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.
Molecular psychiatry
2022 May 26
Mätlik, K;Garton, DR;Montaño-Rodríguez, AR;Olfat, S;Eren, F;Casserly, L;Damdimopoulos, A;Panhelainen, A;Porokuokka, LL;Kopra, JJ;Turconi, G;Schweizer, N;Bereczki, E;Piehl, F;Engberg, G;Cervenka, S;Piepponen, TP;Zhang, FP;Sipilä, P;Jakobsson, J;Sellgren, CM;Erhardt, S;Andressoo, JO;
PMID: 35618883 | DOI: 10.1038/s41380-022-01554-2
bioRxiv : the preprint server for biology
2023 Feb 21
Chen, J;Zheng, Q;Hicks, JL;Trabzonlu, L;Ozbek, B;Jones, T;Vaghasia, A;Larman, TC;Wang, R;Markowski, MC;Denmeade, SR;Pienta, KJ;Hruban, RH;Antonaraskis, ES;Gupta, A;Dang, CV;Yegnasubramanian, S;De Marzo, AM;
PMID: 36865273 | DOI: 10.1101/2023.02.20.529259
The Journal of clinical investigation
2021 Dec 14
Yadav, VK;Berger, JM;Singh, P;Nagarajan, P;Karsenty, G;
PMID: 34905510 | DOI: 10.1172/JCI153752
J Pathol.
2017 Sep 09
Baena-Del Valle JA, Zheng Q, Esopi DM, Rubenstein M, Hubbard GK, Moncaliano MC, Hruszkewycz A, Vaghasia A, Yegnasubramanian S, Wheelan SJ, Meeker AK, Heaphy CM, Graham MK, De Marzo AM.
PMID: 28888037 | DOI: 10.1002/path.4980
Telomerase consists of at least two essential elements, an RNA component hTR or TERC that contains the template for telomere DNA addition, and a catalytic reverse transcriptase (TERT). While expression of TERT has been considered the key rate limiting component for telomerase activity, increasing evidence suggests an important role for the regulation of TERC in telomere maintenance and perhaps other functions in human cancer. By using three orthogonal methods including RNAseq, RT-qPCR, and an analytically validated chromogenic RNA in situ hybridization assay, we report consistent overexpression of TERC in prostate cancer. This overexpression occurs at the precursor stage (e.g. high grade prostatic intraepithelial neoplasia or PIN), and persists throughout all stages of disease progression. Levels of TERC correlate with levels of MYC (a known driver of prostate cancer) in clinical samples and we also show the following: forced reductions of MYC result in decreased TERC levels in 8 cancer cell lines (prostate, lung, breast, and colorectal); forced overexpression of MYC in PCa cell lines, and in the mouse prostate, results in increased TERC levels; human TERC promoter activity is decreased after MYC silencing; and MYC occupies the TERC locus as assessed by chromatin immunoprecipitation (ChIP). Finally, we show that knockdown of TERC by siRNA results in reduced proliferation of prostate cancer cell lines. These studies indicate that TERC is consistently overexpressed in all stages of prostatic adenocarcinoma, and its expression is regulated by MYC. These findings nominate TERC as a novel prostate cancer biomarker and therapeutic target.
Human molecular genetics
2022 Aug 11
Bando, H;Brinkmeier, ML;Castinetti, F;Fang, Q;Lee, MS;Saveanu, A;Albarel, F;Dupuis, C;Brue, T;Camper, SA;
PMID: 35951005 | DOI: 10.1093/hmg/ddac192
Nature communications
2021 Nov 03
Jarmas, AE;Brunskill, EW;Chaturvedi, P;Salomonis, N;Kopan, R;
PMID: 34732708 | DOI: 10.1038/s41467-021-26626-9
Cellular and molecular gastroenterology and hepatology
2021 Dec 29
Kim, TY;Kim, S;Kim, Y;Lee, YS;Lee, S;Lee, SH;Kweon, MN;
PMID: 34971821 | DOI: 10.1016/j.jcmgh.2021.12.015
Prostate.
2018 May 30
Markowski MC, Hubbard GK, Hicks JL, Zheng Q, King A, Esopi D, Rege A, Yegnasubramanian S, Bieberich CJ, De Marzo AM.
PMID: 29851094 | DOI: 10.1002/pros.23657
Abstract
BACKGROUND:
Loss or mutation of PTEN alleles at 10q23 in combination with 8q24 amplification (encompassing MYC) are common findings in aggressive, human prostate cancer. Our group recently developed a transgenic murine model of prostate cancer involving prostate-specific Pten deletion and forced expression of MYC under the control of the Hoxb13 promoter. MYC overexpression cooperated with Pten loss to recapitulate lethal, human prostate cancer.
METHOD:
We now report on the generation of two mouse prostate cancer cell lines, BMPC1 and BMPC2, derived from a lymph node, and liver metastasis, respectively.
