Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing

Aneuploidy frequently arises during human meiosis and is the primary cause of early miscarriage and in vitro fertilization (IVF) failure. Individuals undergoing IVF exhibit significant variability in aneuploidy rates, although the exact genetic causes of the variability in aneuploid egg production remain unclear. Preimplantation genetic testing for aneuploidy (PGT-A) using next-generation sequencing is a standard test for identifying and selecting IVF-derived euploid embryos. The wealth of embryo aneuploidy data and ultra-low coverage whole-genome sequencing (ulc-WGS) data from PGT-A have the potential to discover variants in parental genomes that are associated with aneuploidy risk in their embryos. Using ulc-WGS data from ∼10,000 PGT-A biopsies, we imputed genotype likelihoods of genetic variants in embryo genomes. We then used the imputed variants and embryo aneuploidy calls to perform a genome-wide association study of aneuploidy incidence. Finally, we carried out functional evaluation of the identified candidate gene in a mouse oocyte system. We identified one locus on chromosome 3 that is significantly associated with meiotic aneuploidy risk. One candidate gene, CCDC66, encompassed by this locus, is involved in chromosome segregation during meiosis. Using mouse oocytes, we showed that CCDC66 regulates meiotic progression and chromosome segregation fidelity, especially in older mice. Our work extended the research utility of PGT-A ulc-WGS data by allowing robust association testing and improved the understanding of the genetic contribution to maternal meiotic aneuploidy risk. Importantly, we introduce a generalizable method that has potential to be leveraged for similar association studies that use ulc-WGS data.

Identifying risk genes for embryo aneuploidy using ultra-low coverage whole-genome sequencing

Background

Aneuploidy, the state of a cell containing extra or missing chromosomes, frequently arises during human meiosis and is the primary cause of early miscarriage and maternal age-related in vitro fertilization (IVF) failure. IVF patients exhibit significant variability in aneuploidy rates, although the exact genetic causes of the variability in aneuploid egg production remain unclear. Preimplantation genetic testing for aneuploidy (PGT-A) using ultra-low coverage whole-genome sequencing (ulc-WGS) is a standard test for identifying and selecting IVF-derived embryos with a normal chromosome complement. The wealth of embryo aneuploidy data and ulc-WGS data from PGT-A has potential for discovering variants in paternal genomes that are associated with aneuploidy risk in their embryos.

Methods

Using ulc-WGS data from ∼10,000 PGT-A biopsies, we imputed genotype likelihoods of genetic variants in parental genomes. We then used the imputed variants and aneuploidy calls from the embryos to perform a genome-wide association study of aneuploidy incidence. Finally, we carried out functional evaluation of the identified candidate gene in a mouse oocyte system.

Results

We identified one locus on chromosome 3 that is significantly associated with maternal meiotic aneuploidy risk. One candidate gene, CCDC66, encompassed by this locus, is involved in chromosome segregation during meiosis. Using mouse oocytes, we showed that CCDC66 regulates meiotic progression and chromosome segregation fidelity, especially in older mice.

Conclusions

Our work extended the research utility of PGT-A ulc-WGS data by allowing robust association testing and improved the understanding of the genetic contribution to maternal meiotic aneuploidy risk. Importantly, we introduce a generalizable method that can be leveraged for similar association studies using ulc-WGS data.

Abstract 4245: Drug response metrics and pharmacological profiling using the OncoPanel™ cell-based profiling service

High-throughput, cell-based drug screening platforms are essential to guiding drug discovery programs and can rapidly generate large amounts of pharmacological information about a candidate drug. Drug response data combined with genomic and phenotypic information enables an exploratory analysis that may reveal potential associative biomarkers and deepen the pharmacological profile of a drug. The choice of metric is an important consideration as different metrics will reflect different underlying biological mechanisms. Normalized growth rate inhibition (GR) metrics offer an alternative summary of drug response, and may eliminate bias associated with experimental factors that contribute to variation in growth rate. In these sets of experiments, we used drug response data, generated with the Eurofins OncoPanel cell-based profiling service, to investigate a variety of standard of care compounds against a cell line panel selected for variation in growth rate, cancer indication, cancer hallmark mutational status, and baseline apoptosis rate. Seeding density and incubation times were systematically varied to investigate the relationship between end-point confluence, kinetics, genotype, apoptotic priming, and the robustness of different dose response metrics. Based on these results, select cell lines and standard of care compounds were included in a series of drug-drug combination studies to further investigate the biological underpinning of synergy, at the same time exploring how alternative metrics influence pharmacological profiling experiments. Compounds were added to cells in 10 half-log dilutions, in triplicate, and allowed to incubate for 1, 3, 5, or 10 days. Initial cell density conditions were varied to allow for a final targeted confluence of 30, 80, or 100%. A time-zero plate was fixed at compound addition to allow for GR calculations. Following incubation, the cells were fixed, stained with DAPI, and imaged with a high-content imaging system. Cell proliferation dose response curves were fitted using a 4-parameter log-logistic model with custom curve-fitting software. These data were re-analyzed using the GRmetrics package in R to determine the GR metrics. Summary parameters, including IC50, GR50, and GRmax, were compared in subsequent analyses. For the combination analyses, a 9 x 9 concentration matrix design was used, and Bliss analysis was conducted to assess synergy. Single parameters are typically used to summarize drug responses in cell lines, which are used to classify cell lines as sensitive or resistant to the drug, impacting the interpretation of downstream analyses. We examined the robustness of different parameters, under various growth conditions for select standard of care compounds against a panel of cancer cell lines, and investigated their interpretation on biomarker and drug-drug combination analyses.

