RPPanalyzer Toolbox: An Improved R Package for Analysis of Reverse Phase Protein Array Data

Heyde, Silvia von der; Sonntag, Johanna; Kaschek, Daniel; Bender, Christian; Bues, Johannes; Wachter, Astrid; Timmer, Jens; Korf, Ulrike; Beißbarth, Tim

doi:10.2144/000114205

Cited by 37 publications

(23 citation statements)

References 21 publications

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“…Therefore, background values from fi and dcw for the dorsal hippocampal sections; fi, ic, and str for the intermediate hippocampal sections; and fi and ic for the ventral hippocampal sections were averaged and then this averaged value was subtracted from corresponding images. Finally, R software was used to scale data from several independent stainings/plates using generalized residual sum of squares algorithm to account for batch effects of staining intensities (Kreutz et al, ; von der Heyde et al, ).…”

Section: Methodsmentioning

confidence: 99%

Less means more: The magnitude of synaptic plasticity along the hippocampal dorso‐ventral axis is inversely related to the expression levels of plasticity‐related neurotransmitter receptors

Dubovyk

Manahan‐Vaughan

2017

Hippocampus

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The dorsoventral axis of the hippocampus exhibits functional differentiations with regard to (spatial Vs emotional) learning and information retention (rapid encoding Vs long‐term storage), as well as its sensitivity to neuromodulation and information received from extrahippocampal structures. The mechanisms that underlie these differentiations remain unclear. Here, we explored neurotransmitter receptor expression along the dorsoventral hippocampal axis and compared hippocampal synaptic plasticity in the CA1 region of the dorsal (DH), intermediate (IH) and ventral hippocampi (VH). We observed a very distinct gradient of expression of the N‐methyl‐D‐aspartate receptor GluN2B subunit in the Stratum radiatum (DH< IH< VH). A similar distribution gradient (DH< IH< VH) was evident in the hippocampus for GluN1, the metabotropic glutamate receptors mGlu1 and mGlu2/3, GABAB and the dopamine‐D1 receptor. GABAA exhibited the opposite expression relationship (DH > IH > VH). Neurotransmitter release probability was lowest in DH. Surprisingly, identical afferent stimulation conditions resulted in hippocampal synaptic plasticity that was the most robust in the DH, compared with IH and VH. These data suggest that differences in hippocampal information processing and synaptic plasticity along the dorsoventral axis may relate to specific differences in the expression of plasticity‐related neurotransmitter receptors. This gradient may support the fine‐tuning and specificity of hippocampal synaptic encoding.

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Section: Methodsmentioning

confidence: 99%

Less means more: The magnitude of synaptic plasticity along the hippocampal dorso‐ventral axis is inversely related to the expression levels of plasticity‐related neurotransmitter receptors

Dubovyk

Manahan‐Vaughan

2017

Hippocampus

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“…Signal quantification was performed using an ImageQuant system (GE Healthcare). Replicates of dose response data were scaled and averaged using methods described in (22).…”

Section: Immunoprecipitation and Quantitative Immunoblottingmentioning

confidence: 99%

Downregulation of the TGFβ Pseudoreceptor BAMBI in Non–Small Cell Lung Cancer Enhances TGFβ Signaling and Invasion

et al. 2016

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Non-small cell lung cancer (NSCLC) is characterized by early metastasis and has the highest mortality rate among all solid tumors, with the majority of patients diagnosed at an advanced stage where curative therapeutic options are lacking. In this study, we identify a targetable mechanism involving TGFb elevation that orchestrates tumor progression in this disease. Substantial activation of this pathway was detected in human lung cancer tissues with concomitant downregulation of BAMBI, a negative regulator of the TGFb signaling pathway. Alterations of epithelialto-mesenchymal transition (EMT) marker expression were observed in lung cancer samples compared with tumor-free tissues. Distinct alterations in the DNA methylation of the gene regions encoding TGFb pathway components were detected in NSCLC samples compared with tumor-free lung tissues. In particular, epigenetic silencing of BAMBI was identified as a hallmark of NSCLC. Reconstitution of BAMBI expression in NSCLC cells resulted in a marked reduction of TGFb-induced EMT, migration, and invasion in vitro, along with reduced tumor burden and tumor growth in vivo. In conclusion, our results demonstrate how BAMBI downregulation drives the invasiveness of NSCLC, highlighting TGFb signaling as a candidate therapeutic target in this setting. Cancer Res; 76(13); 3785-801. Ó2016 AACR.

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“…, measurements of total protein on one slide per print run with dyes like Fast Green FCF, Sypro Ruby, or colloidal Gold. The signals obtained reflect the total amount of protein per spot immobilized on the solid phase [69,70]. An alternative approach has been shown in a study where an antibody against single-stranded DNA (ssDNA) can be used as a suitable RPPA normalization parameter [71].…”

Section: Reverse Phase Protein Array-proceduresmentioning

confidence: 99%

Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use

Boellner

Becker

2015

Microarrays

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Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.

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RPPanalyzer Toolbox: An Improved R Package for Analysis of Reverse Phase Protein Array Data

Cited by 37 publications

References 21 publications

Less means more: The magnitude of synaptic plasticity along the hippocampal dorso‐ventral axis is inversely related to the expression levels of plasticity‐related neurotransmitter receptors

Less means more: The magnitude of synaptic plasticity along the hippocampal dorso‐ventral axis is inversely related to the expression levels of plasticity‐related neurotransmitter receptors

Downregulation of the TGFβ Pseudoreceptor BAMBI in Non–Small Cell Lung Cancer Enhances TGFβ Signaling and Invasion

Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use

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