Abstract 1750: Design and development of a novel highly sequence-selective guanine mono-alkylating DNA-interactive ADC payload suitable for solid tumor treatments

Antibody-Drug Conjugates (ADCs) are a fast-growing class of targeted cancer therapeutic agents with over ten approved and greater than 100 in various stages of clinical development.

The pyridinobenzodiazepines (PDDs) are a new class of DNA-interactive sequence-selective Guanine mono-alkylating ADC payloads which contain a sequence recognition component with sufficient span to guide them to specific DNA sequences (e.g., transcription factor binding sites).

A high potency PDD, FGX15-147, has been developed that contains a bi-aryl moiety capable of forming an intramolecular ‘sigma-hole’ interaction with DNA bases, thus providing the molecule with a unique sequence-selectivity profile when compared to other DNA-interactive agents. DNA footprinting data will be presented indicating that the molecule, which spans 8-9 DNA base pairs in the minor groove, has an increased sequence selectivity compared with related analogues, preferring DNA regions containing two guanines 2-4 base pairs apart. FGX15-147 is highly cytotoxic in vitro (e.g., IC50 = 0.30 nM in SW60; 1.6 nM in LIM1215 and 0.142 nM in SW48, after 96 hours incubation), and is thought to exert its activity through a combination of DNA alkylation and inhibiting the binding of important oncogenic transcription factors such as Hypoxia Inducible Factor (HIF) to DNA (demonstrated through an in vitro Transcription Factor Array assay). HIF is known to be involved in the development of a large number of solid malignancies, including pancreatic cancer.

To explore the utility of FGX15-147 as an ADC payload, it was conjugated to trastuzumab in a stochastic manner (DAR 1.6) using a Maleimide-Valine-Alanine linker construct. The resulting ADC exhibited significant in vivo efficacy in a low copy number HER2+ pancreatic cancer Human Tumor Xenograft model using BALB-c mice transplanted with the CAPAN-1 cell line. Complete tumor regression was observed out to 60 days after a single dose of 2 mg/kg comparing favorably to a 10 mg/kg dose of trastuzumab deruxtecan (Enhertu®) in the same study in which substantial tumor regrowth had occurred by 57 days. In a standard mouse model, the FGX15-147-based ADC had a good tolerability profile with a Maximum Tolerated Dose (MTD) of at least 16 mg/kg.

Overall, the favorable tolerability and efficacy profile of FGX15-147 in an ADC format suggests that it represents a potentially valuable approach for the treatment of solid tumors.

Citation Format: Paolo Andriollo, George Procopiou, Daniella M. di Mascio, Paul J. Jackson, Khondaker M. Rahman, Keith R. Fox, David E. Thurston. Design and development of a novel highly sequence-selective guanine mono-alkylating DNA-interactive ADC payload suitable for solid tumor treatments [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 1750.

Abstract 6334: In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors

Antibody-Drug Conjugates (ADCs) are a growing class of therapeutic agents for the treatment of cancer, with thirteen approved and over 100 others in clinical development. The pyridinobenzodiazepine (PDD) platform is a toolbox of sequence-selective, DNA Guanine mono-alkylating ADC payloads with varying potencies and biophysical properties, enabling a payload-based approach to targeting solid tumours and haematological malignancies. We recently reported the development of a lower potency DNA mono-alkylator, FGX20-75, with substantially superior in vivo properties to other DNA alkylating agents and an efficacy/tolerability profile on-par with a topoisomerase inhibitor-based ADC. This molecule is active in the low nanomolar range (i.e., median potency of 6 nM across a 15 cell-line screen), but is sufficiently hydrophilic to allow efficient conjugation to IgG antibodies with Drug Antobody Ratios (DARs) of up to 7. A maleimide-linked analogue of FGX20-75 has been conjugated to a number of antibodies with a DAR of 4. The ADCs produced exhibit significant in vivo efficacy in human tumour xenograft models. For example, in one case, an ADC targeted to an undisclosed antigen produced complete tumour regressions at 10 mg/kg dosing (Q7dx2) in patient-derived xenograft model of osteosarcoma. A substantially increased tolerability profile compared to other DNA-interactive payloads has been observed (e.g., single dose MED of < 1 mg/kg and MTD in mice of up to 80 mg/kg for a DAR 4 construct). Furthermore, in cynomolgus toxicity studies, a HNSTD has yet to be established at 8 mg/kg. Thus, the increase in loading compared to other DNA-interactive payloads compensates for the drop in potency of FGX20-75, resulting in a potent ADC with substantially increased tolerability and potent efficacy in solid tumours. The favourable hydrophobicity profile of the low potency alkylator FGX20-75, and its ease of conjugation to antibodies, along with the significant in vivo efficacy and tolerability of the ADCs produced from it, suggest that this low potency DNA-alkylating payload represents a promising new approach in the treatment of solid tumours.