Citation Format: Charles R. Wageman, Lee R. Cavedine, Vanessa Norman, Natiya Robinson, Tracy Lu, Victoria McBain, Joseph Murphy, Kayla Stehle, Steven M. Garner, Alyssa M. Croff, Brogan A. Epkins, Kristin Dempsey, Alastair J. King, Jesse J. Parry. Drug response metrics and pharmacological profiling using the OncoPanel™ cell-based profiling service [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 4245.

Abstract 2073: Profiling and comparison of breast cancer standard of care agents using the OncoPanel™ cell-based profiling service

Oncology drugs with clinical utility for the treatment of breast cancer span a wide range of different mechanisms and cancer type profiles. Anti-cancer therapies have come a long way from the early use of broad spectrum, cytotoxic agents, with mechanisms that often result in harsh side-effects. The advent of more focused, targeted therapies has afforded the potential for not only fewer side effects, but also the ability to provide more efficacious combination therapies with a greater potential for clinical efficacy. Recent advances have seen the approval of agents targeting CDK4/6, Her2, and PARP over the last ten years. Profiling of candidate molecules for eventual use in a therapeutic setting is an essential component of the drug discovery and development process. Understanding not only the biological potency of a candidate drug, but also the breadth of indications for which it may provide clinical benefit, is paramount in the advancement of molecules for clinical testing. Furthermore, understanding something of both the molecular mechanism and the possibility for combination synergy is an essential part of being able to visualize the full clinical potential of a drug. In the current era of personalized medicine, and understanding of the effect of genomic composition of a particular patient’s tumor on clinical outcome, the ability to evaluate a vast array of genomic signatures is important in being able to successfully direct therapeutic application. Eurofins’ OncoPanel cell-based profiling service provides a convenient way for drug hunters to evaluate not only the potential indication spectrum of a candidate molecule by high-content imaging analysis, but also to identify potentially predictive genomic biomarkers for both sensitivity and resistance to these agents. We have evaluated a range of different approved breast cancer therapeutic agents, using the OncoPanel platform, for their effect on the growth of human tumor cell lines in vitro. These agents span a range of different mechanisms and therapeutic modalities, from broad spectrum cytotoxics to more targeted small molecule and antibody drugs. In this poster, we compare and contrast the different utilities of these drugs, both from the perspective of which tumor types and sub-types are sensitive to these agents, but also with regard to which genomic biomarkers are associated with sensitivity toward them. In doing so, we show how these biomarkers can be useful in not only identifying potentially responsive patient subsets, but also potential combination studies that could be used to improve therapeutic outcome.

Citation Format: Alastair J. King, Lee R. Cavedine, Alyssa M. Croff, Kristin C. Dempsey, Brogan A. Epkins, Steven M. Garner, Tracy Lu, Victoria V. McBain, Joseph W. Murphy, Vanessa L. Norman, Natiya E. Robinson, Kayla A. Stehle, Charles R. Wageman, Jesse J. Parry. Profiling and comparison of breast cancer standard of care agents using the OncoPanel™ cell-based profiling service [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 2073.

Developmental nicotine exposure precipitates multigenerational maternal transmission of nicotine preference and ADHD-like behavioral, rhythmometric, neuropharmacological, and epigenetic anomalies in adolescent mice

Maternal smoking during pregnancy, a form of developmental nicotine exposure (DNE), is associated with increased nicotine use and neurodevelopmental disorders such as ADHD in children. Here, we characterize the behavioral, rhythmometric, neuropharmacological, and epigenetic consequences of DNE in the F1 (first) and F2 (second) generation adolescent offspring of mice exposed to nicotine prior to and throughout breeding. We assessed the effects of passive oral methylphenidate (MPH) administration and voluntary nicotine consumption on home cage activity rhythms and activity and risk-taking behaviors in the open field. Results imply a multigenerational predisposition to nicotine consumption in DNE mice and demonstrate ADHD-like diurnal and nocturnal hyperactivity and anomalies in the rhythmicity of home cage activity that are reversibly rescued by MPH and modulated by voluntary nicotine consumption. DNE mice are hyperactive in the open field and display increased risk-taking behaviors that are normalized by MPH. Pharmacological characterization of nicotinic and dopaminergic systems in striatum and frontal cortex reveals altered expression and dysfunction of nicotinic acetylcholine receptors (nAChRs), hypersensitivity to nicotine-induced nAChR-mediated dopamine release, and impaired dopamine transporter (DAT) function in DNE mice. Global DNA methylation assays indicate DNA methylome deficits in striatum and frontal cortex of DNE mice. Collectively, our data demonstrate that DNE enhances nicotine preference, elicits hyperactivity and risk-taking behaviors, perturbs the rhythmicity of activity, alters nAChR expression and function, impairs DAT function, and causes DNA hypomethylation in striatum and frontal cortex of both first and second-generation adolescent offspring. These findings recapitulate multiple domains of ADHD symptomatology.

