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Bortel P, Hagn G, Skos L, Bileck A, Paulitschke V, Paulitschke P, Gleiter L, Mohr T, Gerner C, Meier-Menches SM. Memory effects of prior subculture may impact the quality of multiomic perturbation profiles. Proc Natl Acad Sci U S A 2024; 121:e2313851121. [PMID: 38976734 PMCID: PMC11260104 DOI: 10.1073/pnas.2313851121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Mass spectrometry-based omics technologies are increasingly used in perturbation studies to map drug effects to biological pathways by identifying significant molecular events. Significance is influenced by fold change and variation of each molecular parameter, but also by multiple testing corrections. While the fold change is largely determined by the biological system, the variation is determined by experimental workflows. Here, it is shown that memory effects of prior subculture can influence the variation of perturbation profiles using the two colon carcinoma cell lines SW480 and HCT116. These memory effects are largely driven by differences in growth states that persist into the perturbation experiment. In SW480 cells, memory effects combined with moderate treatment effects amplify the variation in multiple omics levels, including eicosadomics, proteomics, and phosphoproteomics. With stronger treatment effects, the memory effect was less pronounced, as demonstrated in HCT116 cells. Subculture homogeneity was controlled by real-time monitoring of cell growth. Controlled homogeneous subculture resulted in a perturbation network of 321 causal conjectures based on combined proteomic and phosphoproteomic data, compared to only 58 causal conjectures without controlling subculture homogeneity in SW480 cells. Some cellular responses and regulatory events were identified that extend the mode of action of arsenic trioxide (ATO) only when accounting for these memory effects. Controlled prior subculture led to the finding of a synergistic combination treatment of ATO with the thioredoxin reductase 1 inhibitor auranofin, which may prove useful in the management of NRF2-mediated resistance mechanisms.
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Affiliation(s)
- Patricia Bortel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Gerhard Hagn
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Lukas Skos
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna1090, Austria
| | - Philipp Paulitschke
- PHIO scientific GmbH, Munich81371, Germany
- Faculty of Physics, Ludwig-Maximilians University of Munich, Munich80539, Germany
| | | | - Thomas Mohr
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Center of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna1090, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
| | - Samuel M. Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
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Proteomic Technology "Lens" for Epithelial-Mesenchymal Transition Process Identification in Oncology. Anal Cell Pathol (Amst) 2019; 2019:3565970. [PMID: 31781477 PMCID: PMC6855076 DOI: 10.1155/2019/3565970] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/20/2019] [Accepted: 09/10/2019] [Indexed: 02/08/2023] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a complex transformation process that induces local and distant progression of many malignant tumours. Due to its complex array of proteins that are dynamically over-/underexpressed during this process, proteomic technologies gained their place in the EMT research in the last years. Proteomics has identified new molecular pathways of this process and brought important insights to develop new therapy targets. Various proteomic tools and multiple combinations were developed in this area. Out of the proteomic technology armentarium, mass spectrometry and array technologies are the most used approaches. The main characteristics of the proteomic technology used in this domain are high throughput and detection of minute concentration in small samples. We present herein, using various proteomic technologies, the identification in cancer cell lines and in tumour tissue EMT-related proteins, proteins that are involved in the activation of different cellular pathways. Proteomics has brought besides standard EMT markers (e.g., cell-cell adhesion proteins and transcription factors) other future potential markers for improving diagnosis, monitoring evolution, and developing new therapy targets. Future will increase the proteomic role in clinical investigation and validation of EMT-related biomarkers.
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Paulitschke V, Eichhoff O, Gerner C, Paulitschke P, Bileck A, Mohr T, Cheng PF, Leitner A, Guenova E, Saulite I, Freiberger SN, Irmisch A, Knapp B, Zila N, Chatziisaak T, Stephan J, Mangana J, Kunstfeld R, Pehamberger H, Aebersold R, Dummer R, Levesque MP. Proteomic identification of a marker signature for MAPKi resistance in melanoma. EMBO J 2019; 38:e95874. [PMID: 31267558 PMCID: PMC6669927 DOI: 10.15252/embj.201695874] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
MAPK inhibitors (MAPKi) show outstanding clinical response rates in melanoma patients harbouring BRAF mutations, but resistance is common. The ability of melanoma cells to switch from melanocytic to mesenchymal phenotypes appears to be associated with therapeutic resistance. High-throughput, subcellular proteome analyses and RNAseq on two panels of primary melanoma cells that were either sensitive or resistant to MAPKi revealed that only 15 proteins were sufficient to distinguish between these phenotypes. The two proteins with the highest discriminatory power were PTRF and IGFBP7, which were both highly upregulated in the mesenchymal-resistant cells. Proteomic analysis of CRISPR/Cas-derived PTRF knockouts revealed targets involved in lysosomal activation, endocytosis, pH regulation, EMT, TGFβ signalling and cell migration and adhesion, as well as a significantly reduced invasive index and ability to form spheres in 3D culture. Overexpression of PTRF led to MAPKi resistance, increased cell adhesion and sphere formation. In addition, immunohistochemistry of patient samples showed that PTRF expression levels were a significant biomarker of poor progression-free survival, and IGFBP7 levels in patient sera were shown to be higher after relapse.
