIMENTAL DESIGN:

We developed a CRC-focused Nanostring based CMS classifier that is ideally suited to interrogate archival tissues. We successfully employ this panel in the CMS classification of FFPE tissues from mCRC cohorts, one of which is comprised of paired primary tumors and metastases. Finally, we developed novel mouse implantation models to enable modelling of CRC in vivo at relevant sites.

RESULTS:

Using our classifier we find that the biological hallmarks of mCRC, including CMS, are in general highly similar to those observed in non-metastatic early stage disease. Importantly, our data demonstrate that CMS1 has the worst outcome in relapsed disease, compared to other CMS. Assigning CMS to primary tumors and their matched metastases revealed mostly concordant subtypes between primary and metastasis. Molecular analysis of matched discordant pairs revealed differences in stromal composition at each site. The development of two novel in vivo orthotopic implantation models further reinforces the notion that extrinsic factors may impact on CMS identification in matched primary and metastatic CRC.

CONCLUSION:

We describe the utility of a Nanostring panel for CMS classification of FFPE clinical samples. Our work reveals the impact of intrinsic and extrinsic factors on CRC heterogeneity during disease progression.

Exposure to chronic stress impairs the ability to cope with an acute challenge: Modulation by lurasidone treatment

European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology

2022 Jul 10

Begni, V;Pisano, I;Marizzoni, M;Marchisella, F;Creutzberg, KC;De Rosa, F;Cattaneo, A;Gruca, P;Litwa, E;Papp, M;Riva, MA;
PMID: 35830759 | DOI: 10.1016/j.euroneuro.2022.06.005

Chronic stress represents a major contributor for the development of mental illness. This study aimed to investigate how animals exposed to chronic mild stress (CMS) responded to an acute stress (AS), as a vulnerability's challenge, and to establish the potential effects of the antipsychotic drug lurasidone on such mechanisms. Adult male Wistar rats were exposed or not (controls) to a CMS paradigm for 7 weeks. Starting from the end of week 2, animals were randomized to receive vehicle or lurasidone for 5 weeks. Sucrose intake was used to measure anhedonia. At the end, half of the animals were exposed to an acute stress before sacrifice. Exposure to CMS produced a significant reduction in sucrose consumption, whereas lurasidone progressively normalized such alteration. We found that exposure to AS produced an upregulation of Brain derived neurotrophic factor (Bdnf) in the prefrontal cortex of controls animals. This response was impaired in CMS rats and restored by lurasidone treatment. While in control animals, AS-induced increase of Bdnf mRNA levels was specific for Parvalbumin cells, CMS rats treated with lurasidone show a significant upregulation of Bdnf in pyramidal cells. Furthermore, when investigating the activation of different brain regions, CMS rats showed an impairment in the global response to the acute stressor, that was largely restored by lurasidone treatment. Our results suggest that lurasidone treatment in CMS rats may regulate specific circuits and mechanisms, which will ultimately contribute to boost resilience under stressful challenges.
Yap Promotes Noncanonical Wnt Signals from Cardiomyocytes for Heart Regeneration

Circulation research

2021 Aug 23

Liu, S;Tang, L;Zhao, X;Nguyen, B;Heallen, TR;Li, M;Wang, J;Wang, J;Martin, JF;
PMID: 34424032 | DOI: 10.1161/CIRCRESAHA.121.318966