Citation Format: Paul J. Jackson, Paolo Andriollo, Nicolas Veillard, George Procopiou, David E. Thurston. In vivo efficacy and toxicity of a reduced potency DNA guanine mono-alkylating ADC payload suitable for the treatment of solid tumors [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 6334.

Abstract 1749: A new class of DNA sequence-selective G-A cross-linking antibody-drug conjugate (ADC) payloads

Antibody-Drug Conjugates (ADCs) are rapidly growing in importance as a targeted cancer therapy, with over ten approved, and many currently undergoing clinical trials. ADCs comprise of a cytotoxic agent (i.e., the "payload") conjugated via a chemical linker to a tumor-targeting antibody. There is a demand for novel ADC payloads with unique mechanisms of action, enhanced tolerability profiles and improved physicochemical properties. Such payloads could lead to ADCs with therapeutic efficacy in patients resistant to other therapies, and payloads with reduced hydrophobicity should lead to improved conjugation, minimal aggregation, and higher Drug-Antibody Ratios (DARs).

We report here, studies on a novel class of Cyclopropabenzindole-Pyridinobenzodiazepine (CBI-PDD) payloads, designed through molecular modeling, which form cross-links between Guanine and Adenine bases within the DNA minor groove with defined sequence specificity. Eleven novel analogs will be described which have been structurally modified with various functional groups to allow tunable hydrophobicity, and new vectors through which antibodies may be attached. Most of these analogs are highly cytotoxic, with some exhibiting IC50 values in tumor cells down to the femtomolar range (e.g., FGX37-140, 0.9 pM in both RAJI and Jurkat cells, 72 h incubation). The DNA interactivity of these analogs has been studied using a range of methods such as gel-based DNA footprinting and cross-linking, FRET melting and Transcription Factor (TF) Array assays, the results of which will be described. Overall, the analogs appear to favor the formation of intrastrand rather than interstrand DNA cross-links and can inhibit the DNA binding of several key cancer-related transcription factors such as NFκB.

To explore the potential of these analogs as ADC payloads, one member, FGX8-46, was conjugated to the EGFR-targeting antibody Cetuximab in stochastic fashion (DAR2) to produce Cetuximab-(FGX16-11). This ADC had an unexpectedly high Maximum Tolerated Dose (MTD) in a standard mouse model of at least 45 mg/kg, perhaps reflecting the novel mechanism of action of the payload. It was then evaluated in a Human Tumor Xenograft study based on BALB/c mice transplanted with the EGFR-expressing human colon cancer cell line SW-48 using single doses ranging from 1 mg/kg to 40 mg/kg. Cetuximab-(FGX16-11) was active at all dose levels including 1 mg/kg which provided tumor suppression out to approximately three weeks. Complete tumor suppression out to 50 days was seen with 20 mg/kg.

Overall, the unique mechanism of action, potent cytotoxicity, and excellent in vivo tolerability and significant efficacy in ADC format, make the CBI-PDDs a promising new class of ADC payloads suitable for further development.

Citation Format: George Procopiou, Paul J. Jackson, Daniella M. di Mascio, Jennifer L. Auer, Paolo Andriollo, Ilona Pysz, Khondaker M. Rahman, Keith R. Fox, David E. Thurston. A new class of DNA sequence-selective G-A cross-linking antibody-drug conjugate (ADC) payloads [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 1749.