Abstract 2260: Exploring drug response metrics for biomarker discovery using the OncoPanel™ cell-based profiling service

Using drug response data, generated by the OncoPanelTM cell-based profiling service, we investigated the differences between traditional and normalized growth rate inhibition (GR) metrics in drug sensitivity classification and predictive genomic biomarker discovery. Traditional cellular response parameters can be confounded by numerous growth conditions, especially when the mechanism of action of a drug is coupled to cell cycle processes. Metrics such as IC50 or Emax can be influenced by cellular growth rate, adding bias to the apparent sensitivity to or efficacy of the drug. Use of GR metrics aims to eliminate this bias by normalizing the response data to a per-cell division rate. In this study, we analyzed various parameters for a selection of standard of care compounds when tested against a large panel of cancer cell lines. Compounds were tested against between 213 and 297 different human cancer cell lines. Cells were seeded in 384-well plates and allowed to incubate for 24 hours before acoustic energy-based compound addition was made over 10 half-log concentrations, in triplicate. Initial cell density was captured in a parallel plate to enable cell doubling and end-point GR calculations. After 3 or 10 days of incubation, the cells were fixed, stained with DAPI, and imaged using a high-content imaging platform. Cell proliferation dose response curves were fitted using a 4-parameter log-logistic model within a custom curve-fitting software platform. These same data were then re-analyzed using the GR metrics package developed for the statistical programming language R, to determine GR metrics (GR50 and GRmax). Exploratory analysis was conducted on four parameters: IC50, GR50, GRmax, and number of doublings. IC50 and GR50 were used to classify compounds into drug-resistant or sensitive groups, and GRmax was used to classify each as cytostatic, partially cytostatic, or cytotoxic. Each parameter was used in a predictive genomic biomarker search, using baseline mRNA expression data and mutation data from the COSMIC/Sanger and Broad/CCLE databases. Correlation analysis for doublings and IC50, or GR50, suggests that cell lines with faster doubling rates are associated with drug sensitivity, especially with compounds that target cell cycle processes, such as doxorubicin, carboplatin, cisplatin, and oxaliplatin. Genomic analyses revealed different predictive biomarkers for each choice of parameter. The relationships between significant biomarkers were explored across compounds and cancer cell types. In summary, the methods employed in the OncopanelTM cell-based profiling service enable various dose response parameter estimations, including GR metrics. Through careful use of growth-normalized data, we have expanded our capacity to discover predictive genomic biomarkers that are less influenced by cellular growth conditions.

Citation Format: Charles R. Wageman, Jesse J. Parry, Lee R. Cavedine, Alyssa M. Croff, Steven M. Garner, Brogan A. Epkins, Natiya E. Robinson, Kristin C. Dempsey, Vanessa L. Norman, Usha Warrior, Alastair J. King. Exploring drug response metrics for biomarker discovery using the OncoPanel™ cell-based profiling service [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2260.

Abstract 1391: Establishment and validation of a high-content imaging assay with a 14-day incubation for the testing of epigenetic target-based therapeutics

Given the importance and significance of targeting mutations and epigenetic modification in cancer therapy, we sought to expand on our ability to test drugs with epigenetic modulatory abilities by increasing the exposure time of drugs against cell lines by the OncoPanel™ cell-based profiling service to 14 days. Using historic internal control data, generated in OncoPanel™ cell proliferation assays for 3-, 5-, and 10-day exposures, we were able to calculate the theoretical number of doublings in 14 days for each cell line. This information was used to calculate the seeding density at the time of cell plating that would provide the same endpoint per well density for a select number of cell lines from the panel. Due to the issue of increasing coefficient of variation (CV) with decreasing starting number of cells per well, we eliminated cell lines that had a calculated seeding density of <15 cells per well. For cell line validation, cells were plated at the calculated theoretical density for each cell line in 384-well plates and incubated overnight. A time zero (T0) plate was also seeded for each cell line to allow calculation of the number of doublings in the assay. Test compounds (staurosporine, entinostat, and vorinostat) were added to the assay plates over a range of 10 concentrations, in triplicate, using acoustic liquid transfer. The assay plates were incubated continuously for 7 days, upon which the growth media were removed and replaced with fresh media, followed by re-dosing with compounds. Assay plates were then incubated continuously for an additional 7 days, after which the cells were fixed and stained to allow high-content, fluorescent imaging of nuclei. Data were analyzed as the relative cell count, where the measured fluorescence intensity was transformed to percent of control, as compared with a vehicle-treated control. Cellular response parameters were calculated, using nonlinear regression to a sigmoidal single-site dose response model. The criteria for each cell line to pass quality control included a vehicle CV of <30%, endpoint well confluence, tightness of curve-fit, and an empirically-determined doubling number that was comparable with the calculated number of doublings. Comparison of the doubling numbers was striking and illustrated very high accuracy, adding to the consistency of the assay's performance. In summary, we have validated 110 human cancer cell lines, comprising 16 tissue types, in the 14-day OncoPanel™ proliferation assay, and show comparative analysis of each compound's activity profile from 3-, 5-, 10-, and 14-day incubations. The extended incubation time is highly relevant and useful for testing epigenetic target modulators, which may require a longer-term exposure to show full efficacy, with a greater potential therapeutic outcome.

