Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects

The construction of high-performance microbial cell factories (MCFs) is the centerpiece of biomanufacturing. However, the complex metabolic regulatory network of microorganisms poses great challenges for the efficient design and construction of MCFs. The genome-scale metabolic network models (GSMs) can systematically simulate the metabolic regulation process of microorganisms in silico, providing effective guidance for the rapid design and construction of MCFs. In this review, we summarized the development status of 16 important industrial microbial GSMs, and further outline the technologies or methods that continuously promote high-quality GSMs construction from five aspects: I) Databases and modeling tools facilitate GSMs reconstruction; II) evolving gap-filling technologies; III) constraint-based model reconstruction; IV) advances in algorithms; and V) developed visualization tools. In addition, we also summarized the applications of GSMs in guiding metabolic engineering from four aspects: I) exploring and explaining metabolic features; II) predicting the effects of genetic perturbations on metabolism; III) predicting the optimal phenotype; IV) guiding cell factories construction in practical experiment. Finally, we discussed the development of GSMs, aiming to provide a reference for efficiently reconstructing GSMs and guiding metabolic engineering.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Four-Stage Multi-Physics Simulations to Assist Temperature Sensor Design for Industrial-Scale Coal-Fired Boiler

The growth of renewable energy sources presents a pressing challenge to the operation and maintenance of existing fossil fuel power plants, given that fossil fuel remains the predominant fuel source, responsible for over 60% of electricity generation in the United States. One of the main concerns within these fossil fuel power plants is the unpredictable failure of boiler tubes, resulting in emergency maintenance with significant economic and societal consequences. A reliable high-temperature sensor is necessary for in situ monitoring of boiler tubes and the safety of fossil fuel power plants. In this study, a comprehensive four-stage multi-physics computational framework is developed to assist the design, optimization installation, and operation of the high-temperature stainless-steel and quartz coaxial cable sensor (SSQ-CCS) for coal-fired boiler applications. With the consideration of various operation conditions, we predict the distributions of flue gas temperatures within coal-fired boilers, the temperature correlation between the boiler tube and SSQ-CCS, and the safety of SSQ-CCS. With the simulation-guided sensor installation plan, the newly designed SSQ-CCSs have been employed for field testing for more than 430 days. The computational framework developed in this work can guide the future operation of coal-fired plants and other power plants for the safety prediction of boiler operations.

Online Quantitative Analysis of Perception Uncertainty Based on High-Definition Map

Environmental perception plays a fundamental role in decision-making and is crucial for ensuring the safety of autonomous driving. A pressing challenge is the online evaluation of perception uncertainty, a crucial step towards ensuring the safety and the industrialization of autonomous driving. High-definition maps offer precise information about static elements on the road, along with their topological relationships. As a result, the map can provide valuable prior information for assessing the uncertainty associated with static elements. In this paper, a method for evaluating perception uncertainty online, encompassing both static and dynamic elements, is introduced based on the high-definition map. The proposed method is as follows: Firstly, the uncertainty of static elements in perception, including the uncertainty of their existence and spatial information, was assessed based on the spatial and topological features of the static environmental elements; secondly, an online assessment model for the uncertainty of dynamic elements in perception was constructed. The online evaluation of the static element uncertainty was utilized to infer the dynamic element uncertainty, and then a model for recognizing the driving scenario and weather conditions was constructed to identify the triggering factors of uncertainty in real-time perception during autonomous driving operations, which can further optimize the online assessment model for perception uncertainty. The verification results on the nuScenes dataset show that our uncertainty assessment method based on a high-definition map effectively evaluates the real-time perception results' performance.