Membrane organization of photosystem I complexes in the most abundant phototroph on Earth

Prochlorococcus is a major contributor to primary production, and globally the most abundant photosynthetic genus of picocyanobacteria because it can adapt to highly stratified low-nutrient conditions that are characteristic of the surface ocean. Here, we examine the structural adaptations of the photosynthetic thylakoid membrane that enable different Prochlorococcus ecotypes to occupy high-light, low-light and nutrient-poor ecological niches. We used atomic force microscopy to image the different photosystem I (PSI) membrane architectures of the MED4 (high-light) Prochlorococcus ecotype grown under high-light and low-light conditions in addition to the MIT9313 (low-light) and SS120 (low-light) Prochlorococcus ecotypes grown under low-light conditions. Mass spectrometry quantified the relative abundance of PSI, photosystem II (PSII) and cytochrome b₆f complexes and the various Pcb proteins in the thylakoid membrane. Atomic force microscopy topographs and structural modelling revealed a series of specialized PSI configurations, each adapted to the environmental niche occupied by a particular ecotype. MED4 PSI domains were loosely packed in the thylakoid membrane, whereas PSI in the low-light MIT9313 is organized into a tightly packed pseudo-hexagonal lattice that maximizes harvesting and trapping of light. There are approximately equal levels of PSI and PSII in MED4 and MIT9313, but nearly twofold more PSII than PSI in SS120, which also has a lower content of cytochrome b₆f complexes. SS120 has a different tactic to cope with low-light levels, and SS120 thylakoids contained hundreds of closely packed Pcb-PSI supercomplexes that economize on the extra iron and nitrogen required to assemble PSI-only domains. Thus, the abundance and widespread distribution of Prochlorococcus reflect the strategies that various ecotypes employ for adapting to limitations in light and nutrient levels.

Abstract 211: A new class of sequence-selective DNA cross-linking ADC payloads with increased in vivotolerability

Although five Antibody-Drug Conjugates (ADCs) have been approved and over eighty others are in development, the majority contain payloads belonging to two classes: tubulin inhibitors and DNA interactive agents. Most DNA cross-linking payloads (e.g., the PBD dimers) have potent cytotoxicity but ADCs containing them have high hydrophobicity and a narrow therapeutic window. Thus, there is interest in developing novel payloads which benefit from a potency similar to the PBD dimers but that possess lower hydrophobicity and produce ADCs with a wider Therapeutic Index (TI). The pyridinobenzodiazepines (PDDs) are a new class of guanine-alkylating payloads, and these have been coupled to an adenine-alkylating CXI/duocarmycin pharmacophore to generate molecules that can form G-A DNA cross-links. The lead PDD-CXI payload (FGX-8-46) has a sequence-selectivity profile that differs from other DNA cross-linking agents in that it spans seven to eight base-pairs compared to six to seven for a typical PBD dimer. DNA cleavage experiments have indicated that it cleaves at discrete Adenine-containing sequences of the type 5’-XGXWWWW-3’ (X is any base; W is A/T, and the underlined bases show the cleavage points), and Transcription Factor (TF) Array studies show that it is a potent TF inhibitor, down-regulating several key oncogenic TFs (e.g., NF-κB). In in vitro cell line studies, the G-A cross-linkers have low pM cytotoxicity comparable to the PBD dimers in a wide and diverse range of cell lines, including those from both solid and haematological cancers (e.g., IC50 of ~2 pM in SW-48). This payload class is also compatible with a wide variety of linker technologies, and attachment can be made through either the PDD or CXI units. Importantly, these payloads are significantly less hydrophobic than other equivalent payload classes. ADCs have been generated by conjugating these new payloads to the EGFR-targeting antibody Cetuximab with DARs of between 1.8 and 2.2. The ADCs exhibit potent cytotoxicity in vitro, significant in vivo efficacy and substantially increased tolerability compared to other DNA cross-linking payloads (e.g., the PBD dimer Tesirine). While the G-A cross-linkers retain the cytotoxic potency of the PBD dimers, the “softer” cross-link formed compared to the G-G cross-linking PBD dimers may contribute to the enhanced tolerability profile of this molecular class. The favourable hydrophobicity profile of the PDD-CXI payloads and their ease of conjugation to antibodies, along with their significant in vitro cytotoxicity, in vivo efficacy and tolerability of ADCs produced from them, suggest that they represent a promising new class of ADC payloads.

Citation Format: George Procopiou, Jennifer Auer, Daniella di Mascio, Keith R. Fox, Paolo Andriollo, Ilona Pysz, Francesco Cascio, Nicolas Veillard, K. Miraz Rahman, Paul J. Jackson, David E. Thurston. A new class of sequence-selective DNA cross-linking ADC payloads with increased in vivotolerability [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 211.

