NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

BACKGROUND

Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes.

RESULTS

Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates.

CONCLUSIONS

NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .

Abstract OT1-01-04: Phase 1 study of D-0502, an orally bioavailable SERD with optimized pharmacological and PK/PD property for ER-positive breast cancer

Background: Endocrine therapy such as selective estrogen receptor degrader (SERD) fulvestrant has been used effectively to extend the life of HR+ (ER+ and PR+) and HER2- breast cancer patient, either alone or in combination with CDK4/6 inhibitors such as palbociclib or abemaciclib. D-0502 is an orally bioavailable SERD with potent activity in various HR+ and HER2- breast cancer cell lines and xenograft models. Its combination with palbociclib in both MCF-7 xenograft model and ESR-1 mutated (Y537S) patient derived breast cancer xenograft models resulted in further tumor growth inhibition or regression. Drug metabolism and pharmacokinetic studies both in vitro and in vivo demonstrated that D-0502 exhibits favorable PK profiles suitable for clinical development.

Trial Design: D-0502 is currently being evaluated in a phase 1 trial of women with advanced or metastatic HR+, HER2- breast cancer (MBC) (NCT03471663). This is a multicenter, open-label phase I study of D-0502 single agent and D-0502 in combination with standard dose of palbociclib. The primary objective is to characterize the safety and tolerability of D-0502 and D-0502 in combination with palbociclib, to identify an MTD and/or RP2D. The secondary objective is to evaluate the PK properties and the preliminary anti-tumor activities. Patients will receive D-0502 orally every day and treatment will be administered as 28-day cycles. The study has two parts: Dose Escalation (phase 1a) and Dose Expansion and Combination (phase 1b). In phase Ia, patients will be enrolled using a conventional dose-escalation algorithm (3+3 subjects per dose level) with 4 sequential dose cohorts to identify the MTD and RDE (recommended dose for expansion) in phase 1b) which will be at or below MTD. In phase 1b, there will be 2 cohorts, one is D-0502 single agent administered at RDE and the other is D-0502 in combination with standard dose of palbociclib, each with approximately 12 patients.

Key Eligibility Criteria: Eligible patients included women with confirmed HR+, HER2- MBC who have previously received no more than 2 prior chemotherapies for MBC; ECOG 0-1; evaluable (phase 1a) or measurable (phase 1b) disease (RECIST v1.1); premenopausal or postmenopausal status; adequate hematologic, hepatic and renal functions.

Current Status and Contact Information: At the time of abstract submission, the first cohort of 50 mg patients have started the study treatment. For inquiry of the study, please contact ling.zhang@inventisbio.com.

Citation Format: Zhang L, Dai D, Shi Z, Jiang J, Wang Y. Phase 1 study of D-0502, an orally bioavailable SERD with optimized pharmacological and PK/PD property for ER-positive breast cancer [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 OT1-01-04.

The effect of interactions between a bacterial strain isolated from drinking water and a pathogen surrogate on biofilms formation diverged under static vs flow conditions

AIMS

Interactions with water bacteria affect the incorporation of pathogens into biofilms and thus pathogen control in drinking water systems. This study was to examine the impact of static vs flow conditions on interactions between a pathogen and a water bacterium on pathogen biofilm formation under laboratory settings.

METHODS AND RESULTS

A pathogen surrogate Escherichia coli and a drinking water isolate Stenotrophomonas maltophilia was selected for this study. Biofilm growth was examined under two distinct conditions, in flow cells with continuous medium supply vs in static microtitre plates with batch culture. E. coli biofilm was greatly stimulated (c. 2-1000 times faster) with the presence of S. maltophilia in flow cells, but surprisingly inhibited (c. 65-95% less biomass) in microtitre plates. These divergent effects were explained through various aspects including surface attachment, cellular growth, extracellular signals and autoaggregation.

CONCLUSIONS

Interactions with the same water bacterium resulted in different effects on E. coli biofilm formation when culture conditions changed from static to flow.

SIGNIFICANCE AND IMPACT OF STUDY

This study highlights the complexity of species interactions on biofilm formation and suggests that environmental conditions such as the flow regime can be taken into consideration for the management of microbial contamination in drinking water systems.

Differential Interstrain Susceptibility to Vertebrobasilar Dolichoectasia in a Mouse Model

BACKGROUND AND PURPOSE

Vetebrobasilar dolichoectasia is characterized by arterial elongation, dilation, and tortuosity and leads to high risks of ischemic stroke. Our aim was to investigate the differential susceptibility to elastase-induced vertebrobasilar dolichoectasia induction in 2 different mouse strains.

