Chemosensitivity Profiles Research Articles

Replication Stress is an Actionable Genetic Vulnerability in Desmoplastic Small Round Cell Tumors.

Desmoplastic small round cell tumor (DSRCT) is an aggressive sarcoma subtype that is driven by the EWS-WT1 chimeric transcription factor. The prognosis for DSRCT is poor, and major advances in treating DSCRT have not occurred for over two decades. To identify effective therapeutic approaches to target DSRCT, we conducted a high-throughput drug sensitivity screen in a DSRCT cell line assessing chemosensitivity profiles for 79 small-molecule inhibitors. DSRCT cells were sensitive to PARP and ATR inhibitors (PARPi, ATRi), as monotherapies and in combination. These effects were recapitulated using multiple clinical PARPi and ATRi in three biologically distinct, clinically-relevant models of DSRCT, including cell lines, a patient-derived xenograft (PDX)-derived organoid model, and a cell line-derived xenograft mouse model. Mechanistically, exposure to a combination of PARPi and ATRi caused increased DNA damage, G2/M checkpoint activation, micronuclei accumulation, replication stress, and R-loop formation. EWS-WT1 silencing abrogated these phenotypes and was epistatic with exogenous expression of the R-loop resolution enzyme RNase H1 in reversing the sensitivity to PARPi and ATRi monotherapies. The combination of PARPi and ATRi also induced EWS-WT1-dependent cell-autonomous activation of the cGAS/STING innate immune pathway and cell surface expression of PD-L1. Taken together, these findings point towards a role for EWS-WT1 in generating R-loop-dependent replication stress that leads to a targetable vulnerability, providing a rationale for the clinical assessment of PARPi and ATRi in DSRCT.

The role of SLC39A4 in the prognosis, immune microenvironment, and contribution to malignant behavior in vivo and in vitro of cervical cancer

BackgroundCervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) are becoming more common in younger women. Solute carrier family 39 member 4 (SLC39A4) produces a zinc ion transporter involved in metastasis and invasion of tumors. MethodsThe Cancer Genome Atlas RNA-seq data was used to investigate the expression of SLC39A4 and its prognostic potential. The assessment of the effect of SLC39A4 on cell growth and migration in CESC was conducted using MTT, colony formation, and Transwell assays. SLC39A4 was studied in vivo using a xenograft mouse model, and its functional involvement in oncogenesis was investigated by identifying the associated differentially expressed genes (DEGs). We evaluated the relationships among SLC39A4 levels, chemosensitivity, radiosensitivity and immune infiltration. ResultsSLC39A4 was upregulated in CESC samples, and individuals with greater SLC39A4 mRNA expression had shorter overall survival. SLC39A4 has been identified to be a regulator of tumor cell metastasis and proliferation in vivo and in vitro, with an area under the curve of 0.874 for diagnosing CESC. In total, 948 DEGs were discovered to be enriched in key CESC progression-related signaling pathways. Additionally, intratumoral immune checkpoint and infiltration activity were associated with SLC39A4 expression. High SLC39A4 expression exhibited poor chemosensitivity and radiosensitivity profiles. ConclusionIn conclusion, SLC39A4 is a key regulator of CESC development, prognosis, and the composition of the tumor immune microenvironment. SLC39A4 could be used as a prognostic or diagnostic screening tool and as a potential target for CESC treatment.

SERPINB7 as a prognostic biomarker in cervical cancer: Association with immune infiltration and facilitation of the malignant phenotype

PurposeThe purpose of this study was to investigate the expression patterns, predictive significance, and roles in the immune microenvironment of Serpin Family-B Member 7 (SERPINB7) in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). MethodsThe expression of SERPINB7 and its prognostic relevance were evaluated using RNA-seq data from The Cancer Genome Atlas. SERPINB7 regulation of CESC cell growth and metastasis was investigated using MTT, scratch, and Transwell assays. In vivo effects of SERPINB7 were examined in xenograft model mice and differentially expressed genes (DEGs) associated with SERPINB7 were identified to explore its functional role in oncogenesis. Associations between SERPINB7 levels, chemosensitivity, and immune infiltration were assessed, and mutations and methylation of SERPINB7 were evaluated using the cBioPortal and MethSurv databases, respectively. ResultsSERPINB7 was up-regulated in CESC samples as well as in other tumors, and patients with higher SERPINB7A mRNA levels exhibited shorter overall survival. The area under the curve for the use of SERPINB7 in CESC diagnosis was above 0.9, and the gene was shown to regulate tumor cell proliferation and metastasis in vitro and in vivo. Overall, 398 DEGs enriched in key CESC progression-related signaling pathways were identified. SERPINB7 expression was additionally correlated with intratumoral immune infiltration and immune checkpoint activity. Patients expressing higher SERPINB7 levels exhibited distinct chemosensitivity profiles, and methylation of the SERPINB7 gene was linked to CESC patient prognostic outcomes. ConclusionSERPINB7 was found to be a crucial regulator of CESC progression, prognosis, and the tumor immune microenvironment, highlighting its potential as a diagnostic and prognostic biomarker and target for CESC immunotherapy.