Abstract 217: Development of a rapid and efficient methodology to quantitate thiol detection in antibody-drug conjugates (ADCs)

Antibody-Drug Conjugates (ADCs) are comprised of three distinct components, an antibody, a payload (usually a cytotoxic agent) and a linker (a synthetic chemical chain joining the antibody and payload). Payloads can be conjugated to antibodies in either a stochastic or site-specific manner, with stochastic conjugations usually accomplished through either amine groups of lysine residues or through thiol groups in disulfide bonds located in the hinge region of antibodies. In the latter case, an electrophilic Michael acceptor grouping (e.g., maleimide) of a linker-payload construct reacts with a nucleophilic thiol group of the antibody, forming the ADC. In order for this to occur, disulfide bonds need to be reduced to free thiols. However, knowing the concentration of reactive thiols at different stages during the reduction process can be challenging, and so a more accurate assessment of thiol concentration may allow greater control of the desired average Drug-Antibody Ratio (DAR). Currently, different spectrophotometric (i.e. Ellman’s reagent) and fluorometric assays are used to monitor thiol concentration, but these methods can be expensive, time consuming and inaccurate.

To address these issues, a rapid and efficient fluorescence-based method has been developed to allow the reduction of thiols to be monitored. The method is based on a fluorescein derivative produced via a four-step synthesis starting from commercially available fluorescein sodium salt. In its unreacted form, this novel probe exists in a lactone form. However, once it reacts with a free thiol group, it converts stoichiometrically via opening of the lactone ring to a fluorescent form, thus allowing quantitative determination of the concentration of thiol groups present in solution.

The three antibodies used to trial this procedure (i.e., Trastuzumab, Cetuximab and Rituximab) were reduced using TCEP over a 120 minute period. Aliquots of solution were collected at various time intervals, and incubated with the fluorescein probe for 5 minutes, monitoring fluorescence with a simple fluorimeter. Using this approach, it was possible to accurately assess thiol concentration at each time interval, and relate the overall reduction profile of each antibody to the concentration of reducing agent used. Payloads were then conjugated to the three antibodies at specific timepoints (selected through monitoring thiol reduction) in an effort to generate species with a defined DAR. Overall, the resulting ADCs were found to have average DAR profiles consistent with the measured number of thiols in the reduced antibodies.

When compared with other assays, the developed method gave results with improved reproducibility. Furthermore, the fluorescein probe was less complex and faster to use than other fluorometric kits, and was easy to synthesize, making it a useful new tool in the generation of ADCs.

Citation Format: Ilona Pysz, Paolo Andriollo, Paul J. Jackson, K M. Rahman, David E. Thurston. Development of a rapid and efficient methodology to quantitate thiol detection in antibody-drug conjugates (ADCs) [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 217.

Abstract 738: Development of an HPLC method for the assessment of hydrophobicity of ADC payloads

Antibody-Drug Conjugates (ADCs) are antibodies attached to cytotoxic agents (payloads) through chemically labile linkers. The development of ADCs can fail at various stages, a common cause being a lack of reproducibility in the methods used to attach the payload to the antibody (i.e., the conjugation process) to provide a good yield and uniform drug-antibody ratio (i.e., the DAR). One of the major problems associated with conjugation is the hydrophobicity of a payload which can cause aggregation. The aim of this study was to create a hydrophobicity model to study the physicochemical properties of payloads at an early stage. This should allow their hydrophobicity to be evaluated and optimised at the design stage. A predictive model has been developed based on High Performance Liquid Chromatography (HPLC). Initial work involved development of a gradient reversed-phase HPLC method, and its use in the analysis of multiple reference compounds to establish their relative retention times. This involved the evaluation of a range of reversed-phase columns and solvent systems in order to obtain reproducibility. These initial studies, which utilized a C18 monolithic column for optimum results, demonstrated a clear relationship between the retention time (RT) of the reference compounds and their experimental LogP values obtained from the literature (r = 0.983). Next, a number of commercially available ADC payloads were analysed using the same HPLC method to determine their RT values, and their LogP values were calculated using the ChemDraw software. Payloads studied included Monomethyl Auristatin E (MMAE), Talirine and Tesirine (PBD dimers), Mertansine (DM1) and Calicheamicin. For this group of compounds, the results confirmed that their RT values correlated well with their calculated LogP values (r = 0.94). For example, the payload Talirine, which has a calculated LogP of 3.77, had an RT value of 17 min on the HPLC system equating to a LogP of 3.13 based on the reference compounds. Finally, some novel DNA-interactive payloads (e.g., the pyridinobenzodiazepine FGX-2-62) were evaluated using the same methodology. For FGX-2-62, the calculated LogP varied significantly between different software packages (i.e., 1.47, 3.38 or 4.46 for ChemSketch, MarvinSketch or ChemDraw, respectively). However, its HPLC retention time using the same method was 1.88 min, equating to a LogP of 1.63. This suggests that FGX-2-62 is significantly less hydrophobic than Talirine (e.g., RTs of 1.88 min versus 17 min, respectively), an observation consistent with the ease of conjugation of FGX-2-62 to antibodies without significant aggregation. Overall, these results suggest that HPLC retention time derived from a suitable HPLC method is more reliable than the currently available software-based LogP prediction methods in providing a realistic assessment of the hydrophobicity of novel payloads and their propensity to cause aggregation during conjugation.