MATERIALS AND METHODS

Elastase (25 mU) was injected into the cisterna magna in C57BL/6J (n = 36) and 129/SvEv (SV129) (n = 36) mice. Control animals were injected with heat-inactivated elastase (n = 12 for each strain). At 3, 7, 14, and 28 days after elastase injection, MICROFIL polymer perfusion was performed. The arterial tortuosity index and the percentage increase in diameter were calculated for the basilar artery. Arterial samples were processed for conventional histologic examination, immunostaining, and matrix metalloproteinase expression. A ≥50% increase in diameter and a tortuosity index of ≥10 for the basilar artery were used to indicate success in achieving vertebrobasilar dolichoectasia.

RESULTS

Successful vertebrobasilar dolichoectasia induction was noted in 67% (18 of 27) of the C57BL/6J strain versus 0% (0 of 19) of the SV129 strain (P < .001). Vertebrobasilar dolichoectasia was not observed in sham-operated controls. Both the tortuosity index and diameter increase for the basilar artery were greater in the C57BL/6J strain compared with the SV129 strain (56.3% ± 16.4% versus 21.1% ± 21.6% for diameter, P < .001; 17.4 ± 7.6 versus 10.4 ± 3.8 for tortuosity index, P < .001). Expression of pro-matrix metalloproteinase-2 and pro- and active matrix metalloproteinase-9 was increased in elastase-injected C57BL/6J animals compared with elastase-injected SV129 animals (P = .029, 0.029, and 0.029, respectively). Inflammation scores were significantly higher in C57BL/6J animals versus SV129 animals (P < .001). C57BL/6J subjects demonstrated arterial wall dilation and elongation characterized by internal elastic lamina disruption, muscular layer discontinuity, inflammatory cell infiltration, and high matrix metalloproteinase expression in the media.

CONCLUSIONS

C57BL/6J mice demonstrated greater susceptibility to vertebrobasilar dolichoectasia induction than SV129 mice.

Wall Apposition Is a Key Factor for Aneurysm Occlusion after Flow Diversion: A Histologic Evaluation in 41 Rabbits

BACKGROUND AND PURPOSE

Robust wall apposition for flow-diverter stents may be important for endothelialization. Using a large series of experimental aneurysms treated with the Pipeline Embolization Device, the objectives of this study were to 1) assess interobserver agreement for the evaluation of wall apposition on posttreatment DSA and evaluate its association with aneurysm occlusion, and 2) measure the relationship between wall apposition assessed with histology and aneurysm occlusion rate after treatment.

MATERIALS AND METHODS

Saccular aneurysms were created in 41 rabbits and treated with the Pipeline Embolization Device. DSA was performed just after the deployment of the device and at follow-up. Three investigators independently graded wall apposition on posttreatment DSA as good or poor. A histopathologist blinded to the angiographic results graded the wall apposition on histologic samples. We examined the correlation between angiographic occlusion and wall apposition with histology and angiography.

RESULTS

Wall apposition evaluated on histology was strongly associated with saccular aneurysm occlusion. Sensitivity and specificity of wall apposition to predict complete occlusion at follow-up were 76.9% and 84.0%, respectively, with an overall accuracy of 81.6%. In this experimental study, DSA was suboptimal to assess flow-diverter apposition, with moderate interobserver agreement and low accuracy.

CONCLUSIONS

Good wall apposition is strongly associated with complete occlusion after flow-diverter therapy. In this study, DSA was suboptimal for assessing wall apposition of flow-diverter stents. These findings suggest that improved tools for assessing flow diverter-stent wall apposition are highly relevant.

Myt3 suppression sensitizes islet cells to high glucose-induced cell death via Bim induction

Diabetes is a chronic disease that results from the body's inability to properly control circulating blood glucose levels. The loss of glucose homoeostasis can arise from a loss of β-cell mass because of immune-cell-mediated attack, as in type 1 diabetes, and/or from dysfunction of individual β-cells (in conjunction with target organ insulin resistance), as in type 2 diabetes. A better understanding of the transcriptional pathways regulating islet-cell survival is of great importance for the development of therapeutic strategies that target β-cells for diabetes. To this end, we previously identified the transcription factor Myt3 as a pro-survival factor in islets following acute suppression of Myt3 in vitro. To determine the effects of Myt3 suppression on islet-cell survival in vivo, we used an adenovirus to express an shRNA targeting Myt3 in syngeneic optimal and marginal mass islet transplants, and demonstrate that suppression of Myt3 impairs the function of marginal mass grafts. Analysis of grafts 5 weeks post-transplant revealed that grafts transduced with the shMyt3 adenovirus contained ~20% the number of transduced cells as grafts transduced with a control adenovirus. In fact, increased apoptosis and significant cell loss in the shMyt3-transduced grafts was evident after only 5 days, suggesting that Myt3 suppression sensitizes islet cells to stresses present in the early post-transplant period. Specifically, we find that Myt3 suppression sensitizes islet cells to high glucose-induced cell death via upregulation of the pro-apoptotic Bcl2 family member Bim. Taken together these data suggest that Myt3 may be an important link between glucotoxic and immune signalling pathways.