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Affiliation(s)
- Verena Paulitschke
- Department of DermatologyMedical University of ViennaViennaAustria
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Ossia Eichhoff
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Christopher Gerner
- Department of Analytical ChemistryFaculty of ChemistryUniversity of ViennaViennaAustria
| | - Philipp Paulitschke
- Institute of PhysicsCenter for NanoScienceLudwig Maximilians UniversityMunichGermany
| | - Andrea Bileck
- Department of Analytical ChemistryFaculty of ChemistryUniversity of ViennaViennaAustria
| | - Thomas Mohr
- Department of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterMedical University ViennaViennaAustria
| | - Phil F Cheng
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Alexander Leitner
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Emmanuella Guenova
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Ieva Saulite
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Sandra N Freiberger
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Anja Irmisch
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Bernhard Knapp
- Department of StatisticsProtein Informatics GroupUniversity of OxfordOxfordUK
| | - Nina Zila
- Department of DermatologyMedical University of ViennaViennaAustria
| | | | - Jürgen Stephan
- Institute of PhysicsCenter for NanoScienceLudwig Maximilians UniversityMunichGermany
| | - Joanna Mangana
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Rainer Kunstfeld
- Department of DermatologyMedical University of ViennaViennaAustria
| | | | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Reinhard Dummer
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
| | - Mitchell P Levesque
- Department of DermatologyUniversity of Zurich HospitalUniversity of ZurichZurichSwitzerland
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Does the distribution pattern of brain metastases during BRAF inhibitor therapy reflect phenotype switching? Melanoma Res 2018; 27:231-237. [PMID: 28099366 DOI: 10.1097/cmr.0000000000000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Brain metastases (brain mets) are frequent in metastatic melanoma patients. The aim of this study was to investigate the morphology and progression pattern of brain mets in melanoma patients treated with BRAF inhibitors (BRAFi) compared with patients who did not receive targeted therapy (BRAFi group and control group). The number and size of brain mets were compared between a baseline and a comparative MRI at progression. The number of brain mets was grouped into seven number classes (N=1-4, N=5-10, N=11-20, N=21-30, N=31-40, N=41-50, and N>50) and its difference was reported as the change of class that occurred. The mean size of the newly developed lesions was determined by representative measurements and the evolution of three persisting target lesions was assessed on the basis of modified RECIST criteria. Of 96 patients studied, 42 were in the BRAFi group and 54 were in the control group. Patients under BRAFi treatment had a significantly greater increase in the number of brain mets, where the median change of class for the BRAFi compared with the control group was 2 versus 0 (P<0.01). The mean size of the new lesions was smaller in the BRAFi group. Pre-existing target lesions did not show any prominent or different patterns of how they evolved in either group. Brain mets in patients treated with BRAFi showed a progression pattern characterized by a high propensity to disseminate, which might reflect an in-vivo manifestation of phenotype switching in response to targeted therapy, with a predominance of the invasive/migratory tumor cell phenotype. Drivers of invasiveness may present promising targets for therapeutic interventions.
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Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V. Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases. Clin Proteomics 2018. [PMID: 29541007 PMCID: PMC5844114 DOI: 10.1186/s12014-018-9189-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background MAP 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. Methods Cerebral 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. Results In 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 [Formula: see text] 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. Conclusions Employing 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.
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Affiliation(s)
- Nina Zila
- 1Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.,2Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.,3University of Applied Sciences (FH Campus Wien), Vienna, Austria
| | - Andrea Bileck
- 2Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Besnik Muqaku
- 2Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lukas Janker
- 2Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Ossia M Eichhoff
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Christopher Gerner
- 2Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Verena Paulitschke
- 1Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.,Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
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Abstract
PURPOSE OF REVIEW With incidence of melanoma growing worldwide and new therapies prolonging the survival of patients with advanced disease, complex medical care is needed. RECENT FINDINGS Best care of complicated melanoma cases is achieved in specialized referral centers. Aims to provide optimized melanoma therapy, best patient-reported treatment outcome, and successful clinical and translational research, necessitate a dedicated interdisciplinary team. SUMMARY We report on critical aspects of the interaction between patients, medical care givers, clinical trial and biobanking teams, and emphasize the importance of interdisciplinary tumor boards. Specialized skin cancer nurses and local patient advocacy groups should be involved in patient care and could be the binding link between the patients and the treatment team.
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Abstract
Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate.
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Affiliation(s)
- Deepanwita Sengupta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA; Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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