Citation Format: Ilona Pysz, Paul J. Jackson, Khondaker M. Rahman, David E. Thurston. Development of an HPLC method for the assessment of hydrophobicity of ADC payloads [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 738.

Abstract 5242: Further evidence that the DNA-interactive Pyrrolobenzodiazepine (PBD) Dimer SJG-136 works through a transcription factor inhibition mechanism

The pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are sequence-selective DNA minor-groove interacting agents. The PBD dimer SJG-136 has currently been investigated in Phase II clinical trials in ovarian cancer and leukaemia in the UK and the USA. More recently, PBD dimer analogues are being attached to tumour-targeting antibodies to create Antibody-Drug Conjugates (ADCs), some which are now in Phase 3 clinical trials with many others in pre-clinical and clinical development. Transcription factors (TFs) are sequence-specific DNA-interacting proteins that bind to consensus DNA sequences, thereby controlling transcription. TFs regulate processes such as cell differentiation, proliferation and apoptosis. The interaction of a small-molecule with the consensus DNA recognition sequences of TFs can prevent a TF from interacting with its cognate sequence, thereby inhibiting the expression of genes critical for the survival and proliferation of cancer cells. There is growing evidence that PBDs may exert, at least in part, their pharmacological effect through TF inhibition in addition to the arrest of the replication fork, DNA strand breakage, and inhibition of enzymes including endonucleases and RNA polymerases. For this reason, there is now interest in using PBDs as the basis for a small-molecule strategy to target specific DNA sequences for TF inhibition as a novel anticancer therapy. We have developed a reversed-phase HPLC/MS method as a tool to evaluate the interaction of DNA-binding PBD molecules with oligonucleotides of varying lengths and sequences. Using this methodology, we have demonstrated that the PBD dimer SJG-136 binds to the cognate sequences of the oncogenic transcription factors NF-κB, EGR-1, AP-1 and STAT3. Surprisingly, significant differences in the rate and extent of adduct formation between the different cognate sequences were observed which may explain, at least in part, the differences in potency of SJG-136 in various tumour cell lines. Furthermore, an RT PCR study has been carried out using the human tumour cell lines MDA-MB-231 (breast) and HT-29 (colon) to see whether these transcription factors are affected in vitro. The results were consistent with the HPLC-MS studies in that SJG-136 was shown to significantly down-regulate a number of AP-1- and STAT3-dependent genes such as Bcl-2, VEGF, p53 and survivin. These findings add significantly to knowledge of the mechanism of action of SJG-136 and related PBD compounds, and could be relevant for the correct interpretation of clinical activity of molecules of this type both as standalone agents and as ADC payloads.

Citation Format: Julia Mantaj, Paul J. Jackson, David E. Thurston, Khondaker Miraz Rahman. Further evidence that the DNA-interactive Pyrrolobenzodiazepine (PBD) Dimer SJG-136 works through a transcription factor inhibition mechanism [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 5242. doi:10.1158/1538-7445.AM2017-5242

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.

Hot, humid air decontamination of a C-130 aircraft contaminated with spores of two acrystalliferous Bacillus thuringiensis strains, surrogates for Bacillus anthracis

AIM

To develop test methods and evaluate survival of Bacillus thuringiensis kurstaki cry(-) HD-1 and B. thuringiensis Al Hakam spores after exposure to hot, humid air inside of a C-130 aircraft.

