Targeting MYC Regulation with Polypurine Reverse Hoogsteen Oligonucleotides

The oncogene MYC has key roles in transcription, proliferation, deregulating cellular energetics, and more. Modulating the expression or function of the MYC protein is a viable therapeutic goal in an array of cancer types, and potential inhibitors of MYC with high specificity and selectivity are of great interest. In cancer cells addicted to their aberrant MYC function, suppression can lead to apoptosis, with minimal effects on non-addicted, non-oncogenic cells, providing a wide therapeutic window for specific and efficacious anti-tumor treatment. Within the promoter of MYC lies a GC-rich, G-quadruplex (G4)-forming region, wherein G4 formation is capable of mediating transcriptional downregulation of MYC. Such GC-rich regions of DNA are prime targets for regulation with Polypurine Reverse Hoogsteen hairpins (PPRHs). The current study designed and examined PPRHs targeting the G4-forming and four other GC-rich regions of DNA within the promoter or intronic regions. Six total PPRHs were designed, examined in cell-free conditions for target engagement and in cells for transcriptional modulation, and correlating cytotoxic activity in pancreatic, prostate, neuroblastoma, colorectal, ovarian, and breast cancer cells. Two lead PPRHs, one targeting the promoter G4 and one targeting Intron 1, were identified with high potential for further development as an innovative approach to both G4 stabilization and MYC modulation.

RYBP Sensitizes Cancer Cells to PARP Inhibitors by Regulating ATM Activity

Ring1 and YY1 Binding Protein (RYBP) is a member of the non-canonical polycomb repressive complex 1 (PRC1), and like other PRC1 members, it is best described as a transcriptional regulator. Previously, we showed that RYBP, along with other PRC1 members, is also involved in the DNA damage response. RYBP inhibits recruitment of breast cancer gene 1(BRCA1) complex to DNA damage sites through its binding to K63-linked ubiquitin chains. In addition, ataxia telangiectasia mutated (ATM) kinase serves as an important sensor kinase in early stages of DNA damage response. Here, we report that overexpression of RYBP results in inhibition in both ATM activity and recruitment to DNA damage sites. Cells expressing RYBP show less phosphorylation of the ATM substrate, Chk2, after DNA damage. Due to its ability to inhibit ATM activity, we find that RYBP sensitizes cancer cells to poly-ADP-ribose polymerase (PARP) inhibitors. Although we find a synergistic effect between PARP inhibitor and ATM inhibitor in cancer cells, this synergy is lost in cells expressing RYBP. We also show that overexpression of RYBP hinders cancer cell migration through, at least in part, ATM inhibition. We provide new mechanism(s) by which RYBP expression may sensitize cancer cells to DNA damaging agents and inhibits cancer metastasis.

Design and Characterization of Immune-Stimulating Imidazo[4,5-c]quinoline Antibody-Drug Conjugates

Traditional antibody-drug conjugate (ADC) technology has employed tumor-targeting antibodies to selectively deliver ultrapotent cytotoxins to tumor tissue. While this technology has been highly successful, resulting in the FDA approval of over 10 ADCs, the field continues to struggle with modest efficacy and significant off-target toxicity. Concurrent with the struggles of the ADC field, a new generation of immune-activating therapeutics has arisen, most clearly exemplified by the PD-1/PD-L1 inhibitors that are now part of standard-of-care treatment regimens for a variety of cancers. The success of these immuno-oncology therapeutic agents has prompted the investigation of a variety of new immuno-stimulant approaches, including toll-like receptor (TLR) activators. Herein, we describe the optimization of ADC technology for the selective delivery of a potent series of TLR7 agonists. A series of imidazole[4,5-c]quinoline agonists (as exemplified by compound 1) were shown to selectively agonize the human and mouse TLR7 receptor at low nanomolar concentrations, resulting in the release of IFNα from human peripheral blood mononuclear cells (hPBMCs) and the upregulation of CD86 on antigen-presenting cells. Compound 1 was attached to a deglycosylated (Fc-γ null) HER2-targeting antibody via a cleavable linker, resulting in an ADC (anti-HER2_vc-1) that potently and selectively activated the TLR7 pathway in tumor-associated macrophages via a "bystander" mechanism. We demonstrated that this ADC rapidly released the TLR7 agonist into the media when incubated with HER2+ cells. This release was not observed upon incubation with an isotype control ADC and furthermore was suppressed by co-administration of the naked antibody. In co-culture experiments with HER2+ HCC1954 cells, this ADC induced the activation of the NFκB pathway in mouse macrophages and the release of IFNα from hPBMCs, while a corresponding isotype control ADC did not. Finally, we demonstrated that IP administration of anti-HER2_vc-1 induced complete tumor regression in an HCC1954 xenograft study in SCID beige mice. Unlike related ADC technology that has been reported recently, our technology relies on the passive diffusion of the TLR7 agonist into tumor-associated macrophages rather than Fc-γ-mediated uptake. Based on these observations, we believe that this ADC technology holds significant potential for both oncology and infectious disease applications.

Abstract 675: Facilitating G-quadruplex formation in the KRAS promoter with polypurine reverse Hoogsteen oligonucleotides

KRAS is a GTPase involved in the proliferation signaling of a number of growth factors, such as epidermal growth factor. The protein is mutated or upregulated in an array of cancers, including pancreatic and ovarian cancers, where it correlates with more aggressive and chemoresistant disease. Within the promoter of KRAS lies a G-rich region capable of forming the higher order non-canonical DNA structure, the G-quadruplex (G4). Stabilization of G4 formation in the mid-region of the KRAS promoter downregulates transcription and facilitates decreased growth and chemo-sensitization of pancreatic and ovarian cancer cells with aberrant KRAS signaling. Our collaborative team designed Polypurine Reverse Hoogsteen (PPRH) hairpin oligonucleotides that establish Watson Crick bonds with the pyrimidine strand within the KRAS-mid-G4-forming region to enhance G4 formation, downregulate KRAS transcription and mediate an anti-proliferative effect. In particular, two PPRHs were designed to interact with the 3’ and 5’ ends of the G4-forming region, along with two correlating W:C, and one scramble, controls. The binding of these oligonucleotides to the G4-forming region was verified by gel electrophoresis, and the cell activity was examined in vitro both by luciferase and in pancreatic and ovarian cancer cells. Using a luciferase construct driven by the KRAS promoter, only the PPRHs, and none of the control oligonucleotides, significantly decreased activity. Cytotoxicity experiments in KRAS dependent and independent cell lines demonstrated that PPRHs, but not control oligonucleotides, selectively suppressed proliferation only in the dependent pancreatic and ovarian cancer cell lines. Correlation of the cytotoxic effects of these potential therapeutic PPRHs with transcriptional downregulation is under investigation. PPRH also demonstrated synergistic activity with a KRAS promoter selective G4-stabilizing compound in KRAS-dependent pancreatic cells, and sensitization to standard chemotherapeutic regimens is also being studied. These designed PPRH oligonucleotides selectively stabilize G4 formation within the KRAS mid promoter region, and represent an innovative approach both for G4-stabilization and KRAS modulation with potential for development into novel therapeutics.

Citation Format: Alexandra Maria Psaras, Simonas Valiuska, Veronique Noe, Carlos J. Ciudad, Tracy A. Brooks. Facilitating G-quadruplex formation in the KRAS promoter with polypurine reverse Hoogsteen oligonucleotides [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 675.

Optimization of DOTAP/chol Cationic Lipid Nanoparticles for mRNA, pDNA, and Oligonucleotide Delivery

Lipid nanoparticles (LNPs) can be used as delivery vehicles for nucleic acid biotherapeutics. In fact, LNPs are currently being used in the Pfizer/BioNTech and Moderna COVID-19 vaccines. Cationic LNPs composed of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP)/cholesterol (chol) LNPs have been classified as one of the most efficient gene delivery systems and are being tested in numerous clinical trials. The objective of this study was to examine the effect of the molar ratio of DOTAP/chol, PEGylation, and lipid to mRNA ratio on mRNA transfection, and explore the applications of DOTAP/chol LNPs in pDNA and oligonucleotide transfection. Here we showed that PEGylation significantly decreased mRNA transfection efficiency of DOTAP/chol LNPs. Among non-PEGylated LNP formulations, 1:3 molar ratio of DOTAP/chol in DOTAP/chol LNPs showed the highest mRNA transfection efficiency. Furthermore, the optimal ratio of DOTAP/chol LNPs to mRNA was tested to be 62.5 µM lipid to 1 μg mRNA. More importantly, these mRNA-loaded nanoparticles were stable for 60 days at 4 °C storage without showing reduction in transfection efficacy. We further found that DOTAP/chol LNPs were able to transfect pDNA and oligonucleotides, demonstrating the ability of these LNPs to transport the cargo into the cell nucleus. The influence of various factors in the formulation of DOTAP/chol cationic LNPs is thus described and will help improve drug delivery of nucleic acid-based vaccines and therapies.

