- Primary research
- Open Access
A drug screening assay on cancer cells chronically adapted to acidosis
© The Author(s) 2018
- Received: 4 June 2018
- Accepted: 18 September 2018
- Published: 25 September 2018
Drug screening for the identification of compounds with anticancer activity is commonly performed using cell lines cultured under normal oxygen pressure and physiological pH. However, solid tumors are characterized by a microenvironment with limited access to nutrients, reduced oxygen supply and acidosis. Tumor hypoxia and acidosis have been identified as important drivers of malignant progression and contribute to multicellular resistance to different forms of therapy. Tumor acidosis represents an important mechanism mediating drug resistance thus the identification of drugs active on acid-adapted cells may improve the efficacy of cancer therapy.
Here, we characterized human colon carcinoma cells (HCT116) chronically adapted to grow at pH 6.8 and used them to screen the Prestwick drug library for cytotoxic compounds. Analysis of gene expression profiles in parental and low pH-adapted cells showed several differences relating to cell cycle, metabolism and autophagy.
The screen led to the identification of several compounds which were further selected for their preferential cytotoxicity towards acid-adapted cells. Amongst 11 confirmed hits, we primarily focused our investigation on the benzoporphyrin derivative Verteporfin (VP). VP significantly reduced viability in low pH-adapted HCT116 cells as compared to parental HCT116 cells and normal immortalized epithelial cells. The cytotoxic activity of VP was enhanced by light activation and acidic pH culture conditions, likely via increased acid-dependent drug uptake. VP displayed the unique property to cause light-dependent cross-linking of proteins and resulted in accumulation of polyubiquitinated proteins without inducing inhibition of the proteasome.
Our study provides an example and a tool to identify anticancer drugs targeting acid-adapted cancer cells.
- Tumor acidosis
- Drug resistance
- Drug screening
Tumor cells within a tissue are constantly under the selective pressure of the surrounding environment, characterized by heterogeneity in terms of cellular components, availability of nutrients, fluctuating oxygen levels, poor tissue perfusion and low pH [1, 2]. Such a complex environment is poorly reproduced by standard in vitro culture conditions, which provide excessive levels of nutrients and growth factors, an atmospheric oxygen pressure never reached in human tissues (21%) and the physiological pH conditions of healthy tissues (pH 7.4). Drug-resistance is one of the most important problems in clinical oncology , yet anticancer drugs are normally identified and tested using screening procedures that do not consider the biochemical and physical complexity of solid tumors . This classical approach usually results in the identification of substances that inhibit cell proliferation, but not necessarily affecting the survival of non-proliferating cancer cells. One potential approach to overcome multicellular resistance is the use of multicellular spheroids (MCS), since this 3D culture system better reproduces the oxygen, nutrients and pH gradients observed in human tumor tissues [5, 6]. Results from different studies have indicated that such model systems reduce the chances of selecting anticancer compounds with insufficient pharmacological properties.
One of the simplest biochemical properties affecting drugs’ activity, distribution and intracellular accumulation is their charge status in different pH conditions [7, 8]. Cells within solid tumors are known to be exposed to chronic and/or intermittent acidic conditions as a consequence of high metabolic rates, producing acid metabolites which are not sufficiently removed because of scarce vascular perfusion [1, 9]. Acidification of the extracellular environment causes cell cycle arrest, decreased glycolysis and protein synthesis, autophagy and increased angiogenesis and metastases [8, 10]. Besides promoting malignant progression of tumors, tumor acidosis represents an important mechanism of drug resistance, likely associated with poor drug efficacy [3, 8, 11, 12]. In an attempt to overcome acidosis-mediated drug resistance, we developed a drug screening assay to target the colon cancer HCT116 cell line chronically adapted to acidosis. The screening of the Prestwick library compounds led to the identification of the photosensitizer Verteporfin (VP) as an effective compound with preferential activity towards cells in acidic conditions. We also discovered several aspects of the Verteporfin mechanism of action that raise several cautions with regards to interpretation of experimental results with this drug.