Rationale: During neonatal heart regeneration, the fibrotic response, which is required to prevent cardiac rupture, resolves via poorly understood mechanisms. Deletion of the Hippo pathway gene Sav in adult CMs increases Yap activity and promotes cardiac regeneration, partly by inducing fibrosis resolution. Deletion of Yap in neonatal cardiomyocytes (CMs) leads to increased fibrosis and loss of neonatal heart regeneration, suggesting that Yap inhibits fibrosis by regulating intercellular signaling from CMs to cardiac fibroblasts (CFs). Objective: We investigated the role of Wntless (Wls), which is a direct target gene of Yap, in communication between CMs and CFs during neonatal heart regeneration. Methods and Results: We generated two mouse models to delete Wls specifically in CMs (Myh6-Cas9 combined with AAV9-Wls-gRNAs, and Myh6cre-ERT2/+; Wlsflox/flox mouse). Reanalysis of single-cell RNA-sequencing data revealed that Wnt ligands are expressed in CMs, whereas Wnt receptors are expressed in CFs, suggesting that Wnt signaling is directional from CMs to CFs during neonatal heart regeneration. Wls deletion in neonatal hearts disrupted Wnt signaling, showing as reduced noncanonical Wnt signaling in non-CMs. Four weeks after neonatal heart infarction, heart function was measured by echocardiography. Wls deletion in neonatal hearts after myocardial infarction impairs neonatal heart regeneration, marked by decreased contractile function and increased fibrosis. Wls mutant hearts display CF activation, characterized by increased extracellular matrix secretion, inflammation, and CF proliferation. Conclusions: These data indicate that during neonatal heart regeneration, intercellular signaling from CMs to CFs occurs via noncanonical Wnt signaling to rebuild cardiac architecture after myocardial infarction.
P.0552 The early therapeutic efficacy of lurasidone in a rodent model of depression: a behavioural and biomolecular study

European Neuropsychopharmacology

2021 Dec 01

Pisano, I;Begni, V;Creutzberg, K;Marchisella, F;De Rosa, F;Papp, M;Riva, M;
| DOI: 10.1016/j.euroneuro.2021.10.522

Background: Stress represents a major contributor for the development of mental illness. Accordingly, exposure of adult rats to chronic stress represents a valuable experimental tool to investigate the ability of pharmacological intervention to counteract the adverse effects produced by stress exposure. The aim of this study was to perform a time course analyses of the changes produced by the antipsychotic drug lurasidone in the Chronic Mild Stress (CMS) model, in order to identify early mechanisms that may contribute to its therapeutic activity. Methods: Adult male Wistar rats were left undisturbed or exposed to the CMS paradigm, a well-established model of depression. After two weeks of stress, both controls and CMS rats were randomly divided in two subgroups that received vehicle or lurasidone for five weeks. Sucrose consumption was used to measure anhedonia, a core symptom of depression. Animals were sacrificed after two, three or five weeks of treatment in order to investigate dynamic changes during lurasidone administration. For the sucrose consumption we performed three-way ANOVA and two-way ANOVA with Tukey's posthoc. For the molecular analysis we performed 2-way ANOVA, with Tukey's posthoc for qRT-PCR data and Sidak's posthoc for RNAscope data. Results: CMS rats show a significant reduction in sucrose consumption, (-46% after two weeks, p
Early effects of lurasidone treatment in a chronic mild stress model in male rats

Psychopharmacology

2023 Feb 23

Creutzberg, KC;Begni, V;Marchisella, F;Papp, M;Riva, MA;
PMID: 36820870 | DOI: 10.1007/s00213-023-06343-5

Stress represents a major contributor to the development of mental illness. Accordingly, exposure of adult rats to chronic stress represents a valuable tool to investigate the ability of a pharmacological intervention to counteract the adverse effects produced by stress exposure.The aim of this study was to perform a time course analysis of the treatment with the antipsychotic drug lurasidone in normalizing the anhedonic phenotype in the chronic mild stress (CMS) model in order to identify early mechanisms that may contribute to its therapeutic activity.Male Wistar rats were exposed to CMS or left undisturbed for 7 weeks. After two weeks of stress, both controls and CMS rats were randomly divided into two subgroups that received vehicle or lurasidone for five weeks. Weekly measures of sucrose intake were recorded to evaluate anhedonic behavior, and animals were sacrificed at different weeks of treatment for molecular analyses.We found that CMS-induced anhedonia was progressively improved by lurasidone treatment. Interestingly, after two weeks of lurasidone treatment, 50% of the animals showed a full recovery of the phenotype, which was associated with increased activation of the prefrontal and recruitment of parvalbumin-positive cells that may lead to a restoration of excitatory/inhibitory balance.These results suggest that the capacity of lurasidone to normalize anhedonia at an early stage of treatment may depend on its ability to modulate the function of the prefrontal cortex.
Characterization of early phases of cardiomyopathy syndrome pathogenesis in Atlantic salmon (Salmo salar L.) through various diagnostic methods

