NCI-60 Cancer Cell Line Panel Research Articles

Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors

ABSTRACT Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.

Nutrigenomic gene expression profile of NCI-60 cancer cell lines

Cancer occurs due to uncontrolled growth and proliferation of abnormal cells, which is a result of molecular alterations in genes associated with a variety of cellular processes. In order to support the development of incipient tumors, cancer cells are expected to require a constant and increasing supply of nutrients. Although it is evident that this increase in nutrients demand would be accompanied by adjustments in expression of genes associated with cellular nutrition, little is known about the regulation of these genes and its implication for cancer development and treatment. In this study a literature based list of 90 genes associated with cellular nutrition was compiled and used to stablish nutrigenomic expression signatures across the NCI-60 cancer cell line panel. In order to understand the possible interplay between nutrition genes and cancer genes a literature consolidated gene list of 119 cancer driver genes was used for analysis and comparison. Then, the public available NCI-60 data was used for correlations between nutrigenomic signatures, cancer driver genes and antineoplastic drugs. The results obtained showed several robust correlations between the gene lists and drugs. The expression of GPX2 (Glutathione Peroxidase 2 gene) was strongly correlated with several cancer driver genes and antineoplastic drugs, suggesting that GPX2 may play an important in cancer development and treatment.

Evaluation of novel pyrazol-4-yl pyridine derivatives possessing arylsulfonamide tethers as c-Jun N-terminal kinase (JNK) inhibitors in leukemia cells

A series of 36 pyrazol-4-yl pyridine derivatives (8a-i, 9a-i, 10a-i, and 11a-i) was designed, synthesized, and evaluated for its antiproliferative activity over NCI-60 cancer cell line panel and inhibitory effect against JNK isoforms (JNK1, JNK2, and JNK3). All the synthesized compounds were tested against the NCI-60 cancer cell line panel. Compounds 11b, 11c, 11g, and 11i were selected to determine their GI50s and exerted a superior potency over the reference standard SP600125 against the tested cell lines. 11c showed a GI50 of 1.28 μM against K562 leukemic cells. Vero cells were used to assess 11c cytotoxicity compared to the tested cancer cells. The target compounds were tested against hJNK isoforms in which compound 11e exhibited the highest potency against JNK isoforms with IC50 values of 1.81, 12.7, and 10.5 nM against JNK1, JNK2, and JNK3, respectively. Kinase profiling of 11e showed higher JNK selectivity in 50 kinase panels. Compounds 11c and 11e showed cell population arrest at the G2/M phase, induced early apoptosis, and slightly inhibited beclin-1 production at higher concentrations in K562 leukemia cells relative to SP600125. NanoBRET assay of 11e showed intracellular JNK1 inhibition with an IC50 of 2.81 μM. Also, it inhibited CYP2D6 and 3A4 with different extent and its hERG activity showed little cardiac toxicity with an IC50 of 4.82 μM. hJNK3 was used as a template to generate the hJNK1 crystal structure to explore the binding mode of 11e (PDB ID: 8ENJ) with a resolution of 2.8 °A and showed a typical type I kinase inhibition against hJNK1. Binding energy scores showed that selectivity of 11e towards JNK1 could be attributed to additional hydrophobic interactions relative to JNK3.

Novel hydrazone-isatin derivatives as potential EGFR inhibitors: Synthesis and in vitro pharmacological profiling.

Merging isatin and arylhydrazone moieties constitutes an efficient strategy to access new potential anticancer derivatives. Consequently, 14 hydrazone-isatin derivatives were synthesized and evaluated for their antiproliferative activity against the NCI-60 cancer cell line panel. A kinase assay demonstrated that compound VIIIb inhibited the epidermal growth factor receptor (EGFR), which was confirmed by docking studies, molecular dynamics, and binding free energy calculations. Further characterizations showed that this compound possesses drug-likeness properties, showed a significant decrease of the cell population in the G2/M phase and led to a significant increase in early and late apoptosis, comparable to erlotinib. Also, VIIIb increased the expression of caspase-3 and Bax and decreased the expression of Bcl-2, confirming its potential as a new proapoptotic compound.

Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products

BackgroundIndian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel.MethodsWe examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database.ResultsHierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E.ConclusionThese findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products.

Novel Synthesized N-Ethyl-Piperazinyl-Amides of C2-Substituted Oleanonic and Ursonic Acids Exhibit Cytotoxic Effects through Apoptotic Cell Death Regulation.