Chemical and antibodies
RPMI-1640 (SH30255.01), trypsin (SH40003.12), phosphate-buffered saline (PBS, SH40003.12) and Fetal Bovine Serum (FBS) (SV30160.03) were purchased from HyClone. Sodium Bicarbonate (25080) and RPMI-1640 without NaHCO3 (51800) were purchased from Gibco. Bafilomycin A1 (BafA1, B1793), protease cocktail tablets EDTA-free, phosphatase inhibitors (P5726, P0044) and Verteporfin were purchased from Sigma. Protein assay dye reagent concentrate (500-0006), protein assay standard (5000-0007) and dry milk (170-6404) were purchased from Bio-Rad. The following antibodies were used: LC3B (Cell Signaling Technology, 2775), SQTM1/p62 (BD Biosciences, 610833) and β-actin (Sigma, A5441). HRP-conjugated anti-rabbit (NA934V) and anti-mouse (NXA931) antibodies, ECL system (RPN2106) and PVDF membranes (RPN303F) were purchased from GE Healthcare. The fluorogenic substrate Suc-LLVY-AMC (S-280) was purchased from Boston Biochem (USA).
The colon carcinoma cell line HCT116 was cultured in RPMI-1640 medium supplemented with 10% FBS, antibiotics and 2 g/l NaHCO3. The low pH adapted HCT-116 cell line (AA-HCT116) was obtained by growing the parental cells in RPMI-1640 medium buffered at pH 6.8 (0.15 g/l NaHCO3) for 3 months as previously described [13, 14]. In the settings used, media pH was stable over 48 h and dropped by about 0.1–0.2 units after 3 days in culture for cells kept at pH 6.8 and by 0.3–0.4 units for parental cells. Since parental cells have a higher proliferation rate, so was medium pH dropping faster and cells were passaged every 2–3 days. AA-HCT116 cells were passaged every 4–5 days. The h-TERT RPE1 cell line was cultured in DMEM F12 medium supplemented with 10% FBS and antibiotics. The MelJuSo UbG76V-YFP cell line was cultured in DMEM medium completed with 10% FBS and antibiotics.
Measurements of extracellular acidification rate (ECAR) and oxygen consumption rate (OCR)
HCT116 cells were plated at 60,000 cells/well in 100 µl medium in XF24-well cell plates. Subsequently medium was replaced with 500 µl Seahorse assay medium (1 mM pyruvate, 25 mM glucose and 2 mM glutamine). Oligomycin, FCCP, rotenone and antimycin A were injected according to the Seahorse XF cell mito stress kit. The mitochondrial function was assessed detecting the ECAR and OCR values by using the Seahorse XF analyzer.
Drug screening assay
AA-HCT116 cells were plated at 15,000 cells/well in flat-bottom 96-wells plate, left under the laminar hood for 1 h and then moved to the incubator. On the next day, all plates were treated simultaneously with 10 µM of each of the compounds from the Prestwick chemical library (one compound per well). For each plate, quadruplicate wells were used as untreated controls and quadruplicate wells used for the positive control (VLX600 10 µM) . Plates were then moved back to the incubator and 48 h later cell viability was assessed by the acid phosphatase assay . Hits were identified using a threshold of 70% inhibition of cell viability. Hit confirmation was performed testing each compound in a dose range 0–15 µM in duplicate wells.
Cell viability and clonogenic assay in monolayer and multicellular spheroids cultures
Cells were plated in 96-well plates and the next day treated with different concentrations of the specific compounds. Forty-eight hours after treatment cell viability was evaluated by using the acid phosphatase assay.
For analysis of clonogenic cell survival, HCT116 and AA-HCT116 cells were plated at 300 cells/well in 6-well plates and treated with VP for 8 or 48 h, following culture for 6–8 days in drug-free media. Plates were then washed in PBS and colonies were stained with Giemsa.