Journal of fish diseases

2022 Jun 10

Fritsvold, C;Mikalsen, AB;Haugland, Ø;Tartor, H;Sindre, H;
PMID: 35686455 | DOI: 10.1111/jfd.13659

Since the first description of cardiomyopathy syndrome (CMS) in Atlantic salmon, in 1985, the disease caused by piscine myocarditisvirus (PMCV) has become a common problem in Atlantic salmon farming, not only in Norway, but also in other salmon farming countries like Scotland and Ireland. In the last years, CMS has been ranked as the most important salmon viral disease in Norway regarding both mortality and economic losses. Detailed knowledge of infection and pathogenesis is still lacking, a decade after the causal agent was first described, and there is a need for a wider range of methods/tools for diagnostic and research purposes. In this study, we compared the detection of PMCV- and CMS-related tissue lesions using previously used and well-known methods like histopathology and real-time RT-PCR to immunohistochemistry (IHC), a less used method, and a new method, RNAscope in situ hybridization. Tissue samples of three different cardiac compartments, mid-kidney and skin/muscle tissue were compared with non-lethal parallel samplings of blood and mucus. The development of pathological cardiac lesions observed in this experiment was in accordance with previous descriptions of CMS. Our results indicate a viremic phase 10- to 20-day post-challenge (dpc) preceding the cardiac lesions. In this early phase, virus could also be detected in relatively high amount in mid-kidney by real-time RT-PCR. Plasma and/or mid-kidney samples may, therefore, be candidates to screen for early-phase PMCV infection. The RNAscope in situ hybridization method showed higher sensitivity and robustness compared with the immunohistochemistry and may be a valuable support to histopathology in CMS diagnostics, especially in cases of untypical lesions or mixed infections.
Coupled myovascular expansion directs cardiac growth and regeneration

Development (Cambridge, England)

2022 Sep 15

DeBenedittis, P;Karpurapu, A;Henry, A;Thomas, MC;McCord, TJ;Brezitski, K;Prasad, A;Baker, CE;Kobayashi, Y;Shah, SH;Kontos, CD;Tata, PR;Lumbers, RT;Karra, R;
PMID: 36134690 | DOI: 10.1242/dev.200654

Heart regeneration requires multiple cell types to enable cardiomyocyte (CM) proliferation. How these cells interact to create growth niches is unclear. Here, we profile proliferation kinetics of cardiac endothelial cells (CECs) and CMs in the neonatal mouse heart and find that they are spatiotemporally coupled. We show that coupled myovascular expansion during cardiac growth or regeneration is dependent upon VEGF-VEGFR2 signaling, as genetic deletion of Vegfr2 from CECs or inhibition of VEGFA abrogates both CEC and CM proliferation. Repair of cryoinjury displays poor spatial coupling of CEC and CM proliferation. Boosting CEC density after cryoinjury with virus encoding Vegfa enhances regeneration. Using Mendelian randomization, we demonstrate that circulating VEGFA levels are positively linked with human myocardial mass, suggesting that Vegfa can stimulate human cardiac growth. Our work demonstrates the importance of coupled CEC and CM expansion and reveals a myovascular niche that may be therapeutically targeted for heart regeneration.
Involvement of Scratch2 in GalR1-mediated depression-like behaviors in the rat ventral periaqueductal gray