Citation Format: Jesse J. Parry, Vanessa L. Norman, Charles R. Wageman, Lee R. Cavedine, Timothy J. Sindelar, Alyssa M. Croff, Steven M. Garner, Brogan A. Epkins, Natiya E. Robinson, Kristin C. Dempsey, Usha Warrior, Alastair J. King. Establishment and validation of a high-content imaging assay with a 14-day incubation for the testing of epigenetic target-based therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1391.

The interaction of the Chrna5 D398N variant with developmental nicotine exposure

A single nucleotide polymorphism (SNP) in CHRNA5 (rs16969968, change from an aspartic acid [D] to asparagine [N] at position 398 of the human α5 nicotinic acetylcholine receptor subunit) has been associated with increased risk for nicotine dependence. Consequently, carriers of the risk variant may be at elevated risk for in utero nicotine exposure. To assess whether this gene-environment interaction might impact nicotine intake in developmental nicotine-exposed offspring, we utilized a mouse expressing this human SNP. D and N dams drank nicotine (100 μg/mL) in 0.2% saccharin water or 0.2% saccharin water alone (vehicle) as their sole source of fluid from 30 days prior to breeding until weaning of offspring. The nicotine (D Nic, N Nic) or vehicle (D Veh, N Veh) exposed offspring underwent a 2-bottle choice test between postnatal ages of 30 to 46 days. N Nic offspring consumed the most nicotine at the highest concentration (400 μg/mL) compared with all other groups. In contrast, D Nic offspring drank the least amount of nicotine at all concentrations tested. Nicotine-stimulated dopamine (DA) release measured from striatal synaptosomes was increased in D Nic offspring, while decreased in N Nic offspring relative to their genotype-matched controls. These data suggest that the α5 variant influences the effect of developmental nicotine exposure on nicotine intake of exposed offspring. This gene-environment interaction on striatal DA release may provide motivation for increased nicotine seeking in N Nic offspring and reduced consumption in D Nic offspring.

TC299423, a Novel Agonist for Nicotinic Acetylcholine Receptors

(E)-5-(Pyrimidin-5-yl)-1,2,3,4,7,8-hexahydroazocine (TC299423) is a novel agonist for nicotinic acetylcholine receptors (nAChRs). We examined its efficacy, affinity, and potency for α6β2^∗ (α6β2-containing), α4β2^∗, and α3β4^∗ nAChRs, using [¹²⁵I]-epibatidine binding, whole-cell patch-clamp recordings, synaptosomal ⁸⁶Rb⁺ efflux, [³H]-dopamine release, and [³H]-acetylcholine release. TC299423 displayed an EC₅₀ of 30–60 nM for α6β2^∗ nAChRs in patch-clamp recordings and [³H]-dopamine release assays. Its potency for α6β2^∗ in these assays was 2.5-fold greater than that for α4β2^∗, and much greater than that for α3β4^∗-mediated [³H]-acetylcholine release. We observed no major off-target binding on 70 diverse molecular targets. TC299423 was bioavailable after intraperitoneal or oral administration. Locomotor assays, measured with gain-of-function, mutant α6 (α6L9′S) nAChR mice, show that TC299423 elicits α6β2^∗ nAChR-mediated responses at low doses. Conditioned place preference assays show that low-dose TC299423 also produces significant reward in α6L9′S mice, and modest reward in WT mice, through a mechanism that probably involves α6(non-α4)β2^∗ nAChRs. However, TC299423 did not suppress nicotine self-administration in rats, indicating that it did not block nicotine reinforcement in the dosage range that was tested. In a hot-plate test, TC299423 evoked antinociceptive responses in mice similar to those of nicotine. TC299423 and nicotine similarly inhibited mouse marble burying as a measure of anxiolytic effects. Taken together, our data suggest that TC299423 will be a useful small-molecule agonist for future in vitro and in vivo studies of nAChR function and physiology.

Abstract 2116: Combining the power of different profiling approaches to better understand the activity of kinase inhibitor drugs

Profiling of inhibitors for eventual therapeutic use is an essential part of drug discovery and development. Evaluating the in vitro potency of kinase inhibitors in a wide panel of enzyme assays is critical, not only to guiding SAR knowledge for improving drug design, but also for assessing selectivity, which has long-reaching consequences for both biological activity and safety. Evaluation of the same inhibitors in cellular models yields information on the activity of these inhibitors in a more physiologically relevant environment. However, while some selective kinase inhibitors show predictably selective profiles in cell proliferation assays, others do not. Thus, the biological context in which a kinase inhibitor functions, and the signaling networks influenced by inhibition of both the desired target and off-target activities, help to define how that inhibitor will work in a cellular setting and, ultimately, in a therapeutic application. We demonstrate the power of profiling several well-known kinase inhibitors in complementary panel assays, to predict behavior that has implications for clinical activity. The in vitro profiles of selective (trametinib, vemurafenib) and less selective (dasatinib, sorafenib) kinase inhibitors are shown and compared. With careful evaluation of their in vitro enzyme activity profiles in Eurofins’ KinaseProfiler™ panel, cellular response profiles in OncoPanel™, and predictive biomarker identification by univariate genomic analysis, a fuller picture of these inhibitors’ biological activity can be generated, and may be applied to predicting the therapeutic potential of such inhibitors. While, in some cases, clinical response is seen as expected, this kind of comprehensive analysis opens up the possibility for expanding clinical utility of an asset by potential repurposing for other indications. Collectively, this demonstrates not only the need to understand an inhibitor’s fundamental activity(ies) at its designated target(s), but also the importance of considering cellular context, when assessing its maximum potential clinical utility.