Clonogenic cell survival was also assessed on HCT116 MCS treated with different compounds. Briefly, MCS were obtained by a modification of the hanging-drop method applied to 96-well plates as previously described . After drug treatment for 3 days, the MCS were collected, washed in PBS, and a single cell suspension was obtained after incubation with Accutase (Biolegend, 423201). Equal volumes of cells for each treatment condition were plated in triplicate in 6-well plates for 6–8 days, followed by staining the colonies with Giemsa. The software ImageJ was used to perform semi-automated colony counting.
Analysis of intracellular VP accumulation
Cells were plated in black 96-wells plates (Costar) and allowed to adhere overnight.
On the next day, VP was added in a range 0–15 μM for 4 h. After removal of drug containing medium, cells were extensively washed with PBS. VP fluorescence was recorded with excitation wavelength of 450 nm and an emission wavelength of 695 nm  using a fluorescence microplate reader Tecan Infinite M1000 (Tecan, Männedorf, Switzerland). For each condition quadruplicate wells were used and VP fluorescence was normalized to protein content for each well.
Qualitative analysis of intracellular VP was performed by laser-scanning fluorescence microscopy with a Leica confocal microscope.
Studies on autophagic flux
Analysis of the autophagic flux by Western blot was done on different cell lines. Experiments were performed by plating cells in their appropriate medium and allowing them to adhere overnight. On the next day, VP was added at specified concentrations for 4, 8 or 24 h and BafA1 (100 nM) was added during the last 2 h of incubation. Cells were then collected for Western blotting. Analysis of the autophagic flux was performed using the ratio of normalised levels of LC3-II in the presence and absence of BafA1. All experiments were performed in darkness conditions.
Cells were washed with PBS on ice and collected by scraping in cold PBS. The cell pellet was lysed in RIPA buffer (150 mM NaCl, 50 mM Tris pH 7.4, 1% Nonidet P-40, 0.1% SDS and 0.5% sodium deoxycholate) in presence of protease and phosphatase inhibitors. The protein concentration was determined using the Biorad Protein Assay (Biorad Laboratories) and equal amount of proteins (20 µg) was loaded on pre-casted acrylamide gels (4–12% SDS-PAGE, NuPage). The proteins were transferred from the gel to PVDF membrane for 2 h at 4 °C. Red Ponceau staining of the membranes verified the proper loading and transfer. Membranes were blocked in 5% blotting grade dry milk in TBS with 0.1% Tween (TBS-T) for 1 h at room temperature and then incubated with primary antibodies diluted in 5% BSA in TBS-T overnight at 4 °C. The next day membranes were washed and incubated for 1 h at room temperature with the appropriate HRP-conjugated secondary antibody and the binding was revealed by the ECL system.
Analysis of proteasomal activity
The fluorogenic substrate Suc-LLVY-AMC was used to measure the chymotrypsin-like activity of the proteasome on cellular lysates. Briefly, cells were treated with VP or BZ for 4 h, lysed in presence of 0.05% NP40, 1 µM DTT and 2 µM ATP, followed by the addition of Suc-LLVY-AMC (10 μM). Fluorescence intensity was recorded using a Tecan Infinite M1000 microplate reader with excitation wavelength 380 nm and emission wavelength 460 nm.
The cell line MelJuSo UbG76 V-YFP was used as reporter of proteasome inhibition . Cells were plated overnight and then exposed to VP or BZ. Detection of accumulated Ub-YFP was performed by Western blot analysis using an anti-GFP antibody.
