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Supplemental Table 1. Comparison among Q-RT-PCR, ISH-TMA and IHC for the detection of ErbB-2 in breast cancers. IHC ISH-TMA Q-RT-PCR Q-RT-PCR range Q-RT-PCR score 0 0 0* 0 0 0 0* 0 0 0 1 0 0 0 1 0 0 0 1 0 0 1 2 0 1 1 2 0 0 0 3 0 0 0 3 0 0 0 3 0 0 0 3 0 0 0 3 x<10 0 1 1 3 0 0 0 4 0 0 0 5 0 0 0 5 0 0 0 5 0 1 1 5 0 0 0 6 0 0 0 8 0 0 0 8 0 1 1 8 0 0 1 8 0 1 1 11 1 1 1 11 1 1 1 11 1 1 0 12 1 1 1 13 10<x<20 1 0 1 13 1 1 1 16 1 1 1 17 1 2 1 17 1 2 2 22 2 2 2 43 2 20<x<100 3 2 74 2 3 2 86 2 3 3 213 3 3 3 259 x>100 3 3 3 362 3 Legend to Supplemental Table 1. This experiment was set up to demonstrate that there is good semi-quantitative correlation between the levels of expression detected by ISH-TMA, IHC and Q-RT-PCR. We compared the three methods on levels of ErbB-2 expression in breast cancer, since ErbB-2 is overexpressed in breast cancers, over a wide range of levels. 1 Thirty-nine primary infiltrating ductal carcinomas were divided into two aliquots, one of which was snap-frozen in liquid nitrogen and stored at –80°C for RNA extraction, and the other was fixed in buffered formalin and embedded in paraffin blocks for TMA construction. All frozen sections were reviewed by a pathologist before analysis and selected for cellularity (at least 70% of tumor cells), before RNA extraction. Column “Q-RT-PCR”: The cohort of 39 breast cancer patients was analyzed by Q-RT-PCR. The housekeeping gene ß-actin was used for the normalization. Results were expressed as relative levels of ErbB-2 mRNA, referred to a sample, called calibrator, chosen to represent 1X expression of this gene. The calibrator was a breast cancer cell line (MCF-7) that was analyzed on every assay plate with the unknown samples. The amount of target, normalized to the endogenous reference (ß-actin) and relative to the calibrator, was defined by ∆∆Ct method as described by Livak K (Sequence Detectro User Bulletin 2; Applied Biosystems). Specifically, the formula is applied as follows: Target amount = 2 -∆∆Ct where ∆∆Ct = [Ct (HER-2/neu sample) – Ct (ß-actin sample)] – [Ct (HER-2/neu calibrator) – Ct (ß-actin calibrator)]. The two samples labeled with an asterisk (0*) gave no amplification after 40 cycles. Cores from paraffin blocks, corresponding to these cases, were then arrayed on a TMA (in duplicate) and subjected to ISH with an ErbB-2-specific riboprobe. ISH scores were assigned as described in Methods (column “ISH-TMA”). Parallel sections of the TMA were also evaluated by IHC. Immunohistochemical staining for ErbB-2 was performed using the primary Ab (anti-HER-2/neu, DAKO, Carpinteria, CA, 1:2000 dilution) followed by detection with the Dako EnVision+ system, peroxidase (DAKO). Briefly, formalin-fixed, paraffin-embedded tissue sections were deparaffinized, rehydrated, pretreated in 0.25 mM EDTA pH 8.0 at 95°C and exposed to the primary antibody for 60 min at room temperature. Positive and negative controls were included in each experiment. ErbB-2 overexpression was evaluated according to the scoring system recommended by the DAKO HercepTest: score 0, no staining or membrane staining in <10% of the tumor cells; score 1, barely perceptible membrane staining in >10% of the tumor cells; score 2, weak-to-moderate staining of the entire membrane in >10% of the tumor cells; score 3, strong staining of the entire membrane in >10% of the tumor cells. Scores of 2 and 3 were considered to represent overexpression. Since data from ISH-TMA and IHC analyses are discontinuous, whereas those obtained by Q-RT-PCR analyses are continuous, we transformed