Strong Connection of Single-Wall Carbon Nanotube Fibers with a Copper Substrate Using an Intermediate Nickel Layer

Lightweight carbon nanotube fibers (CNTFs) with high electrical conductivity and high tensile strength are considered to be an ideal wiring medium for a wide range of applications. However, connecting CNTFs with metals by soldering is extremely difficult due to the nonreactive nature and poor wettability of CNTs. Here we report a strong connection between single-wall CNTFs (SWCNTFs) and a Cu matrix by introducing an intermediate Ni layer, which enables the formation of mechanically strong and electrically conductive joints between SWCNTFs and a eutectic Sn-37Pb alloy. The electrical resistance change rate (ΔR/R0) of Ni-SWCNTF/solder-Cu interconnects only decreases ∼29.8% after 450 thermal shock cycles between temperatures of -196 and 150 °C, which is 8.2 times lower than that without the Ni layer. First-principles calculations indicate that the introduction of the Ni layer significantly improves the heterogeneous interfacial bond strength of the Ni-SWCNTF/solder-Cu connections.

Enrichment of Large-Diameter Semiconducting Single-Walled Carbon Nanotubes by Conjugated Polymer-Assisted Separation

Semiconducting single-walled carbon nanotubes (s-SWCNTs) with large diameters are highly desired in the construction of high performance optoelectronic devices. However, it is difficult to selectively prepare large-diameter s-SWCNTs since their structure and chemical stability are quite similar with their metallic counterparts. In this work, we use SWCNTs with large diameter as a raw material, conjugated polymer of regioregular poly-(3-dodecylthiophene) (rr-P3DDT) with long side chain as a wrapping agent to selectively separate large-diameter s-SWCNTs. It is found that s-SWCNTs with a diameter of ~1.9 nm are effectively enriched, which shows a clean surface. By using the sorted s-SWCNTs as a channel material, we constructed thin-film transistors showing charge-carrier mobilities higher than 10 cm² V^-1 s^-1 and on/off ratios higher than 10³.

Escherichia coli inhibits endometriosis by inducing M1 polarity of peritoneal macrophages and the IL-1 signaling pathway

The development of endometriosis is closely linked to macrophages, and the type M1 macrophage has been hypothesized to play an inhibitory role in its progression. Escherichia coli induces macrophage polarization toward M1 in numerous diseases and differs in the reproductive tract of patients with and without endometriosis; however, its specific role in endometriosis development remains unknown. Therefore, in this study, E. coli was selected as a stimulator to induce macrophages, and its effects on the growth of endometriosis lesions in vitro and in vivo were investigated using C57BL/6N female mice and endometrial cells. It was revealed that E. coli inhibited the migration and proliferation of co-cultured endometrial cells by IL-1 in vitro and prevented the growth of lesions and induced macrophage polarization toward M1 in vivo. However, this change was counteracted by C-C motif chemokine receptor 2 inhibitors, suggesting that it was associated with bone marrow-derived macrophages. Overall, the presence of E. coli in the abdominal cavity may be a protective factor for endometriosis.

Real-Time Evaluation of Perception Uncertainty and Validity Verification of Autonomous Driving

Deep neural network algorithms have achieved impressive performance in object detection. Real-time evaluation of perception uncertainty from deep neural network algorithms is indispensable for safe driving in autonomous vehicles. More research is required to determine how to assess the effectiveness and uncertainty of perception findings in real-time.This paper proposes a novel real-time evaluation method combining multi-source perception fusion and deep ensemble. The effectiveness of single-frame perception results is evaluated in real-time. Then, the spatial uncertainty of the detected objects and influencing factors are analyzed. Finally, the accuracy of spatial uncertainty is validated with the ground truth in the KITTI dataset. The research results show that the evaluation of perception effectiveness can reach 92% accuracy, and a positive correlation with the ground truth is found for both the uncertainty and the error. The spatial uncertainty is related to the distance and occlusion degree of detected objects.