Preclinical Testing of a Novel Thin Film Nitinol Flow-Diversion Stent in a Rabbit Elastase Aneurysm Model

BACKGROUND AND PURPOSE

Thin film nitinol can be processed to produce a thin microporous sheet with a low percentage of metal coverage (<20%) and high pore attenuation (∼70 pores/mm(2)) for flow diversion. We present in vivo results from the treatment of experimental rabbit aneurysms by using a thin film nitinol-based flow-diversion device.

MATERIALS AND METHODS

Nineteen aneurysms in the rabbit elastase aneurysm model were treated with a single thin film nitinol flow diverter. Devices were also placed over 17 lumbar arteries to model perianeurysmal branch arteries of the intracranial circulation. Angiography was performed at 2 weeks (n = 7), 1 month (n = 8), and 3 months (n = 4) immediately before sacrifice. Aneurysm occlusion was graded on a 3-point scale (grade I, complete occlusion; grade II, near-complete occlusion; grade III, incomplete occlusion). Toluidine blue staining was used for histologic evaluation. En face CD31 immunofluorescent staining was performed to quantify neck endothelialization.

RESULTS

Markedly reduced intra-aneurysmal flow was observed on angiography immediately after device placement in all aneurysms. Grade I or II occlusion was noted in 4 (57%) aneurysms at 2-week, in 6 (75%) aneurysms at 4-week, and in 3 (75%) aneurysms at 12-week follow-up. All 17 lumbar arteries were patent. CD31 staining showed that 75% ± 16% of the aneurysm neck region was endothelialized. Histopathology demonstrated incorporation of the thin film nitinol flow diverter into the vessel wall and no evidence of excessive neointimal hyperplasia.

CONCLUSIONS

In this rabbit model, the thin film nitinol flow diverter achieved high rates of aneurysm occlusion and promoted tissue in-growth and aneurysm neck healing, even early after implantation.

Comparison of predictive scores of symptomatic intracerebral haemorrhage after stroke thrombolysis in a single centre

Symptomatic intracerebral haemorrhage following thrombolysis for ischaemic stroke causes significant morbidity and mortality. This study assessed which of four risk scores (SEDAN, HAT, GRASPS and SITS) best predicts symptomatic intracerebral haemorrhage.

METHODS

Data from 431 patients treated at Aberdeen Royal Infirmary (2003-2013) were extracted from a thrombolysis database. Score performance was compared using area under the curve.

RESULTS

Any intracerebral haemorrhage occurred in 12% of patients (53/413); 11% fulfilling the SITS-MOST symptomatic intracerebral haemorrhage definition (6/53), 34% the ECASS II definition (18/53), and 43% the National Institute of Neurological Disorder and Stroke definition (23/53). Stroke severity, as defined by the National Institutes of Health Stroke Scale, significantly improved after 24 hours in patients without intracerebral haemorrhage, but not in those with. Significant symptomatic intracerebral haemorrhage predictors were age, glucose, stroke severity, hyperdense middle cerebral artery on CT scan, ASPECTS score and anti-platelet therapy. The haemorrhage after thrombolysis score performed best at predicting symptomatic intracerebral haemorrhage (area under the curve 0.67-0.78, p < 0.001).

CONCLUSION

The haemorrhage after thrombolysis score uses the least variables and has the best predictive value for symptomatic intracerebral haemorrhage. Using predictive scores for clinical decision making depends on estimation of overall benefits as well as risk.

Evaluation of the Angiographic Grading Scale in Aneurysms Treated with the WEB Device in 80 Rabbits: Correlation with Histologic Evaluation

BACKGROUND AND PURPOSE

The WEB Occlusion Score has been proposed to assess angiographic outcomes for intracranial aneurysms treated with the Woven EndoBridge (WEB) device. Using a large series of experimental aneurysms treated with the WEB, we had the following objectives: 1) to compare angiographic outcomes as measured by the WEB Occlusion Scale with histologic results, and 2) to assess interobserver and intraobserver agreement of the WEB Occlusion Scale.

MATERIALS AND METHODS

Intracranial aneurysms were created in 80 rabbits and treated with WEB devices. Animals were sacrificed at last follow-up for histologic evaluation. DSA was performed just after the deployment of the device and at follow-up. Four investigators independently and retrospectively graded the DSA twice according to the WEB Occlusion Scale. One histopathologist blinded to the angiographic results graded the occlusion according to a 4-point scale patterned on the WEB Occlusion Scale. Intra- and interobserver agreement were evaluated for DSA. Follow-up angiographic grading and histologic reference were compared to determine the WEB Occlusion Scale accuracy for complete (with or without recess filling) versus incomplete occlusion and adequate (complete occlusion or neck remnant) versus inadequate occlusion.