Abstract A061: Utility of patient-derived organoids for precision pharmacotyping, phenotypic screens, and modeling of pancreatic disease

Abstract Pancreatic ductal adenocarcinoma (PDA) is projected to soon become the second leading cause of cancer death. Aberrant glycosylation is a hallmark of PDA, but the impact of glycosylation remains vastly understudied in PDA. Additionally, a lack of disease models that recapitulate glycosylation differences observed in human disease has hampered efforts to leverage glycan changes as therapeutic strategies. To address these needs, human patient-derived organoids (PDOs) were employed to address three major questions. First, the use of PDOs in drug screening experiments to characterize therapeutic sensitivity and resistance (i.e. “pharmacotyping”) is a promising precision medicine approach to inform clinical decisions. However, the extent to which different sources of basement membrane extracts (BMEs) in which PDOs are cultured contribute to organoid chemosensitivity profiles is unknown. Mouse and human PDA organoids representing a range of PDA disease stages (early, late, and metastasis) were subjected to a chemotherapy and targeted therapy pharmacotyping panel in different commercial BMEs. Differences in growth kinetics and drug response were analyzed. RNA-seq was performed to determine the impact of BME source on gene expression programs. Results from this work will provide key insights regarding optimal growth of pancreatic PDOs as well as the impact of exogenous factors on pharmacotyping results. Second, elevated serum levels of the glycan CA19-9 are observed in more than 75% of PDA patients. Recent evidence demonstrated that CA19-9 promotes pancreatitis and accelerates pancreatic tumorigenesis in mice, phenotypes that are reversible with the use of CA19-9-targeting antibodies. However, how CA19-9 synthesis is regulated is unknown. We developed organoid high-throughput screens to identify compounds that impact CA19-9 production. Continuing this screen across a library of hPDOs will lay the foundation for the identification of new therapeutic candidates and the understanding of regulators of glycosylation in PDA. Lastly, the pancreatitis is a major risk factor for the development of PDA, with hereditary pancreatitis patients having a 40-55% cumulative risk of developing PDA. However, reliable organoid models of human pancreatitis are lacking. To address this need, we optimized methods to derive PDOs from chronic pancreatitis specimens of genetic and non-genetic etiology. Human chronic pancreatitis organoids underwent multi-omic characterization and credentialing in order to provide the field with more representative models of pancreatitis in humans and a platform to explore early detection strategies and study pancreatic disease progression. Overall, we demonstrate the broad utility of PDOs to identify early detection biomarkers and targetable vulnerabilities in PDA. These models are a renewable resource for the field, enabling elucidation of the molecular underpinnings of the increased susceptibility of chronic pancreatitis to PDA and other fundamental aspects of PDA biology. Citation Format: Jan Lumibao, Shira Okhovat, Kristina Peck, Dannielle Engle. Utility of patient-derived organoids for precision pharmacotyping, phenotypic screens, and modeling of pancreatic disease [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A061.

Predicting the chemosensitivity of pancreatic cancer cells as a personalized therapy.

Annually, approx. 4000 patients are diagnosed with pancreatic cancer in Poland, and the number of deaths is close to the number of diagnoses. Such a high morbidity/mortality ratio is caused by a high percentage of unresectable lesions (about 80%) and chemoresistance, which, among other things, is due to the specific desmoplastic environment. Currently, there are 2 main systemic treatment regimens for pancreatic cancer: FOLFIRINOX (which is a combination of folic acid, fluorouracil (5-FU), irinotecan, and oxaliplatin) and combined treatment with nab-paclitaxel plus gemcitabine (NPXL+GMC). In order to increase the effectiveness of systemic treatments for individual patients, cell lines derived from resected pancreatic tumors were developed and their chemosensitivity to various agents was examined. The hypothesis was that patients may benefit from individualization of chemotherapy. Patients with histopathologically confirmed pancreatic cancer were operated on using irreversible electroporation (IRE) procedure. After isolating and establishing individual cell lines, chemosensitivity to 5-FU, GMC and NPXL was determined using MTT assay in primary and metastatic cell cultures. Three primary cell lines were isolated for the prediction of chemosensitivity. Gemcitabine was shown to be more effective at lower doses compared to 5-FU, while NPXL was more effective than 5-FU, and both of these were less effective in metastatic cells. Pancreatic cancer cell chemoresistance was confirmed in stage IV. Determination of chemosensitivity profiles using cell lines may help in the selection of systemic treatments for individual patients. This method can be the basis for a personalized planned chemotherapeutic protocol.

Establishment and Biochemical Characterization of a Multidrug-resistant Promyelocytic Leukemia Cell Line HL-60/CDDP

The present study reports on the establishment, validation and biochemical characterization of a novel chemoresistant variant of the HL-60 acute myeloid leukemia (AML) cell line developed at the Laboratory of Experimental Chemotherapy at the Faculty of Pharmacy of MU-Sofia. Selection of the chemoresistant strain (HL-60/CDDP) has been carried out by prolonged serial exposures of the parent chemosensitive HL-60 cell line to gradually increasing concentrations of the metal complex. In its final variant, the resultant HL-60/CDDP test system showed significantly altered chemosensitivity profiles to the Pt(II)-based drugs cisplatin, carboplatin, oxaliplatin and was maintained in an RPMI-1640 medium containing 25 μM cisplatin. The promyelocytic cells also showed diminished susceptibility to differentiation therapy with arsenic trioxide As2O3. The emergence of the multiresistant phenotype is suggested to be most likely due to common biochemical properties of the screened compounds, including their strong affinity and high reactivity with sulfhydryl SH-groups. The presented study is focused on elucidating the multidrug resistance patterns in the newly established leukemic model that can be used as a potential test system for exploring the drug-resistance reversal capacity of various drugs and experimental compounds.