Efficient Fabrication of High-Quality Single-Walled Carbon Nanotubes and Their Macroscopic Conductive Fibers

High-purity and well-graphitized single-walled carbon nanotubes (SWCNTs) with excellent physiochemical properties are ideal building blocks for the assembly of various CNT macrostructures for a wide range of applications. We report the preparation of high-quality SWCNTs on a large scale using a floating catalyst chemical vapor deposition (FCCVD) method. Under the optimum conditions, the conversion rate of the carbon source to SWCNTs reached 28.8%, and 20.4% of the metal nanoparticles were active for SWCNT growth, which are 15% and ∼400 times higher than those previously reported for FCCVD synthesis, respectively. As a result, the prepared SWCNTs have a very low residual catalyst content of ∼1.9 wt % and a high rapid oxidation temperature of 717 °C. Using these high-quality SWCNTs, we spun macroscopic SWCNT fibers by a wet-spinning process. The resulting fibers had a high electrical conductivity of 6.67 MS/m, which is 32% higher than the best value previously reported for SWCNT fibers.

Neutrophil-lymphocyte ratio and hypersensitive C-reaction protein are associated with miscarriage during the second trimester of pregnancy

This study investigated whether biomarkers in the second trimester of pregnancy, including the white blood cell (WBC) count, neutrophil-lymphocyte ratio (NLR), hypersensitive C-reactive protein (hs-CRP) concentration, and procalcitonin (PCT) concentration, were associated with miscarriage during the second trimester of pregnancy. Sixty-two asymptomatic patients in their second trimester of pregnancy were included in the control group (group A). Among 67 patients diagnosed with late threatened miscarriage, 46 patients with ongoing pregnancy were included in group B and 21 patients with subsequent miscarriage were included in group C. The serum of these patients was collected and the biomarkers were analyzed. A paired-samples t-test was used for the comparison between the groups before and after the miscarriage. Statistical significance was set at p<0.05. Receiver operating characteristic curve (ROC) analysis was performed to evaluate the predictive value of different biomarkers for miscarriage during the second trimester of pregnancy. WBC count, neutrophil percentage, and hs-CRP levels were significantly higher in group C than in groups A and B (p<0.05). Lymphocyte percentage and albumin levels decreased significantly from group A to group C (p<0.05). In contrast, NLR increased significantly from group A to group C (p<0.05). There was a significant decrease in the WBC count, neutrophil percentage, hemoglobin concentration, and post-miscarriage NLR among the cases with miscarriage (p<0.05). The area under the curve of WBC count, NLR, hs-CRP, and the combination of these three factors for the prediction of late miscarriage varied from 78.0% to 82.6%. The combination of these three factors had the highest specificity of 91.1%, while hs-CRP had the highest sensitivity of 88.9%. WBC count, NLR, and hs-CRP levels are strongly associated with miscarriage during the second trimester of pregnancy, indicating that they are potential predictive biomarkers.

MicroRNA-26b-5p promotes development of neonatal respiratory distress syndrome by inhibiting differentiation of mesenchymal stem cells to type II of alveolar epithelial cells via regulating Wnt5a

OBJECTIVE

The aim was to investigate the role of microRNA-26b-5p in regulating mesenchymal stem cells (MSCs) differentiation to type II of alveolar epithelial cells (AECII) in the disease course of neonatal respiratory distress syndrome (NRDS).

MATERIALS AND METHODS

MSCs were first derived from rat bone marrow. In vitro induction of MSCs differentiation to AECII was conducted by SAGM. The mRNA levels of microRNA-26b-5p, Wnt5a, and AECII-related genes (Occludin, KGF, CK18, SpA, SpB, and SpC) during the process of cell differentiation were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). Enzyme-linked immunosorbent assay (ELISA) was conducted for detecting levels of inflammatory factors tumor necrosis factor-α (TNF-α), interferon-α (INF-α), and interleukin-1 (IL-1) in cell supernatant. Dual-luciferase reporter gene assay was then carried out to verify the regulatory effect of microRNA-26b-5p on Wnt5a. MicroRNA-26b-5p expression in serum samples of NRDS neonates and healthy neonates was detected by qRT-PCR as well.

RESULTS

MicroRNA-26b-5p was overexpressed in NRDS neonates than those of healthy neonates. Besides, microRNA-26b-5p was highly expressed in the process of MSCs differentiation to AECII. MicroRNA-26b-5p overexpression remarkably inhibited AECII differentiation and Wnt5a expression. Levels of TNF-α, INF-α, and IL-1 in cell supernatant during differentiation induction were elevated. The regulatory effects of microRNA-26b-5p on AECII differentiation, Wnt5a expression, and inflammatory response were reversed by Wnt5a overexpression.