RESULTS:
Both cell lines demonstrate a phenotype consistent with adenocarcinoma and grew under standard tissue culture conditions. Androgen receptor (AR) protein expression is minimal (BMPC1) or absent (BMPC2) consistent with AR loss observed in the BMPC mouse model of invasive adenocarcinoma. Growth in media containing charcoal-stripped serum resulted in an increase in AR mRNA in BMPC1 cells with no effect on protein expression, unless androgens were added, in which case AR protein was stabilized, and showed nuclear localization. AR expression in BMPC2 cells was not effected by growth media or treatment with androgens. Treatment with an anti-androgen/castration or androgen supplemented media did not affect in vitro or in vivo growth of either cell line, irrespective of nuclear AR detection.
DISCUSSION:
These cell lines are a novel model of androgen-insensitive prostatic adenocarcinoma driven by MYC over-expression and Pten loss.
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.
PLoS Genet.
2015 Dec 17
Kumar A, Kopra J, Varendi K, Porokuokka LL, Panhelainen A, Kuure S, Marshall P, Karalija N, Härma MA, Vilenius C, Lilleväli K, Tekko T, Mijatovic J, Pulkkinen N, Jakobson M, Jakobson M, Ola R, Palm E, Lindahl M, Strömberg I, Võikar V, Piepponen TP, Saarma
PMID: 26681446 | DOI: 10.1371/journal.pgen.1005710.
Degeneration of nigrostriatal dopaminergic system is the principal lesion in Parkinson's disease. Because glial cell line-derived neurotrophic factor (GDNF) promotes survival of dopamine neurons in vitro and in vivo, intracranial delivery of GDNF has been attempted for Parkinson's disease treatment but with variable success. For improving GDNF-based therapies, knowledge on physiological role of endogenous GDNF at the sites of its expression is important. However, due to limitations of existing genetic model systems, such knowledge is scarce. Here, we report that prevention of transcription of Gdnf 3'UTR in Gdnf endogenous locus yields GDNF hypermorphic mice with increased, but spatially unchanged GDNF expression, enabling analysis of postnatal GDNF function. We found that increased level of GDNF in the central nervous system increases the number of adult dopamine neurons in the substantia nigra pars compacta and the number of dopaminergic terminals in the dorsal striatum. At the functional level, GDNF levels increased striatal tissue dopamine levels and augmented striatal dopamine release and re-uptake. In a proteasome inhibitor lactacystin-induced model of Parkinson's disease GDNF hypermorphic mice were protected from the reduction in striatal dopamine and failure of dopaminergic system function. Importantly, adverse phenotypic effects associated with spatially unregulated GDNF applications were not observed. Enhanced GDNF levels up-regulated striatal dopamine transporter activity by at least five fold resulting in enhanced susceptibility to 6-OHDA, a toxin transported into dopamine neurons by DAT. Further, we report how GDNF levels regulate kidney development and identify microRNAs miR-9, miR-96, miR-133, and miR-146a as negative regulators of GDNF expression via interaction with Gdnf 3'UTR in vitro. Our results reveal the role of GDNF in nigrostriatal dopamine system postnatal development and adult function, and highlight the importance of correct spatial expression of GDNF. Furthermore, our results suggest that 3'UTR targeting may constitute a useful tool in analyzing gene function.
Proc Natl Acad Sci U S A.
2018 Nov 15
Shen H, Marino RAM, McDevitt RA, Bi GH, Chen K, Madeo G, Lee PT, Liang Y, De Biase LM, Su TP, Xi ZX, Bonci A.
PMID: 30442663 | DOI: 10.1073/pnas.1800886115
A subset of midbrain dopamine (DA) neurons express vesicular glutamate transporter 2 (VgluT2), which facilitates synaptic vesicle loading of glutamate. Recent studies indicate that such expression can modulate DA-dependent reward behaviors, but little is known about functional consequences of DA neuron VgluT2 expression in neurodegenerative diseases like Parkinson's disease (PD). Here, we report that selective deletion of VgluT2 in DA neurons in conditional VgluT2-KO (VgluT2-cKO) mice abolished glutamate release from DA neurons, reduced their expression of brain-derived neurotrophic factor (BDNF) and tyrosine receptor kinase B (TrkB), and exacerbated the pathological effects of exposure to the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Furthermore, viral rescue of VgluT2 expression in DA neurons of VglutT2-cKO mice restored BDNF/TrkB expression and attenuated MPTP-induced DA neuron loss and locomotor impairment. Together, these findings indicate that VgluT2 expression in DA neurons is neuroprotective. Genetic or environmental factors causing reduced expression or function of VgluT2 in DA neurons may place some individuals at increased risk for DA neuron degeneration. Therefore, maintaining physiological expression and function of VgluT2 in DA neurons may represent a valid molecular target for the development of preventive therapeutic interventions for PD.
Science advances
2022 Feb 25
Zhang, K;Erkan, EP;Jamalzadeh, S;Dai, J;Andersson, N;Kaipio, K;Lamminen, T;Mansuri, N;Huhtinen, K;Carpén, O;Hietanen, S;Oikkonen, J;Hynninen, J;Virtanen, A;Häkkinen, A;Hautaniemi, S;Vähärautio, A;
PMID: 35196078 | DOI: 10.1126/sciadv.abm1831
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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