Targeted Downregulation of MYC through G-quadruplex Stabilization by DNAi

Modulating the expression or function of the enigmatic MYC protein has demonstrated efficacy in an array of cancer types and a marked potential therapeutic index and safety profile. Despite its high therapeutic value, specific and selective inhibitors or downregulating therapeutics have proven difficult to develop. In the current study, we expanded our work on a MYC promoter G-quadruplex (G4) stabilizing DNA clamp to develop an oligonucleotide interfering DNA (DNAi) therapeutic. We explored six DNAi for G4-stabilization through EMSA, DMS footprinting, and thermal stability studies, focusing on the DNAi 5T as the lead therapeutic. 5T, but not its scramble control 5Tscr, was then shown to enter the nucleus, modulate cell viability, and decrease MYC expression through G4-stabilization. DNAi 5T is thus described to be our lead DNAi, targeting MYC regulation through stabilization of the higher-order DNA G4 structure in the proximal promoter, and it is poised for further preclinical development as an anticancer therapeutic.

Abstract 1246: Anticancer activitiy of indolo[2,3-c]quinoline stabilization of the KRAS promoter G4mid structure

KRAS is a well validated anti-cancer therapeutic target; many active drug discovery programs are ongoing with foci on individual mutant isoforms, necessitating a wide array of drugs to be developed and missing cancers with dysregulation of non-mutant KRAS. Transcriptional down-regulation has been demonstrated to be lethal to tumor cells with aberrant KRAS signaling, irrespective of mutational status, and to potentially have a wide therapeutic window. G-quadruplex (G4) formation within KRAS's core promoter offers a molecular target to decrease the gene expression. Targeted G4-stabilization within the KRAS promoter targets cancer cells' acquired addiction to the transforming event of aberrant KRAS signaling through an activating mutation or protein overexpression, and thus is applicable to both of these deviant states. Small molecules that specifically inhibit transcriptional expression of KRAS genes have great potential for patients whose tumors have disregulated KRAS function. In the current works, compounds clarify the physiologically relevant G4 within the KRAS promoter (G4mid) through a combination of ex vivo screening, luciferase, cytotoxicity, and transcriptional regulation assays. A small set of novel indolo[2,3-c]quinoline compounds were synthesized and a newly optimized FRET Melt2 assay with a Z' score of >0.5 was used to determine KRAS G4mid stabilization efficacy and selectivity. Compounds were then examined for KRAS promoter stabilization using a luciferase assay, pancreatic and ovarian cancer cytotoxicity by an MTS assay, and correlative changes in KRAS transcription as measured by multiplexed qPCR. JM-222 is the lead indolo[2,3-c]quinoline compound that demonstrates KRAS G4mid selective stabilization and promoter regulation, cancer cell cytotoxicity and altered KRAS transcription. These works highlight the function of G4mid in regulating KRAS transcription, novel synthetic methods for indolo[2,3-c]quinoline synthesis, the improved utility of the FRET Melt2 assay, and the overall potential for small compound-mediated KRAS promoter G4 stabilization for patients harboring tumors with aberrant KRAS signaling.

Citation Format: Alexandra Maria Psaras, Jared Miller, L. Nathan Tumey, Tracy A. Brooks. Anticancer activitiy of indolo[2,3-c]quinoline stabilization of the KRAS promoter G4mid structure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1246.

Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells

G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC.

Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures

Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.

Abstract 2168: Nucleic acid clamp-mediated recognition and transcriptional modulation of MYC oncogenes through the stabilization of G-quadruplexes

G-quadruplexes (G4s) tend to cluster around biologically important regions such as promoters of DNA, 5’-UTR of mRNA and telomeres. Modulating the stability of G4 as in these regulatory sequences is an emerging approach for cancer treatment. MYC proto-oncogene is overexpressed in over 80% of tumor types, contributing to deregulated cancer cell proliferation. Silencing MYC expression has been demonstrated to be an effective approach to inhibit tumor growth. Among all the silencing strategies, stabilizing MYC promoter G4 that serves as an on-off switch for the transcription of MYC has been explored by the targeting of small molecules. However, the binding specificity of small molecule retarded the drug development process. Exploring novel MYC G4-targeting strategies is necessary to potentiate the pharmacological specificity of MYC G4 modulation. Here, we adopted a nucleic acid clamp based approach to recognize and stabilize the physiologically predominant MYC G4. Previously, a clamp (clamp A) was been demonstrated to recognize the physiologically relevant MYC G4 with high specificity and to downregulate MYC promoter activity. In the current research, we modified and optimized this clamp to allow for flexibility with labeling and monitoring techniques. The original 18 Å polyethylene glycol phosphate linker connecting the 5’ and 3’ regions of clamp A were substituted with thymine bases of varying lengths; 5 thymines were found to be optimal. The binding specificity and MYC G4 recognizing ability of this optimized clamp A T5 were confirmed by EMSA and ECD; the G4 stabilizing ability of clamp A T5 was demonstrated by DMS footprinting. The cytotoxicity of clamp A T5 was examined by MTS assay on HEK-293 and MCF-7 cells. The intracellular localization of clamp A T5 is being determined microscopically with a 6-FAM-labeled clamp A T5 after being transfected into and incubated with HEK-293 and MCF-7 cells for 48 hr. Nuclear localization is being examined by co-staining with DAPI, and MYC promoter localization is being determined by clustering with a MYC FISH probe. The modification of the clamp is both cost-effective, and enables the detailed study of intracellular functions. This clamp has potential as both a diagnostic tool to inform the use of MYC G4-targeted small molecules, and as a nanotherapeutic.

Citation Format: Taisen Hao, Tracy A. Brooks. Nucleic acid clamp-mediated recognition and transcriptional modulation of MYC oncogenes through the stabilization of G-quadruplexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2168. doi:10.1158/1538-7445.AM2017-2168

Nucleic acid clamp-mediated recognition and stabilization of the physiologically relevant MYC promoter G-quadruplex

The MYC proto-oncogene is upregulated, often at the transcriptional level, in ∼80% of all cancers. MYC's promoter is governed by a higher order G-quadruplex (G4) structure in the NHE III₁ region. Under a variety of conditions, multiple isoforms have been described to form from the first four continuous guanine runs (G4_1–4) predominating under the physiologically relevant supercoiled conditions. In the current study, short oligonucleotides complementing the 5′- and 3′-regions flanking the G4 have been connected by an abasic linker to form G4 clamps, varying both linker length and G4 isoform being targeted. Clamp A with an 18 Å linker was found to have marked affinity for its target isomer (G4_1–4) over the other major structures (G4_2–5 and G4_1–5, recognized by clamps B and C, respectively), and to be able to shift equilibrating DNA to foster greater G4 formation. In addition, clamp A, but not B or C, is able to modulate MYC promoter activity with a significant and dose-dependent effect on transcription driven by the Del4 plasmid. This linked clamp-mediated approach to G4 recognition represents a novel therapeutic mechanism with specificity for an individual promoter structure, amenable to a large array of promoters.

Abstract 2914: Biphenylene and bipyridine connected benzofuran compounds as novel regulators of kRAS transcription

Pancreatic cancer is the fourth most deadly cancer with 5 year survival rate of ∼6%. One of the major attributes of pancreatic cancer is kRAS mutations. kRAS is a proto-oncogene with intrinsic GTPase activity, and is responsible for cell proliferation, division, and apoptosis. kRAS mutations are observed in >95% of pancreatic adenocarcinoma and in 30% all human tumors. When mutated it leads to continuous activity and uncontrolled proliferation which results in increased tumorigenicity and poor prognosis. Downregulating kRAS expression has shown to halt proliferation and leads to cellular death in pancreatic cancer models, but to date no small molecule capable of such transcriptional silencing has been described. A novel series of molecules with either biphenylene or bipyridine spacer connecting the terminal benzofuran ring was synthesized using solution phase chemistry. Tertiary amine side chains were incorporated to the C2-position of the benzofuran ring to improve the DNA binding affinity of these compounds. The synthesized compounds were purified using a “catch and release” method employing the sulfonic acid based resins. The eleven novel compounds were screened in parallel for their ability to stabilize G-quadruplex structures in the kRAS promoter, and to downregulate kRAS promoter activity. Two of the compounds increased the thermal profile of non-canonical DNA formations in the promoter region by >5 °C; however, on the whole these compounds did not seem to function as G-quadruplex-stabilizing agents. Eight compounds significantly decreased luciferase expression under the explicit control of the kRAS promoter by up to 75%, by compound BF 4.3, through an as-yet unknown mechanism of action. The compound series was examined for the inhibition of cellular viability in two mutant kRAS pancreatic cancer cell lines - Panc-1 and MIA PaCa-2; in both cell lines the compounds containing the bipyridine spacer had greater cytotoxic effects with IC50's of ∼30 μM, consistently. qPCR is being used to confirm the decrease in promoter activity in native cellular conditions. These agents are intriguing in both their novel scaffold and their unexpected activity decreasing kRAS expression in a mechanism unrelated to higher order DNA structures. Ultimately, down regulation of kRAS transcription will provide a novel therapeutic approach for pancreatic cancer and improve the prognosis of this highly lethal disease.