CONCLUSIONS

MicroRNA-26b-5p inhibits MSCs differentiation to AECII via inhibiting Wnt5a expression through the Wnt pathway.

[Changes of retinal structure after systemic immunosuppressive treatment in eyes with Vogt-Koyanagi-Harada disease]

Objective: To assess structural changes in retina after systemic immunosuppressive treatment in Vogt-Koyanagi-Harada (VKH) disease using spectral-domain optical coherence tomography (SD-OCT). Methods: The clinical data of 17 VKH cases (34 eyes) who consecutively attended the Beijing Tongren Hospital between December 2015 and December 2019 were retrospectively reviewed. All the patients had acute or subacute onset, and underwent high-dose systemic corticosteroid and/or immunosuppressive treatment, with a followed-up time of at least 6 months. At the end of follow-up, the intraocular inflammation was controlled, and oral prednisone was withdrawn or being adjusted to less than 10 mg/day. The SD-OCT features of the included eyes were analyzed before treatment, 1 week, 1 month and 3 months after treatment, and at the last visit. Results: A total of 17 cases (34 eyes; 6 males and 11 females) were included, with an age of (42.2±10.6) years, and were followed up for (9.4±3.3) months. At 1 week after initiating treatment, the percentage of the eyes with extensive/multiple or multifocal retinal detachment in the macular region, membranous structures and intraretinal cysts, and undulations and bumps of retinal pigment epithelium (RPE) decreased (5.9% vs 100%, 2.9% vs 47.1%, 5.9% vs 70.6%, 11.8% vs 58.8%, respectively, all P<0.001). There was statistical significant difference of the percentage of ellipsoid zone and external limiting membrane (ELM) disruptions before treatment, at 3 months and the last visit (100% vs 35.3%, 64.7% vs 52.9%, 41.2% vs 26.5%, respectively, all P<0.001). At the last visit, there were statistical significant differences of the best corrected vision acuity (BCVA) between the intact ellipsoid zone group (20 eyes) and the discontinuous group (14 eyes), as well as between the intact ELM group (25 eyes) and the discontinuous group (9 eyes), respectively [0 (0, 0.05) vs 0.10 (0.03, 0.33) (log MAR), P=0.004; 0 (0, 0.07) vs 0.22 (0.05, 0.40) (log MAR), P=0.005]. Conclusions: The edema of choroid and retina subsided obviously at 1 week after initiating treatment. The extent of damage and recovery ability of ellipsoid zone and ELM were different before treatment, at 3 months and the last visit. At the last visit, the outer retinal layers failed to recover completely in some patients, and were related to the BCVA.

The accuracy of bone mineral density measurement using dual-energy spectral CT and quantitative CT: a comparative phantom study

AIM

To compare bone mineral density (BMD) measurement accuracy by dual-energy spectral computed tomography (CT) and quantitative CT (QCT) using an anthropomorphic European spine phantom (ESP).

MATERIALS AND METHODS

An ESP containing three hydroxyapatite inserts with densities of 50, 100, and 200 mg/cm³ was scanned 10 times each using spectral CT and QCT protocols. Their BMD values were measured using hydroxyapatite-based spectral CT material decomposition images and QCT images and compared with the true values in ESP.

RESULTS

Both protocols had good repeatability in BMD measurement with low coefficient-of-variance (spectral CT: <2.31%; QCT: <1.17%). There were biases in BMD measurement for the 50, 100, and 200 mg/cm³ hydroxyapatite insert with relative errors of 2.34% (48.83±1.13 mg/cm³), 2% (98±1.25 mg/cm³) and 5.96% (188.09±2.11 mg/cm³), in spectral CT, and 11% (55.5±0.65 mg/cm³), 9.85% (109.85±0.42 mg/cm³) and 4.04% (208.07±0.54 mg/cm³) in QCT, respectively.