RNA sequencing and bioinformatics
RNA sequencing was performed in biological triplicate using Strand-specific TruSeq library preparation and Ribo-Zero ribosomal depletion. Tophat2, HTSeq, and DESeq 2 were utilized for alignment, quantification, and differential expression analysis, respectively, with the hg19 genome and Ensembl v73 [20–22]. All bioinformatics were preformed in the R programming language  and scripts related to the differential expression analysis, gene ontology analysis, and community detection analysis are publically available (https://github.com/GranderLab/acidAdaptedRNAseq) as an R package facilitating reproduction of the analysis and associated figures. Principal component analysis and hierarchical clustering was performed using the prcomp and heatmap.2 functions, respectively, within the R statistical environment. Data was centered and scaled (mean = 0, sd = 1) for each gene previous to clustering and regularize log transformed previous to PCA.
Gene ontology term enrichment
Significant (alpha < 0.05) genes in the differential expression analysis were used for biological processes GO term enrichment analysis with the topGO software . All quantified genes, defined as counts per million > 1 in at least 3 samples, were utilized as the gene universe. Terms with less than 5 annotated genes were not included in the significance testing procedure. Significance testing was performed using the classic Fisher method and the top 1000 terms with the lowest p-value were included in downstream analysis unless otherwise specified.
Community detection analysis
To understand the relationship between the significant GO terms, the GO graph was retrieved for all significant (alpha < 0.05) GO terms using the GOSim Bioconductor package [25, 26]. The GO graph was then utilized for community detection via the spin-glass algorithm  from the igraph package  using a maximum of 200 possible spin states. The authority score was subsequently calculated for all nodes in the GO graph to determine the node with the highest in-degree for each community . The GO graph was then collapsed on the nodes with the highest authority scores (community node) by merging all nodes into said node and simplifying the graphs edges. In cases when several nodes had identical authority scores equaling the max authority score for that community’s nodes, one was chosen at random to represent the community. All nodes not presently contained in the collapsed graph, were merged into the graph and edges were re-drawn between the merged nodes and the community node. Results were visualized with the graph package .
All data were obtained from at least three experimental replicates and presented as mean ± SEM, if not otherwise indicated. Data analysis was performed using Graphpad Prism 6.0 (GraphPad Software, CA). Differences between groups were analysed with parametric or non-parametric tests according to the distribution of the values. The specific test used is indicated in figure legends. The significance level was set as P < 0.05.
Acid-adapted HCT116 cells are resistant towards many clinically used drugs
Phenotypic and transcriptomic profile of acid-adapted cancer cells
We utilized RNA-seq data to perform differential expression analysis and discovered 4796 genes to be significantly (alpha < 0.05) altered in AA-HCT116 cells vs. their parental cell line, with 1283 of these genes exhibiting a fold change > 2 (Additional file 1: Figure S1A).
Thus, AA-HCT116 cells maintained under acidic conditions showed characteristics resembling less differentiated cells and with a decreased proliferation rate, further supporting the use of these cells as a model system for identification of compounds targeting cancer cells under these clinically relevant conditions.
Screening of the Prestwick library of known drugs
Hit compounds from Prestwick compound library
Methyl benzethonium chloride
Treatment of age-related macular degeneration
Activity of Verteporfin in acidic and metabolically-stressed colon cancer cells
VP (trade name Visudyne®) is a benzoporphyrine derivative used as a photodynamic agent for the treatment of macular degeneration, with limited toxicity. Recent studies have proposed that VP has anticancer activity both in vitro and in preclinical animal models [35, 36]. Moreover, VP has been suggested as a specific inhibitor of the YAP-1 protein whose role is important in the biology of colon carcinoma .