A series of novel hybrid chalcone N-ethyl-piperazinyl amide derivatives of oleanonic and ursonic acids were synthesized, and their cytotoxic potential was evaluated in vitro against the NCI-60 cancer cell line panel. Compounds 4 and 6 exhibited the highest overall anticancer activity, with GI50 values in some cases reaching nanomolar values. Thus, the two compounds were further assessed in detail in order to identify a possible apoptosis- and antiangiogenic-based mechanism of action induced by the assessed compounds. DAPI staining revealed that both compounds induced nuclei condensation and overall cell morphological changes consistent with apoptotic cell death. rtPCR analysis showed that up-regulation of pro-apoptotic Bak gene combined with the down-regulation of the pro-survival Bcl-XL and Bcl-2 genes caused altered ratios between the pro-apoptotic and anti-apoptotic proteins’ levels, leading to overall induced apoptosis. Molecular docking analysis revealed that both compounds exhibited high scores for Bcl-XL inhibition, suggesting that compounds may induce apoptotic cell death through targeted anti-apoptotic protein inhibition, as well. Ex vivo determinations showed that both compounds did not significantly alter the angiogenesis process on the tested cell lines.

3-Pyridinylidene Derivatives of Chemically Modified Lupane and Ursane Triterpenes as Promising Anticancer Agents by Targeting Apoptosis.

Cancer persists as a global challenge due to the extent to which conventional anticancer therapies pose high risks counterbalanced with their therapeutic benefit. Naturally occurring substances stand as an important safer alternative source for anticancer drug development. In the current study, a series of modified lupane and ursane derivatives was subjected to in vitro screening on the NCI-60 cancer cell line panel. Compounds 6 and 7 have been identified as highly active with GI50 values ranging from 0.03 µM to 5.9 µM (compound 6) and 0.18–1.53 µM (compound 7). Thus, these two compounds were further assessed in detail in order to identify a possible antiproliferative mechanism of action. DAPI (4′,6-diamidino-2-phenylindole) staining revealed that both compounds induced nuclei condensation and overall cell morphological changes consistent with apoptotic cell death. rtPCR analysis showed that both compounds induced upregulation of proapoptotic Bak and Bad genes while downregulating Bcl-XL and Bcl-2 antiapoptotic genes. Molecular docking analysis revealed that both compounds exhibited high scores for Bcl-XL inhibition, while compound 7 showed higher in silico Bcl-XL inhibition potential as compared to the native inhibitor ATB-737, suggesting that compounds may induce apoptotic cell death through targeted antiapoptotic protein inhibition, as well.

Novel A-Ring Chalcone Derivatives of Oleanolic and Ursolic Amides with Anti-Proliferative Effect Mediated through ROS-Triggered Apoptosis.

A series of A-ring modified oleanolic and ursolic acid derivatives including C28 amides (3-oxo-C2-nicotinoylidene/furfurylidene, 3β-hydroxy-C2-nicotinoylidene, 3β-nicotinoyloxy-, 2-cyano-3,4-seco-4(23)-ene, indolo-, lactame and azepane) were synthesized and screened for their cytotoxic activity against the NCI-60 cancer cell line panel. The results of the first assay of thirty-two tested compounds showed that eleven derivatives exhibited cytotoxicity against cancer cells, and six of them were selected for complete dose–response studies. A systematic study of local SARs has been carried out by comparative analysis of potency distributions and similarity relationships among the synthesized compounds using network-like similarity graphs. Among the oleanane type triterpenoids, C2-[4-pyridinylidene]-oleanonic C28-morpholinyl amide exhibited sub-micromolar potencies against 15 different tumor cell lines and revealed particular selectivity for non-small cell lung cancer (HOP-92) with a GI50 value of 0.0347 μM. On the other hand, superior results were observed for C2-[3-pyridinylidene]-ursonic N-methyl-piperazinyl amide 29, which exhibited a broad-spectrum inhibition activity with GI50 < 1 μM against 33 tumor cell lines and <2 μM against all 60 cell lines. This compound has been further evaluated for cell cycle analysis to decipher the mechanism of action. The data indicate that compound 29 could exhibit both cytostatic and cytotoxic activity, depending on the cell line evaluated. The cytostatic activity appears to be determined by induction of the cell cycle arrest at the S (MCF-7, SH-SY5Y cells) or G0/G1 phases (A549 cells), whereas cytotoxicity of the compound against normal cells is nonspecific and arises from apoptosis without significant alterations in cell cycle distribution (HEK293 cells). Our results suggest that the antiproliferative effect of compound 29 is mediated through ROS-triggered apoptosis that involves mitochondrial membrane potential depolarization and caspase activation.

