2-Aminobenzothiazoles Inhibit Virulence Gene Expression and Block Polymyxin Resistance in Salmonella enterica

One promising strategy to combat antibiotic-resistant bacteria is to develop compounds that block bacterial defenses against antibacterial conditions produced by the innate immune system. Salmonella enterica, which causes food-borne gastroenteritis and typhoid fever, requires histidine kinases (HKs) to resist innate immune defenses such as cationic antimicrobial peptides (CAMPs). Herein, we report that 2-aminobenzothiazoles block histidine kinase-dependent phenotypes in Salmonella enterica serotype Typhimurium. We found that 2-aminobenzothiazoles inhibited growth under low Mg²⁺ , a stressful condition that requires histidine kinase-mediated responses, and decreased expression of the virulence genes pagC and pagK. Furthermore, we discovered that 2-aminobenzothiazoles weaken Salmonella's resistance to polymyxin B and polymyxin E, which are last-line antibiotics and models for host defense CAMPs. These findings raise the possibilities that 2-aminobenzothiazoles can block HK-mediated bacterial defenses and can be used in combination with polymyxins to treat infections caused by Salmonella.

Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action

Aromatase inhibitors (AIs) reduce breast cancer recurrence and prolong survival, but up to 30% of patients exhibit recurrence. Using a genome-wide association study of patients entered on MA.27, a phase III randomized trial of anastrozole versus exemestane, we identified a single nucleotide polymorphism (SNP) in CUB And Sushi multiple domains 1 (CSMD1) associated with breast cancer–free interval, with the variant allele associated with fewer distant recurrences. Mechanistically, CSMD1 regulates CYP19 expression in an SNP- and drug-dependent fashion, and this regulation is different among 3 AIs: anastrozole, exemestane, and letrozole. Overexpression of CSMD1 sensitized AI-resistant cells to anastrozole but not to the other 2 AIs. The SNP in CSMD1 that was associated with increased CSMD1 and CYP19 expression levels increased anastrozole sensitivity, but not letrozole or exemestane sensitivity. Anastrozole degrades estrogen receptor α (ERα), especially in the presence of estradiol (E2). ER⁺ breast cancer organoids and AI- or fulvestrant-resistant breast cancer cells were more sensitive to anastrozole plus E2 than to AI alone. Our findings suggest that the CSMD1 SNP might help to predict AI response, and anastrozole plus E2 serves as a potential new therapeutic strategy for patients with AI- or fulvestrant-resistant breast cancers.

A germline variation within the CSMD1 gene predicts aromatase inhibitor response in breast cancer.

Abstract LB-103: The interaction between SNP genotype and aromatase inhibitor treatment response in early breast cancer