Citation Format: Harshul Batra, Mohammad K. Islam, David E. Thurston, Khondaker M. Rahman, Tracy A. Brooks. Biphenylene and bipyridine connected benzofuran compounds as novel regulators of kRAS transcription. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2914.

Abstract 1254: Small molecule targeting of the kRAS mid-G-quadruplex for potential pancreatic cancer therapeutics

Pancreatic cancer is disproportionally lethal (7% of all cancer deaths), as compared to its incidence (3% of cancer incidences) within the United States. One of the most important genetic alterations in pancreatic cancer is within the kRAS oncogene. Over 60% of all pancreatic cancers, and up to 95% of pancreatic ductal adenocarcinomas, harbor mutations in this oncogene. While approaches to therapeutically modulate kRAS activity have not yielded clinical agents, downregulation of expression shows promise in preclinical models. To date, no molecular target has allowed for small molecule mediated downregulation of kRAS expression; however, the promoter region holds promise for a new approach. The kRAS promoter has three distinct guanine-rich regions capable of forming higher order non-B-DNA structures, G-quadruplexes (G4s). In particular the middle (mid) of these three regions forms a stable, inducible, and transcriptionally silencing G4 structures, whereas the more distal (far) region forms no such structure, and the more proximal (near) region has little to no biological function. The structure of this mid-region G4 has been elucidated by electromobility shift assay, DMS footprinting, and circular dichroism (CD). Small molecules capable of stabilizing this structure have been screened from the NCI Diversity Set III by the FRET melt assay, confirmed by CD, and examined for their downregulation of kRAS promoter activity. From the 1600 compounds, the indoloquinolone NSC 317605 is the lead molecule identified. It is particularly interesting as it prefers the mid-, as opposed to the near-, G4 and significantly reduces kRAS promoter activity. This is in contrast to the ellipticine NSC 176327, which favors the near-, over the mid-, G4 and does not decrease kRAS promoter activity. The effect of each compound on cell viability on kRAS transcription is under examination in a panel of pancreatic cancer cells. These works support previous findings that the mid-, and not the near-G4, harbors the potential to transcriptionally downregulate kRAS, and identify a new scaffold for future development.

Brooks Lab startup funds, DoD, Rhianna Morgan GSC Grant, University of Mississippi School of Pharmacy

Citation Format: Rhianna K. Morgan, Tracy A. Brooks. Small molecule targeting of the kRAS mid-G-quadruplex for potential pancreatic cancer therapeutics. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1254.

Identification and characterization of a new G-quadruplex forming region within the kRAS promoter as a transcriptional regulator

kRAS is one of the most prevalent oncogenic aberrations. It is either upregulated or mutationally activated in a multitude of cancers, including pancreatic, lung, and colon cancers. While a significant effort has been made to develop drugs that target kRAS, their clinical activity has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel mechanism and molecular target to downregulate kRAS expression--a previously undescribed G-quadruplex (G4) secondary structure within the proximal promoter acting as a transcriptional silencer. There are three distinct guanine-rich regions within the core kRAS promoter, including a previously examined region (G4near). Of these regions, the most distal region does not form an inducible and stable structure, whereas the two more proximal regions (termed near and mid) do form strong G4s. G4near is predominantly a tri-stacked structure with a discontinuous guanine run incorporated; G4mid consists of seven distinct runs of continuous guanines and forms numerous competing isoforms, including a stable three-tetrad stacked mixed parallel and antiparallel loop structures with longer loops of up to 10 nucleotides. Comprehensive analysis of the regulation of transcription by higher order structures has revealed that the guanine-rich region in the middle of the core promoter, termed G4mid, is a stronger repressor of promoter activity than G4near. Using the extensive guanine-rich region of the kRAS core promoter, and particularly the G4mid structure, as the primary target, future drug discovery programs will have potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic, ovarian, lung, and colon cancers.

Abstract 5419: Structure elucidation of G-quadruplex within the mid-region of the kRAS promoter and identification of stabilizing small molecules as promising transcriptional silencers

Over 60% of pancreatic cancers harbor mutations in the kRAS oncogene, whose promoter has three distinct guanine-rich regions (near, mid, and far) capable of forming higher order G-quadruplexes (G4s). These important structures have transcriptional silencing potential and stabilizing compounds cause selective apoptosis in kRAS-addicted cells. Previous works in our laboratory have identified the mid-G4 region as having the highest silencing capacity, with little apparent roles for the near- or far-G4 regions. The structure of this mid-region G4 is being elucidated by electromobility shift assay, DNA polymerase stop assay, DMS footprinting, and circular dichroism (CD). In addition, small molecules are being screened by the Förster Resonance Energy Transfer (FRET) melt assay and confirmed by CD for their stabilization potential. We have identified multiple, equilibrating, intramolecular G4s forming within the mid-region of the kRAS promoter. Varying buffer conditions (cations, dehydration, and molecular crowding) affect these formations; the predominating isoform is a tetra-stacked mixed parallel and antiparallel structure with an 8:15:7 loop configuration. Over 1,600 compounds have been screened and several are being pursued as leads. Several compounds selectively stabilized the mid-G4 and suppress kRAS transcription. Our work highlights the mid-G4-forming region of the kRAS promoter a therapeutic target with the utmost promise for pancreatic cancer, and further features the stabilizing potential of targeted compounds. Studies are ongoing to vet the potential of other “hit” compounds from the FRET screen, as well as to elucidate the structure of the kRAS mid-G4 in chromosomal DNA.

Brooks Lab startup funds, DoD, Rhianna Morgan GSC Grant, University of Mississippi School of Pharmacy

Citation Format: Rhianna K. Morgan, Tracy A. Brooks, Khondaker M. Rahman. Structure elucidation of G-quadruplex within the mid-region of the kRAS promoter and identification of stabilizing small molecules as promising transcriptional silencers. [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 5419. doi:10.1158/1538-7445.AM2015-5419

Abstract 2137: The effect of the transcription factor MAZ on kRAS transcription: a role for the G-quadruplex

kRAS is a GTPase protein affecting normal cell proliferation, division, and apoptosis. It is mutated in >30% of all cancers, particularly in 60-90% of pancreatic cancers. Mutated kRAS leads to continuous activity and uncontrolled proliferation. To date there have been no successful clinical agents targeting mutant kRAS activity. Modulating kRAS expression has shown anti-proliferative promise as an approach in pancreatic cancer models, but is not a main avenue of pursuit for clinical development due to lack of a molecular target. Our lab is focused on the regulation of kRAS transcription through a variety of G-rich regions of DNA in the promoter capable of forming non-B-DNA structures termed G-quadruplexes (G4s). In the current study, we sought to determine the effect of the transcription factor MAZ on the regulation of kRAS, with a particular focus on the three putative G4-forming regions (herein termed near, mid, and far in reference to their relative proximity to the transcriptional start site). In a study of the kRAS promoter using a series of luciferase plasmids, MAZ expression led to a concentration-dependent decrease in promoter activity. This action was localized to interactions with the mid-G4-forming region. In the context of a more multifaceted intracellular mileu as found in the pancreatic cancer cell lines MiaPaCa-2, Panc-1, and BxPc3, the effects of MAZ were much more complex. In particular, 48 hr post-transfection with MAZ expression plasmids, monitoring of kRAS transcription revealed a cell line-specific modulation with an increase in kRAS expression in Panc-1 cells only, confirming a previous study, and no changes noted in either the MiaPaCa-2 or the Bx-Pc3 cells. Further studies are ongoing evaluating the direct binding of MAZ to the various G-rich regions in those cell lines, as well as determining the DNA structure (single-stranded, double-stranded, or G4-DNA) to which the MAZ protein is binding. Ultimately, an understanding of the regulation of this G-rich region of DNA, by MAZ or any other transcription factors such as Sp1 or p53, is an important part of the larger puzzle leading to a targeted drug discovery program focused on G4-regulation. Ultimately, G4-stabilization-mediated down regulation of kRAS has high potential for anti-cancer efficacy in pancreatic cancers, where there is a dire need for novel therapeutic development.