CONCLUSION

BMD can be accurately measured using either QCT or spectral CT, and spectral CT has smaller bias than QCT.

Molecular cloning and functional characterisation of duck (Anas platyrhynchos) tumour necrosis factor receptor-associated factor 3

1. Tumour necrosis factor receptor-associated factor 3 (TRAF3) is a key regulator of innate immunity and acquired immunity, and has a salient anti-viral role. 2. In this experiment, the duck TRAF3 (DuTRAF3) gene was cloned according to the Anas platyrhynchos TRAF3 sequence to explore its function. The TRAF3 open reading frame contains 1704 bp that encode a protein of 567 amino acids, which contain a RING finger domain, two zinc finger motifs, a coiled-coil region, and a MATH domain. 3. Reverse transcription-polymerase chain reaction showed that DuTRAF3 was expressed in all the examined tissues, with a comparatively higher expression in the spleen and brain tissues. 4. In HEK293T cells, DuTRAF3 overexpression resulted in a significantly increased NF-κB activity and interferon (IFN)-β promoter activation. 5. Following resiquimod (R848) and poly(I:C) stimulation of duck peripheral blood mononuclear cells (PBMCs), the expressions of TRAF3 and IFN-β were significantly upregulated; in addition, following R848 stimulation, the mRNA levels of IL-6, IL-8 and IL-10 were also significantly upregulated. After infection with the Newcastle Disease Virus LaSota vaccine strain, the mRNA levels of IL-6 and IL-10 were significantly upregulated, while that of TRAF3 was downregulated. 6. These results suggest that DuTRAF3 has an important role to play in innate antiviral immune responses.

Gradient magnet design for simultaneous detection of electrons and positrons in the intermediate MeV range

We report the design and development of a compact electron and positron spectrometer based on tapered neodymium iron boron magnets to characterize the pairs generated in laser-matter experiments. The tapered design forms a gradient magnetic field component allowing energy dependent focusing of the dispersed charged particles along a chosen detector plane. The mirror symmetric design allows for simultaneous detection of pairs with energies from 2 MeV to 500 MeV with an accuracy of ≤10% in the wide energy range from 5 to 110 MeV for a parallel beam incident on a circular aperture of 20 mm. The energy resolution drops to ≤20% for 4-90 MeV range for a divergent beam originating from a point source at 20 cm away (i.e., a solid angle of ∼8 milli steradians), with ≤10% accuracy still maintained in the narrower energy range from 10 to 55 MeV. It offers higher solid angle acceptance, even for the divergent beam, compared to the conventional pinhole aperture-based spectrometers. The proposed gradient magnet is suitable for the detection of low flux and/or monoenergetic type electron/positron beams with finite transverse sizes and offers unparalleled advantages for gamma-ray spectroscopy in the intermediate MeV range.

Abstract P4-14-13: Pertuzumab (P) use in first-line HER2-positive metastatic breast cancer (mBC) in US community oncology practices: Treatment patterns and outcomes

Background: Pertuzumab was FDA-approved in 6/2012 for use in first-line in combination with trastuzumab (H) and docetaxel for patients (pts) with HER2-positive mBC. This retrospective study investigated the clinical characteristics, treatment patterns, safety, and outcomes for pts with HER2-positive mBC who received a P-containing regimen in first-line in US community oncology practices.

Methods: This study utilized iKnowMed electronic health records, Claims Data Warehouse, and Social Security Death Index. Pts with HER2-positive mBC, who received a P-containing regimen between 6/2012 and 6/2014 and were followed through 12/2014, had ≥2 visits within the McKesson Specialty Health/US Oncology Network, and were not on clinical trials during the study period, were eligible.