Purpose: To determine genetic variants that could differentiate aromatase inhibitors (AIs) efficacy in early stage breast cancer. Experimental Design: We performed a stratified cox-proportional hazards analysis utilizing stratification factors and other covariates examining Breast Cancer Free Interval (BCFI) SNP-treatment interaction in Caucasian patients entered on the MA.27 trial. This analysis involved 4465 patients (2226 on anastrozole and 2239 on exemestane arm) including 245 (121 on anastrozole and 124 events on exemestane arm) with a breast event. Preclinical laboratory studies included luciferase activity, chromatin immunoprecipitation (ChIP) assay, and cell migration assays. Results: We identified 887 SNPs with a p-value <1E-4 that could differentiate anastrozole from exemestane efficacy. We next used GTEx databases to determine whether these SNPs might be cis-eQTLs with nearby genes, and found that 95 SNPs were eQTL with 14 genes. Functional validation of SNP effect in these 14 genes on response to anastrozole and exemestane revealed that 3 SNPs showed genotype-dependent differences between anastrozole and exemestane. Two of the three SNPs, rs1877193 and rs6735923 located upstream of LY75 gene, were associated with higher LY75 gene expression. Our drug-SNP interaction GWAS showed that both SNPs were associated with better BCFI for exemestane compared to anastrozole (HR= 0.447, 0.458). The SNP rs62293499 located downstream of the GPR160 gene was also associated with better BCFI for exemestane compared to anastrozole (HR=0.433). Interestingly, all 3 SNPs were associated with worse outcome (shorter BCFI) in anastrozole treated patients (HR=1.39~1.58), but with longer BCFI in the exemestane treated patients (HR=0.58~0.71) based on our GWAS results in MA.27 trial. However, all 3 SNPs showed no association with BCFI if the two treatment arms, anastrozole and exemestane, were combined (HR=0.92~1.08). Consistently, cells with Ly75 or GPR160 SNP variant genotypes were more sensitive to exemestane compared to anastrozole. Mechanistically, the 3 SNPs regulated estrogen receptor-dependant LY75 and GPR160 expression. LY75 suppression induced epithelial-to-mesenchymal transition (EMT) in breast cancer cell lines, accompanied by increased migratory capacity in vitro. LY75 knockdown also resulted in predominant downregulation of functional pathways such as cell proliferation, while pathways associated with mesenchymal stimulation were generally increased. GPR160 knockdown also resulted in downregulation of cell proliferation pathways. Conclusions: This SNP genotype and AI treatment interaction clinical study revealed unique genetic variants that differentiate anastrozole and exemestane efficacy. The signals were lost in the GWAS analysis when anastrozole and exemestane were combined. Preclinical laboratory studies revealed novel functions of LY75 and GPR160 in breast cancer. These findings represent potential steps towards individualized AI therapy.

Citation Format: Junmei Cairns, James N. Ingle, Krishna R. Kalari, Lois E. Shepherd, Matthew J. Ellis, Paul E. Goss, Poulami Barman, Erin E. Carlson, Matthew P. Goetz, Richard M. Weinshilboum, Liewei Wang. The interaction between SNP genotype and aromatase inhibitor treatment response in early breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-103.

Enzyme-targeted fluorescent small-molecule probes for bacterial imaging

Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.

Mechanistic Studies of Bioorthogonal ATP Analogues for Assessment of Histidine Kinase Autophosphorylation

Phosphorylation is an essential protein modification and is most commonly associated with hydroxyl-containing amino acids via an adenosine triphosphate (ATP) substrate. The last decades have brought greater appreciation to the roles that phosphorylation of myriad amino acids plays in biological signaling, metabolism, and gene transcription. Histidine phosphorylation occurs in both eukaryotes and prokaryotes but has been shown to dominate signaling networks in the latter due to its role in microbial two-component systems. Methods to investigate histidine phosphorylation have lagged behind those to study serine, threonine, and tyrosine modifications due to its inherent instability and the historical view that this protein modification was rare. An important strategy to overcome the reactivity of phosphohistidine is the development of substrate-based probes with altered chemical properties that improve modification longevity but that do not suffer from poor recognition or transfer by the protein. Here, we present combined experimental and computational studies to better understand the molecular requirements for efficient histidine phosphorylation by comparison of the native kinase substrate, ATP, and alkylated ATP derivatives. While recognition of the substrates by the histidine kinases is an important parameter for the formation of phosphohistidine derivatives, reaction sterics also affect the outcome. In addition, we found that stability of the resulting phosphohistidine moieties correlates with the stability of their hydrolysis products, specifically with their free energy in solution. Interestingly, alkylation dramatically affects the stability of the phosphohistidine derivatives at very acidic pH values. These results provide critical mechanistic insights into histidine phosphorylation and will facilitate the design of future probes to study enzymatic histidine phosphorylation.