Synthesis of messagenin and platanic acid chalcone derivatives and their biological potential

The chalcone derivatives of 20-oxo-lupanes have been synthesised and screened for some types of biological activity. Ozonolysis of lupanes afforded 20-oxo-derivatives with the following condensation using different aromatic aldehydes by Claisen‒Schmidt reaction to the target compounds. The E configuration of 19-[3-(pyridin-3-yl)-prop-2-en-1-one]-fragment was established by X-ray analysis. Screening of cytotoxic activity against NCI-60 cancer cell line panel revealed, that messagenin derivative 9 has the highest activity with GI50 value ranged from 0.304 to 0.804 μM. A colorimetric SRB assay revealed for the 2,30-bis-furfurylidene derivative 11 and 30-bromo-20-oxo-29-nor-3,28-diacetoxy-betulin 16 cytotoxic activity against breast carcinoma MCF-7 and ovarian carcinoma A2780 cell lines. Compounds 11 and 13 acted also as inhibitors of the enzyme α-glucosidase (from S. saccharomyces) with IC50 values of 1.76 μM and 3.3 μM thus being 97- and 52-fold more active than standard acarbose. Antiviral potency of compounds 12 and 14 against HCMV, HSV-1 and HPV is also discussed.

Molecular genomic features associated with invitro response of the NCI-60 cancer cell line panel to natural products.

Natural products remain a significant source of anticancer chemotherapeutics. The search for targeted drugs for cancer treatment includes consideration of natural products, which may provide new opportunities for antitumor cytotoxicity as single agents or in combination therapy. We examined the association of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with invitro response to treatment with 1302 small molecules which included natural products, semisynthetic natural product derivatives, and synthetic compounds based on a natural product pharmacophore from the Developmental Therapeutics Program of the US National Cancer Institute's database. These compounds were obtained from a variety of plant, marine, and microbial species. Molecular information utilized for the analysis included expression measures for 23059 annotated transcripts, lncRNAs, and miRNAs, and data on protein-changing single nucleotide variants in 211 cancer-related genes. We found associations of expression of multiple genes including SLFN11, CYP2J2, EPHX1, GPC1, ELF3, and MGMT involved in DNA damage repair, NOTCH family members, ABC and SLC transporters, and both mutations in tyrosine kinases and BRAF V600E with NCI-60 responses to specific categories of natural products. Hierarchical clustering identified groups of natural products, which correlated with a specific mechanism of action. Specifically, several natural product clusters were associated with SLFN11 gene expression, suggesting that potential action of these compounds may involve DNA damage. The associations between gene expression or genome alterations of functionally relevant genes with the response of cancer cells to natural products provide new information about potential mechanisms of action of these identified clusters of compounds with potentially similar biological effects. This information will assist in future drug discovery and in design of new targeted cancer chemotherapy agents.

Could microtubule inhibitors be the best choice of therapy in gastric cancer with high immune activity: mutant DYNC1H1 as a biomarker.

Immune checkpoint blockade (ICB) has achieved unprecedented breakthroughs in various cancers, including gastric cancer (GC) with high immune activity (MSI-H or TMB-H), yet clinical benefits from ICB were moderate. Here we aimed to identify the most appropriate drugs which can improve outcomes in GC. We firstly compared MSI-H and TMB-H GC samples with normal samples in TCGA-STAD cohort, respectively. After that, Connectivity Map database repurposed nine candidate drugs (CMap score < -90). Then, microtubule inhibitors (MTIs) were screened as the significant candidate drugs with their representative gene sets strongly enriched (p < 0.05) via GSEA. GDSC database validated higher activities of some MTIs in GC cells with MSI-H and TMB-H (p < 0.05). Furthermore, some MTIs activities were positively associated with mutant Dynein Cytoplasmic 1 Heavy Chain 1 (DYNC1H1) (p < 0.05) based on NCI-60 cancer cell line panel. DYNC1H1 was high frequently alteration in GC and was positively associated with TMB-H and MSI-H. Mutant DYNC1H1 may be accompanied with down-regulation of MTIs-related genes in GC or change the binding pocket to sensitize MTIs. Overall, this study suggested that some MTIs may be the best candidate drugs to treat GC with high immune activity, especially patients with DYNC1H1 mutated.

First person profile: William Sellers, MD: Dr. Sellers has helped to shape the field of cancer genomics and, alongside his colleagues, is working toward its ultimate goal-to move from therapy to cure.