Phosphoproteomic Analysis of Primary Myeloma Patient Samples Identifies Distinct Phosphorylation Signatures Correlating with Chemo-Sensitivity Profiles in an Ex Vivo Drug Sensitivity Testing Platform

Introduction: Multiple myeloma (MM) is characterized by the clonal expansion of plasma cells in the bone marrow resulting in end-organ damage. Despite an extensive increase in the five-year survival rate in recent years, MM is still considered an incurable disease as patients will repeatedly relapse and develop resistance to current chemotherapies. A key focus for the personalization of myeloma therapy is understanding the biological mechanisms of drug resistance and identifying clinically useful biomarkers of therapeutic response. Highly efficient techniques for the enrichment of phosphorylated peptides followed by high resolution mass spectrometry facilitates the quantitation of thousands of site-specific phosphorylation events. Here, we have performed a phosphoproteomic analysis on MM cell lysates stratified based on their ex vivo drug response profiles to advance our understanding of drug resistance mechanisms.Materials and Methods: CD138 + plasma cells were isolated from 20 adult MM patient bone marrow aspirates at diagnosis (n=7) or relapse (n=13). Samples were grouped based on ex vivo drug sensitivity and resistance testing (DSRT) as follows: highly sensitive (Group I), sensitive (Group II), resistant (Group III), highly resistant (Group IV) [1]. For the phosphoproteomic analysis, peptides were generated and purified using the filter aided sample preparation (FASP) protocol. Peptide tandem mass tag (TMT) labelling, Fe 3+ immobilized metal ion affinity chromatography (IMAC), synchronous precursor selection (SPS), and triple stage tandem mass spectrometry (MS3) was performed. Nonenriched peptides were used for proteomic analysis. Resulting data was analysed using MaxQuant, followed by normalization of phosphosite intensities using the internal reference scale (IRS) method, and statistical analysis using Perseus. Functional enrichment and kinase enrichment analyses were performed on significant phosphoproteins using g:profiler and KEA2, respectively.Results: Our quantitative MS-based phosphoproteomic analysis identified 2,945 phosphorylation sites on 2,232 phosphopeptides from 690 phosphoproteins. Of these phosphorylation sites, 176 were significantly changed between all four DSRT groups and 267 were significantly changed between Group I and Group IV (False Discovery Rate (FDR) < 0.05). Hierarchical clustering was performed to highlight the distinct phosphoproteomic profiles associated with each DSRT group, of which the very sensitive (Group I) and very resistant (Group IV) subgroups demonstrated a well-defined separation (Fig. 1A, 1B). KEGG pathway analysis and gene ontology (GO) analysis of significantly increased phosphorylated proteins in Group IV compared to Group I MM patients demonstrated an increased phosphorylation of proteins associated with tight junctions, the Rap1 signalling pathway and the phosphatidylinositol signalling system; indicating an upregulation of cell adhesion associated processes in drug resistant MM. Phosphoproteins increased in abundance in Group I compared to Group IV MM patients revealed an increased phosphorylation of proteins involved in translation and RNA processing including the spliceosome, RNA transport and RNA binding pathways (Fig. 1C). We identified filamin A serine 2152, RAS guanyl-releasing protein 2 serine 576 and proto-oncogene tyrosine-protein kinase Src serine 17 as increased in Group IV MM, and nuclease-sensitive element-binding protein 1 (YBX1) serine 165, CD44 serine 697 and Bcl2-associated agonist of cell death (BAD) serine 99 as increased in Group I MM. KEA of the upregulated phosphoproteome in Group IV revealed an enrichment of cyclin dependent kinase 1 (CDK1) and ribosomal s6 kinases (RPS6K) whereas casein kinase 2 (CK2) and the glycolysis-associated kinases were enriched in Group I (Fig. 1D).Conclusion: Our study has generated a phosphoproteomic dataset demonstrating distinct phosphorylation signatures associated with drug sensitivity in clinical MM plasma cells. The identification of phosphorylation events associated with drug resistance provides a basis for further exploration of these events and associated signalling pathways to further understand drug resistance mechanisms in MM and identify potential biomarkers of therapeutic response and targets for drug re-sensitization in MM.

A transcriptomic signature to predict adjuvant gemcitabine sensitivity in pancreatic adenocarcinoma

Chemotherapy is the only systemic treatment approved for pancreatic ductal adenocarcinoma (PDAC), with a selection of regimens based on patients' performance status and expected efficacy. The establishment of a potent stratification associated with chemotherapeutic efficacy could potentially improve prognosis by tailoring treatments. Concomitant chemosensitivity and genome-wide RNA profiles were carried out on preclinical models (primary cell cultures and patient-derived xenografts) derived from patients with PDAC included in the PaCaOmics program (NCT01692873). The RNA-based stratification was tested in a monocentric cohort and validated in a multicentric cohort, both retrospectively collected from resected PDAC samples (67 and 368 patients, respectively). Forty-three (65%) and 203 (55%) patients received adjuvant gemcitabine in the monocentric and the multicentric cohorts, respectively. The relationships between predicted gemcitabine sensitivity and patients' overall survival (OS) and disease-free survival were investigated. The GemPred RNA signature was derived from preclinical models, defining gemcitabine sensitive PDAC as GemPred+. Among the patients who received gemcitabine in the test and validation cohorts, the GemPred+ patients had a higher OS than GemPred- (P= 0.046 and P= 0.00216). In both cohorts, the GemPred stratification was not associated with OS among patients who did not receive gemcitabine. Among gemcitabine-treated patients, GemPred+ patients had significantly higher OS than the GemPred-: 91.3 months [95% confidence interval (CI): 61.2-not reached] versus 33 months (95% CI: 24-35.2); hazard ratio 0.403 (95% CI: 0.221-0.735, P= 0.00216). The interaction test for gemcitabine and GemPred+ stratification was significant (P= 0.0245). Multivariate analysis in the gemcitabine-treated population retained an independent predictive value. The RNA-based GemPred stratification predicts the benefit of adjuvant gemcitabine in PDAC patients.