METHODS AND RESULTS

Bacillus thuringiensis spores were either pre-inoculated on 1 × 2 or 2 × 2 cm substrates or aerosolized inside the cargo hold of a C-130 and allowed to dry. Dirty, complex surfaces (10 × 10 cm) swabbed after spore dispersal showed a deposition of 8-10 log10 m(-2) through the entire cargo hold. After hot, humid air decontamination at 75-80°C, 70-90% relative humidity for 7 days, 87 of 98 test swabs covering 0·98 m(2) , showed complete spore inactivation. There was a total of 1·67 log10 live CFU detected in 11 of the test swabs. Spore inactivation in the 98 test swabs was measured at 7·06 log10 m(-2) .

CONCLUSIONS

Laboratory test methods for hot, humid air decontamination were scaled for a large-scale aircraft field test. The C-130 field test demonstrated that hot, humid air can be successfully used to decontaminate an aircraft.

SIGNIFICANCE AND IMPACT OF THE STUDY

Transition of a new technology from research and development to acquisition at a Technology Readiness Level 7 is unprecedented.

Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing

Bacillus anthracis is the potentially lethal etiologic agent of anthrax disease, and is a significant concern in the realm of biodefense. One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis. We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background. We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples. We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid. Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database. Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis. We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing. Our results, in combination with the capacity of sequencing for providing insights into the genomic characteristics of complex and novel organisms, suggest that these platforms should be considered important components of a biosurveillance strategy.

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

BACKGROUND

Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.

RESULTS

Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population phiPT values, p < 0.01).

CONCLUSION

Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue

A small number of conserved canonical single nucleotide polymorphisms (canSNP) that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient’s B. anthracis genotype into 1 of 12 subgroups. Reconstruction of the pagA gene also showed a unique SNP that defines a new lineage for B. anthracis.

Evaluating Burkholderia pseudomallei Bip proteins as vaccines and Bip antibodies as detection agents

Burkholderia pseudomallei is a biothreat agent and an important natural pathogen, causing melioidosis in humans and animals. A type III secretion system (TTSS-3) has been shown to be critical for virulence. Because TTSS components from other pathogens have been used successfully as diagnostic agents and as experimental vaccines, it was investigated whether this was the case for BipB, BipC and BipD, components of B. pseudomallei's TTSS-3. The sequences of BipB, BipC and BipD were found to be highly conserved among B. pseudomallei and B. mallei isolates. A collection of monoclonal antibodies (mAbs) specific for each Bip protein was obtained. Most recognized both native and denatured Bip protein. Burkholderia pseudomallei or B. mallei did not express detectable BipB or BipD under the growth conditions used. However, anti-BipD mAbs did recognize the TTSS needle structures of a Shigella strain engineered to express BipD. The authors did not find that BipB, BipC or BipD are protective antigens because vaccination of mice with any single protein did not result in protection against experimental melioidosis. Enzyme-linked immunosorbent assay (ELISA) studies showed that human melioidosis patients had antibodies to BipB and BipD. However, these ELISAs had low diagnostic accuracy in endemic regions, possibly due to previous patient exposure to B. pseudomallei.

The complete genome sequence of Bacillus thuringiensis Al Hakam

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).

Fatal pneumonia among metalworkers due to inhalation exposure to Bacillus cereus Containing Bacillus anthracis toxin genes

Bacillus cereus pneumonia is unusual in nonimmunocompromised hosts. We describe fatal cases in 2 metalworkers and the associated investigation. Anthrax toxin genes were identified in B. cereus isolates from both patients using polymerase chain reaction. Finding anthrax toxin genes in non-Bacillus anthracis isolates has, to our knowledge, only been reported once previously.

Genetic diversity among Botulinum Neurotoxin-producing clostridial strains

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism.

Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes

Bacillus cereus is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and other more serious infections. In one such infection, B. cereus G9241 was identified as the causative agent of a severe pneumonia in a Louisiana welder in 1994. This isolate was found to harbor most of the B. anthracis virulence plasmid pXO1 (13). Here we report the characterization of two clinical and one environmental B. cereus isolate collected during an investigation of two fatal pneumonia cases in Texas metal workers. Molecular subtyping revealed that the two cases were not caused by the same strain. However, one of the three isolates was indistinguishable from B. cereus G9241. PCR analysis demonstrated that both clinical isolates contained B. anthracis pXO1 toxin genes. One clinical isolate and the environmental isolate collected from that victim's worksite contained the cap A, B, and C genes required for capsule biosynthesis in B. anthracis. Both clinical isolates expressed a capsule; however, neither was composed of poly-D-glutamic acid. Although most B. cereus isolates are not opportunistic pathogens and only a limited number cause food-borne illnesses, these results demonstrate that some B. cereus strains can cause severe and even fatal infections in patients who appear to be otherwise healthy.

Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis

Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.

Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates

DNA from over 300 Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis isolates was analyzed by fluorescent amplified fragment length polymorphism (AFLP). B. thuringiensis and B. cereus isolates were from diverse sources and locations, including soil, clinical isolates and food products causing diarrheal and emetic outbreaks, and type strains from the American Type Culture Collection, and over 200 B. thuringiensis isolates representing 36 serovars or subspecies were from the U.S. Department of Agriculture collection. Twenty-four diverse B. anthracis isolates were also included. Phylogenetic analysis of AFLP data revealed extensive diversity within B. thuringiensis and B. cereus compared to the monomorphic nature of B. anthracis. All of the B. anthracis strains were more closely related to each other than to any other Bacillus isolate, while B. cereus and B. thuringiensis strains populated the entire tree. Ten distinct branches were defined, with many branches containing both B. cereus and B. thuringiensis isolates. A single branch contained all the B. anthracis isolates plus an unusual B. thuringiensis isolate that is pathogenic in mice. In contrast, B. thuringiensis subsp. kurstaki (ATCC 33679) and other isolates used to prepare insecticides mapped distal to the B. anthracis isolates. The interspersion of B. cereus and B. thuringiensis isolates within the phylogenetic tree suggests that phenotypic traits used to distinguish between these two species do not reflect the genomic content of the different isolates and that horizontal gene transfer plays an important role in establishing the phenotype of each of these microbes. B. thuringiensis isolates of a particular subspecies tended to cluster together.

Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis

The three species of the group 1 bacilli, Bacillus anthracis, B. cereus, and B. thuringiensis, are genetically very closely related. All inhabit soil habitats but exhibit different phenotypes. B. anthracis is the causative agent of anthrax and is phylogenetically monomorphic, while B. cereus and B. thuringiensis are genetically more diverse. An amplified fragment length polymorphism analysis described here demonstrates genetic diversity among a collection of non-anthrax-causing Bacillus species, some of which show significant similarity to B. anthracis. Suppression subtractive hybridization was then used to characterize the genomic differences that distinguish three of the non-anthrax-causing bacilli from B. anthracis Ames. Ninety-three DNA sequences that were present in B. anthracis but absent from the non-anthrax-causing Bacillus genomes were isolated. Furthermore, 28 of these sequences were not found in a collection of 10 non-anthrax-causing Bacillus species but were present in all members of a representative collection of B. anthracis strains. These sequences map to distinct loci on the B. anthracis genome and can be assayed simultaneously in multiplex PCR assays for rapid and highly specific DNA-based detection of B. anthracis.

Random amplified polymorphic DNA and amplified fragment length polymorphism analyses of Pasteurella multocida isolates from fatal fowl cholera infections

Fowl cholera, a disease caused by Pasteurella multocida, continues to be a major problem for the poultry industry. The sources of pathogenic organisms responsible for most sporadic epidemics remain unconfirmed, although attenuated vaccines that retain a low level of virulence have occasionally been implicated in outbreaks of the disease. One of the vaccines most commonly used to prevent fowl cholera is the M-9 strain. In the present study, 61 clinical isolates from turkeys that died of fowl cholera from 1997 to 1999 on 36 Utah farms were analyzed and compared to the M-9 vaccine strain. Genetic analyses of the isolates were done by random amplified polymorphic DNA (RAPD) analysis and amplified fragment length polymorphism (AFLP) fingerprinting. The results of these genetic analyses were correlated with the vaccination status of the flock, isolate serotype, and geographic location. Although both genetic techniques effectively identified similar subtle genomic differences, RAPD analysis provided only 77% of the detail provided by AFLP analysis. While a relationship between genetic profile and serotype was evident, no significant relationship indicating geographic influence was found (P = 0.351). Interestingly, organisms isolated from vaccinated flocks were significantly closer genetically to the M-9 vaccine strain than isolates from unvaccinated birds were (P = 0.020). Statistical analyses revealed that this relationship could not have been determined by serotyping alone (P = 0.320), demonstrating the value of AFLP and RAPD analyses in the characterization of disease-causing strains.