Citation Format: Alastair J. King, Jesse J. Parry, Samantha C. Burkart, Lee R. Cavedine, Alyssa M. Cracchiolo, Brogan A. Epkins, Steven M. Garner, Timothy J. Sindelar, Charles R. Wageman, Stephen P. Davies, Andrew Plater, Anna M. Woodward, Usha Warrior. Combining the power of different profiling approaches to better understand the activity of kinase inhibitor drugs [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 2116. doi:10.1158/1538-7445.AM2017-2116

Abstract 5787: Validation of spheroids with long-term incubation for high-throughput screening

The OncoPanel™ service has established 100 genomically-characterized human tumor cell lines as targets for the screening of compounds in 3D spheroid models. We sought to (1) expand the cell line capability of the service and (2) validate the cell lines in a long-term (10-day) assay. For the cell line expansion, cells were plated at two densities in 384-well, spheroid-promoting plates, and were incubated for 3 days to allow formation of spheroids. The growth media were then removed and replaced with media containing the hypoxia probe, Lox-1. Twenty-four hours later, the ability to form spheroids was determined by bright-field, high-content imaging, and fluorescent detection of the Lox-1 probe in the hypoxic core of the spheroids. Cells were then seeded in assay plates at pre-determined densities, along with a time zero (T0) plate, and were incubated for 4 days to allow spheroid formation. Spheroid formation was verified by bright-field, high-content imaging, as previously mentioned. The growth media were removed and replaced with fresh media, followed by the addition of staurosporine over a range of 10 concentrations, using acoustic liquid transfer. At this time, the T0 plate was processed for subsequent doubling calculations. The assay plates were incubated for 10 days, re-imaged, and the spheroids were lysed using CellTiter-Glo® 3D viability reagent. Data were analyzed as the relative cell count, where the measured bioluminescence intensity was transformed to percent of control, as compared with a vehicle-treated control. Cellular response parameters were calculated using nonlinear regression to a sigmoidal single-site dose response model. A vehicle CV of <30% was required, as one criterion, for each cell line to pass quality control. Based on our tests of spheroid formation in the expansion cell lines, we have added 36 cell lines to the spheroid- or loose aggregate-forming cell line panel, with 20 cell lines validated in the long-term assay. Through the use of high-throughput screening and high-content imaging, we can verify and validate spheroid formation and growth in a 384-well format, with which we can test agents for drug discovery projects and provide value for potentially greater therapeutic outcomes.

Citation Format: Jesse J. Parry, Steven M. Garner, Lee R. Cavedine, Alyssa M. Cracchiolo, Brogan A. Epkins, Samantha C. Burkart, Timothy J. Sindelar, Charles R. Wageman, Usha Warrior, Alastair J. King. Validation of spheroids with long-term incubation for high-throughput screening [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 5787. doi:10.1158/1538-7445.AM2017-5787

Synthesis, Nicotinic Acetylcholine Binding, and in Vitro and in Vivo Pharmacological Properties of 2'-Fluoro-(carbamoylpyridinyl)deschloroepibatidine Analogues

In this study, we report the synthesis, nAChR in vitro and in vivo pharmacological properties of 2'-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues (5, 6a,b, and 7a,b), which are analogues of our lead structure epibatidine. All of the analogues had subnanomolar binding affinity for α4β2*-nAChRs, and all were potent antagonists of α4β2-nAChRs in an in vitro functional assay. Analogues 6a,b were also highly selective for α4β2- relative to α3β4- and α7-nAChRs. Surprisingly, all of the analogues were exceptionally potent antagonists of nicotine-induced antinociception in the mouse tail-flick test, relative to standard nAChR antagonists such as DHβE. 2'-Fluoro-(4-carbamoyl-3-pyridinyl)deschloroepitabidine (6a) displayed an attractive combination of properties, including subnanomolar binding affinity (Ki = 0.07 nM), submicromolar inhibition of α4β2-nAChRs in the functional assay (IC50 = 0.46 μM) with a high degree of selectivity for α4β2- relative to the α3β4/α7-nAChRs (54-/348-fold, respectively), potent inhibition of [(3)H]dopamine release mediated by α4β2*- and α6β2*-nAChRs in a synaptosomal preparation (IC50 = 21 and 32 nM, respectively), and an AD50 of 0.007 μg/kg as an antagonist of nicotine induced antinociception in the mouse tail-flick test which is 64 250 times more potent than DHβE. These data suggest that compound 6a will be highly useful as a pharmacological tool for studying nAChRs and merits further development.