In silico analysis of DYNLL1 expression in ovarian cancer chemoresistance.

Ovarian cancer (OC) is the most lethal gynecological cancer and chemoresistance is responsible for the treatment failure and unfavorable clinical outcome in this disease. The deletion of DYNLL1 was reported to result in increased chemoresistance in BRCA1-mutant high-grade serous ovarian carcinoma cells. Considering its role in chemoresistance, a better understanding of DYNLL1 expression is needed to develop novel strategies in the treatment of OC. In the current study, we aimed to investigate the differential expression of DYNLL1 in OC with respect to cell types, chemosensitivity profiles, certain drug treatments, and cancer progression. DYNLL1 levels were analyzed using expression profiling data sets from Gene Expression Omnibus and quantitative reverse-transcription polymerase chain reaction in R. We found that the level of DYNLL1 was higher in OC histotypes compared with normal ovarian cells. DYNLL1 expression is decreased in OC cells of epithelial type; but, it is increased in OC cells of stromal type, compared with matched control cells. Chemoresistant OC cells were shown to have lower DYNLL1 expression than chemosensitive OC cells. Carboplatin and NSC319726 treatments resulted in slightly decreased DYNLL1 expression and DYNLL1 levels were decreased in the course of cancer progression in OC epithelial cells. The results suggest that changes in DYNLL1 expression in OC might be cell-type dependent and lower DYNLL1 levels may be associated with increased chemoresistance in OC. Although further studies are needed, certain drugs and cancer progression may lead to lower DYNLL1 levels, possibly resulting in increased chemoresistance. Therefore, it can be stated that DYNLL1 might be an important player in OC progression and chemoresistance.

The Effect of Olaparib and Bortezomib Combination Treatment on Ovarian Cancer Cell Lines

Objective: Ovarian cancer (OC) is the deadliest gynecologic malignancy and has a poor survival rate due to late diagnosis and chemoresistance development. In the standard treatment of OC, platinum-based chemotherapeutics are used. However, following several rounds of chemotherapy, these drugs’ efficacy eventually becomes limited due to the development of chemoresistance in most patients who previously responded to this treatment. Therefore, overcoming chemoresistance in the treatment of OC is of high importance. In this study, we investigated the effect of combinatorial inhibition of poly(ADPribose) polymerase (PARP) and proteasome by olaparib and bortezomib on chemosensitive and chemoresistant OC cell lines. Materials and Methods: We used sulphorhodamine B assay to screen cell viability following drug treatments alone or in combination, and used the cytotoxicity data to model the effect of drugs on cell death in R programming environment. In addition to olaparib and bortezomib, we performed cytotoxicity screenings where we applied cisplatin to OC cells. We also carried out flow cytometry analysis to quantify apoptotic cells following treatments. Results: We showed that combination treatment was more effective on chemosensitive OC cell lines when cisplatin was not used. In the presence of cisplatin, olaparib and bortezomib combination treatment resulted in higher cytotoxicity in chemoresistant OC lines compared to chemosensitive OC cell lines. Combinatorial inhibition of PARP and proteasome led to a higher number of apoptotic cells in OV2008 chemosensitive cell line compared to drugs alone. Conclusion: Our data shows that olaparib and bortezomib combination treatment might show promise in vivo in the treatment of OC. Also, the efficacy of this combination treatment might be dependent on OC cells’ chemosensitivity profiles.

Precise Modeling of IKZF1 Alterations in Human B-Cell Acute Lymphoblastic Leukemia Cell Lines Reveals Distinct Chemosensitivity, Homing, and Engraftment Properties