Citation Format: Harshul Batra, Tracy A. Brooks. The effect of the transcription factor MAZ on kRAS transcription: a role for the G-quadruplex. [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 2137. doi:10.1158/1538-7445.AM2015-2137

Abstract 2110: Modulating NRAS mRNA translation by nucleic acid clamp-mediated stabilization of the 5′- UTR G-quadruplex

NRAS, a proto-oncogene belonging to the RAS oncogene superfamily, is a intracellular signal cascade mediator, with intrinsic GTPase activity, functioning to initiate the MAPK cell signaling pathway. Among the RAS oncogene superfamily that is mutated in approximately 30% of all cancers, the NRAS mutation accounts for about 15% of RAS related human malignancies, particularly myeloid leukemias and cutaneous melanomas. Recently, a stable G-quadruplex (G4) was previously identified in the 5′-untranslated region (UTR) of NRAS mRNA. This G4 functioned as a translational silencer, downregulating NRAS protein and leading to the hypothesis that a small nucleic acid clamp could be optimized to facilitate the formation of specifically this G4, decrease NRAS expression, and facilitate cell death in melanoma cells. In the present study, a set of clamps were designed and examined for their ability to facilitate the formation of a G4 in the 5′-UTR sequence of NRAS. These clamps are comprised of ribonucleotides complementary to the RNA 5′- and 3′-regions flanking the G4-forming sequence held together by a small linker element. Based on binding studies consisting of electromobility shift assays and circular dichroism, an optimal flank length and linker length was chosen for cellular studies. Effects on cellular viability and NRAS expression are being examined in leukemia and melanoma cells, and RNA ChIP-Seq is being used to localize the intracellular activity of the clamps to the 5′-UTR. These nucleic acid clamps offer a high degree of selectivity for G4s over linear RNA facilitated by the small linker region; moreover, the approach of complementary nucleotides, versus small molecule-mediated G4 stabilization, allows for specificity for just one G4 out of all of the intracellular structures. This approach not only provides a solid base for developing the clamp into a non-small molecule cancer therapy, but also opens a new window for modulating oncogenic gene expression at the transcriptional or translational levels. The current study, in particular, offers a novel approach to anti-NRAS-mediated therapies for the treatment of myeloid leukemias and cutaneous melanomas.

Citation Format: Taisen Hao, Tracy A. Brooks. Modulating NRAS mRNA translation by nucleic acid clamp-mediated stabilization of the 5′- UTR G-quadruplex. [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 2110. doi:10.1158/1538-7445.AM2015-2110

Effect of interior loop length on the thermal stability and pK(a) of i-motif DNA

The four-stranded i-motif (iM) conformation of cytosine-rich DNA is important in a wide variety of biochemical systems ranging from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C·C(+) base pair. Fundamental studies that aim to understand how the lengths of loops connecting the protonated C·C(+) pairs affect intramolecular iM physical properties are described here. We characterized both the thermal stability and the pK(a) of intramolecular iMs with differing loop lengths, in both dilute solutions and solutions containing molecular crowding agents. Our results showed that intramolecular iMs with longer central loops form at pHs and temperatures higher than those of iMs with longer outer loops. Our studies also showed that increases in thermal stability of iMs when molecular crowding agents are present are dependent on the loop that is lengthened. However, the increase in pK(a) for iMs when molecular crowding agents are present is insensitive to loop length. Importantly, we also determined the proton activity of solutions containing high concentrations of molecular crowding agents to ascertain whether the increase in pK(a) of an iM is caused by alteration of this activity in buffered solutions. We determined that crowding agents alone increase the apparent pK(a) of a number of small molecules as well as iMs but that increases to iM pK(a) were greater than that expected from a shift in proton activity.

Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA

DNA sequences with the potential to form secondary structures such as i-motifs (iMs) and G-quadruplexes (G4s) are abundant in the promoters of several oncogenes and, in some instances, are known to regulate gene expression. Recently, iM-forming DNA strands have also been employed as functional units in nanodevices, ranging from drug delivery systems to nanocircuitry. To understand both the mechanism of gene regulation by iMs and how to use them more efficiently in nanotechnological applications, it is essential to have a thorough knowledge of factors that govern their conformational states and stabilities. Most of the prior work to characterize the conformational dynamics of iMs have been done with iM-forming synthetic constructs like tandem (CCT)_n repeats and in standard dilute buffer systems. Here, we present a systematic study on the consequences of epigenetic modifications, molecular crowding, and degree of hydration on the stabilities of an iM-forming sequence from the promoter of the c-myc gene. Our results indicate that 5-hydroxymethylation of cytosines destabilized the iMs against thermal and pH-dependent melting; contrarily, 5-methylcytosine modification stabilized the iMs. Under molecular crowding conditions (PEG-300, 40% w/v), the thermal stability of iMs increased by ∼10 °C, and the pK_a was raised from 6.1 ± 0.1 to 7.0 ± 0.1. Lastly, the iM’s stability at varying degrees of hydration in 1,2-dimethoxyethane, 2-methoxyethanol, ethylene glycol, 1,3-propanediol, and glycerol cosolvents indicated that the iMs are stabilized by dehydration because of the release of water molecules when folded. Our results highlight the importance of considering the effects of epigenetic modifications, molecular crowding, and the degree of hydration on iM structural dynamics. For example, the incorporation of 5-methylycytosines and 5-hydroxymethlycytosines in iMs could be useful for fine-tuning the pH- or temperature-dependent folding/unfolding of an iM. Variations in the degree of hydration of iMs may also provide an additional control of the folded/unfolded state of iMs without having to change the pH of the surrounding matrix.

Abstract 4374: Identification of novel, biologically relevant, G-quadruplexes formed within the critical promoter of kRAS as promising molecular targets

To date, kRAS is one of, if not the, most established oncogenic anomalies identified. It is either upregulated or mutationally activated in a variety of cancers, most notably pancreatic adenocarcinoma, non-small cell lung and colon cancers. Pancreatic cancer carries the highest mortality rate of all cancers, with only a 3-6 month median survival, and a 5-year survival of <5%. Lung and colon cancers harboring a mutant kRAS are associated with a worsened prognosis and shorter disease-free survival, and such mutations are independent factors for poor prognosis. To date no attempts to modulate kRAS activity, localization, or signaling have produced clinically active moieties; there is a desperate need for new, kRAS-focused therapeutics. Various silencing technologies have demonstrated that decreasing kRAS expression is sufficient to produce cancer cell kill, and the presented works describe a novel target to downregulate kRAS expression - secondary structures within the proximal promoter, which contains a unique string of G-rich DNA. Negative superhelicity induced by transcription results in this region opening up to form unique secondary structures called G-quadruplexes (G4s). These G4s most often act as silencer elements, forming globular structures that mask binding sites for transcriptional factors, allowing for specific molecular targeting by small molecule drugs, modulating transcription, and protein expression. The G-rich region of the kRAS promoter is extensive, containing three separate putative G4-forming regions. Initial works described the near G4 as a unique ‘kinked’ structure, as well as described two compounds that stabilize different isoforms of this structure, but do not appear to contribute much to the transcriptional control of kRAS. Further elucidation of promoter activity has highlighted new, and more biologically important, G4s existing more distally from the transcriptional state site. Stabilization of this region in a plasmid system significantly decreases luciferase expression, and the mid-G4-forming region forms several stable, complex, structures. These formations have been examined by EMSA, polymerase stop, and footprinting methods. From these data, the elucidated predominant structures are currently the target of further studies with the ultimate goal of describing a new molecular structure, and its dynamic regulation, for future drug development.

Citation Format: Chi-Fan Hockings, Kristen M. Greer, Tracy A. Brooks. Identification of novel, biologically relevant, G-quadruplexes formed within the critical promoter of kRAS as promising molecular targets. [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 4374. doi:10.1158/1538-7445.AM2013-4374

Anticancer activity and cellular repression of c-MYC by the G-quadruplex-stabilizing 11-piperazinylquindoline is not dependent on direct targeting of the G-quadruplex in the c-MYC promoter

This G-rich region of the c-MYC promoter has been shown to form a G-quadruplex structure that acts as a silencer element for c-MYC transcriptional control. In the present work, we have synthesized a series of 11-substituted quindoline analogues as c-MYC G-quadruplex-stabilizing compounds, and the cell-free and in vitro activity of these compounds were evaluated. Two lead compounds (4 and 12) demonstrated good cell-free profiles, and compound 4 (2-(4-(10H-indolo[3,2-b]quinolin-11-yl)piperazin-1-yl)-N,N-dimethylethanamine) significantly down-regulated c-MYC expression. However, despite the good cell-free activity and the effect of these compounds on c-MYC gene expression, we have demonstrated, using a cellular assay in a Burkitt's lymphoma cell line (CA46-specific), that these effects were not mediated through targeting of the c-MYC G-quadruplex. Thus, caution should be used in assigning the effects of G-quadruplex-interactive compounds that lower c-MYC to direct targeting of these promoter elements unless this assay, or similar ones, demonstrates direct targeting of the G-quadruplex in cells.