the Q-RT-PCR values into discontinuous data (1). The discontinuous Q-RT-PCR scores (column “Q- RT-PCR score”) are shown along with the ranges of actual values used to attribute the score (column “Q-RT-PCR range”). Pearson Correlation was calculated in Excel Software (Microsoft). The Pearson Correlation Coefficients were Q-RT-PCR vs. ISH- TMA, r = 0.906; Q-RT-PCR vs. IHC, r = 0.909; ISH-TMA vs. IHC, r = 0.910. To test if the frequency of the observed values of expression between ISH, IHC and PCR are evenly distributed, a chi square test was performed (ISH vs. IHC, Chi = 2.15 and P=0.54; ISH vs. PCR, Chi = 3.85 and P = 0.27; IHC vs. PCR, Chi = 2.41 and P = 0.49), confirming that the three method used in the analysis are not significantly different. Twenty of the 39 samples displayed in this Table are the same used in a previously published validation of ISH vs. Q-RT-PCR of ErbB-2 expression (2). 2 References to Supplemental Table 1 1. Ginestier, C., Charafe-Jauffret, E., Bertucci, F., et al. Distinct and complementary information provided by use of tissue and DNA microarrays in the study of breast tumor markers. Am J Pathol 2002;161:1223-33. 2. Nicassio, F., Bianchi, F., Capra, M., et al. A cancer-specific transcriptional signature in human neoplasia. J Clin Invest 2005;115:3015-25. 3 Supplemental Table 2. List of screened kinases. Symbol Sugen Aliases Group Name cDNA Acc AAK1 AAK1 KIAA1048 OTHER AP2 associated kinase 1 NM_014911 ACVR1C ALK7 ALK7, ACVRLK7 TKL Activin A receptor, type IC AY127050 ADCK1 ADCK1 ADCK1 ATYPICAL AarF domain containing kinase 1 BC058906 ADRBK2 BARK2 GRK3, BARK2 AGC Adrenergic, beta, receptor kinase 2 NM_005160 ALS2CR2 STLK6 ILPIP STE Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2 NM_018571 ALS2CR7 PFTAIRE2 CMGC Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7 BC038807 ANKK1 SgK288 ANKK1, PKK2 TKL Ankyrin repeat and kinase domain containing 1 AF487542 AURKA AurA AIK, STK6 OTHER Aurora kinase A NM_003600 AURKB AurB STK12, AIK2, ARK2 OTHER Aurora kinase B NM_004217 BRSK1 BRSK1 KIAA1811 CAMK BR serine/threonine kinase 1 NM_032430 BRSK2 BRSK2 PEN11B, STK29, SAD1 CAMK BR serine/threonine kinase 2 NM_003957 BUB1 BUB1 BUB1, BUB1L, BUB1A OTHER BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) NM_004336 C9orf96* SgK071 OTHER Chromosome 9 open reading frame 96 NM_153710 CAMK1D CaMK1d CKLIK CAMK Calcium/calmodulin-dependent protein kinase ID AF286366 CAMK2D CaMK2d CAMKD CAMK Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta NM_001221 CAMKK1 CaMKK1 CAMKKA OTHER Calcium/calmodulin-dependent protein kinase kinase 1, alpha AF425301 CAMKK2 CaMKK2 CAMKK, CAMKKB OTHER Calcium/calmodulin-dependent protein kinase kinase 2, beta AF287631 CDKL3 CDKL3 NKIAMRE CMGC Cyclin-dependent kinase-like 3 NM_016508 CDKL4 CDKL4 CMGC Cyclin-dependent kinase-like 4 NM_001009565 CIT CRIK CRIK, STK21 AGC Citron (rho-interacting, serine/threonine kinase 21) NM_007174 CLK2 CLK2 hCLK2 CMGC CDC-like kinase 2 NM_003993 CLK4 CLK4 CMGC CDC-like kinase 4 NM_020666 4 CRK7 CRK7 CRKR, KIAA0904 CMGC CDC2-related protein kinase 7 NM_016507 CSNK1A1L CK1a2 CK1 Casein kinase 1, alpha 1-like BC028723 DCAMKL2 DCAMKL2 DCDC3, DCK2 CAMK Doublecortin and CaM kinase-like 2 NM_152619 DCAMKL3 DCAMKL3 KIAA1765 CAMK Doublecortin and CaM kinase-like 3 AB051552 DYRK3 DYRK3 DYRK5, RED, REDK CMGC Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3 BC015501 EIF2AK1 HRI HRI, KIAA1369 OTHER Eukaryotic translation initiation factor 2-alpha kinase 1 NM_014413 EIF2AK4 GCN2_d2 GCN2, KIAA1338 OTHER Eukaryotic translation initiation factor 2 alpha kinase 4 NM_001013703 ERN2 