Around 20% of pediatric and the majority of adults with B-cell acute lymphoblastic leukemia (B-ALL) suffer relapse, and prognosis after relapse is very poor. Therefore, identifying those at risk for treatment failure and improving their outcome is imperative. In B-ALL, deletions and mutations of the gene IKAROS family zinc finger 1 (IKZF1) are associated with an increased risk of relapse. IKZF1 encodes the IKAROS protein, which is a master lymphoid regulatory transcription factor and chromatin remodeler. Somatic IKZF1 lesions are thought to be secondarily acquired, arising in lymphoblasts with existing driver genetic lesions, most commonly co-occurring with BCR-ABL1 fusion, activating kinase fusions of Ph-like disease and deregulated DUX4 and ERG. In B-ALL, mono- or bi-allelic deletions of the entire gene, as well as intragenic deletions occur. One of the most common perturbations of IKZF1 in B-ALL is an intragenic deletion of a 50-kilobase (kb) region containing exons 4-7, resulting in the expression of a dominant-negative isoform, IK6. Recently published clinical data show potentially conflicting results over the benefits of therapy intensification in IKZF1-mutant cases (Clappier et al., 2015; Hinze et al., 2017; & Yeoh, et al., 2018). Human cell models of these deletions are needed, as there may be unknown functional differences among mutation types, and the available body of data relies on clinical statistical associations, in vitro RNA interference, viral overexpression of IK6, and mouse models.We used the CRISPR/Cas9 system in the human B-ALL cell lines Nalm-6 and REH by electroporation with sgRNA-Cas9 ribonucleoprotein complexes (RNPs) to generate IKZF1-mutant clones. We identified single cell-derived clonal lines with IKZF1 frameshift mutations in one or both alleles by Sanger sequencing and TIDE decomposition. We confirmed ablation of protein expression by immunoblotting. We treated the IKZF1-mutant clonal cell lines with chemotherapeutic agents commonly used to treat B-ALL and calculated the IC50 by Annexin V/7-AAD double-negative population after 48-72 hour treatment. Compared to IKZF1-wild type Nalm-6 cells, Nalm-6 IKZF1-/- clones exhibited profound resistance to dexamethasone and modest but significant resistance to most other chemotherapeutics tested including vincristine, asparaginase, and daunorubicin. In contrast, these cell lines were more sensitive to the nucleoside analog, cytarabine (Panel A). We next analyzed gene expression profiles by RNA-seq and observed that IKZF1-/- clones are characterized by a stem cell-like gene expression signature and activation of the JAK/STAT pathway (Panel B). Transplantation into immunodeficient NOD scid gamma (NSG) mice demonstrated that IKZF1 deletion leads to enhanced engraftment, significantly increased bone marrow homing, and reduced survival time (Panel D).We also employed a novel CRISPR/Cas9 homology-directed repair (HDR) strategy to generate clonal cell lines expressing IK6 under control of the endogenous promoter, which represents a significant advantage to many previous studies utilizing viral overexpression. We electroporated the cells with sgRNA-Cas9 RNPs along with a 3kb commercially synthesized double-stranded DNA HDR template that knocks-in exon 8 with a GFP tag directly following exon 3. Using this strategy, we were able to isolate heterozygous clones (IKZF1IK6/+) from both Nalm-6 (Panel C) and REH cell lines using flow cytometry sorting for GFP-positive cells. We confirmed precise HDR by Sanger sequencing and immunoblotting. When transplanted into immunodeficient mice, IKZF1IK6/+ cells showed delayed engraftment and disease onset, but profound splenic infiltration, consistent with a more indolent, infiltrative disease phenotype (Panels D & E). Ongoing drug treatment assays suggest the chemosensitivity profiles of IKZF1IK6/+ and IKZF1IK6/- clonal cell lines are distinct from their isogenic IKZF1-/- counterparts.Our data support clinical studies reporting that IKZF1-mutated B-ALL is an aggressive, infiltrative, and treatment-resistant disease. Notable differences in drug response and in vivo dynamics in xenografts exist between IKZF1-/- cells and IKZF1IK6/+ cells. Detailed delineation of the exact IKZF1 status in ALL patients at diagnosis may be informative in more accurately determining risk stratification and the most effective therapeutic regimen. DisclosuresNo relevant conflicts of interest to declare.

Secdrug: A Computational Method for Discovering Novel Secondary Drug Combinations Using Large-Scale Pharmacogenomics Databases

Drug resistance is a major obstacle in achieving complete and sustained therapeutic effect in cancer chemotherapy. Chemo-resistance may also lead to over-dosing and unwanted exposure to ineffective anti-tumor agents thereby increasing the risk of negative side-effects and the cost of drug development. Therefore, our goal is to utilize a large-scale pharmacogenomics database (Genomics of Drug Sensitivity in Cancer or GDSC, the largest public resource of drug-sensitivity data on over 250 drugs in more than 1000 human cancer cell lines of common and rare types of adult and childhood cancers of diverse origin) and develop a prediction method to identify novel secondary drug combination regimens that may effectively reverse drug resistance.We utilized a greedy algorithm-based set-covering computational optimization method followed by a regularization technique to seek all secondary drugs that could kill maximum number of cell lines of the test disease (B-Cell cancers) resistant to the test drug (the Proteasome inhibitor/PI drug Bortezomib/Bz/Velcade) in a sequential manner ordered by the number of cell lines killed. The predicted top secondary drug combinations in PI-resistant B-cell cancers are shown in Figure 1.To validate our prediction results, we treated human multiple myeloma cell lines (HMCLs) highly resistant to the proteasome inhibitors Bortezomib, Carfilzomob, Oprozomib and Ixazomib with the predicted best secondary drugs. Figure 2 depicts In vitro chemo-sensitivity profiles of PI-resistant HMCLs and other B-cell cancer cell lines showing percent survival compared to untreated control at increasing concentrations of secondary drugs, as single agents or in combination.Furthermore, for each drug in the predicted drug combination, we identified differentially expressed (DE) genes by comparing the expression profiles between extraordinary- sensitive and resistant cell lines. These significantly regulated DE genes were used to identify pathways associated with the successful drug combinations.Finally, we developed an R software package secDrug based on this computational pipeline for predicting novel secondary therapies in chemotherapy-resistant cancers. secDrug takes a query of any cancer type and any test drug, and outputs a list of the top secondary drug combinations with confidence score and biological pathway visualization. Thus, secDrug has potential application in clinical decision-making for discovering resistance-reversing cancer chemotherapy regimens. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness

Osteosarcoma (OS) is an aggressive sarcoma, where novel treatment approaches are required. Genomic studies suggest that a subset of OS, including OS tumour cell lines (TCLs), exhibit genomic loss of heterozygosity (LOH) patterns reminiscent of BRCA1 or BRCA2 mutant tumours. This raises the possibility that PARP inhibitors (PARPi), used to treat BRCA1/2 mutant cancers, could be used to target OS. Using high-throughput drug sensitivity screening we generated chemosensitivity profiles for 79 small molecule inhibitors, including three clinical PARPi. Drug screening was performed in 88 tumour cell lines, including 18 OS TCLs. This identified known sensitivity effects in OS TCLs, such as sensitivity to FGFR inhibitors. When compared to BRCA1/2 mutant TCLs, OS TCLs, with the exception of LM7, were PARPi resistant, including those with previously determined BRCAness LoH profiles. Post-screen validation experiments confirmed PARPi sensitivity in LM7 cells as well as a defect in the ability to form nuclear RAD51 foci in response to DNA damage. LM7 provides one OS model for the study of PARPi sensitivity through a potential defect in RAD51-mediated DNA repair. The drug sensitivity dataset we generated in 88 TCLs could also serve as a resource for the study of drug sensitivity effects in OS.