Abstract 4757: Design and optimization of linked nucleic acid (LNA) probes to detect the c-MYC G-quadruplex

The c-MYC oncogene is upregulated in almost 80% of cancers, and in some cases is the causative oncogenic factor. It is regulated at the transcriptional level with up to 90% initiating at the P1 and P2 promoters. The NHE III1 element regulates this region, which consists of a unique guanine-rich string of DNA capable of adopting at least three topologies: single stranded, double stranded (ds) and the non-B-DNA G-quadruplex (G4) structure. G4s are formed when two or more tetrads stack, each comprised of four guanines bonded by Hoogsteen hydrogen bonds, stabilized with monovalent cations. Putative G4 forming regions have at least four runs of three or more consecutive guanines separated by varying nucleotides that comprise the loop structures. The c-MYC G4 structure has been elucidated to involve guanine runs 1α4 (G41-4) or 2Δ5 (G42-5) (of six total runs) in a parallel formation. Regulatory proteins have been identified, and small molecule compounds are under investigation to stabilize the G4 element and downregulate c-MYC expression. In parallel to these efforts, we are developing linked nucleic acid (LNA)-biotin bridge probes to be used as diagnostic tools to identify these formations in biopsies in order to inform therapeutic regimens. Molecular models of the two G4 isoforms were used to determine the distance occupied by the secondary structure to be between 16.4α16.6 angstroms; various length nucleic acid sequences flanking a 17.7α30 angstrom linker were screened and optimized. Probes were shown to be structure specific - either for the c-MYC G41-4 (probe 1a) or the G42-5 (probe 1b) - by EMSA analysis. The probes were amenable to internal biotinylation for ongoing pull-down assays, but truncation of the 5′-complementary sequence limited affinity. Interestingly, the LNA probes thermally stabilized the c-MYC G4 in a unique pattern and are also being examined for their potential therapeutic efficacy. Experiments are underway to show that these hybrid probes will bind intracellularly and show the frequency of G4 formation in quiescent versus activated cells, and following treatment with c-MYC G4-interactive compounds. Through these works, we highlight for the first time that a ‘FISH’-type probe can be developed and used to selectively detect the formation of the c-MYC G4 in vitro. Up to 80% cancer patients overexpress c-MYC and are candidates for G4-targeted therapies currently under development. The developed probes will be of great utility as companion diagnostics in selecting patients for G4-therapeutics and truly personalized medicine.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4757. doi:1538-7445.AM2012-4757

Abstract 1829: Small molecule stabilization of the kRAS promoter G-quadruplex as a target for novel pancreatic cancer therapeutics

kRAS is one of, if not the, most prevalent oncogenic aberrations identified to date. It is either upregulated or mutationally activated in a multitude of cancers, including close to 100% of pancreatic adenocarcinomas. Pancreatic cancer carries the highest mortality rate of all cancers, with only a 3-6 month median survival, and a 5-year survival of <5%. There is a desperate need for new therapeutics, particularly those targeting kRAS. This is not a new concept; due to the common nature of the kRAS mutation a significant effort has been made to develop drugs that target its activated form. However, the clinical activity of those drugs has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel target to downregulate kRAS expression - secondary structures within the proximal promoter, which contains a unique string of G-rich DNA. Negative superhelicity induced by transcription results in this region opening up to form unique secondary structures called G-quadruplexes (G4s). These G4s most often act as silencer elements, forming globular structures that mask binding sites for transcriptional factors, allowing for specific molecular targeting by small molecule drugs, modulating transcription, and protein expression. Using the confirmed major isoform - a unique ‘kinked’ structure - as the primary target, we undertook a screening effort in order to identify potential G4-stabilizing small molecules. Several hundred compounds were screened, and two chemical classes consistently emerged: ellipticines (E) and quindolines (Q). The lead compounds from each pharmacophore are NSC176327 (E-14) and Quindoline i (Q-i), respectively, each of which has previously been demonstrated to stabilize other G4 structures (such as the parallel structure found within the MYC promoter.) What is most intriguing is the clear difference in isoform stabilization with these compounds; E-14 stabilizes the major kinked isoform, whereas Q-i is a bit more promiscuous and stabilizes several isoforms as demonstrated by FRET melt, the Polymerase Stop Assay and DMS footprinting. Both of these compounds demonstrate cytotoxicity, as measured by MTS, at 24 and 72 h, in a variety of pancreatic cell lines, with E-14 being notably more potent. Cytotoxicity is is being correlated to changes in kRAS mRNA expression. G4s have emerged as a potential DNA target with great potential for specificity as they are more globular than nascent DNA, and each carry some degree of distinctiveness. Using the kRAS proximal promoter G4 structure as the primary target, a drug discovery program will have great potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic adenocarcinomas, as well as childhood leukemias, ovarian, lung, and colon cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1829. doi:1538-7445.AM2012-1829

The physiological and behavioral response of pigs castrated with and without anesthesia or analgesia

Surgical castration is a common management practice performed on male pigs to prevent the occurrence of boar taint. Surgical castration is known to cause physiological and behavioral changes in pigs indicative of pain-induced distress; however, it is commonly performed without pain relief. The objective of this study was to evaluate the effectiveness of carbon dioxide gas (CO(2)) anesthesia and a non-steroidal anti-inflammatory drug (NSAID) to alleviate the pain caused by castration. At 3 d of age, male pigs were either control handled (CON), castrated without pain relief (CAS), given an NSAID and then immediately castrated (CAS+NSAID), anesthetized with CO(2) and then castrated (CAS+CO2), or anesthetized with CO(2) and given an NSAID at the time of castration (CAS+BOTH). Blood samples were collected before castration, and at 30, 60, 120, and 180 min, 24 h, and 3 d after castration or handling for analysis of cortisol, C-Reactive protein (CRP), and substance-P (SP) concentrations. This study was then repeated using the same treatment groups, and the behavioral response to castration and handling were measured using a 1-min scan sampling procedure. The percentage of stress vocalizations was recorded during the administration of all treatments. Anesthesia and analgesia did not effectively reduce (P > 0.05) the cortisol response to surgical castration. Overall, CRP concentrations were greater (P < 0.05) in CAS+CO2 pigs as compared with CON pigs. Sixty minutes after castration or handling, SP concentrations were greater (P < 0.08) in pigs given CO(2) anesthesia (CO2, CAS+CO2, and CAS+BOTH) than CON, CAS, and CAS+NSAID pigs. Pigs castrated without pain relief spent more (P < 0.001) time lying without contact than all other treatments during the first 30 min after castration, but thereafter CAS+CO2 pigs spent more (P < 0.001) time lying without contact than other treatments. During the first 30 min after the treatments were applied, CAS+CO2 pigs spent more (P < 0.01) time displaying pain-like behaviors than CON, CAS, CAS+NSAID, and CAS+BOTH pigs. The percentage of stress vocalizations was greater (P < 0.05) in CAS and CAS+NSAID pigs than all other treatments. Neither CO(2) anesthesia nor a NSAID, given separately or combined, markedly reduced the pain-induced distress caused by castration in pigs. More research is needed to evaluate practical methods of on-farm pain relief for pigs.

Demonstration that drug-targeted down-regulation of MYC in non-Hodgkins lymphoma is directly mediated through the promoter G-quadruplex

Most transcription of the MYC proto-oncogene initiates in the near upstream promoter, within which lies the nuclease hypersensitive element (NHE) III(1) region containing the CT-element. This dynamic stretch of DNA can form at least three different topologies: single-stranded DNA, double-stranded DNA, or higher order secondary structures that silence transcription. In the current report, we identify the ellipticine analog GQC-05 (NSC338258) as a high affinity, potent, and selective stabilizer of the MYC G-quadruplex (G4). In cells, GQC-05 induced cytotoxicity with corresponding decreased MYC mRNA and altered protein binding to the NHE III(1) region, in agreement with a G4 stabilizing compound. We further describe a unique feature of the Burkitt's lymphoma cell line CA46 that allowed us to clearly demonstrate the mechanism and location of action of GQC-05 within this region of DNA and through the G4. Most importantly, these data present, as far as we are aware, the most direct evidence of intracellular G4-mediated control of a particular promoter.

Tight junctions contain oligomeric protein assembly critical for maintaining blood-brain barrier integrity in vivo

Tight junctions (TJs) are major components of the blood-brain barrier (BBB) that physically obstruct the interendothelial space and restrict paracellular diffusion of blood-borne substances from the peripheral circulation to the CNS. TJs are dynamic structures whose intricate arrangement of oligomeric transmembrane and accessory proteins rapidly alters in response to external stressors to produce changes in BBB permeability. In this study, we investigate the constitutive trafficking of the TJ transmembrane proteins occludin and claudin-5 that are essential for forming the TJ seal between microvascular endothelial cells that inhibits paracellular diffusion. Using a novel, detergent-free OptiPrep density-gradient method to fractionate rat cerebral microvessels, we identify a plasma membrane lipid raft domain that contains oligomeric occludin and claudin-5. Our data suggest that oligomerization of occludin involves disulfide bond formation within transmembrane regions, and that assembly of the TJ oligomeric protein complex is facilitated by an oligomeric caveolin scaffold. This is the first time that distribution of oligomeric TJ transmembrane proteins within plasma membrane lipid rafts at the BBB has been examined in vivo. The findings reported in this study are critical to understand the mechanism of assembly of the TJ multiprotein complex that is essential for maintaining BBB integrity.

