Abstract
Experimental models closely representing in vivo conditions allow investigating mechanisms of resistance. Our aims were to establish a live-cell biobank of malignant pleural mesothelioma (MPM) samples and to obtain proof of principle that primary culture chemoresistant models, mimicking tumor progression observed in patients, can be obtained in vitro, providing a useful tool to investigate underlying mechanisms. Primary mesothelioma cultures were established from 235 samples between 2007 and 2014. Of two MPM patients, primary cultures obtained at different time points: at initial diagnosis, after neoadjuvant treatment at surgery and/or after tumor recurrence, were deeply investigated. Cells and corresponding tumor tissue were characterized by mesothelial protein and gene expression analysis. In addition, primary cultures from chemo naive patients were exposed to increasing doses of cisplatin/pemetrexed during three months and compared with non-treated cells in a cytotoxicity assay, and by selected profiling of senescence markers. In vitro chemoresistance in the primary mesothelioma cell cultures was associated with increased Thy1 (CD90) expression. Thy1 expression in MPM samples was significantly associated with poor overall survival in the TCGA MPM cohort. Our results illustrate that the establishment of a large live-cell MPM biobank contributes to a better understanding of therapy resistance observed in vivo, which eventually may lead to a more logical approach for developing new treatment strategies.
Introduction
Malignant pleural mesothelioma (MPM) is an asbestos-related cancer arising from mesothelial cells of the pleura. The prognosis of MPM patients is poor [median survival of 12 months ()] likely because in most cases diagnosis is made in advanced disease stages. A recent large-scale study based on pathological samples has comprehensively characterized most genetic alterations and distinct molecular profiles in MPM (). However, there is still the need of experimental models to define cancer driver activity of a given genetic alteration, like it has been done with the Nf2-(–) and Bap1-deficient mice (, ). Experimental models may closely resemble in vivo conditions and allow for the testing of novel therapeutic approaches to understand their mechanism of action.
Moreover, experimental models allow for the investigation of resistance mechanisms. Patient-derived xenografts in humanized NSG mice (https://www.jax.org/news-and-insights/jax-blog/2015/april/the-next-big-thing-in-cancer-modeling-patient-derived-xenografts-in-humaniz) would represent the best overall model but currently are difficult to implement for routine purposes. In contrast, cell lines are an easy accessible disease model () that is still accepted for certain investigations, such as molecular mechanism of drug action. Primary mesothelioma cultures were shown as valid model for mechanisms of resistance to pemetrexed, which, in combination with platinum compounds, is a component of current MPM standard neoadjuvant treatment (). According to Cellosaurus (http://web.expasy.org/cgi-bin/cellosaurus/search) there are 402 human mesothelioma cell lines available. Of these cell models, only 11 have a well-profiled genotype (https://portals.broadinstitute.org/ccle/home) and for 45, fingerprinting for identification is available. In addition, long-term passaging leads to genetic drift caused by genomic instability. A recent study () demonstrated an upregulation of glycolytic and oxidative phosphorylation in commercial lines compared to primary cultures. In addition, primary cells maintain expression of podoplanin, which is lost in commercial lines and they show activation of the type I interferon signaling pathway ().
In this study, we tested the hypothesis whether molecular profiling of primary mesothelioma cell culture obtained from patients with MPM are helpful to understand the mechanisms of acquired resistance to cisplatin/pemetrexed treatment in vivo.
Materials and Methods
Tumor
Tissue samples were obtained from patients treated for MPM at the Department of Medical Oncology and Department of Thoracic Surgery between January 2007 and December 2014. The study has been approved by the Zurich Cantonal Ethics Committee (reference numbers StV 24-2005 and 29-2009). Written informed consent was obtained from all patients. Tumor samples obtained from diagnostic biopsies prior to neoadjuvant chemotherapy and the corresponding resection specimens were processed immediately for total RNA extraction using Qiagen RNAeasy kit (Qiagen, Hilden, Germany). In addition, another part of the tumor samples was embedded in OCT and immediately frozen at −80°C. The remaining tumor samples were fixed in 4% buffered formaldehyde for paraffin embedding.