VP alters levels of polyubiquitinated proteins without inhibition of the proteasome
We reasoned that disturbance of SQSTM1 function might alter the dynamics of the UPS in AA-HCT116 cells. Utilizing the RNA-seq data, we could identify a clear differential expression of UPS-related genes in AA-HCT116 cells, suggesting that changes in the UPS could be responsible for the increased sensitivity of AA-HCT116 cells to VP treatment (Fig. 7b). Gene ontology (GO) analysis further supported this observation, revealing enrichment of several UPS related gene ontology terms (Additional file 3: Figure S3D). As observed for Bortezomib (BZ), a known proteasome inhibitor, VP treatment also induced a concentration-dependent accumulation of poly-ubiquitinated proteins and concurrent decrease in the amount of free ubiquitin (Fig. 7c), which normally indicates defective proteasomal degradation and/or deubiquitination activity. Interestingly, VP seems to induce the appearance of polyubiquitin complexes with MW higher than those induced by Bortezomib, suggesting some differences in the mechanism of action of these two drugs. To investigate this possibility, we used Suc LLVY-AMC, a fluorogenic substrate for measuring the chymotrypsin-like peptidase activity of the 20S proteasome. HCT116 and AA-HCT116 cells were treated with 1 and 5 µM VP, with BZ used as positive control. As shown in Fig. 7d–e, while the proteolytic activity of the proteasome was strongly reduced by treatment with BZ, no major effects were observed on either of the cell lines treated with VP. Consistent with this observation, VP did not affect degradation of the proteasome substrate UbG76 V-YFP in the MelJuSo reporter cell line, indicating that proteasomal degradation is fully functional in VP-treated cells (Fig. 7f). Moreover, unlike BZ, VP does not affect the expression of cyclin-dependent kinase inhibitor CDKN1A, a protein whose turnover is regulated by proteasomal degradation (Fig. 7g). Due to the light-dependent effects of VP on cell viability, we assessed the effects of light exposure during the treatment and protein extraction steps. As shown in Additional file 3: Figure S3E, the presence of high MW polyubiquitinated proteins was observed when all experimental procedures were conducted in presence of light. In contrast no polyubiquitinated proteins were observed when all procedures were conducted in complete darkness. Taken together, these experiments show that although VP induced the accumulation of high MW ubiquitinated proteins, this effect is light dependent and not due to inhibition of proteasomal activity.
Tumor acidosis has been acknowledged as an important feature of solid tumors that can dramatically alter pathobiology of the disease [8, 10]. Although it has been known that acidosis also negatively modulates drug sensitivity, few studies have aimed to identify agents with preferential activity towards cancer cells cultured in acidic conditions. Standard 2D cell culture has long been applied for the identification of compounds with activities on either proliferation or cell survival in preclinical settings. Conventional culture conditions imply the use of media with high glucose content, non-physiological oxygen pressure and alkaline pH set at 7.4. Overall, such conditions are poorly representative of the complex physiological environment that cancer cells experience in vivo and hence drug screening performed in these simplified conditions might overestimate the potential clinical efficacy of identified compounds. With the aim to partially overcome such limitations, we developed and characterized HCT116 cells chronically adapted to low pH culture conditions. To our knowledge, the characterization of the transcriptome of acid adapted cells has thus far been limited. RNAseq analysis was applied to define major differences between parental and adapted cell lines, as summarized in Fig. 3. Although the full characterization and validation of these data was not in the scope of this study, the analysis suggests distinct biological properties of the low pH adapted AA-HCT116 cells, including a slower proliferation rate and an increased expression of several markers implicated in autophagy and cell differentiation. In line with previous reports on other cell types [34, 43], AA-HCT116 cells show upregulation of several autophagy genes. AA-HCT116 cells also upregulate the expression of CD274 (PDL-1), a molecule whose expression on tumor cells mediates immunosuppression by inhibiting the activation of CTL and NK cells. Interestingly, acidosis is known to have a strong immunosuppressive activity, thus modulation of tumor acidosis has been suggested as a mechanism to improve immune therapy [44–46].
An initial pilot screen with clinically used anticancer drugs showed that nearly all drugs had a lower cytotoxicity on AA-HCT116 as compared to parental HCT116 cells, confirming that cells chronically adapted to acidosis are resistant to many chemotherapeutics. Interestingly, Everolimus was recently reported to selectively target melanoma cells adapted to acidic pH  and in our study the activity of Everolimus and Sorafenib was similar in the two cell lines.