Evaluation of the in vitro Chemosensitivity and Correlation with Clinical Outcomes in Lung Cancer using the ATP-TCA.

Multiple drug resistance (MDR) to chemotherapeutic agents often leads to a failure to respond to chemotherapy. We utilized an in vitro chemosensitivity test to identify sensitive and effective chemotherapeutic drugs and further elucidated the correlation between the in vivo chemosensitivity and clinical outcomes. Here, we evaluated the in vitro chemosensitivity and MDR of 120 lung cancer patients to eight singledrug chemotherapies and of 291 lung cancer patients to seven chemotherapy regimens using an ATP-based tumor chemosensitivity assay (ATP-TCA). Additionally, the chemosensitivity profiles of lung adenocarcinoma patients (284 cases) and lung squamous cell carcinoma patients (90 cases) to these single-drug and chemotherapy regimens were compared. Furthermore, the correlations between the chemosensitivity and clinical outcomes were investigated in 16 stage III squamous cell carcinoma patients. PTX (51.7%), TXT (43.3%), GEM (12.5%), PTX+DDP (62.5%), TXT+L-OHP (54.3%) and VP-16+DDP (16.2%) had the highest in vitro chemosensitivity rates. Approximately 31.7% of patients developed resistance to all eight single-drug chemotherapies, and 25.8% of patients displayed resistance to all seven chemotherapy regimens. In addition, lung squamous cell carcinoma was significantly more sensitive to GEM and MTA+DDP than lung adenocarcinoma (P<0.05). Further analysis showed that patients with higher drug sensitivity tended to have longer disease-free survival (18 months vs. 8.5 months) than patients displaying drug resistance (P<0.05). These results suggest that the implementation of in vitro drug susceptibility testing before chemotherapy can effectively prevent the occurrence of primary drug resistance and inappropriate drug treatment.

Using patient-derived xenograft models of colorectal liver metastases to predict chemosensitivity

BackgroundFew in vivo models for colorectal cancer have been demonstrated to show external validity by accurately predicting clinical patient outcomes. Patient-derived xenograft (PDX) models of cancer have characteristics that might provide a form of translational research leading to personalized cancer care. The aim of this pilot study was to assess the feasibility of using PDXs as a platform for predicting patient colorectal liver metastases responses, in this case by correlating PDX and patient tumor responses to either folinic acid, fluorouracil plus oxaliplatin or folinic acid, fluorouracil plus irinotecan-based regimens. MethodsSixteen patients underwent potentially curative resection of colorectal liver metastases, and tumors were grafted into NOD.CB17-Prkdcscid/Arc mice. Mice were divided into groups to determine relative tumor growth in response to treatment. Tumors were analyzed by immunohistochemistry for Ki67 and Excision repair cross-complementation group 1. ResultsAn engraftment rate of 81% was achieved. Overall, there was a 67% positive match rate between eligible patient and PDX chemosensitivity profiles. There was a significant difference in relative decrease in Ki67 expression between sensitive/stable versus resistant PDXs for both treatment regimens. There was no statistically significant correlation between baseline ERCC1 expression and response to Oxaliplatin + 5-Fluorouracil in the PDXs. ConclusionsThis pilot study supports the feasibility of using PDX models of advanced colorectal cancer in larger studies to potentially predict patient chemosensitivity profiles.

Human lung adenocarcinoma cell cultures derived from malignant pleural effusions as model system to predict patients chemosensitivity.

BackgroundLung cancer is the leading cause of cancer related deaths and Malignant Pleural Effusion (MPE) is a frequent complication. Current therapies suffer from lack of efficacy in a great percentage of cases, especially when cancer is diagnosed at a late stage. Moreover patients’ responses vary and the outcome is unpredictable. Therefore, the identification of patients who will benefit most of chemotherapy treatment is important for accurate prognostication and better outcome. In this study, using malignant pleural effusions (MPE) from non-small cell lung cancer (NSCLC) patients, we established a collection of patient-derived Adenocarcinoma cultures which were characterized for their sensitivity to chemotherapeutic drugs used in the clinical practice.MethodsTumor cells present in MPEs of patients with NSCLC were isolated by density gradient centrifugation, placed in culture and genotyped by next generation sequencing. In a subset of cases patient derived xenografts (PDX) were obtained upon tumor cell inoculation in rag2/IL2 knock-out mice. Isolated primary cultures were characterized and tested for drug sensitivity by in vitro proliferation assays. Additivity, antagonism or synergy for combinatorial treatments were determined by analysis with the Calcusyn software.ResultsWe have optimized isolation procedures and culture conditions to expand in vitro primary cultures from Malignant Pleural Effusions (MPEs) of patients affected by lung adenocarcinomas, the most frequent form of non small cell lung cancer. Using this approach we have been able to establish 16 primary cultures from MPEs. Cells were banked at low passages and were characterized for their mutational pattern by next generation sequencing for most common driver mutations in lung cancer. Moreover, amplified cultures were shown to engraft with high efficiency when injected in immunocompromised mice. Cancer cell sensitivity to drugs used in standard chemotherapy regimens was assessed either individually or in combination. Differential chemosensitivity and different mutation profiles were observed which suggests that this isolation method could provide a platform for predicting the efficacy of chemotherapy in the clinical setting. Most importantly for six patients it was possible to establish a correlation between drug response in vitro and response to therapy in the clinic.ConclusionsResults obtained using primary cultured cells from MPEs underscore the heterogeneity of NSCLC in advanced stage as indicated by drug response and mutation profile. Comparison of data obtained from in vitro assays with patients’ responses to therapy leads to the conclusion that this strategy may provide a potentially useful approach for evaluating individual chemosensitivity profile and tailor the therapy accordingly. Furthermore, combining MPE-derived primary cultures with their genomic testing allows to identify patients eligible to trials with novel targeted agents.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-016-0816-x) contains supplementary material, which is available to authorized users.