Cell Culture and Senescence-Associated-β-Gal Activity
Primary mesothelioma cell cultures were generated as previously described (). In order to establish a model for chemoresistance, two primary cultures from chemotherapy-naive epithelioid MPM specimens were continually exposed to low doses of cisplatin and pemetrexed according to a previously published method of cisplatin-resistance in ovarian cancer cell lines (). These two cultures originated from two MPM patients. The first primary culture was taken from a biopsy of a male 69-year-old patient (P95), who had an epithelioid MPM (Figures S1 and S2 in Supplementary Material) and was enrolled into the SAKK17/04 study (). The patient, therefore, underwent extrapleural pneumonectomy after neoadjuvant chemotherapy but relapsed 15 months later. He died 27 months after the initial diagnosis. The second culture was established from a female, 50-year-old patient (P236) with papillary epithelioid tumor morphology (Figure S1 in Supplementary Material). The patient underwent partial pleurectomy (Figure S2 in Supplementary Material) but relapsed 19 months later and was operated again, followed by chemotherapy. Unfortunately, the patient died 3 years after the first surgery. In the two chemo-naive primary cultures, cells were treated with cisplatin at the initial dose of 3 and 1 nM pemetrexed. The treatment was conducted in three cycles, including 4 days of treatment and 3 days of recovery time. The concentration was doubled and the procedure was repeated until the concentration of cisplatin and pemetrexed reached 48 and 16 nM, respectively. Chemoresistance induction was evaluated based on the cytotoxicity to a subsequent exposure to cisplatin and pemetrexed. Doubling time was estimated as previously described (). Primary cells were authenticated by DNA fingerprinting of short tandem repeat loci (Microsynth, Switzerland). Senescence-associated-β-gal activity was determined as previously described ().
Relative Gene Expression
To extract RNA, Qiagen RNeasy kit was used. cDNA was determined as previously described (). Selected gene expression [primers are listed in Table S1 in Supplementary Material and (–) analysis using MIQE compliant protocols ()] was conducted as previously described.
Western Blotting
Whole cellular protein extracts were prepared in 95°C Laemmli sample buffer and mechanically sheared by pressing few times through syringes (26 G). Protein concentration was determined using a Pierce™ 660 nm Protein Assay (Thermo Scientific). A total of 5 µg protein per extract was separated on denaturing 10–20% gradient SDS-PAGE gels. Proteins were transferred on PVDF transfer membranes (0.45 µm, Perkin Elmer). Membranes were probed with the following primary antibodies: anti-calretinin (Sigma, HPA007306), mouse anti-actin (#69100) from MP Biomedicals, N-Cadherin (BD Biosciences, 610920), YAP (Cell Signaling 4912), Mesothelin (Rockland Inc. 200-301-A88), GATA4 (C-20) (Santa Cruz sc-1237), p62 (Progen GP62-C), LC3B (Cell Signaling 2775S), p53 (DO-1) (Santa Cruz sc-126), Thy1 (H-110) (Santa Cruz sc-9163), and γ-H2AX (Millipore 05-636). Membranes were then incubated with the secondary antibody rabbit anti-mouse IgG-HRP (A-5420) from Antell, and goat anti-rabbit IgG-HRP (#7074) from Cell Signaling. The signals were detected by enhanced chemiluminescence (ECL™ Western Blotting Reagents, GE Healthcare) and detected on photosensitive film (Super RX Fuji x-Ray Film, Fujifilm). Proteins were quantitated with densitometry using Image J software (Version 1.42q, USA).