In vitro and in vivo neuronal nicotinic receptor properties of (+)- and (-)-pyrido[3,4]homotropane [(+)- and (-)-PHT]: (+)-PHT is a potent and selective full agonist at α6β2 containing neuronal nicotinic acetylcholine receptors

Pyrido[3,4]homotropane (PHT) is a conformationally rigid, high affinity analogue of nicotine. (+)-PHT was previously shown to be 266 times more potent than (-)-PHT for inhibition of [(3)H]epibatidine binding to nAChRs but had no antinociceptive activity in mouse tail-flick or hot-plate tests and was not a nicotinic antagonist even when administered intrathecally. While (-)-PHT had no agonist activity, it was a potent, nicotinic antagonist in the test. Here, electrophysiological studies with rat nAChRs show (+)-PHT to be a low efficacy partial agonist selective for α4β2-nAChRs, relative to α3β4-nAChRs (15-fold) and α7-nAChRs (45-fold). (-)-PHT was an antagonist with selectivity for α3β4, relative to α4β2- (3-fold) and α7- (11-fold) nAChRs. In [(3)H]DA release studies in mice, (+)-PHT was 10-fold more potent than (-)-PHT at α4β2*-nAChRs and 30-fold more potent at α6β2*-nAChRs. Studies using α5KO mice suggested that much of the activity at α4β2*-nAChRs is mediated by the α4β2α5-nAChR subtype. In conditioned place preference studies, (-)-PHT was more potent than (+)-PHT in blocking nicotine reward. Off-target screens showed (+)- and (-)-PHT to be highly selective for nAChRs. The high potency, full agonism of (+)- and (-)-PHT at α6*-nAChR contrasts with the partial agonism observed for α4*-nAChR, making these ligands intriguing probes for learning more about the pharmacophores for various nAChRs.

α6β2*-subtype nicotinic acetylcholine receptors are more sensitive than α4β2*-subtype receptors to regulation by chronic nicotine administration

Nicotinic acetylcholine receptors (nAChR) of the α6β2* subtype (where *indicates the possible presence of additional subunits) are prominently expressed on dopaminergic neurons. Because of this, their role in tobacco use and nicotine dependence has received much attention. Previous studies have demonstrated that α6β2*-nAChR are down-regulated following chronic nicotine exposure (unlike other subtypes that have been investigated - most prominently α4β2* nAChR). This study examines, for the first time, effects across a comprehensive chronic nicotine dose range. Chronic nicotine dose-responses and quantitative ligand-binding autoradiography were used to define nicotine sensitivity of changes in α4β2*-nAChR and α6β2*-nAChR expression. α6β2*-nAChR down-regulation by chronic nicotine exposure in dopaminergic and optic-tract nuclei was ≈three-fold more sensitive than up-regulation of α4β2*-nAChR. In contrast, nAChR-mediated [(3) H]-dopamine release from dopamine-terminal region synaptosomal preparations changed only in response to chronic treatment with high nicotine doses, whereas dopaminergic parameters (transporter expression and activity, dopamine receptor expression) were largely unchanged. Functional measures in olfactory tubercle preparations were made for the first time; both nAChR expression levels and nAChR-mediated functional measures changed differently between striatum and olfactory tubercles. These results show that functional changes measured using synaptosomal [(3) H]-DA release are primarily owing to changes in nAChR, rather than in dopaminergic, function. This study examined dose-response relationships for murine α6β2*-nicotinic acetylcholine receptor (nAChR) down-regulation by chronic nicotine treatment. The ID50 value for α6β2* down-regulation (35 nM) is ≈ 3x lower than the ED50 value for α4β2* nAChR up-regulation (95 nM), both well within the range reached by human smokers. Chronic nicotine treatment altered α6β2*- and α4β2*-nAChR-mediated [(3) H]-dopamine release from striatal and olfactory tubercle synaptosomes, but dopaminergic parameters were largely unaffected. We conclude that functional changes are primarily driven by altered nAChR activity.

Effectiveness of nicotinic agonists as desensitizers at presynaptic α4β2- and α4α5β2-nicotinic acetylcholine receptors

INTRODUCTION

Nicotine interacts with nicotinic acetylcholine receptors (nAChRs) and modifies neuronal functions. The net result of nicotine exposure is difficult to assess because multiple nAChR subtypes exist and are expressed on multiple classes of neurons. Nicotine, unlike the natural agonist acetylcholine, remains in tissues for hours, and during this extended exposure nAChRs desensitize. Therefore, agonists can block the natural functions of nAChRs. Higher nicotine concentrations are required to desensitize α4β2-nAChRs containing the α5 subunit. The aim of these experiments was to determine if this property holds true for compounds other than nicotine.

METHODS

[(3)H]-dopamine release from crude mouse striatal synaptosomal preparations was used to measure activation and desensitization of the [(α4β2)2β2] and [(α4β2)2α5] nAChR subtypes. Affinity was measured by competition with [(125)I]-epibatidine.