ATCT-14CHEMOSENSITIVITY OF PRIMARY AND METASTATIC CNS TUMORS TO 4-DEMETHYL-4-CHOLESTERYLOXYCARBONYLPENCLOMEDINE (DM-CHOC-PEN) AND TEMOZOLOMIDE

BACKGROUND: The efficacy of TMZ in the treatment of high-grade astrocytomas is limited by drug-resistance mediated by O6-methylguanine-DNA methyltransferase (MGMT). Brain metastases are difficult to treat and currently no standard chemotherapeutic therapies exist. 4-Demethyl-4-cholesteryloxycarbonylpenclomedine (DM-CHOC-PEN) is a polychlorinated pyridine cholesteryl carbonate whose mechanism of action is via alkylation of DNA at N7-guanine. This agent has had early therapeutic success in treating both primary and metastatic CNS malignancies in Phase I and Phase II clinical trials. METHODS: To better understand the sensitivity and mechanisms of resistance in primary and metastatic CNS tumors, we collected tissue from subjects (n = 38) enrolled between March 2014 - January 2015 for chemosensitivity studies. These included high-grade astrocytomas (9), metastatic brain tumors (6) meningiomas (6), and other more benign tumors such as pituitary adenomas (4), hemangioblastoma (1), and chondrosarcoma (1). Using viable tumor cell explants from surgery, cells were grown under standard conditions (RPMI/FBS, 5%CO2, 37°C), in vitro chemosensitivity profiles were obtained comparing DM-CHOC-PEN vs. TMZ and other commonly used anti-cancer agents. RESULTS: Tumor cells exhibited higher susceptibility to DM-CHOC-PEN than to TMZ (RR = 3.19, p = 0.0029, 95% confidence interval [CI], 1.3-7.8 vs. TMZ). In a subgroup analysis of high-grade astrocytomas, atypical meningiomas, and secondary metastases in this cohort, an association was noted between TMZ-resistance (µIC50 = 3.3, S.D. = 0.46) and DM-CHOC-PEN-sensitivity (µIC50 = 1.0, S.D = 0.26) using two-sample independent, Student's t-test with Fisher's exact P-value (p = 0.0001, t(23.72) = 4.5, df = 27.17). CONCLUSIONS: These preliminary results suggest that DM-CHOC-PEN may promote cell death in tumors possessing acquired MGMT-mediated drug-resistance. Furthermore, it supports roles for this promising new agent in the treatment of primary and metastatic brain tumors and in treatment of high-grade astrocytomas, either in combination with TMZ or alone in cases of TMZ-resistance.

Temporal bone carcinoma: a first glance beyond the conventional clinical and pathological prognostic factors

Temporal bone squamous cell carcinoma (TBSCC) is an uncommon, aggressive malignancy with a poor prognosis in advanced cases. The dismal outcome is partially related to: the lack of reliable clinical or pathological prognostic factors and the largely unstandardized surgical and integrated treatments adopted. There is an undeniable need for novel diagnostic/therapeutic strategies to improve the prognosis. The purpose of this critical review was to explore the level of available knowledge concerning the molecular markers involved in the biology of TBSCC that have a prognostic potential. The Pub-Med and Scopus electronic databases were searched without publication date limits for studies investigating molecular markers in cohorts of patients with primary TBSCC. The search terms used were: "temporal bone cancer", "temporal bone carcinoma", "temporal bone malignancy", "ear cancer", "ear carcinoma", and "ear malignancy". We decided preliminarily not to consider series with less than five cases. Nine retrospective case series of TBSCC were found in which different analytical techniques had been used to study the role of several biomarkers (HPV, vimentin, transforming growth factor β, CD105, RECK, matrix metalloproteinase-9, MASPIN, EBV, p16, TP53 mutation, pSTAT3, relaxin-2). CD105 expression (in tumor vessel endothelial cells) and MASPIN cytoplasmic expression (in carcinoma cells) were, respectively, found directly and inversely related with the neoplasm's recurrence rate. CD105 expression was also inversely related with disease-free survival in TBSCC. A future goal of such analyses should be to ascertain the radio- and chemo-sensitivity profiles of individual TBSCCs, enabling truly personalized therapies. A further, more ambitious goal will be to find targets for therapeutic agents that might prove crucial in improving the disease-specific survival for patients with advanced TBSCC.