Abstract 4422: Direct demonstration of c-MYC G-quadruplex stabilization in vitro: elucidating the CA46 system

Many cancers harbor reciprocal chromosomal translocations that can lead to the activation of proto-oncogenes, inactivation of tumor-suppressor genes and/or generation of oncogenic chimera. In Non-Hodgkin Burkitt's lymphoma (BL) there is a characteristic translocation of the c-MYC gene on chromosome 8q24 to one of three immunoglobulin genes on chromosomes 14, 2, or 22. The resulting product leads to c-MYC upregulation. ∼90% of c-MYC gene transcription is initiated by the P1 and P2 promoters, just upstream of which lies the guanine-rich NHE III1 control element. This is a very dynamic stretch of DNA, capable of forming at least three different DNA topologies: single stranded, double stranded and the G-quadruplex (G4) DNA. The G4 is a transcriptional silencer, and thus an attractive target for anti-cancer therapeutics. Using two BL cell lines (RAJI and CA46) we directly demonstrate the formation of a G4 in the c-MYC promoter. Using a small molecule compound, we clearly show specific activity dependent on the existence and regulation of this structure. The BL reciprocal translocation t(8;14) maintains G4-mediated control of c-MYC on both chromosomes in RAJI, but only on the non-translocated (NT) chromosome in CA46. The translocated (T) chromosome's rate of transcription is 1000-fold greater than the NT, making the T the major allele, and the NT the minor allele. Thus, RAJI harbors G4-mediated control of both alleles and is expected to be more sensitive to G4-interactive compounds than CA46, which lost G4 control on the major allele. Indeed, GQC-05 (NSC338258), previously demonstrated to bind and stabilize the c-MYC G4, had greater cytotoxicity in the RAJI cell line. This compound demonstrated a rapid and time-dependent downregulation of c-MYC mRNA in RAJI, but no overt c-MYC effect in CA46. We were able to distinguish, using primers specific to exons 1 or 2, between the NT and T mRNA products, respectively. Remarkably, GQC-05 rapidly and significantly downregulated c-MYC mRNA from the NT allele in CA46 cells, where the G4 maintains transcriptional control. As a negative control, we examined the effects of GQC-05 on both exons in RAJI cells; no differential effect was observed. Doxorubicin is a non-G4 interactive compound that also decreases c-MYC expression in CA46 cells, but does not show this ‘exon-specific’ effect. Chromatin immunoprecipitation confirmed GQC-05 changes protein binding to the G4-region of the c-MYC promoter, with decreased transcription factor, and altered G4-regulatory factor, binding. Our work elucidates the primary mechanism of action for GQC-05 as stabilization of the c-MYC G4, leading to transcriptional downregulation. More importantly, we unambiguously demonstrate the formation and regulation of the c-MYC G4 in vitro and for the first time are able to evaluate c-MYC G4-targeted compounds in a whole cell system with this newly described CA46 model.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4422. doi:10.1158/1538-7445.AM2011-4422

Increased MYC gene copy number correlates with increased mRNA levels in diffuse large B-cell lymphoma

BACKGROUND

Translocations involving the MYC gene and increased MYC mRNA levels are associated with poor outcome in diffuse large B-cell lymphoma. However, the presence of increased MYC gene copy number and/or polysomy of chromosome 8 have not been previously described.

DESIGN AND METHODS

Utilizing dual color chromogenic in situ hybridization, we investigated MYC gene copy and chromosome 8 centromere numbers in 52 cases of diffuse large B-cell lymphoma. Cases were divided into those with "increased" or "not increased" MYC gene copy number for comparison with MYC mRNA levels, Ki-67 values, and survival.

RESULTS

Increased MYC gene copy number was present in 38% of cases. Overall, the average MYC mRNA level was 2398 (range, 342 - 9783) and the percentage of nuclei positive for Ki-67 was 57.5% (range, 20-87%). Within the group with increased MYC copy number, the MYC mRNA values ranged from 816 to 5912 (average, 2843) and the Ki-67 values ranged from 23% to 83% (average, 57%). Within the group with not increased MYC copy number, MYC mRNA values ranged from 342 to 9783 (average, 2118) and the Ki-67 values ranged from 20% to 87% (average, 58%). There was a statistically significant relationship between increased MYC gene copy number and increased MYC mRNA (P=0.034) and a trend toward a relationship between increased mRNA and higher Ki-67 values.

CONCLUSIONS

This is the first report that low level copy number increases are common in diffuse large B-cell lymphoma and that these changes correlate with MYC mRNA in a statistically significant manner. MYC copy number changes are an additional possible molecular mechanism that may result in increased mRNA and, likely, high proliferation and poor outcome.

Targeting MYC Expression through G-Quadruplexes

In this review, the authors describe a novel mechanism for control of MYC expression that involves a four-stranded DNA structure, termed a G-quadruplex, amenable to small molecule targeting. The DNA element involved in this mechanism, the nuclease hypersensitive element III(1) (NHE III(1)), is just upstream of the P1 promoter and is subjected to dynamic stress (negative superhelicity) resulting from transcription. This is sufficient to convert the duplex DNA to a G-quadruplex on the purine-rich strand and an i-motif of the pyrimidine-rich strand, which displaces the activating transcription factors to silence gene expression. Specific proteins have been identified, NM23-H2 and nucleolin, that resolve and fold the G-quadruplex to activate and silence MYC expression, respectively. Inhibition of the activity of NM23-H2 molecules that bind to the G-quadruplex silences gene expression, and redistribution of nucleolin from the nucleolus to the nucleoplasm is expected to inhibit MYC. The authors also describe the mechanism of action of Quarfloxin, a first-in-class G-quadruplex-interactive compound that involves the redistribution of nucleolin from the nucleolus to the nucleoplasm. G-quadruplexes have been best known as test-tube oddities for more than four decades. However, during the past decade, they have emerged as likely players in a number of important biological processes, including transcriptional control. Only time will tell if these odd DNA structures will assume the role of an established receptor class, but it is clear from the scientific literature that there is a dramatic increase in interest in this little-known area in the past few years.

Making sense of G-quadruplex and i-motif functions in oncogene promoters

The presence and biological importance of DNA secondary structures in eukaryotic promoters are becoming increasingly recognized among chemists and biologists as bioinformatics in vitro and in vivo evidence for these structures in the c-Myc, c-Kit, KRAS, PDGF-A, hTERT, Rb, RET and Hif-1alpha promoters accumulates. Nevertheless, the evidence remains largely circumstantial. This minireview differs from previous ones in that here we examine the diversity of G-quadruplex and i-motif structures in promoter elements and attempt to categorize the different types of arrangements in which they are found. For the c-Myc G-quadruplex and Bcl-2 i-motif, we summarize recent biological and structural studies.

Molecular cloning of the human platelet-derived growth factor receptor beta (PDGFR-beta) promoter and drug targeting of the G-quadruplex-forming region to repress PDGFR-beta expression

To understand the mechanisms controlling platelet-derived growth factor receptor beta (PDGFR-beta) expression in malignancies, we have cloned and characterized the first functional promoter of the human PDGFR-beta gene, which has been confirmed by luciferase reporter gene assays. The transcription initiation sites were mapped by primer extension. Promoter deletion experiments demonstrate that the proximal, highly GC-rich region (positions -165 to -139) of the human PDGFR-beta promoter is crucial for basal promoter activity. This region is sensitive to S1 nuclease and likely to assume a non-B-form DNA secondary structure within the supercoiled plasmid. The G-rich strand in this region contains a series of runs of three or more guanines that can form multiple different G-quadruplex structures, which have been subsequently assessed by circular dichroism. A Taq polymerase stop assay has shown that three different G-quadruplex-interactive drugs can each selectively stabilize different G-quadruplex structures of the human PDGFR-beta promoter. However, in transfection experiments, only telomestatin significantly reduced the human PDGFR-beta basal promoter activity relative to the control. Furthermore, the PDGFR-beta mRNA level in Daoy cells was significantly decreased after treatment with 1 muM telomestatin for 24 h. Therefore, we propose that ligand-mediated stabilization of specific G-quadruplex structures in the human PDGFR-beta promoter can modulate its transcription.

Abstract 3681: Helping Eve overcome ADAM: Characterization of the G-quadruplex in the ADAM15 core promoter

Breast cancer is the most common form of cancer in women, whose lethality is only surpassed by lung cancer. Through the last quarter-century there have been significant advances in detection and treatment options, such as Herceptin for HER2/neu positive cancers. While the development of targeted biological agents has greatly improved patient outcome, up to 70% of patients remain de novo refractory, relapse on therapy, or develop resistance. There is a pressing and eminent need for novel therapies to synergize with, or resensitize to, standard treatments. Enter ADAM15, with known zymogen, secretase, and disintegrin activies. This catalytically active member of the ADAM family is normally expressed in early embryonic development and is aberrantly expressed in various cancers, including breast. ADAM15 promotes extracellular shedding of E-cadherin, a soluble ligand for the HER2/neu receptor, leading to activation, increased motility, and proliferation. Seven independent microarray studies have shown that ADAM15 and HER2/neu are simultaneously upregulated in several stages of breast cancer, where their overexpression correlates with more aggressive and invasive disease.