RESULTS

Nine compounds of varying affinity and efficacy were tested. All compounds partially desensitized both subtypes; concentration necessary for desensitization correlated with binding site affinity but not efficacy. All compounds showed a similar, significant shift in concentration necessary for a 50% effect when the α5 subunit was included (averaging 8-fold higher). The extent of desensitization produced by a 10-min exposure did not correlate with affinity or efficacy of compound.

CONCLUSION

Full or partial nicotinic agonists used as medications may effectively desensitize α4β2-nAChRs. However, significantly higher concentrations of all compounds tested were required to elicit desensitization of α4α5β2-nAChRs than α4β2-nAChRs. If desensitization is the important property for a smoking cessation drug, basic screening at both subtypes may provide a mechanistic foundation for effectiveness.

CC4, a dimer of cytisine, is a selective partial agonist at α4β2/α6β2 nAChR with improved selectivity for tobacco smoking cessation

BACKGROUND AND PURPOSE

Many of the addictive and rewarding effects of nicotine are due to its actions on the neuronal nicotinic ACh receptor (nAChR) subtypes expressed in dopaminergic mesocorticolimbic cells. The partial agonists, cytisine and varenicline, are helpful smoking cessation aids. These drugs have a number of side effects that limit their usefulness. The aim of this study was to investigate the preclinical pharmacology of the cytisine dimer1,2-bisN-cytisinylethane (CC4).

EXPERIMENTAL APPROACH

The effects of CC4 on nAChRs were investigated using in vitro assays and animal behaviours.

KEY RESULTS

When electrophysiologically tested using heterologously expressed human subtypes, CC4 was less efficacious than cytisine on neuronal α4β2, α3β4, α7 and muscle-type receptors, and had no effect on 5-hydroxytryptamine3 receptors. Acting through α4β2 and α6β2 nAChRs, CC4 is a partial agonist of nAChR-mediated striatal dopamine release and, when co-incubated with nicotine, prevented nicotine's maximal effect on this response. In addition, it had low affinity for, and was less efficacious than nicotine and cytisine on the α3β4 and α7-nAChR subtypes. Like cytisine and nicotine, CC4-induced conditioned place preference (CPP), and its self-administration shows an inverted-U dose-response curve. Pretreatment with non-reinforcing doses of CC4 significantly reduced nicotine-induced self-administration and CPP without affecting motor functions.

CONCLUSION AND IMPLICATIONS

Our in vitro and in vivo findings reveal that CC4 selectively reduces behaviours associated with nicotine addiction consistent with the partial agonist selectivity of CC4 for β2-nAChRs. The results support the possible development of CC4 or its derivatives as a promising drug for tobacco smoking cessation.

A novel α-conotoxin MII-sensitive nicotinic acetylcholine receptor modulates [(3) H]-GABA release in the superficial layers of the mouse superior colliculus

Mouse superficial superior colliculus (SuSC) contains dense GABAergic innervation and diverse nicotinic acetylcholine receptor subtypes. Pharmacological and genetic approaches were used to investigate the subunit compositions of nicotinic acetylcholine receptors (nAChR) expressed on mouse SuSC GABAergic terminals. [(125) I]-Epibatidine competition-binding studies revealed that the α3β2* and α6β2* nicotinic subtype-selective peptide α-conotoxin MII-blocked binding to 40 ± 5% of SuSC nAChRs. Acetylcholine-evoked [(3) H]-GABA release from SuSC crude synaptosomal preparations is calcium dependent, blocked by the voltage-sensitive calcium channel blocker, cadmium, and the nAChR antagonist mecamylamine, but is unaffected by muscarinic, glutamatergic, P2X and 5-HT3 receptor antagonists. Approximately 50% of nAChR-mediated SuSC [(3) H]-GABA release is inhibited by α-conotoxin MII. However, the highly α6β2*-subtype-selective α-conotoxin PIA did not affect [(3) H]-GABA release. Nicotinic subunit-null mutant mouse experiments revealed that ACh-stimulated SuSC [(3) H]-GABA release is entirely β2 subunit-dependent. α4 subunit deletion decreased total function by >90%, and eliminated α-conotoxin MII-resistant release. ACh-stimulated SuSC [(3) H]-GABA release was unaffected by β3, α5 or α6 nicotinic subunit deletions. Together, these data suggest that a significant proportion of mouse SuSC nicotinic agonist-evoked GABA-release is mediated by a novel, α-conotoxin MII-sensitive α3α4β2 nAChR. The remaining α-conotoxin MII-resistant, nAChR agonist-evoked SuSC GABA release appears to be mediated via α4β2* subtype nAChRs.