Harnessing β-Lactam Antibiotics for Illumination of the Activity of Penicillin-Binding Proteins in Bacillus subtilis

Selective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis in Bacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam antibiotics from different structural subclasses using a fluorescence-based assay. Most compounds readily labeled PBP1, PBP2a, PBP2b, or PBP4. Almost all penicillin scaffolds were coselective for all or combinations of PBP2a, 2b, and 4. Cephalosporins, on the other hand, possessed the lowest IC₅₀ values for PBP1 alone or along with PBP4 (ceftriaxone, cefoxitin) and 2b (cefotaxime) or 2a, 2b, and 4 (cephalothin). Overall, five selective inhibitors for PBP1 (aztreonam, faropenem, piperacillin, cefuroxime, and cefsulodin), one selective inhibitor for PBP5 (6-aminopenicillanic acid), and various coselective inhibitors for other PBPs in B. subtilis were discovered. Surprisingly, carbapenems strongly inhibited PBP3, formerly shown to have low affinity for β-lactams and speculated to be involved in β-lactam resistance in B. subtilis. To investigate the specific roles of PBP3, we developed activity-based probes based on the meropenem core and utilized them to monitor the activity of PBP3 in living cells. We showed that PBP3 activity localizes as patches in single cells and concentrates as a ring at the septum and the division site during the cell growth cycle. Our activity-based approach enabled spatial resolution of the transpeptidation activity of individual PBPs in this model microorganism, which was not possible with previous chemical and biological approaches.

Chemical tools for selective activity profiling of bacterial penicillin-binding proteins

Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.

Anastrozole has an Association between Degree of Estrogen Suppression and Outcomes in Early Breast Cancer and is a Ligand for Estrogen Receptor α

PURPOSE

To determine if the degree of estrogen suppression with aromatase inhibitors (AI: anastrozole, exemestane, letrozole) is associated with efficacy in early-stage breast cancer, and to examine for differences in the mechanism of action between the three AIs.

EXPERIMENTAL DESIGN

Matched case-control studies [247 matched sets from MA.27 (anastrozole vs. exemestane) and PreFace (letrozole) trials] were undertaken to assess whether estrone (E1) or estradiol (E2) concentrations after 6 months of adjuvant therapy were associated with risk of an early breast cancer event (EBCE). Preclinical laboratory studies included luciferase activity, cell proliferation, radio-labeled ligand estrogen receptor binding, surface plasmon resonance ligand receptor binding, and nuclear magnetic resonance assays.

RESULTS

Women with E1 ≥1.3 pg/mL and E2 ≥0.5 pg/mL after 6 months of AI treatment had a 2.2-fold increase in risk (P = 0.0005) of an EBCE, and in the anastrozole subgroup, the increase in risk of an EBCE was 3.0-fold (P = 0.001). Preclinical laboratory studies examined mechanisms of action in addition to aromatase inhibition and showed that only anastrozole could directly bind to estrogen receptor α (ERα), activate estrogen response element-dependent transcription, and stimulate growth of an aromatase-deficient CYP19A1^-/- T47D breast cancer cell line.

CONCLUSIONS

This matched case-control clinical study revealed that levels of estrone and estradiol above identified thresholds after 6 months of adjuvant anastrozole treatment were associated with increased risk of an EBCE. Preclinical laboratory studies revealed that anastrozole, but not exemestane or letrozole, is a ligand for ERα. These findings represent potential steps towards individualized anastrozole therapy.

Ion Mobility Mass Spectrometry as an Efficient Tool for Identification of Streptorubin B in Streptomyces coelicolor M145

Ion mobility spectrometry was utilized to corroborate the identity of streptorubin B (2) as the natural product produced by Streptomyces coelicolor. Natural product 2 was initially assigned as butylcycloheptylprodigiosin (3), and only relatively recently was this assignment clarified. We present additional evidence of this assignment by comparing collisional cross sections (Ω) of synthetic standards of 2, 3, and metacycloprodigiosin (4) to the cyclic prodiginine produced by S. coelicolor. Calculated theoretical Ω values demonstrate that cyclic prodiginines could be identified without standards. This work highlights ion mobility as an efficient tool for the dereplication of natural products.