First person profile: William Sellers, MD: Dr. Sellers has helped to shape the field of cancer genomics and, alongside his colleagues, is working toward its ultimate goal-to move from therapy to cure.

Evaluation of Cytotoxicity and α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids.

A series of two new and twenty earlier synthesized branched extra-amino-triterpenoids obtained by the direct coupling of betulinic/betulonic acids with polymethylenpolyamines, or by the cyanoethylation of lupane type alcohols, oximes, amines, and amides with the following reduction were evaluated for cytotoxicity toward the NCI-60 cancer cell line panel, α-glucosidase inhibitory, and antimicrobial activities. Lupane carboxamides, conjugates with diaminopropane, triethylenetetramine, and branched C3-cyanoethylated polyamine methyl betulonate showed high cytotoxic activity against most of the tested cancer cell lines with GI50 that ranged from 1.09 to 54.40 µM. Betulonic acid C28-conjugate with triethylenetetramine and C3,C28-bis-aminopropoxy-betulin were found to be potent micromolar inhibitors of yeast α-glucosidase and to simultaneously inhibit the endosomal reticulum α-glucosidase, rendering them as potentially capable to suppress tumor invasiveness and neovascularization, in addition to the direct cytotoxicity. Plausible mechanisms of cytotoxic action and underlying disrupted molecular pathways were elucidated with CellMinner pattern analysis and Gene Ontology enrichment analysis, according to which the lead compounds exert multi-target antiproliferative activity associated with oxidative stress induction and chromatin structure alteration. The betulonic acid diethylentriamine conjugate showed partial activity against methicillin-resistant S. aureus and the fungi C. neoformans. These results show that triterpenic polyamines, being analogs of steroidal squalamine and trodusquemine, are important substances for the search of new drugs with anticancer, antidiabetic, and antimicrobial activities.

Design, characterization and quantum chemical computations of a novel series of pyrazoles derivatives with potential anti-proinflammatory response

The synthesis and characterization of the full family of 11 pyrazoles were performed by means of UV–Vis, FTIR, 1H NMR, 13C NMR, two-dimensional NMR experiments and DFT simulations. As pyrazoles are known for showing diverse biological actions, they were also tested in the NCI-60 cancer cell line panel, showing moderate to good activity against different cell lines. Furthermore, the anti-proinflammatory activity test of a set of pyrazoles of the form (E)-4-((4-bromophenyl)diazenyl)-3,5-dimethyl-1-R-phenyl-1H-pyrazole was performed, this is based on the study of the blockage of the increase in intracellular [Ca2+] observed in response to platelet-activating factor (PAF) treatment of four pyrazoles (i.e.6, 8, 9 and 10), which successfully displayed [Ca2+] channel inhibition. Therefore, the obtained intracellular [Ca2+] signal results indicate that the pyrazole family characterized in this study, in particular compounds 6 and 10, are potent blockers of the PAF-initiated Ca2+ signaling that mediates the hyperpermeability typically observed during the development of inflammation.

Synthesis, evaluation of cytotoxicity, and antimicrobial activity of A-azepano- and A-seco-3-amino-C28-aminolupanes

A series of new C28-amino-lupanes bearing A-azepano- and A-seco-3-amino-fragments was synthesized from 3,28-dioximino-betulin and evaluated for cytotoxicity toward the NCI-60 cancer cell line panel and antimicrobial activity against key ESKAPE pathogens. A-azepano-28-amino-betulin exhibited remarkable activities with GI50 ranging from 1.16 to 2.27 μM against all panel with the highest activity toward leukemia, colon cancer, non-small cell lung cancer and breast cancer. The replacement of the hydroxyl group at C28 in the structure of azepanobetulin to the amino group did not show a strong effect on the cytotoxic activity. Both compounds were ∼5 and ∼4 times more active than doxorubicin against colon cancer HCT-15 and ovarian cancer NCI/ADR-RES cell lines, thus these A-azepano-lupane triterpenoids are the promising agents for future anticancer drug development. The ability of A-azepanobetulin to inhibit cell growth may be associated with its cytostatic effect, which, depending on the cell line, is associated with the arrest either S or G1 phase of cell cycle. 3-Amino-3,4-seco-28-amino-lup-4(23),20(29)-dien exhibited significant bacteriostatic effect against methicillin-resistant Staphylococcus aureus (MIC ≤ 0.25 μg/mL) that exceeds the effect of the clinically used antibiotic vancomycin.

