Mass Spectrometry-Based Serum and Plasma Peptidome Profiling for Prediction of Treatment Outcome in Patients With Solid Malignancies

Labots, Mariëtte; Schütte, Lisette M.; Mijn, Johannes C. van der; Pham, Thang V.; Jiménez, Connie R.; Verheul, Henk M.W.

doi:10.1634/theoncologist.2014-0101

Cited by 22 publications

(10 citation statements)

References 82 publications

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“…Mass spectroscopy is the most commonly reported technique for the recent investigations screening the LMWF for disease‐related information, probing and profiling proteomic information of hundreds of candidate disease biomarkers without the need for a priori knowledge of their existence or relevance to disease states . Facing the complexity of human serum, most approaches aiming for the identification and validation of LMWF diagnostic biomarkers have introduced HMWF depletion in their protocols .…”

Section: Results and Discussionmentioning

confidence: 99%

Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy

et al. 2016

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Vibrational spectroscopic techniques can detect small variations in molecular content, linked with disease, showing promise for screening and early diagnosis. Biological fluids, particularly blood serum, are potentially valuable for diagnosis purposes. The so-called Low Molecular Weight Fraction (LMWF) contains the associated peptidome and metabolome and has been identified as potentially the most relevant molecular population for disease-associated biomarker research. Although vibrational spectroscopy can deliver a specific chemical fingerprint of the samples, the High Molecular Weight Fraction (HMWF), composed of the most abundant serum proteins, strongly dominates the response and ultimately makes the detection of minor spectral variations a challenging task. Spectroscopic detection of potential serum biomarkers present at relatively low concentrations can be improved using pre-analytical depletion of the HMWF. In the present study, human serum fractionation by centrifugal filtration was used prior to analysis by Attenuated Total Reflection infrared spectroscopy. Using a model sample based on glycine spiked serum, it is demonstrated that the screening of the LMWF can be applied to quantify blinded concentrations up to 50 times lower. Moreover, the approach is easily transferable to different bodily fluids which would support the development of more efficient and suitable clinical protocols exploring vibrational spectroscopy based ex-vivo diagnostic tools

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Section: Results and Discussionmentioning

confidence: 99%

Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy

et al. 2016

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“…43 Aside from appropriate analytical test performance, critical factors to bringing biomarker discovery to approved clinical diagnostics include clearly defined intended use within a target population and utilization of appropriate specimens in preliminary validation studies to obtain sufficient evidence for well-designed validation studies at multiple clinical sites. 43, 44, 45 In conclusion, specific activity of recombinant kinases can be adequately measured on the PTK microarray. For its use with more complex samples containing multiple kinases, the array peptides need further optimization for specificity.…”

Section: Discussionmentioning

confidence: 88%

“…An alternative method to obtain insight into tumor kinase activity is provided using mass spectrometry-based phosphoproteomics. 46 This method provides information on thousands of phosphopeptides per sample but in contrast requires sub- or low milligram-range amounts of protein 47 , which is at the high end of the amount that can be obtained in daily clinical practice from a tumor biopsy (Labots et al , Cancer Res 2015;75(15 Suppl):abstract nr 2007 45 ). Taken together, we aim to enhance the differential potential of the PTK array by using mass spectrometry-based phosphoproteomics to select more discriminative peptides and to enable clinical validation of this assay.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer

et al. 2016

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Personalized cancer medicine aims to accurately predict the response of individual patients to targeted therapies, including tyrosine kinase inhibitors (TKIs). Clinical implementation of this concept requires a robust selection tool. Here, using both cancer cell lines and tumor tissue from patients, we evaluated a high-throughput tyrosine kinase peptide substrate array to determine its readiness as a selection tool for TKI therapy. We found linearly increasing phosphorylation signal intensities of peptides representing kinase activity along the kinetic curve of the assay with 7.5–10 μg of lysate protein and up to 400 μM adenosine triphosphate (ATP). Basal kinase activity profiles were reproducible with intra- and inter-experiment coefficients of variation of <15% and <20%, respectively. Evaluation of 14 tumor cell lines and tissues showed similar consistently high phosphorylated peptides in their basal profiles. Incubation of four patient-derived tumor lysates with the TKIs dasatinib, sunitinib, sorafenib and erlotinib primarily caused inhibition of substrates that were highly phosphorylated in the basal profile analyses. Using recombinant Src and Axl kinase, relative substrate specificity was demonstrated for a subset of peptides, as their phosphorylation was reverted by co-incubation with a specific inhibitor. In conclusion, we demonstrated robust technical specifications of this high-throughput tyrosine kinase peptide microarray. These features required as little as 5–7 μg of protein per sample, facilitating clinical implementation as a TKI selection tool. However, currently available peptide substrates can benefit from an enhancement of the differential potential for complex samples such as tumor lysates. We propose that mass spectrometry-based phosphoproteomics may provide such an enhancement by identifying more discriminative peptides.

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“…Apolipoproteins might be another interesting group for further investigation. In patients with good treatment response they were significantly up-regulated and have already been described as a probable prognostic factor and can be predictive for survival [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases

et al. 2018

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BackgroundMAP kinase inhibitor (MAPKi) therapy for BRAF mutated melanoma is characterized by high response rates but development of drug resistance within a median progression-free survival (PFS) of 9–12 months. Understanding mechanisms of resistance and identifying effective therapeutic alternatives is one of the most important scientific challenges in melanoma. Using proteomics, we want to specifically gain insight into the pathophysiological process of cerebral metastases.MethodsCerebral metastases from melanoma patients were initially analyzed by a LC–MS shotgun approach performed on a QExactive HF hybrid quadrupole-orbitrap mass spectrometer. For further validation steps after bioinformatics analysis, a targeted LC-QQQ-MS approach, as well as Western blot, immunohistochemistry and immunocytochemistry was performed.ResultsIn this pilot study, we were able to identify 5977 proteins by LC–MS analysis (data are available via ProteomeXchange with identifier PXD007592). Based on PFS, samples were classified into good responders (PFS ≥ 6 months) and poor responders (PFS 3 months). By evaluating these proteomic profiles according to gene ontology (GO) terms, KEGG pathways and gene set enrichment analysis (GSEA), we could characterize differences between the two distinct groups. We detected an EMT feature (up-regulation of N-cadherin) as classifier between the two groups, V-type proton ATPases, cell adhesion proteins and several transporter and exchanger proteins to be significantly up-regulated in poor responding patients, whereas good responders showed an immune activation, among other features. We identified class-discriminating proteins based on nearest shrunken centroids, validated and quantified this signature by a targeted approach and could correlate parts of this signature with resistance using the CPL/MUW proteome database and survival of patients by TCGA analysis. We further validated an EMT-like signature as a major discriminator between good and poor responders on primary melanoma cells derived from cerebral metastases. Higher immune activity is demonstrated in patients with good response to MAPKi by immunohistochemical staining of biopsy samples of cerebral melanoma metastases.ConclusionsEmploying proteomic analysis, we confirmed known extra-cerebral resistance mechanisms in the cerebral metastases and further discovered possible brain specific mechanisms of drug efflux, which might serve as treatment targets or as predictive markers for these kinds of metastasis.Electronic supplementary materialThe online version of this article (10.1186/s12014-018-9189-x) contains supplementary material, which is available to authorized users.

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Mass Spectrometry-Based Serum and Plasma Peptidome Profiling for Prediction of Treatment Outcome in Patients With Solid Malignancies

Cited by 22 publications

References 82 publications

Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy

Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy

Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases

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