Chronic exposure to complex metal oxide nanoparticles elicits rapid resistance in Shewanella oneidensis MR-1

Engineered nanoparticles are incorporated into numerous emerging technologies because of their unique physical and chemical properties. Many of these properties facilitate novel interactions, including both intentional and accidental effects on biological systems. Silver-containing particles are widely used as antimicrobial agents and recent evidence indicates that bacteria rapidly become resistant to these nanoparticles. Much less studied is the chronic exposure of bacteria to particles that were not designed to interact with microorganisms. For example, previous work has demonstrated that the lithium intercalated battery cathode nanosheet, nickel manganese cobalt oxide (NMC), is cytotoxic and causes a significant delay in growth of Shewanella oneidensis MR-1 upon acute exposure. Here, we report that S. oneidensis MR-1 rapidly adapts to chronic NMC exposure and is subsequently able to survive in much higher concentrations of these particles, providing the first evidence of permanent bacterial resistance following exposure to nanoparticles that were not intended as antibacterial agents. We also found that when NMC-adapted bacteria were subjected to only the metal ions released from this material, their specific growth rates were higher than when exposed to the nanoparticle. As such, we provide here the first demonstration of bacterial resistance to complex metal oxide nanoparticles with an adaptation mechanism that cannot be fully explained by multi-metal adaptation. Importantly, this adaptation persists even after the organism has been grown in pristine media for multiple generations, indicating that S. oneidensis MR-1 has developed permanent resistance to NMC.

PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient

PURPOSE

The majority of patients with cancer receive treatments that are minimally informed by omics data. We propose a precision medicine computational framework, PANOPLY (Precision Cancer Genomic Report: Single Sample Inventory), to identify and prioritize drug targets and cancer therapy regimens.

MATERIALS AND METHODS

The PANOPLY approach integrates clinical data with germline and somatic features obtained from multiomics platforms and applies machine learning and network analysis approaches in the context of the individual patient and matched controls. The PANOPLY workflow uses the following four steps: selection of matched controls to the patient of interest; identification of patient-specific genomic events; identification of suitable drugs using the driver-gene network and random forest analyses; and provision of an integrated multiomics case report of the patient with prioritization of anticancer drugs.

RESULTS

The PANOPLY workflow can be executed on a stand-alone virtual machine and is also available for download as an R package. We applied the method to an institutional breast cancer neoadjuvant chemotherapy study that collected clinical and genomic data as well as patient-derived xenografts to investigate the prioritization offered by PANOPLY. In a chemotherapy-resistant patient-derived xenograft model, we found that that the prioritized drug, olaparib, was more effective than placebo in treating the tumor ( P < .05). We also applied PANOPLY to in-house and publicly accessible multiomics tumor data sets with therapeutic response or survival data available.

CONCLUSION

PANOPLY shows promise as a means to prioritize drugs on the basis of clinical and multiomics data for an individual patient with cancer. Additional studies are needed to confirm this approach.

Structure Elucidation of Macrolide Antibiotics Using MSn Analysis and Deuterium Labelling

The 14- and 16-membered macrolide antibiotics are an important structural class. Ubiquitously produced by a number of bacterial strains, namely actinomycetes, purification and structure elucidation of the wide array of analogs is challenging, both for discovery efforts and methodologies to monitor for byproducts, metabolites, and contaminants. Collision-induced dissociation mass spectrometry offers an attractive solution, enabling characterization of mixtures, and providing a wealth of structural information. However, interpretation of these spectra can be difficult. We present a study of 14- and 16-membered macrolide antibiotics, including MSⁿ analysis for unprecedented depth of coverage, and complimentary analysis with D₂O and H₂¹⁸O labeling to elucidate fragmentation mechanisms. These analyses contrast the behaviors of varying classes of macrolides and highlight how analogues can be identified in relation to similar structures, which will provide utility for future studies of novel macrolides, as well as impurities, metabolites, and degradation products of pharmaceuticals. Graphical Abstract.

Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach

Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.

Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.

Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2

Anastrozole is a widely prescribed aromatase inhibitor for the therapy of estrogen receptor positive (ER+) breast cancer. We performed a genome‐wide association study (GWAS) for plasma anastrozole concentrations in 687 postmenopausal women with ER+ breast cancer. The top single‐nucleotide polymorphism (SNP) signal mapped across SLC38A7 (rs11648166, P = 2.3E‐08), which we showed to encode an anastrozole influx transporter. The second most significant signal (rs28845026, P = 5.4E‐08) mapped near ALPPL2 and displayed epistasis with the SLC38A7 signal. Both of these SNPs were cis expression quantitative trait loci (eQTL)s for these genes, and patients homozygous for variant genotypes for both SNPs had the highest drug concentrations, the highest SLC38A7 expression, and the lowest ALPPL2 expression. In summary, our GWAS identified a novel gene encoding an anastrozole transporter, SLC38A7, as well as epistatic interaction between SNPs in that gene and SNPs near ALPPL2 that influenced both the expression of the transporter and anastrozole plasma concentrations.

Abstract P1-03-04: Molecular subtyping of androgen receptor-positive patients using gene expression profiles

Breast cancer is a heterogeneous disease, and unsupervised clustering approaches using gene expression data have identified 3-6 distinct subtypes of triple negative breast cancer (TNBC). A genomically and clinically distinct subtype of TNBC is referred to as LAR (Luminal Androgen Receptor). Tumors with this subtype typically express high levels of the AR and exhibit alterations within genes involved in the PI3K pathway (e.g. PIK3CA mutations). Prospective studies are underway using drugs that target the AR alone or in combination with PI3K and CDK 4/6 inhibitors. Given the importance of accurately identifying this subtype, we sought to develop an online tool that uses submitted gene expression data to confidently characterize LAR samples by corroborating the classification with previously published clustering approaches.

Methods: We have investigated TNBC RNA-Seq data from The Cancer Genome Atlas (TCGA) breast cancer study (N=123 samples) by cluster analysis. Analysis of the average silhouette width in both biased and unbiased K-means clustering approaches demonstrated LAR and basal as two distinct and significant clusters. A shrunken centroid model of 426 differentially expressed genes, named as CABAL (Clustering Among BAsal and Luminal androgen receptor), was constructed by comparing LAR and basal subtypes.

Results: We applied the CABAL model to classify the four TNBC microarray datasets that were previously used in clustering experiments as well as an independent RNA-Seq data cohort. Non-negative matrix factorization (NMF) and fuzzy clustering were applied to the samples (N=1046). Clustering similarity among the methods was assessed with the adjusted rand index, and CABAL demonstrated significant similarity with both fuzzy and NMF clustering methods. Similarly, hierarchical clustering analysis performed on the pooled cohort of 1046 samples recapitulated the CABAL classification with an area under the receiver operating curve of 0.91.

Conclusions: Confident and robust identification of samples with the LAR phenotype is paramount in the assessment of clinical associations and therapeutic efficacy. To facilitate LAR identification, we have provided a web-based prediction tool of the CABAL classification, integrated with the NMF and fuzzy clustering results to identify candidate LAR samples. The end user is provided with the pair-wise adjusted rand indexes, thus reinforcing in the clustering characterizations. Further, our online LAR depiction tool provides a set of graphical and tabular summaries, which will be illustrated, while providing additional molecular characterizations of the PAM50 and Metabric classifications. The availability of this tool could advance the genomic research and treatment of TNBC patients.

Citation Format: Thompson KJ, Alaparthi T, Sinnwell JP, Carlson EE, Tang X, Bockol M, Vedell PT, Ingle JN, Suman V, Weinshilboum RM, Wang L, Boughey JC, Kalari KR, Goetz MP. Molecular subtyping of androgen receptor-positive patients using gene expression profiles [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-03-04.

Abstract P3-06-10: Multiscale modeling of omics data for precision breast cancer treatment

Introduction: The vast majority of cancer patients continue to receive treatments that are minimally informed by omics data. In the case of breast cancer, only ER and HER2 are routinely used for treatment selection. There is a particular need for personalized treatment in individuals with primary and secondary drug resistance or aggressive breast cancers. Emerging bioinformatics and statistical methods have made a fundamental impact on cancer research. However, challenges remains with regard to patient-centric data analysis and providing genomic data guidance to oncologists. There exists a large number of FDA approved anti-neoplastic drugs used to treat cancers other than breast and the development of innovative informatics methods and algorithms to repurpose those drugs should benefit breast cancer patients.