Immunofluorescence
Primary cells were grown on 12-mm glass coverslips in 24-well plates. Cells were fixed for 10 min with 4% paraformaldehyde and permeabilized with 0.05% saponin for 5 min. The cells were then incubated over night at 4°C with Calretinin (N-term) (Sigma HPA007306), Podoplanin (D2-40) (Dako M3619), YAP1 (Cell Signaling 4912), Ki67 (Abcam ab8191), Phalloidin 488 (molecular probes A12379), Thy1 (H-110) (Santa Cruz sc-9163), and N-Cadherin from Dako (M3613) diluted in PBS containing 1% bovine serum albumin. Secondary antibodies, Alexa Fluor 488-conjugated goat anti-rabbit IgG (Life Technologies A11034) and Alexa Fluor 555-conjugated goat anti-mouse IgG (Life Technologies A21424) antibody was added for 1 h at RT. Nuclear DNA was stained using DAPI. Coverslips were mounted using Prolong Gold antifade reagent (Life Technologies). Images were acquired using an Olympus BX61 microscope (Schwerzenbach, Switzerland) equipped with an F-view camera for conventional fluorescence imaging. The image capture was controlled with the AnalySISPro software (Soft Imaging System, Münster, Germany).
Surface Phenotyping
Cells resuspended in ice-cold PBS/2mM EDTA were incubated with antibodies against Thy1 (H-110) (Santa Cruz sc-9163) at 4°C for 30 min in the dark. Secondary antibody (PE-labeled, Dianova) was incubated at 4°C for 30 min in the dark. After washing with PBS cells were resuspended in ice-cold PBS/2mM EDTA and fluorescence was measured on an Attune flow cytometer (Applied Biosystems) and analyzed with the Attune cytometric software v1.2.5 (Applied Biosystems).
Genetic Alterations
For DNA isolation from formalin-fixed, paraffin-embedded (FFPE) tissue, two punches of 0.6 mm were taken from the tumor of each FFPE Block. DNA was extracted using the Maxwell 16 FFPE Tissue LEV DNA Purification Kit (Promega) according to the manufacturer’s protocol. Isolated DNA was diluted in nuclease-free water and the concentration was measured by fluorometric quantitation using the Qubit 2.0 fluorometer (Thermo Fisher Scientific).
For targeted amplicon-based sequencing, we developed a custom-designed Ion AmpliSeq MPM Panel (Thermo Fisher Scientific), covering the coding regions of 30 genes that were reported to be commonly mutated in MPM. 10 ng of either FFPE tumor or primary cell DNA were used as an input for library preparation, following the Ion AmpliSeq DNA Library Preparation user guide (Thermo Fisher Scientific). Template preparation and sequencing was performed according to the manufacturer’s protocol (Ion PI Hi-Q OT2 200 Kit User Guide and Ion PI Hi-Q Sequencing 200 Kit, Thermo Fisher Scientific). Alignment, variant calling, and filtering of the resulting data were performed with Ion Reporter 5.0 (Thermo Fisher Scientific). The filtering chain included removal of all synonymous mutations, variants that are found in the UCSC Common SNPs database, variants with an allele ratio below 10% or a read count below 50. Additionally, all mutations were visually inspected, using the Integrative Genomics Viewer Software (Broad Institute).
For array-based genome wide copy number analysis, OncoScan FFPE microarrays (Affymetrix) were conducted at IMGM Laboratories GmbH (Martinsried, Germany). An input amount of 79.2 ng DNA was used for the assay. Molecular inversion probe processing was carried out according to the OncoScan FFPE Assay Kit Protocol (Affymetrix). For data analysis, the AGCC Viewer v4.2.1567 and the OncoScan Console v1.3.0.39 were used (Affymetrix). Copy number variation (CNV) and loss of heterozygosity (LOH) analysis was performed using the Nexus Express for OncoScan v3.1 software. CNVs were visualized using Circos19. Oncoscan have been deposited in GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109305).