Abstract 4128: Extensive morphological heterogeneity of circulating and selected high metastatic variants and differential chemosensitivity of human prostate cancer in mouse models

Abstract Circulating PC-3-GFP human prostate cancer cells were collected from the blood from nude mice orthotopically implanted with PC-3-GFP. In parallel experiments, a highly metastatic PC-3-GFP cell line was developed by injecting parental PC-3-GFP to the footpad of nude mice which metastasized to inguinal lymph nodes from which the cancer cells were collected and were re-injected to the footpad. After 6 cycles, the PC-3-GFP cells collected from inguinal lymph nodes (PC-3-GFP-LN) and were injected to the footpad. PC-3-GFP-LN showed 100% metastasis to major lymph nodes (popliteal, inguinal, axillary, and cervical), and 100% metastasis to bone and lung. PC-3-GFP-CTC and PC-3-GFP-LN were cultured in vitro, and their morphology and chemo-sensitivity were comparing to the parental PC-3-GFP cells. Highly pleomorphic subpopulations of prostate cancer cells were identified in PC-3-GFP-CTC and PC-3-GFP-LN. The different cell subtypes included characteristic high malignancy features such as high nucleus to cytoplasmic (N/C) ratios and giant cell formation as a result of abnormal mitoses. Variations in growth rate, plating efficiency, size, shape, and number of the nuclei and nucleoli were observed. The results suggest extensive tumor heterogeneity in both sublines. The giant cells, contain multiple nuclei, cannot survive by themselves and need small cells around them in order to proliferate. However, giant cells also can produce smaller cells, which divide further. The ratio of giant cells/total cells were significantly higher in PC-3-GFP-LN compared to parental cells. However, the morphology of cells from lung metastasis and bone metastasis showed lung and bone epithelial features such as squamous on shape and tightly packed together. PC-3-GFP-CTC had similar sensitivity to both cisplatinum and docetaxel when compared to PC-3-parental cells. PC-3-GFP-LN was resistant. In contrast, PC-3-GFP-LN was sensitive to the traditional Chinese medicine (TCM) herbal mixture LQ similar to the parental cells. These results demonstrate that circulating tumor cells (CTCs) and selected high metastatic variants can be extensively heterogeneous and have different chemosensitivity profiles, suggesting new approaches to treatment such as with TCM. Citation Format: Lei Zhang, Chengyu Wu, Robert. M Hoffman. Extensive morphological heterogeneity of circulating and selected high metastatic variants and differential chemosensitivity of human prostate cancer in mouse models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4128. doi:10.1158/1538-7445.AM2015-4128

Abstract 3381: Overcoming resistance to BRAF inhibitors in colon cancer and melanoma cell lines.

Abstract Mutations in the B-raf oncogene constitutively activate the RAF-MEK-ERK signaling pathway, a key regulator of cell proliferation and survival. The most common BRAF mutation (V600E) occurs in approximately 70% of primary melanomas and 10% of colorectal cancers. Melanoma patients carrying the BRAF(V600) mutation respond with frequency of 80% to the BRAF inhibitor vemurafenib, while colon cancer patients respond at a rate of 5% only, indicative of intrinsic resistance. Moreover, clinical benefit is further limited by the rapid emergence of acquired resistance among vemurafenib responders. Combination therapy targeting both BRAF(V600E) and possible escape pathways appears to be a promising approach to reverse resistance to BRAF inhibitors. Here, we present the molecular characterization and in vitro chemosensitivity profiles of 20 melanoma and 20 human colorectal cancer cell lines. Four of the colon and 11 of the melanoma cell lines were established at Oncotest from patient-derived tumor xenografts (PDX). Molecular profiles include the mutation status of BRAF, PIK3CA, KRAS, and NRAS (exon sequencing) and protein levels for components of the MAPK, EGFR and PI3K/AKT pathways (Western blot analysis). Sensitivity profiles for inhibitors of BRAF, MEK, EGFR and PI3K were determined in vitro using a fluorescence-based survival and proliferation assay. Overcoming resistance to BRAF inhibitors was investigated by combination of vemurafenib with other inhibitors of the RAF-MEK-ERK pathway or inhibitors of potential escape pathways like EGFR, PI3K/AKT or c-MET and evaluated by combination index according to Chou-Talalay. In line with the clinical situation, the BRAF V600E substitution was found in 13/20 (65%) of the melanoma and only in 4/20 (20%) of the colon cancer cell lines. BRAF and NRAS mutations were mutually exclusive in melanoma cell lines and KRAS mutations did not occur at all. Among the colon cancer cell lines, in addition to the BRAF(v600E) mutation, alteration in KRAS (10/20 cell lines), PIK3CA (6/20) and NRAS (1/20) were detected. Chemosensitivity profiling revealed intrinsic resistance to BRAF inhibitors for 3/13 (23%) BRAF(V600E) melanoma cell lines and for 3/4 (75%) BRAF(V600E) colon cancer cell lines. Reversal of the resistance of BRAF inhibitor-insensitive melanoma cell lines was recorded as synergism between vemurafenib and inhibitors of vasious kinases (c-MET, AKT, PI3K, MEK, or EGFR. A particularly strong synergistic interaction was found for vemurafenib and the c-MET inhibitor SU11274, irrespective of BRAF status. For colon cancer cell lines, the strongest synergisms were detected for the combinations of vemurafenib with inhibitors of c-MET, EGFR, PI3K, AKT and MEK. Displaying similar mutation and chemosensitivity profiles as melanomas and colon cancers in the clinic, the present cell line panels represent valuable tools to investigate the reversal of resistance towards BRAF inhibitors. Citation Format: Gerhard Kelter, Rebekka Krumbach, Torsten Giesemann, Vincent Vuaroqueaux, Thomas Metz, Thomas Metcalfe, Heinz-Herbert Fiebig. Overcoming resistance to BRAF inhibitors in colon cancer and melanoma cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3381. doi:10.1158/1538-7445.AM2013-3381