We have examined a unique string of GC-rich DNA within the critical core promoter of ADAM15. This region of DNA consists of seven tandem runs of three or more consecutive guanines. Under superhelical stress produced by the transcriptional complex, this region can relax from duplex DNA to form an intrastrand secondary structure known as a G-quadruplex. These globular entities generally serve as silencing elements for gene transcription. Furthermore, the topology of each G-quadruplex is as unique as a fingerprint. This allows for specific therapeutic targeting, offering a unique opportunity for treatment and selectivity over normal cells thus providing a potentially wide therapeutic window. Circular dichroism (CD) studies have confirmed the formation of a mixed parallel/anti-parallel G-quadruplex. Further CD analysis of the minimal G-quadruplex forming fragments has shown the capability of forming four unique thermally stable species. Electrophoretic mobility shift assay indicates the strongest intramolecular G-quadruplex formation in the 5′- and 3′-end runs of guanine, with minor intermolecular formations in the 3′-mid sequence, and a relatively unstable 5′-mid formation. To specifically determine which guanines are involved in the formation of the G-quadruplex and predict biologically relevant three-dimensional structures, DMS footprinting was performed on the full-length sequence and each of the four dissected regions. The pursuant data was used to build a molecular model of the structure. Full characterization of the G-quadruplex species formed will allow for specific drug targeting and stabilization, and the further development of novel, targeted therapeutics.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3681.

Abstract 1386: A novel approach to develop anti-VEGFR2/KDR therapeutics: characterizing and targeting the G-quadruplex

The anti-angiogenic approach is traditionally considered for solid malignancies, but increasing evidence has also highlighted its involvement in the progression of hematological oncologies. Angiogenesis, including expression of key proteins, is aberrant in blood cancers such as leukemias, lymphomas, and myelomas, in addition to many solid malignancies, including pancreatic cancer. The most critical mediator of oncogenic angiogenesis is vascular endothelial growth factor (VEGF), which is recognized by two high-affinity receptor tyrosine kinases, VEGFR1 and VEGFR2 (KDR gene). VEGFR2 is necessary for the survival, growth, and differentiation of endothelial cells as its downstream effects include activation of the MAPK and the PI3K pathways, and its upregulation is observed under conditions of pathological angiogenesis. While VEGF/VEGFR2 signaling is known to act in a paracrine manner on endothelial cells, autocrine signaling has been observed in both malignant cells and hematopoietic stem cells. For endothelial and hematological malignancies, both autocrine and paracrine pathways can be targeted with anti-VEGFR2 therapies, potentially doubling the clinical efficacy. Intriguingly, the promoter region of KDR contains a GC-rich region of DNA within its the core promoter located −120 to −31 basepairs (bp) upstream of the transcriptional start site (TSS), putatively able to form several G-quadruplexes. These are unique DNA secondary structures that often serve as transcriptional silencer elements. In the present study, G-quadruplex formation has been isolated −80 to −38 bp upstream of the TSS, which contains five strings of guanines that form a mixed parallel/anti-parallel G-quadruplex, as determined by circular dichroism. The cleavage pattern of DMS footprinting and the major stop product of the polymerase stop assay confirmed that the dominant isoform is a parallel G-quadruplex occurring within the four 3’ runs of guanines. Mutant studies were performed to further determine guanines integral to G-quadruplex formation. An electrophoretic mobility shift assay was used to confirm the formation of a biologically relevant intramolecular structure. High-throughput screening identified a novel KDR-interactive agent, NSC643735, which thermally stabilized the G-quadruplex. This compound is currently being tested in vitro, and has high potential to transcriptionally downregulate KDR mRNA and, subsequently, VEGFR2 protein. These data characterizing the formation of a unique secondary structure in an important oncogene are promising to develop novel and specific anti-KDR therapy for the treatment of hematological and solid malignancies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1386.

The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics

MYC is deregulated in most tumour types, but an effective means to selectively target its aberrant expression is not yet available. Supercoiling that is induced by transcription has been demonstrated to have dynamic effects on DNA in the MYC promoter element: it converts duplex DNA to non-duplex DNA structures, even at considerable distances from the transcriptional start site. These non-duplex DNA structures, which control both turning on and off of transcription and the rate of transcription firing, are amenable to small-molecule targeting. This dynamic system provides a unique opportunity for the treatment of tumours in which MYC is an important oncogene.

Occludin oligomeric assembly at tight junctions of the blood-brain barrier is disrupted by peripheral inflammatory hyperalgesia

Tight junctions (TJs) at the blood-brain barrier (BBB) dynamically alter paracellular diffusion of blood-borne substances from the peripheral circulation to the CNS in response to external stressors, such as pain, inflammation, and hypoxia. In this study, we investigated the effect of lambda-carrageenan-induced peripheral inflammatory pain (i.e., hyperalgesia) on the oligomeric assembly of the key TJ transmembrane protein, occludin. Oligomerization of integral membrane proteins is a critical step in TJ complex assembly that enables the generation of tightly packed, large multiprotein complexes capable of physically obliterating the interendothelial space to inhibit paracellular diffusion. Intact microvessels isolated from rat brains were fractionated by detergent-free density gradient centrifugation, and gradient fractions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis/ Western blot. Injection of lambda-carrageenan into the rat hind paw produced after 3 h a marked change in the relative amounts of oligomeric, dimeric, and monomeric occludin isoforms associated with different plasma membrane lipid raft domains and intracellular compartments in endothelial cells at the BBB. Our findings suggest that increased BBB permeability (i.e., leak) associated with lambda-carrageenan-induced peripheral inflammatory pain is promoted by the disruption of disulfide-bonded occludin oligomeric assemblies, which renders them incapable of forming an impermeant physical barrier to paracellular transport.

Peripheral inflammatory hyperalgesia modulates morphine delivery to the brain: a role for P-glycoprotein

P-glycoprotein (Pgp, ABCB1) is a critical efflux transporter at the blood-brain barrier (BBB) where its luminal location and substrate promiscuity limit the brain distribution of numerous therapeutics. Moreover, Pgp is known to confer multi-drug resistance in cancer chemotherapy and brain diseases, such as epilepsy, and is highly regulated by inflammatory mediators. The involvement of inflammatory processes in neuropathological states has led us to investigate the effects of peripheral inflammatory hyperalgesia on transport properties at the BBB. In the present study, we examined the effects of lambda-carrageenan-induced inflammatory pain (CIP) on brain endothelium regulation of Pgp. Western blot analysis of enriched brain microvessel fractions showed increased Pgp expression 3 h post-CIP. In situ brain perfusion studies paralleled these findings with decreased brain uptake of the Pgp substrate and opiate analgesic, [(3)H] morphine. Cyclosporin A-mediated inhibition of Pgp enhanced the uptake of morphine in lambda-carrageenan and control animals. This indicates that the CIP induced decrease in morphine transport was the result of an increase in Pgp activity at the BBB. Furthermore, antinociception studies showed decreased morphine analgesia following CIP. The observation that CIP modulates Pgp at the BBB in vivo is critical to understanding BBB regulation during inflammatory disease states.

Biphasic cytoarchitecture and functional changes in the BBB induced by chronic inflammatory pain

The blood-brain barrier (BBB) is a dynamic system which maintains brain homeostasis and limits CNS penetration via interactions of transmembrane and intracellular proteins. Inflammatory pain (IP) is a condition underlying several diseases with known BBB perturbations, including stroke, Parkinson's, multiple sclerosis and Alzheimer's. Exploring the underlying pathology of chronic IP, we demonstrated alterations in BBB paracellular permeability with correlating changes in tight junction (TJ) proteins: occludin and claudin-5. The present study examines the IP-induced molecular changes leading to a loss in functional BBB integrity. IP was induced by injection of Complete Freund's Adjuvant (CFA) into the plantar surface of the right hindpaw of female Sprague-Dawley rats. Inflammation and hyperalgesia were confirmed, and BBB paracellular permeability was assessed by in situ brain perfusion of [14C]sucrose (paracellular diffusion marker). The permeability of the BBB was significantly increased at 24 and 72 h post-CFA. Analysis of the TJ proteins, which control the paracellular pathway, demonstrated decreased claudin-5 expression at 24 h, and an increase at 48 and 72 h post-injection. Occludin expression was significantly decreased 72 h post-CFA. Expression of junction adhesion molecule-1 (JAM-1) increased 48 h and decreased by 72 h post-CFA. Confocal microscopy demonstrated continuous expression of both occludin and JAM-1, each co-localizing with ZO-1. The increased claudin-5 expression was not limited to the junction. These results provide evidence that chronic IP causes dramatic alterations in specific cytoarchitectural proteins and demonstrate alterations in molecular properties during CFA, resulting in significant changes in BBB paracellular permeability.

The 4′-O-benzylated doxorubicin analog WP744 overcomes resistance mediated by P-glycoprotein, multidrug resistance protein and breast cancer resistance protein in cell lines and acute myeloid leukemia cells

BACKGROUND

The synthetic 4'-O-benzylated doxorubicin analog WP744 was designed to abrogate transport by the multidrug resistance (MDR)-associated ATP-binding cassette (ABC) proteins P-glycoprotein (Pgp) and multidrug resistance protein (MRP-1). We compared its uptake and cytotoxicity with those of doxorubicin and daunorubicin in cell lines overexpressing Pgp, MRP-1 or breast cancer resistance protein (BCRP) and in acute myeloid leukemia (AML) cells.

METHODS

Cellular uptake was studied by flow cytometry and cytotoxicity in 96-h 96-well cultures in cell lines overexpressing Pgp, MRP-1 or wild type (BCRP(R482)) or mutant (BCRP(R482T), BCRP(R482G)) BCRP and in pre-treatment AML marrow cells.