Statistics
Data are expressed as mean ± SD. Statistical analysis was performed using Mann–Whitney U tests using StatView 5.0.1 (SAS institute) and t-test using GraphPad. Differences were considered statistically significant at p < 0.05.
Results
Primary Cultures Reflect Tumor Characteristics
Between 2007 and 2014, 235 surgical samples were obtained and processed, as described in Figure 1A. After preservation of tumor material for histopathological evaluation, remaining parts of the tumor were processed in order to extract RNA. Derived cDNA was then used for quality control assays, i.e., for calculation of the MPM score (), allowing to determine that 82% of the samples contained at least 50% tumor cells. In case of large representative tumor tissue, additional parts of the fresh sample were used to establish primary cultures, either in the presence of serum () or in the absence of serum (), for enzymatic analysis () or in situ hybridization (). Successful primary cultures from “bona fide” tumor samples, defined as sufficiently growing cells for collecting RNA and total protein lysates, and preparing frozen stocks, was achieved in 68% of initial samples (159/235).
Figure 1
Primary cultures from two patients (P236 and P95) for whom samples were available at different stages of the disease (for nomenclature defining the different samples from these patients see Figure S2 in Supplementary Material) and where we had observed maintenance of epithelioid histology in one (P236) and epithelial to mesenchymal transition (EMT) in the second (P95), were selected for this proof of principle study. It is worth noting that EMT was evaluated on surgical specimens excluding any diagnostic bias introduced by single biopsy analysis. For these two patients, established primary cultures from different time points were compared with matching initial tumor samples by short tandem repeat analysis (Table S2 in Supplementary Material), Oncoscan CNV testing, and amplicon panel sequencing (Figure 1B). While few genetic alterations were present in P236, consistent with current knowledge on papillary mesothelioma (
N-cadherin, mesothelin, and calretinin MPM biomarker mRNA and protein expression was determined (Figure 1C) and decreasing calretinin expression reflected the evolution of the tumor. A high level of YAP expression was observed in all cultures. Culture heterogeneity was evidenced in one of the patient (P236_cells) by immunofluorescence analysis, revealing that not all cells stained for podoplanin (D2-40), Ki-67, nuclear YAP, or nuclear calretinin, while all cells expressed N-cadherin (Figure 1D). Changes in mesothelin, calretinin and podoplanin gene expression levels were also evaluated in tumor samples (Figure 1E). Differences observed in vivo for selected mRNAs involved either in differentiation (HES1, RUNX2), EMT (GREM1, CTGF), senescence (PUMA, LOX, PAI1), drug transport (SLC22A4, ABCC1), cell cycle (CALB2 (
Development of Chemoresistance Is Accompanied by Increased Levels of DNA Damage, Autophagy and Senescence Marker β-Galactosidase
Malignant pleural mesothelioma chemoresistance models have been described after 96 h exposure of human mesothelioma cell lines to high doses of pemetrexed (
Figure 2

(A) Establishment in vitro of chemoresistant cell lines by exposure to gradually increasing doses of cisplatin/pemetrexed. (B) Cis/pem line established from patient P236A_cells is chemoresistant compared to control when challenged with pemetrexed/cisplatin. Two-way ANOVA with Bonferroni’s post hoc test, *p < 0.01.
We have previously described the occurrence of senescence in MPM patients treated with chemotherapy (
Figure 3

(A) Senescence-associated beta-galactosidase staining in control and cis/pem adapted primary cultures from patient malignant pleural mesothelioma (MPM) 236 and MPM95. Scale bar 25 µm. (B) Expression of senescence-associated secretion phenotype-associated GATA-4 and autophagy activation LC3B and p62. (C) DNA-damage response markers γ-H2AX and p53 stabilization.