Low concentrations of nicotine differentially desensitize nicotinic acetylcholine receptors that include α5 or α6 subunits and that mediate synaptosomal neurotransmitter release

Desensitization is a complex property of nicotinic acetylcholine receptors (nAChR). Several subtypes of nAChR have high sensitivity to nicotine and mediate effects of nicotine at concentrations found in blood of tobacco smokers. Desensitization of some of these receptor subtypes has been studied in model systems, however, other subtypes have been difficult to express heterologously in native forms. In addition, model systems may not have the same accessory molecules and post-translational modifications found in native populations. We have used wild-type and subunit null mutant mice to study desensitization properties of the high sensitivity α4β2-nAChRs including those that have α5 subunits at both GABAergic and dopaminergic nerve terminals. In addition, we have studied the desensitization of one subtype of α6β2-nAChRs at dopaminergic terminals using α4 subunit null mutant mice. Exposure to low nicotine concentrations, leads to rapid, but partial desensitization of activity mediated by these receptors. α4β2-nAChRs including α5 subunits show faster rates of recovery from desensitization than α4β2-nAChRs without α5. Inclusion of the α5 subunit significantly shifts the concentration response for desensitization to higher values, indicating that receptors with α5 subunits are less desensitized by a 10-min exposure to low concentrations of nicotine. Receptors with α6 subunits appear to desensitize to a lesser degree than those with α4 subunits, indicating that α6β2-nAChRs are somewhat resistant to desensitization by nicotine. These results highlight the importance of studying various receptor subtypes in native systems and how they may differentially respond to nicotine and to nicotinic drugs.

Structural differences determine the relative selectivity of nicotinic compounds for native alpha 4 beta 2*-, alpha 6 beta 2*-, alpha 3 beta 4*- and alpha 7-nicotine acetylcholine receptors

Mammalian brain expresses multiple nicotinic acetylcholine receptor (nAChR) subtypes that differ in subunit composition, sites of expression and pharmacological and functional properties. Among known subtypes of receptors, alpha 4 beta 2* and alpha 6 beta 2*-nAChR have the highest affinity for nicotine (where * indicates possibility of other subunits). The alpha 4 beta 2*-nAChRs are widely distributed, while alpha 6 beta 2*-nAChR are restricted to a few regions. Both subtypes modulate release of dopamine from the dopaminergic neurons of the mesoaccumbens pathway thought to be essential for reward and addiction. alpha 4 beta 2*-nAChR also modulate GABA release in these areas. Identification of selective compounds would facilitate study of nAChR subtypes. An improved understanding of the role of nAChR subtypes may help in developing more effective smoking cessation aids with fewer side effects than current therapeutics. We have screened a series of nicotinic compounds that vary in the distance between the pyridine and the cationic center, in steric bulk, and in flexibility of the molecule. These compounds were screened using membrane binding and synaptosomal function assays, or recordings from GH4C1 cells expressing h alpha 7, to determine affinity, potency and efficacy at four subtypes of nAChRs found in brain, alpha 4 beta 2*, alpha 6 beta 2*, alpha 7 and alpha 3 beta 4*. In addition, physiological assays in gain-of-function mutant mice were used to assess in vivo activity at alpha 4 beta 2* and alpha 6 beta 2*-nAChRs. This approach has identified several compounds with agonist or partial agonist activity that display improved selectivity for alpha 6 beta 2*-nAChR.

Evaluation of structurally diverse neuronal nicotinic receptor ligands for selectivity at the alpha6( *) subtype

Direct comparison of pyridine versus pyrimidine substituents on a small but diverse set of ligands indicates that the pyrimidine substitution has the potential to enhance affinity and/or functional activity at alpha6 subunit-containing neuronal nicotinic receptors (NNRs) and decrease activation of ganglionic nicotinic receptors, depending on the scaffold. The ramifications of this structure-activity relationship are discussed in the context of the design of small molecules targeting smoking cessation.

Selectivity of ABT-089 for alpha4beta2* and alpha6beta2* nicotinic acetylcholine receptors in brain

Numerous pharmaceutical efforts have targeted neuronal nicotinic receptors (nAChRs) for amelioration of cognitive deficits. While alpha4beta2 and alpha7 are the more prominent nAChR in brain, other heteromeric nAChR can have important impact on agonist pharmacology. ABT-089 is a pioneer nAChR agonist found to enhance cognitive function with an exceptionally low incidence of adverse effects. To further investigate the mechanism of action of ABT-089, we evaluated its function in mouse brain preparations in which we have characterized the subunit composition of native nAChR. Among alpha4beta2*-nAChR, ABT-089 had partial agonist activity (7-23% of nicotine) and high selectivity for alpha4alpha5beta2 nAChR as evidenced by loss of activity in thalamus of alpha5(-/-) mice. ABT-089 stimulated [(3)H]-dopamine release (57%) exceeded the activity at alpha4beta2* nAChR, that could be explained by the activity at alpha6beta2* nAChR. The concentration-response relationship for ABT-089 stimulation of alpha6beta2* nAChR was biphasic. EC(50) and efficacy values for ABT-089, respectively, were 28 microM and 98% at the less sensitive alpha6beta2* nAChR and 0.11 microM and 36% at the more sensitive subtype (the most sensitive target for ABT-089 identified to date). ABT-089 had essentially no agonist or antagonist activity at concentrations <or=300 microM at alpha3beta4-nAChR measured by [(3)H]-acetylcholine release from interpeduncular nucleus. Thus, ABT-089 is a beta2* nAChR ligand with demonstrable agonist activity at alpha4beta2* and alpha6beta2* receptors. As one form of alpha6beta2* nAChR is sensitive to sub-muM concentrations, we propose that this receptor in particular may contribute to the enhanced cognitive performance following low doses of ABT-089.