RESULTS

Uptake and cytotoxicity of WP744 were consistently greater than those of doxorubicin and daunorubicin at equimolar concentrations in all cell lines studied and in AML cells.

CONCLUSION

WP744 overcomes transport by Pgp, MRP-1 and BCRP in cell lines and AML cells and is a promising agent for clinical development in AML and other malignancies with broad-spectrum multidrug resistance.

Design, synthesis and structure-activity relationships of novel taxane-based multidrug resistance reversal agents

A series of novel taxane-based multidrug resistance (MDR) reversal agents (TRAs) has been designed and synthesized. Structure-activity relationship (SAR) study clearly indicates that modification of the C-7 position with hydrophobic arenecarbonylcinnamoyl groups brings about high potency against drug efflux mediated by P-glycoprotein (P-gp). Six TRAs exhibit ability to modulate a wide range of ATP-binding cassette (ABC) transporters, such as P-gp, multidrug resistance-associated protein 1 (MRP1), and breast cancer resistance protein (BCRP), which may serve as novel broad-spectrum modulators of ABC transporters.

Chronic inflammatory pain leads to increased blood-brain barrier permeability and tight junction protein alterations

The blood-brain barrier (BBB) maintains brain homeostasis by limiting entry of substances to the central nervous system through interaction of transmembrane and intracellular proteins that make up endothelial cell tight junctions (TJs). Recently it was shown that the BBB can be modulated by disease pathologies including inflammatory pain. This study examined the effects of chronic inflammatory pain on the functional and molecular integrity of the BBB. Inflammatory pain was induced by injection of complete Freund's adjuvant (CFA) into the right plantar hindpaw in female Sprague-Dawley rats under halothane anesthesia; control animals were injected with saline. Edema and hyperalgesia were assessed by plethysmography and infrared paw-withdrawal latency. At 72 h postinjection, significant edema formation and hyperalgesia were noted in the CFA-treated rats. Examination of permeability of the BBB by in situ perfusion of [14C]sucrose while rats were under pentobarbital anesthesia demonstrated that CFA treatment significantly increased brain sucrose uptake. Western blot analysis of BBB TJ proteins showed no change in expression of zonula occludens-1 (an accessory protein) or actin (a cytoskeletal protein) with CFA treatment. Expression of the transmembrane TJ proteins occludin and claudin-3 and -5 significantly changed with CFA treatment with a 60% decrease in occludin, a 450% increase in claudin-3, and a 615% increase in claudin-5 expression. This study demonstrates that during chronic inflammatory pain, alterations in BBB function are associated with changes in specific transmembrane TJ proteins.

Structure-activity analysis of taxane-based broad-spectrum multidrug resistance modulators

BACKGROUND

Clinical drug resistance is frequently associated with overexpression of the multidrug resistance (MDR) proteins P-glycoprotein (Pgp), multidrug resistance protein (MRP-1) and breast cancer resistance protein (BCRP). Taxanes are substrates for Pgp and MRP-1, but not BCRP. Taxane-based reversal agents (tRAs) are non-cytotoxic MDR modulators previously examined for broad-spectrum modulation of Pgp, MRP-1 and BCRP.

MATERIALS AND METHODS

Modulation by tRAs was studied by flow cytometry and resistance to taxanes was studied in cytotoxicity assays in the parental HL60/wt, 8226/wt and MCF7/S, and the resistant HL60/ADR, 8226/Dox6, 8226/MR20 and MCF7 AdVp3000 cell lines. Amino acid sequence (BLAST) alignments were performed using ClustalW.

RESULTS

Structure-activity analysis demonstrated greatest alignment of BCRP with the transmembrane 7-12 region of Pgp and identified tRA side groups that contributed or were detrimental to modulation.

CONCLUSION

Identification of tRA side groups contributing to modulation of Pgp, MRP-1 and BCRP will allow the design of a next generation of tRAs and will optimize their potential clinical applicability.

Broad-spectrum modulation of ATP-binding cassette transport proteins by the taxane derivatives ortataxel (IDN-5109, BAY 59-8862) and tRA96023

PURPOSE

The taxanes paclitaxel and docetaxel are substrates for P-glycoprotein (Pgp), an ATP-binding cassette (ABC) transport protein associated with multidrug resistance (MDR). In contrast, the synthetic taxane ortataxel (BAY 59-8862, IDN-5109) is effective against Pgp-expressing cells by virtue of modulation of Pgp-mediated transport. The synthetic taxane tRA96023 also modulates Pgp and is noncytotoxic due to removal of the tubulin-binding side chain at the C-13 position of the taxane backbone. We studied the effects of ortataxel and tRA96023 on the other MDR-associated ABC transport proteins, multidrug resistance protein (MRP-1) and breast cancer resistance protein (BCRP, MXR, ABCG2).

METHODS

Modulation of mitoxantrone, daunorubicin and doxorubicin retention and cytotoxicity by ortataxel and tRA96023 was studied in established cell lines overexpressing Pgp, MRP-1 and wild type (BCRP(R482)) and mutant (BCRP(R482T)) BCRP, and was compared with modulation by the established Pgp-, MRP-1- and BCRP-specific modulators PSC-833, probenecid and fumitremorgin C, respectively.

RESULTS

Ortataxel effectively modulated drug retention and cytotoxicity in cell lines overexpressing MRP-1 and BCRP(R482), in addition to Pgp. tRA96023 modulated drug retention and cytotoxicity in cell lines overexpressing BCRP(R482) and Pgp, but not those overexpressing MRP-1. Neither ortataxel nor tRA96023 modulated BCRP(R482T).

CONCLUSIONS

The synthetic taxane derivatives ortataxel and tRA96023 are broad-spectrum ABC protein modulators. Further studies will seek to identify a noncytotoxic synthetic taxane that modulates Pgp, MRP-1 and BCRP.

Taxane-based reversal agents modulate drug resistance mediated by P-glycoprotein, multidrug resistance protein, and breast cancer resistance protein

Overexpression of ATP-binding cassette transport proteins, including P-glycoprotein (Pgp), multidrug resistance (MDR) protein (MRP-1), and breast cancer resistance protein (BCRP), is a well-characterized mechanism of MDR in tumor cells. Although the cytotoxic taxanes paclitaxel and docetaxel are substrates for Pgp-mediated efflux, the semisynthetic taxane analogue ortataxel inhibits drug efflux mediated by Pgp as well as, as we recently demonstrated, MRP-1 and BCRP. Nevertheless, ortataxel is not optimal for development as a clinical MDR modulator because of its cytotoxicity [corrected]. We sought to identify noncytotoxic taxane-based broad-spectrum modulators from a library of noncytotoxic taxane-based reversal agents (tRAs) designed by eliminating the C-13 side chain of the taxane molecule, which inhibits microtubule depolymerization. Twenty tRAs, selected based on modulation of paclitaxel cytotoxicity in Pgp-overexpressing MDA435/LCC6(mdr1) cells, were studied for modulation of retention and cytotoxicity of substrates of MRP-1 and BCRP as well as Pgp in established cell lines overexpressing each of these transporters. Four tRAs modulated MRP-1 and 17 modulated BCRP in addition to Pgp. The four broad-spectrum tRAs strongly modulated daunorubicin and mitoxantrone efflux and enhanced their cytotoxicity in cell lines overexpressing the three MDRs, decreasing IC(50) values by as much as 97% [corrected]. These tRAs, especially tRA 98006, have promise for development as clinical broad-spectrum MDR modulators and warrant more preclinical analysis to determine pharmacokinetic interactions and efficacy.

Construction and characterization of an effector strain of Streptococcus mutans for replacement therapy of dental caries

An effector strain has been constructed for use in the replacement therapy of dental caries. Recombinant DNA methods were used to make the Streptococcus mutans supercolonizing strain, JH1140, lactate dehydrogenase deficient by deleting virtually all of the ldh open reading frame (ORF). To compensate for the resulting metabolic imbalance, a supplemental alcohol dehydrogenase activity was introduced by substituting the adhB ORF from Zymomonas mobilis in place of the deleted ldh ORF. The resulting clone, BCS3-L1, was found to produce no detectable lactic acid during growth on a variety of carbon sources, and it produced significantly less total acid due to its increased production of ethanol and acetoin. BCS3-L1 was significantly less cariogenic than JH1140 in both gnotobiotic- and conventional-rodent models. It colonized the teeth of conventional rats as well as JH1140 in both aggressive-displacement and preemptive-colonization models. No gross or microscopic abnormalities of major organs were associated with oral colonization of rats with BCS3-L1 for 6 months. Acid-producing revertants of BCS3-L1 were not observed in samples taken from infected animals (reversion frequency, <10(-3)) or by screening cultures grown in vitro, where no revertants were observed among 10(5) colonies examined on pH indicator medium. The reduced pathogenic potential of BCS3-L1, its strong colonization potential, and its genetic stability suggest that this strain is well suited to serve as an effector strain in the replacement therapy of dental caries in humans.