Results: Of the 322 pts who received a P-containing regimen in the first-line setting, 25% were ≥65 years of age, 63% were post-menopausal, 61% had hormone receptor-positive mBC, 84% had a performance status of 0 or 1, and 76% had a Charlson Comorbidities Index of 0. Twenty-one percent of pts had 1 site of metastasis noted, 32% had 2 sites, and 47% had 3 or more sites. Pts with de novo mBC made up 40% of this cohort. Of the pts with recurrent mBC, over 60% received H in the early-stage BC setting. In the first-line mBC setting, 93% of the 322 pts received H+P+taxane, and 7% received H+P with other chemotherapy agent(s). Common adverse events reported included: fatigue (49%), diarrhea (44%), nausea (33%), peripheral neuropathy (33%), neutropenia (24%), and rash (22%). Further analyses including outcomes of these 322 pts will be presented.

Conclusions: First-line P was given in combination with H and chemotherapy agent(s) (93% taxane). No new safety signals were observed. More details on the clinical characteristics, specific treatment patterns, and safety will be presented, along with the progression-free survival of these pts receiving first-line P-containing therapy in a real-world setting.

Citation Format: Robert N, Goertz H-P, Asmar L, Tseng W-Y, Jiao X, Portera C, Yoo B, Patt D, Antao V. Pertuzumab (P) use in first-line HER2-positive metastatic breast cancer (mBC) in US community oncology practices: Treatment patterns and outcomes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-14-13.

Evaluation of Immune Profiles and MicroRNA Expression Profiles in Peripheral Blood Mononuclear Cells of Long-Term Stable Liver Transplant Recipients and Recipients With Acute Rejection Episodes

OBJECTIVE

This study aimed to document the difference of immunophenotypes in peripheral blood mononuclear cells (PBMCs) between long-term stable liver transplant recipients and recipients with acute rejection. We also sought to identify whether there is any correlation between microRNA (miRNA) expression profile and the differential immunoprofile in these 2 groups to establish a specific miRNA biomarker to identify potential liver transplant recipients.

METHODS

PBMCs were isolated from 53 stable liver transplant recipients (STA group) and 15 liver transplant recipients with repeated biopsy-proven rejection episodes admitted to our hospital. Immunoprofiles were analyzed by means of flow cytometry. Analysis of miRNA expression in the PBMCs was performed by means of real-time polymerase chain reaction.

RESULTS

The immune profiling analysis showed increased frequency of peripheral natural killer cells and regulatory T cells in stable liver transplant recipients compared with the acute rejection recipients and healthy volunteers (P < .05). There was no significant difference in the immune cell levels (CD19(+) B cells, CD4(+) T cells, and CD8(+) T cells) in PBMCs among the transplant recipient groups and healthy control subjects. Three miRNAs, miR-18b, miR-340, and miR-106b, were up-regulated in the PBMCs of the STA recipients compared with recipients with acute rejection.

CONCLUSIONS

These results suggest that miR-18b, miR-340, and miR-106b, which regulate the expression of specific immunophenotypes, can be used as potential biomarkers to identify long-term stable liver transplant recipients from recipients with acute rejection.

Abstract P1-07-05: The cell fate factor DACH1 represses YB-1-mediated oncogenic transcription and translation

The epithelial-mesenchymal transition (EMT) enhances cellular invasiveness and confers tumor cells with cancer stem cell like characteristics, through transcriptional and translational mechanisms. The mechanisms maintaining transcriptional and translational repression of EMT and cellular invasion are poorly understood. The Drosophila homologue of DACH1, the Dac gene is a key member of the retinal determination gene network that specifies organismal development. The dachshund (dac), eya1, eyes-absent (eya), twin of eyeless (toy), teashirt (tsh) and sinoculues (so) are expressed in progenitor cells, contributing to development of the eye and genitalia. Loss of DACH1 expression contributes to the expansion of neural progenitors, muscle satellite cell differentiation and breast cancer stem cells. In recent studies Dachshund repressed breast cancer stem cell expansion. DACH1 expression is reduced in a variety of human cancers including prostate, ovarian and human breast cancer.