Synthesis, modification, and biological activity of propargylated methyl dihydroquinopimarates

The introduction of the alkynyl moiety to the abietane diterpenic core by modification of the cycle E of methyl dihydroquinopimarate is described. The arylpropargyl, aminopropargyl, and 1,2,3-triazole derivatives are synthesized via Sonogashira reaction, Mannich reaction and click-chemistry, correspondingly. The antitumor effect towards the NCI-60 cancer cell line panel and antimicrobial activity against key ESKAPE pathogens of the synthesized compounds were studied in vitro. The cytotoxicity and hemolytic activity of the abietane derivatives was tested using HEK293 human embryonic kidney cell line and the human red blood cells, correspondingly. The methyl dihydroquinopimarate propargyl analogs showed high antitumor activity against leukemia (CCRF-CEM; SR), non-small cell lung cancer (NCI-H522), melanoma (LOX IMVI; MALME-3M), ovarian cancer (IGROV1), and renal cancer (786-0; UO-31) cell lines. The Mannich’s diterpene bases with pyrrolidine and diethylamine fragments exhibited fungicidal activity towards Cr. neoformans (MIC= 16 μg/ml), while possessing low toxicity. The described modifications of the abietane diterpenoids have great potential for further development of new cytotoxic and fungicidal compounds.

Design, synthesis and biological evaluation of 6-substituted quinolines derived from cabozantinib as c-Met inhibitors.

Based on the cabozantinib scaffold, novel c-Met inhibitors were rationalized from the limited knowledge of structure-activity relationships for the quinoline 6-position. Emphasis was given to modifications capable of engaging in additional polar interactions with the c-Met active site. In addition, ortho-fluorinations of the terminal benzene ring were explored. Fifteen new molecules were synthesized and evaluated in a c-Met enzymatic binding assay. A wide range of substituents were tolerated in the quinoline 6-position, while the ortho-fluorinations performed were shown to give considerable reductions in the c-Met binding affinity. The antiproliferative effects of the compounds were evaluated in the NCI60 cancer cell line panel. Most notably, compounds 15b and 18b were able to inhibit cell proliferation more efficiently than cabozantinib in leukemia, CNS, and breast cancer cell lines. The in vitro data agreed well with the in silico docking results, where additional hydrogen bonding was identified in the enzymatic pocket for the para-amino substituted 15b and 18b.

Abstract 4246: Association of transcriptional levels of folate-mediated one-carbon metabolism related genes in cancer cell lines with drug treatment response

Abstract Folate-mediated one-carbon metabolism (OCM) is essential for growth and survival of cancer cells. It affects biosynthesis of nucleotides and amino acids, regulation of redox status, methylation of nucleic acids and proteins, and genome maintenance. We investigated whether the response of cancer cells to antitumor therapy treatment may be partially influenced by variation in expression of one-carbon metabolism genes. We used publicly available gene expression data and drug response measures for 251 antitumor agents in 635 cancer cell lines with matching information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources. We examined whether pre-treatment expression levels of OCM-related genes were associated with drug response. Among the 34 OCM genes examined, expression of GART, TYMS, SHMT2, MTR, ALDH2, BHMT, MAT2B, MTHFD2, NNMT, and SLC46A1 showed modest correlations with response to treatment with a variety of antitumor agents. Higher expression levels of the SLC46A1 transporter gene were associated with resistance to multiple drugs, whereas elevated expression of GART, TYMS, SHMT2, MTR, BHMT, and MAT2B was associated with chemosensitivity to multiple antitumor agents. NNMT expression was bimodally distributed and showed different directions of association with various agents. Correlation of increased NNMT expression with sensitivity to dasatinib was validated in the NCI-60 cancer cell line panel. Expression of several OCM genes was strongly associated with expression of multiple components of drug target pathways. For example, expression of both TYMS and GART was strongly positively correlated with BRCA1 expression, NNMT expression was associated with expression of multiple drug target genes including EGFR and ABL2, and the expression of TYMS, DHFR, and SHMT1 was positively correlated with AURKB expression. Pretreatment expression levels of many OCM genes including DHFR, TYMS, ATIC, GART, AHCY, MTHFD1, SLC19A1, and multiple other genes were positively correlated with each other, suggesting their co-regulation. In contrast, NNMT expression was negatively correlated with expression of several other OCM genes. Further studies could investigate whether correlations of expression levels of individual OCM genes with drug response are related to specific metabolic roles of these genes or whether such associations may be due to the general increase in cellular growth and proliferation and tumor progression, which may affect sensitivity to cancer treatment. Citation Format: Julia Krushkal, Suleyman Vural, Dong-Joon Min. Association of transcriptional levels of folate-mediated one-carbon metabolism related genes in cancer cell lines with drug treatment response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4246.