Increase in Thy1 Expression in Acquired-Chemoresistance Line
In order to get more insight into events occurring during the development of chemoresistance in primary cultures from patient P236 exposed to cisplatin/pemetrexed, we analyzed the mRNA expression of autophagy/senescence-associated IL-6 and PAI-1 (
Figure 4

(A) Expression of senescence-associated genes IL-6 and PAI-1 and THY1/lnc RP11-334E6.12 during chemoresistance development or tumor progression. (B) Immunofluorescence analysis of Thy1 expression cis/pem and control lines and original primary cultures from tumor samples of malignant pleural mesothelioma (MPM) 236 during tumor progression. (C) Flow cytometry analysis of Thy1 expression in cis/pem vs. control line. (D) lnc RP11-334E6.12 mRNA expression correlates with THY1 expression in MPM tumors.
In the process of trying to better understand mechanisms regulating Thy1 expression, we realized that we had used primers (
Discussion
A national effort in UK has resulted in the establishment of 26 primary mesothelioma cultures within the UK Mesobank (
Primary cultures in cancer research are of high value. Indeed, they represent primary intermediate before growth as xenograft, which, although providing a three-dimensional tissue environment have high-cost and low-throughput capacity. We have highlighted (
Although high-quality repositories such as biobanks and biomolecular resource infrastructures are being established (
In the primary culture from the patient with abundant chromosomal instability (P95), a basal level of chemoresistance associated with senescence-associated phenotype was observed. This is consistent with the presence of the gain of function p53 mutation observed in this patient. Indeed p53Arg280Threo, although not fully oncogenic, has been shown to increase growth in soft agar of p53-deficient cells (
The tumor from the second patient (P236) was of epithelioid morphology, maintaining the same histotype throughout the course of the disease and displayed absence of gross genetic abnormalities. In this context, it is worth noting that in triple negative breast cancer, 26% of cancers lack gross genetic abnormalities and this is likely because they originate from an epithelial precursor with stemness properties (
Primary mesothelioma cultures obtained at a 4-year interval have already been shown to demonstrate increased drug resistance but underlying mechanisms have not been examined yet (
Statements
Ethics statement
Zurich Cantonal Ethics Committee (reference numbers StV 24-2005 and 29-2009).
Author contributions
EF-B and PW designed experiments. KO, JK-R, and EF-B carried out experiments and interpreted data. KO, JK-R, and EF-B generated figures. KO and EF-B wrote the manuscript. All authors read and approved the final manuscript.
Funding
This work was supported by the Swiss National Science Foundation Sinergia grant CRSII3 147697, the Stiftung für Angewandte Krebsforschung and Zürich Krebsliga. Funding bodies had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
Acknowledgments
We are grateful to Gabriela Ziltener and Manuel Ronner for skillful assistance.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Supplementary material
The Supplementary Material for this article can be found online at http://www.frontiersin.org/articles/10.3389/fonc.2018.00040/full#supplementary-material.
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Summary
Keywords
mesothelioma, primary culture, tumor progression, chemoresistance, genetic profiling, mutations, copy number, cisplatin and pemetrexed
Citation
Oehl K, Kresoja-Rakic J, Opitz I, Vrugt B, Weder W, Stahel R, Wild P and Felley-Bosco E (2018) Live-Cell Mesothelioma Biobank to Explore Mechanisms of Tumor Progression. Front. Oncol. 8:40. doi: 10.3389/fonc.2018.00040
Received
13 October 2017
Accepted
05 February 2018
Published
23 February 2018
Volume
8 - 2018
Edited by
Marco Lucchi, University of Pisa, Italy
Reviewed by
Janaki Deepak, University of Maryland, Baltimore, United States; Anca Maria Cimpean, University of Medicine and Pharmacy, Timisoara, Romania
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Copyright
© 2018 Oehl, Kresoja-Rakic, Opitz, Vrugt, Weder, Stahel, Wild and Felley-Bosco.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Emanuela Felley-Bosco, emanuela.felley-bosco@usz.ch
Specialty section: This article was submitted to Thoracic Oncology, a section of the journal Frontiers in Oncology
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