These findings prompted us to use systematic screening to identify compounds with cytotoxic activity also against acid-adapted colon carcinoma cells, leading to the identification of VP as an interesting hit, with equipotent activity also on the adapted cell line. VP has been safely used as a photosensitizer in photodynamic therapy (PDT) of acute macular degeneration and it is under investigation in PDT of pancreatic cancer . Recently, it was suggested that VP specifically targets Yes-associated protein 1 (YAP1), a transcriptional coactivator in the Hippo signaling pathway . Based on this report, VP has been used as a pharmacological tool to study the protumorigenic activity of YAP1 in several cancer models [49–51]. Moreover, some studies have also suggested that VP inhibits YAP activity in the absence of light activation [39, 52]. However, a very recent study has shown that VP demonstrate activity against cancer cell lines that is independent of YAP1 and instead dependent on the ability to induce high MW protein oligomers, in particular STAT3 and SQSTM1 . In fact, VP was recently shown to induce cross-linking of SQSTM1 . In line with these studies, we observed that treatment with VP induces the accumulation of protein oligomers, including SQSTM1, GRP78 and mTOR.
Here, we extend these studies to demonstrate that the activity of VP towards cancer cells is pH-dependent and light-dependent and associated with protein cross-linking and alterations of polyubiquitinated proteins. The exact mechanism by which VP induces such a phenomenon is still unclear. However, we could exclude any involvement of the proteasome since we did not observe any inhibition of proteasomal function upon VP treatment using three different methods. Importantly, we observed that treatment of cells and protein extraction in complete darkness totally abolished the effects of VP on the observed accumulation of poly-ubiquitinated proteins, suggesting that extreme care should be taken in experimental studies addressing the mechanism of action of this drug, as recently pointed out by Kostantinou and colleagues . In fact, contrary to many studies where exposure to ambient light is not specifically addressed in experimental procedures, these authors present strong experimental evidence that cross-linked oligomers and formation of high MW complexes is mostly a light dependent mechanism. In line with this, we observed that the effects of VP on cell viability was also light-dependent since exposure of VP to ambient light for 30 min before treatment greatly increased VP effects in both HCT116 and AA-HCT116 cells.
Although the scope of this study was not to unravel the molecular mechanism by which VP affects cancer cell viability, we observed that VP has a preferential activity towards colon cancer cells grown in acidic conditions. This might be simply related to the higher intracellular availability of VP in both AA-HCT116 and parental HCT116 cells transiently exposed to acidic medium. This behavior may be predicted by the acidic pKa of the compound, which likely facilitates the uptake and intracellular availability.
In conclusion, our study describes the phenotypic and transcriptomic profile of acid adapted colon cancer cells. We used these cells to screen a library of FDA-approved compounds and identified Verteporfin as a hit compound preferentially targeting acidic cancer cells. Given that VP (Visudyne®) is already available for therapeutic applications, its use as anticancer agent might be easily translated into clinical oncology for specific cancer types.
Tumor acidosis is an important factor underlying poor efficacy of anticancer drugs. We have characterized cancer cells chronically adapted to acidosis and used them as a tool to screen for drugs, leading to the identification of Verteporfin as an effective drug preferentially targeting acidic cells. To our knowledge this is the first study assessing the relevance of tumor acidosis in a drug screening perspective.
PP, JTS, NB, MM, IK, DY performed experiments and data analysis; TL, MH, PD, SL designed the study and analysed data, ADM designed the study and led the project. PP, JTS, PD, TL, MH, SL and ADM wrote and reviewed the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Availability of data and materials
Data and reagents are available upon request to ADM. RNAseq data are publicly available as specified in the text.
Consent for publication
Ethics approval and consent to participate
This work was supported by Grants from the Swedish Cancer Society (Grant # CAN 2012/415), the Association for International Cancer Research (Grant #11-0522) and the Robert Lundberg Foundation.
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