RESULTS

Inter- and intraobserver weighted κ for the angiographic WEB Occlusion Scale were, respectively, 0.76 and 0.76, indicating substantial agreement. The sensitivity and specificity of the WEB Occlusion Scale for complete occlusion at follow-up compared with the histologic reference standard were, respectively, 75% and 83.3%, with an overall accuracy of 80%. Similarly, for adequate occlusion at follow-up, sensitivity was 97.7%, specificity was 64.9%, and overall accuracy was 82.5%.

CONCLUSIONS

The WEB Occlusion Scale appears to be consistent, reliable, and accurate compared with a histologic reference standard.

Differential Gene Expression in Coiled versus Flow-Diverter-Treated Aneurysms: RNA Sequencing Analysis in a Rabbit Aneurysm Model

BACKGROUND AND PURPOSE

The biologic mechanisms leading to aneurysm healing or rare complications such as delayed aneurysm ruptures after flow-diverter placement remain poorly understood. We used RNA sequencing following implantation of coils or flow diverters in elastase aneurysms in rabbits to identify genes and pathways of potential interest.

MATERIALS AND METHODS

Aneurysms were treated with coils (n = 5) or flow diverters (n = 4) or were left untreated for controls (n = 6). Messenger RNA was isolated from the aneurysms at 4 weeks following treatment. RNA samples were processed by using RNA-sequencing technology and were analyzed by using the Ingenuity Pathway Analysis tool.

RESULTS

With RNA sequencing for coiled versus untreated aneurysms, 464/9990 genes (4.6%) were differentially expressed (58 down-regulated, 406 up-regulated). When we compared flow-diverter versus untreated aneurysms, 177/10,041 (1.8%) genes were differentially expressed (8 down-regulated, 169 up-regulated). When we compared flow-diverter versus coiled aneurysms, 13/9982 (0.13%) genes were differentially expressed (8 down-regulated, 5 up-regulated). Keratin 8 was overexpressed in flow diverters versus coils. This molecule may potentially play a critical role in delayed ruptures due to plasmin production. We identified overregulation of apelin in flow diverters, supporting the preponderance of endothelialization, whereas we found overexpression of molecules implicated in wound healing (dectin 1 and hedgehog interacting protein) for coiled aneurysms. Furthermore, we identified metallopeptidases 1, 12, and 13 as overexpressed in coiled versus untreated aneurysms.

CONCLUSIONS

We observed different physiopathologic responses after endovascular treatment with various devices. Flow diverters promote endothelialization but express molecules that could potentially explain the rare delayed ruptures. Coils promote wound healing and express genes potentially implicated in the recurrence of coiled aneurysms.

RNA-Sequencing Analysis of Messenger RNA/MicroRNA in a Rabbit Aneurysm Model Identifies Pathways and Genes of Interest

BACKGROUND AND PURPOSE

Rabbit aneurysm models are used for the testing of embolization devices and elucidating the mechanisms of human intracranial aneurysm growth and healing. We used RNA-sequencing technology to identify genes relevant to induced rabbit aneurysm biology and to identify genes and pathways of potential clinical interest. This process included sequencing microRNAs, which are important regulatory noncoding RNAs.

MATERIALS AND METHODS

Elastase-induced saccular aneurysms were created at the origin of the right common carotid artery in 6 rabbits. Messenger RNA and microRNA were isolated from the aneurysm and from the control left common carotid artery at 12 weeks and processed by using RNA-sequencing technology. The results from RNA sequencing were analyzed by using the Ingenuity Pathway Analysis tool.

RESULTS

A total of 9396 genes were analyzed by using RNA sequencing, 648 (6.9%) of which were found to be significantly differentially expressed between the aneurysms and control tissues (P < .05; false-discovery rate, <0.01; fold change, >2 or <.5). Of these genes, 614 were mapped successfully, 143 were down-regulated, and 471 were up-regulated in the aneurysms as compared with controls. Using the same criteria for significance, 3 microRNAs were identified as down-regulated and 5 were identified as up-regulated. Pathway analysis associated these genes with inflammatory response, cellular migration, and coagulation, among other functions and pathologies.

CONCLUSIONS

RNA-sequencing analysis of rabbit aneurysms revealed differential regulation of some key pathways, including inflammation and antigen presentation. ANKRD1 and TACR1 were identified as genes of interest in the regulation of matrix metalloproteinases.