Methods and Results: We have developed precision care systems (such as PANOPLY and CORPUS) to identify personalized therapies for an individual patient and to deliver genomic reports in a standard, searchable format so that a researcher or an oncologist can quickly navigate through molecular data and obtain prioritized drugs and targets.The PANOPLY (Precision cancer genomics report: single sample inventory) algorithm applies machine learning and topology-based network analysis methods to integrate multi-omics profiles and clinical data; individual-specific molecular alterations are identified and compared with a set of matched-controls having similar clinical data. Since there is a lack of a “gold standard” dataset to test such algorithms, we simulated 500 case-control sets and evaluated drug predictions across multiple simulation scenarios. We applied the PANOPLY algorithm to The Cancer Genome Atlas (TCGA) breast cancer cohort, which consists of multi-omics data and clinical data. In addition, PANOPLY was also applied to an in-house neoadjuvant breast cancer study (BEAUTY) that consists of multi-omics data, clinical data, and patient-derived xenografts (PDXs). In the TCGA breast cancer study we obtained survival data to determine the cases and matched-controls; and in the BEAUTY, we used pathologic complete response (pCR) as an outcome to determine responders and non-responders. Recurrent targetable alterations were not enriched in patients without pCR in the BEAUTY study. We have applied the PANOPLY to non-responder patients to identify individual specific alterations, dysregulated networks, drug targets, and drugs for each patient and stored them as case reports in CORPUS (Computational Oncology Reports and Precision therapeUticS), a web-based repository that allows clinicians to review genomic reports. Using comprehensive “omic” data derived from a triple negative breast cancer patient who had pre and post-neoadjuvant chemotherapy PDXs, PANOPLY prioritized the PARP inhibitors as the top class of drug. Using the PDX models available from this patient, we tested olaparib and confirmed the in vivo antitumor activity (more effective than vehicle with a p-value &lt; 0.05 in the PDXs). Further studies to confirm PANOPLY findings are currently underway.

Conclusions: In summary, the PANOPLY and CORPUS systems incorporate molecular data together with clinical data to provide genomic reports with proposed drug targets to advance or enable precision breast cancer care.

Citation Format: Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Alaparthi T, Yu J, Vedell PT, Kalmbach MT, Bockol MA, Hossain A, Weinshilboum RM, Boughey JC, Wang L, Suman VJ, Goetz MP. Multiscale modeling of omics data for precision breast cancer treatment [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-10.

Biological impact of nanoscale lithium intercalating complex metal oxides to model bacterium B. subtilis

The wide applications of lithium intercalating complex metal oxides in energy storage devices call for a better understanding of their environmental impact at the end of their life cycle. In this study, we examine the biological impact of a panel of nanoscale lithium nickel manganese cobalt oxides (Li _x Ni _y Mn _z Co_1-y-z O₂, 0 < x, y, z < 1, abbreviated to NMCs) to a model Gram-positive bacterium, Bacillus subtilis, in terms of cellular respiration and growth. A highly sensitive single-cell gel electrophoresis method is also applied for the first time to understand the genotoxicity of these nanomaterials to bacterial cells. Results from these assays indicate that the free Ni and Co ions released from the incongruent dissolution of the NMC material in B. subtilis growth medium induced both hindered growth and cellular respiration. More remarkably, the DNA damage induced by the combination of the two ions in solution is comparable to that induced by the NMC material, which suggests that the free Ni and Co ions are responsible for the toxicity observed. A material redesign by enriching Mn is also presented. The combined approaches of evaluating their impact on bacterial growth, respiration, and DNA damage at a single-cell level, as well as other phenotypical changes allows us to probe the nanomaterials and bacterial cells from a mechanistic prospective, and provides a useful means to an understanding of bacterial response to new potential environmental stressors.