IRE2 IRE1b OTHER Endoplasmic reticulum to nucleus signalling 2 NM_033266 FLJ23356* SgK196 OTHER Hypothetical protein FLJ23356 NM_032237 FLJ25006 SgK494 AGC Hypothetical protein FLJ25006 NM_144610 HIPK2 HIPK2 CMGC Homeodomain interacting protein kinase 2 NM_022740 HIPK4 HIPK4 CMGC Homeodomain interacting protein kinase 4 BC034501 HUNK HUNK CAMK Hormonally upregulated Neu-associated kinase NM_014586 IRAK3* IRAK3 IRAK-M TKL Interleukin-1 receptor-associated kinase 3 BC057800 KALRN Trad HAPIP, DUO, TRAD CAMK Kalirin, RhoGEF kinase NM_007064 KIAA0999 QSK KIAA0999 CAMK KIAA0999 protein NM_025164 KSR2 KSR2 TKL Kinase suppressor of ras 2 AY345972 LATS2 LATS2 AGC LATS, large tumor suppressor, homolog 2 (Drosophila) NM_014572 LIMK1 LIMK1 LIMK1, LIMK TKL LIM domain kinase 1 NM_002314 LIMK2 LIMK2 TKL LIM domain kinase 2 NM_016733 LOC340156 SgK085 LOC340156 CAMK hypothetical protein LOC340156 NM_001012418 LOC91461 SgK493 OTHER Hypothetical protein BC007901 NM_138370 LRRK2 LRRK2 DARDARIN TKL Leucine-rich repeat kinase 2 XM_058513 LYK5* STLK5 STRAD STE Protein kinase LYK5 NM_001003786 MAP3K15 MAP3K7 FLJ16518 STE Mitogen-activated protein kinase kinase kinase 15 NM_001001671 5 MAP3K6 MAP3K6 MAPKKK6 STE Mitogen-activated protein kinase kinase kinase 6 AF100318 MAP3K9 MLK1 MLK1 TKL Mitogen-activated protein kinase kinase kinase 9 NM_033141 MAP4K1 HPK1 HPK1 STE Mitogen-activated protein kinase kinase kinase kinase 1 NM_007181 MAP4K3 KHS2 MAPKKKK3, GLK, RAB8IPL1 STE Mitogen-activated protein kinase kinase kinase kinase 3 NM_003618 MAP4K4 ZC1/HGK HGK STE Mitogen-activated protein kinase kinase kinase kinase 4 NM_004834 MAPK15 Erk7 ERK8 CMGC Mitogen-activated protein kinase 15 AY065978 MASK MST4 MST4 STE Mst3 and SOK1-related kinase NM_016542 MASTL MASTL FLJ14813 GENE AGC Microtubule associated serine/threonine kinase-like NM_032844 MELK MELK KIAA0175, HPK38 CAMK Maternal embryonic leucine zipper kinase NM_014791 MGC16169* TBCK OTHER Hypothetical protein MGC16169 NM_033115 MGC42105 NIM1 MGC42105 CAMK Hypothetical protein MGC42105 NM_153361 MINK1 ZC3/MINK MINK, B55, MAP4K6 STE Misshapen-like kinase 1 (zebrafish) NM_015716 MLCK caMLCK LOC91807 CAMK Cardiac-MyBP-C associated Ca/CaM kinase NM_182493 MLKL* MLKL FLJ34389 OTHER Mixed lineage kinase domain-like BC028141 MYLK2 skMLCK KMLC, MLCK CAMK Myosin light chain kinase 2, skeletal muscle NM_033118 MYO3B
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    Current Heart Failure Reports (2020) 17:234–246 https://doi.org/10.1007/s11897-020-00475-x TRANSLATIONAL RESEARCH IN HEART FAILURE (J BACKS & M VAN DEN HOOGENHOF, SECTION EDITORS) New Insights in RBM20 Cardiomyopathy D. Lennermann1,2 & J. Backs1,2 & M. M. G. van den Hoogenhof1,2 Published online: 13 August 2020 # The Author(s) 2020 Abstract Purpose of Review This review aims to give an update on recent findings related to the cardiac splicing factor RNA-binding motif protein 20 (RBM20) and RBM20 cardiomyopathy, a form of dilated cardiomyopathy caused by mutations in RBM20. Recent Findings While most research on RBM20 splicing targets has focused on titin (TTN), multiple studies over the last years have shown that other splicing targets of RBM20 including Ca2+/calmodulin-dependent kinase IIδ (CAMK2D) might be critically involved in the development of RBM20 cardiomyopathy. In this regard, loss of RBM20 causes an abnormal intracellular calcium handling, which may relate to the arrhythmogenic presentation of RBM20 cardiomyopathy. In addition, RBM20 presents clinically in a highly gender-specific manner, with male patients suffering from an earlier disease onset and