Abstract 4789: Predicting sensitivity to Lantern Pharma’s pipeline drug candidate LP-184 using the Response Algorithm for Drug Positioning and Rescue

Abstract LP-184 is a DNA Damage Repair inhibitor being developed by Lantern Pharma primarily as a non-hormone, non-chemotherapy option for the growing indication of taxane- and hormone-resistant metastatic prostate cancer. LP-184 is a next-generation analog of Irofulven with broad anti-tumor activity that counteracts multi-drug resistance pathways and is potentially synergistic with many classes of anticancer agents. LP-184 has a favorable therapeutic index and pharmacokinetic profile. Knowledge about its shared mechanism of action with Irofulven and potential biomarkers implicated in induction of bioactivation and synthetic lethal interactions is available. To advance LP-184 into clinical stages and achieve accelerated approval, Lantern Pharma is employing its proprietary Artificial Intelligence (AI)-driven technology. Lantern Pharma has developed a technology platform termed RADRTM that can be used to construct responder/ non-responder profiles based on gene expression signatures and predict true responders before conducting a clinical trial in order to achieve higher success rates. RADRTM is an Al-based machine learning approach for candidate biomarker identification and patient stratification. RADRTM is a combination of three automated modules working sequentially to generate drug- and tumor-specific gene signatures predictive of response. RADRTM emphasizes the integration of biological knowledge, data-driven feature selection, and robust Al algorithms to derive biomarkers in a hypothesis-free manner. In analytic demonstrations, RADRTM was able to achieve an average accuracy of 85% in validation tests using preclinical datasets associated with selected solid tumor indications and approved drugs. As part of RADRTM drug model building and development, we used a dataset showing preclinical efficacy of our pipeline oncology candidate LP-184. We obtained baseline cell line gene expression profiles covering more than 18,000 transcripts per cell line and corresponding LP-184 sensitivity records from the NCI60 cancer cell line panel. Using RADRTM, we derived a panel of 10 genes whose expression levels are predictive of overall response at an accuracy of 100%. Thus, RADRTM was able to identify the top 10 genes for prediction of either drug sensitivity or insensitivity, demonstrating the hypothesis-free identification of biomarkers with biological relevance and statistical rigor and having highest possible prediction accuracy. Genes from the final 10 predictive list were found to be functionally involved in LP-184-specific induction of bioactivation and are in agreement with its mechanism of action. These preliminary biomarker analyses will be further validated using LP-184 sensitivity and pre-treatment gene expression data derived from ex vivo models of fresh prostate tumor biopsy samples. Citation Format: Aditya Kulkarni, Umesh Kathad, Yuvanesh Vedaraju, Barry Henderson, Gregory Tobin, Panna Sharma, Arun Asaithambi. Predicting sensitivity to Lantern Pharma’s pipeline drug candidate LP-184 using the Response Algorithm for Drug Positioning and Rescue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4789.

Association of transcriptional levels of folate-mediated one-carbon metabolism-related genes in cancer cell lines with drug treatment response

Folate-mediated one-carbon metabolism is essential for growth and survival of cancer cells. We investigated whether the response of cancer cells to antitumor treatment may be partially influenced by variation in expression of one-carbon metabolism genes. We used cancer cell line information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources to examine whether variation in pretreatment expression of one-carbon metabolism-related genes was associated with response to treatment. GART, TYMS, SHMT2, MTR, ALDH2, BHMT, MAT2B, MTHFD2, NNMT, and SLC46A1 showed modest statistically significant correlations with response to a variety of antitumor agents. Higher expression levels of SLC46A1 were associated with resistance to multiple agents, whereas elevated expression of GART, TYMS, SHMT2, MTR, BHMT, and MAT2B was associated with chemosensitivity to multiple drugs. NNMT expression was bimodally distributed and showed different directions of association with various agents. Correlation of increased NNMT expression with sensitivity to dasatinib was validated in the NCI-60 cancer cell line panel. Pretreatment expression levels were correlated among many one-carbon metabolism genes. Expression of several folate genes was strongly associated with expression of multiple components of drug target pathways. Molecular mechanisms underlying associations of one-carbon metabolism gene with drug response require further investigation.