Tiny Things with Enormous Impact: Nanotechnology in the Fight Against Infectious Disease

Nanoparticles have exceptional properties that make them outstanding candidates for improving diagnostics and the treatment of infectious disease. Their small size, distinctive intrinsic properties, and ability to be decorated with a variety of complex functionalities make them uniquely capable of detection and targeting of certain diseases. Nanotechnology has the ability to increase the sensitivity of detection methods, the potency and ease of treatment, and the effectiveness of vaccinations. However, major challenges remain to their application in low-resource settings due in large part to the sensitivity of these particles to their local environment, a property that makes them both exceptional for detection and prone to complications or failure during synthesis and utilization. These challenges are likely to be solved only by continued and enhanced communication across scientific disciplines, for example, medical doctors and diagnosticians providing information about what is needed in new technologies. This information will enable materials scientists and engineers to rapidly address the corresponding technical challenges, such as the scalable and reproducible generation of nontoxic and stable, yet responsible nanoparticles.

Exploration of the Effects of γ-Phosphate-Modified ATP Analogues on Histidine Kinase Autophosphorylation

While two-component systems (TCSs), composed of a sensor histidine kinase (HK) and a response regulator, are the main signaling pathways in bacteria, global TCS activity remains poorly described. Here, we report the kinetic parameters of the HK autophosphorylation reaction using previously uncharacterized γ-phosphate-modified ATP analogues to further elucidate their utility as activity-based probes for global TCS analysis. Given the increased stability of thiophosphorylated histidine in comparison to that of the native phosphoryl modification, which is attributed to the decreased electrophilicity of this moiety, we anticipated that ATPγS may be turned over much more slowly by the HKs. Surprisingly, we found this not to be the case, with the turnover numbers decreasing <1 order of magnitude. Instead, we found that alkylation of the thiophosphate had a much more dramatic effect on turnover and, in one case, the binding affinity of this substrate analogue (BODIPY-FL-ATPγS).

Disarming the virulence arsenal of Pseudomonas aeruginosa by blocking two-component system signaling

Pseudomonas aeruginosa infections have reached a “critical” threat status making novel therapeutic approaches required.

Pseudomonas aeruginosa infections have reached a “critical” threat status making novel therapeutic approaches required. Inhibiting key signaling enzymes known as the histidine kinases (HKs), which are heavily involved with its pathogenicity, has been postulated to be an effective new strategy for treatment. Herein, we demonstrate the potential of this approach with benzothiazole-based HK inhibitors that perturb multiple virulence pathways in the burn wound P. aeruginosa isolate, PA14. Specifically, our compounds significantly reduce the level of toxic metabolites generated by this organism that are involved in quorum-sensing and redox-balancing mechanisms. They also decrease the ability of this organism to swarm and attach to surfaces, likely by influencing their motility appendages. Quantitative transcription analysis of inhibitor-treated cultures showed substantial perturbations to multiple pathways including expression of response regulator GacA, the cognate partner of the “super regulator” of virulence, HK GacS, as well as flagella and pili formation. These promising results establish that blocking of bacterial signaling in P. aeruginosa has dramatic consequences on virulence behaviours, especially in the context of surface-associated infections.

Screening serine/threonine and tyrosine kinase inhibitors for histidine kinase inhibition

Histidine kinases of bacterial two-component systems are promising antibacterial targets. Despite their varied, numerous roles, enzymes in the histidine kinase superfamily share a catalytic core that may be exploited to inhibit multiple histidine kinases simultaneously. Characterized by the Bergerat fold, the features of the histidine kinase ATP-binding domain are not found in serine/threonine and tyrosine kinases. However, because each kinase family binds the same ATP substrate, we sought to determine if published serine/threonine and tyrosine kinase inhibitors contained scaffolds that would also inhibit histidine kinases. Using select assays, 222 inhibitors from the Roche Published Kinase Set were screened for binding, deactivation, and aggregation of histidine kinases. Not only do the results of our screen support the distinctions between ATP-binding domains of different kinase families, but the lead molecule identified also presents inspiration for further histidine kinase inhibitor development.