Proceedings of the National Academy of Sciences of the United States of America

2021 Jun 15

Yang, Y;Li, Y;Liu, B;Li, C;Liu, Z;Deng, J;Luo, H;Li, X;Wu, J;Li, H;Wang, CY;Zhao, M;Wu, H;Lallemend, F;Svenningsson, P;Hökfelt, TGM;Xu, ZD;
PMID: 34108238 | DOI: 10.1073/pnas.1922586118

Galanin receptor1 (GalR1) transcript levels are elevated in the rat ventral periaqueductal gray (vPAG) after chronic mild stress (CMS) and are related to depression-like behavior. To explore the mechanisms underlying the elevated GalR1 expression, we carried out molecular biological experiments in vitro and in animal behavioral experiments in vivo. It was found that a restricted upstream region of the GalR1 gene, from -250 to -220, harbors an E-box and plays a negative role in the GalR1 promoter activity. The transcription factor Scratch2 bound to the E-box to down-regulate GalR1 promoter activity and lower expression levels of the GalR1 gene. The expression of Scratch2 was significantly decreased in the vPAG of CMS rats. Importantly, local knockdown of Scratch2 in the vPAG caused elevated expression of GalR1 in the same region, as well as depression-like behaviors. RNAscope analysis revealed that GalR1 mRNA is expressed together with Scratch2 in both GABA and glutamate neurons. Taking these data together, our study further supports the involvement of GalR1 in mood control and suggests a role for Scratch2 as a regulator of depression-like behavior by repressing the GalR1 gene in the vPAG.
CSF2-dependent monocyte education in the pathogenesis of ANCA-induced glomerulonephritis

Annals of the rheumatic diseases

2022 Apr 13

Rousselle, A;Sonnemann, J;Amann, K;Mildner, A;Lodka, D;Kling, L;Bieringer, M;Schneider, U;Leutz, A;Enghard, P;Kettritz, R;Schreiber, A;
PMID: 35418479 | DOI: 10.1136/annrheumdis-2021-221984

Myeloid cell activation by antineutrophil cytoplasmic antibody (ANCA) is pivotal for necrotising vasculitis, including necrotising crescentic glomerulonephritis (NCGN). In contrast to neutrophils, the contribution of classical monocyte (CM) and non-classical monocyte (NCM) remains poorly defined. We tested the hypothesis that CMs contribute to antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and that colony-stimulating factor-2 (CSF2, granulocyte-macrophage colony-stimulating factor (GM-CSF)) is an important monocyte-directed disease modifier.Myeloperoxidase (MPO)-immunised MPO-/- mice were transplanted with haematopoietic cells from wild-type (WT) mice, C-C chemokine receptor 2 (CCR2)-/- mice to abrogate CM, or transcription factor CCAAT-enhancer-binding protein beta (C/EBPβ)-/- mice to reduce NCM, respectively. Monocytes were stimulated with CSF2, and CSF2 receptor subunit beta (CSF2rb)-deficient mice were used. Urinary monocytes and CSF2 were quantified and kidney Csf2 expression was analysed. CSF2-blocking antibody was used in the nephrotoxic nephritis (NTN) model.Compared with WT mice, CCR2-/- chimeric mice showed reduced circulating CM and were protected from NCGN. C/EBPβ-/- chimeric mice lacked NCM but developed NCGN similar to WT chimeric mice. Kidney and urinary CSF2 were upregulated in AAV mice. CSF2 increased the ability of ANCA-stimulated monocytes to generate interleukin-1β and to promote TH17 effector cell polarisation. CSF2rb-/- chimeric mice harboured reduced numbers of kidney TH17 cells and were protected from NCGN. CSF2 neutralisation reduced renal damage in the NTN model. Finally, patients with active AAV displayed increased urinary CM numbers, CSF2 levels and expression of GM-CSF in infiltrating renal cells.CMs but not NCMs are important for inducing kidney damage in AAV. CSF2 is a crucial pathological factor by modulating monocyte proinflammatory functions and thereby TH17 cell polarisation.
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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

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