a more severe disease progression. Summary Further research on RBM20, and treatment of RBM20 cardiomyopathy, will need to consider both the multitude and relative contribution of the different splicing targets and related pathways, as well as gender differences. Keywords RBM20 . Dilated cardiomyopathy . CaMKIIδ . Calcium handling . Gender differences . Titin Introduction (ARVC), where a small number of genes account for most of the genetic causes, DCM-causing mutations have been ob- Dilated cardiomyopathy (DCM), as defined by left ventricular served in a variety of genes of diverse ontology [2].
  • Anti-CLK2 Antibody (ARG66787)

    Anti-CLK2 Antibody (ARG66787)

    Product datasheet [email protected] ARG66787 Package: 100 μg anti-CLK2 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes CLK2 Tested Reactivity Hu Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name CLK2 Antigen Species Human Immunogen Synthetic peptide between aa. 1-50 of Human CLK2. Conjugation Un-conjugated Alternate Names CDC-like kinase 2; Dual specificity protein kinase CLK2; EC 2.7.12.1 Application Instructions Application table Application Dilution IHC-P 1:100 - 1:300 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control COLO205 and A549 Calculated Mw 60 kDa Observed Size ~ 60 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS, 0.02% Sodium azide, 50% Glycerol and 0.5% BSA. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol and 0.5% BSA Concentration 1 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/3 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol CLK2 Gene Full Name CDC-like kinase 2 Background This gene encodes a dual specificity protein kinase that phosphorylates serine/threonine and tyrosine- containing substrates.
  • The Dual Role of Micrornas in Colorectal Cancer Progression

    The Dual Role of Micrornas in Colorectal Cancer Progression

    International Journal of Molecular Sciences Review The Dual Role of MicroRNAs in Colorectal Cancer Progression Lei Ding 1,2,†, Zhenwei Lan 1,2,†, Xianhui Xiong 1,2, Hongshun Ao 1,2, Yingting Feng 1,2, Huan Gu 1,2, Min Yu 1,2 and Qinghua Cui 1,2,* 1 Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; [email protected] (L.D.); [email protected] (Z.L.); [email protected] (X.X.); [email protected] (H.A.); [email protected] (Y.F.); [email protected] (H.G.); [email protected] (M.Y.) 2 Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China * Correspondence: [email protected]; Tel.: +86-871-65031412 † These authors contributed equally to this work. Received: 29 August 2018; Accepted: 13 September 2018; Published: 17 September 2018 Abstract: Colorectal cancer (CRC) is responsible for one of the major cancer incidence and mortality worldwide. It is well known that MicroRNAs (miRNAs) play vital roles in maintaining the cell development and other physiological processes, as well as, the aberrant expression of numerous miRNAs involved in CRC progression. MiRNAs are a class of small, endogenous, non-coding, single-stranded RNAs that bind to the 3’-untranslated region (30-UTR) complementary sequences of their target mRNA, resulting in mRNA degradation or inhibition of its translation as a post-transcriptional regulators. Moreover, miRNAs also can target the long non-coding RNA (lncRNA) to regulate the expression of its target genes involved in proliferation and metastasis of CRC. The functions of these dysregulated miRNAs appear to be context specific, with evidence of having a dual role in both oncogenes and tumor suppression depending on the cellular environment in which they are expressed.