Herein, the cell fate-determination factor Dachshund (DACH1), suppressed EMT via repression of cytoplasmic translational induction of Snail by inactivating the Y box-binding protein (YB-1). In the nucleus, DACH1 antagonized YB-1-mediated oncogenic transcriptional modules governing cell invasion. DACH1 blocked YB-1-induced mammary tumor growth and EMT in mice. In basal-like breast cancer (BLBC) the reduced expression of DACH1 and increased YB-1, correlated with poor metastasis free survival. The loss of DACH1 suppression of both cytoplasmic translational and nuclear transcriptional events governing EMT and tumor invasion may contribute to poor prognosis in BLBC.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-07-05.

Abstract P5-04-04: CCR5 antagonists block basal breast cancer and prostate cancer metastasis in vivo

The identification of new therapeutic targets and treatments to reduce tumor metastasis homing requires alternative interrogation approaches. The roles of the chemokine CCL5 and its receptor CCR5 in breast cancer progression are controversial. Cancer metastasis is regulated by chemokines in the microenvironment. Chemokines bind to cell surface receptors that belong to the G-protein-coupled receptor family (GPCRs), controlling diverse biological and pathological processes from immune surveillance, inflammation, and cancer. Previous studies of human breast cancer and breast cancer cell lines demonstrated that the chemokine receptors CXCR4 and CCR7 are expressed in breast cancer cells, malignant breast tumors, and metastasis. Their related ligands, CXCL12 (SDF1) and CCL21, are also expressed at the site of metastasis. Subsequent studies identified altered expression of CCL5 (RANTES) in breast cancer patients, correlating with disease progression. CCL5 can be expressed and secreted either by breast cancer cells or by non-malignant stromal cells at the primary or metastatic sites. However, the roles of CCL5 and its receptors in breast cancer are not fully understood. CCL5 facilitates disease progression by recruiting and modulating the activity of inflammatory cells, which subsequently remodel the tumor microenvironment. Accordingly, inhibition of CCR5 by a peptide antagonist reduced leukocyte infiltration and reduced tumor growth after subcutaneous injection of 410.4 mammary carcinoma cells into immunocompetent mice. Our recent microarray analysis of 2,254 human breast cancers demonstrated increased expression of CCL5 and its receptor CCR5, but not CCR3, in the basal and HER-2 genetic subtypes of breast cancer. Interrogation of pathways activated in patient normal breast vs. tumor identified up regulation of a CCR5 signaling module. At the same time, we also extended our research to prostate cancers. Using isogenic oncogene transformed breast and prostate cancer cell lines we show oncogene transformation induces CCR5 expression in breast and prostate epithelial cells. Further we show that the subpopulation of cells that express functional CCR5 display increased invasiveness. Studies in vivo demonstrated that CCR5 promoted metastasis homing. The FDA approved CCR5 antagonists Maraviroc or Vicriviroc, developed to block CCR5 HIV co-receptor function, reduced in vitro invasion of basal breast cancer and prostate cancer cell lines without affecting cell proliferation or viability. In a series of preclinical mouse models, used at equivalent doses to those used in treatment of humans for HIV, Maraviroc decreased breast pulmonary metastasis. The isogenic prostate cancer cell lines metastasized to bones in immune-competent mice representing an ideal model for testing anti-metastasis therapies. CCR5 was expressed in the metastasis in the bones. Maraviroc reduced prostate cancer metastasis to brain, bones and lungs. Our findings provide evidence for a key role of CCL5/CCR5 in the metastasis of basal breast cancer and prostate cancer cell lines and suggest that CCR5 antagonists may be used as an adjuvant therapy to reduce the risk of metastasis in patients with the basal breast cancer subtype and prostate cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-04-04.

MicroRNAs and cancer stem cells: the sword and the shield

Emerging chemotherapy drugs and targeted therapies have been widely applied in anticancer treatment and have given oncologists a promising future. Nevertheless, regeneration and recurrence are still huge obstacles on the way to cure cancer. Cancer stem cells (CSCs) are capable of self-renewal, tumor initiation, recurrence, metastasis, therapy resistance, and reside as a subset in many, if not all, cancers. Therefore, therapeutics specifically targeting and killing CSCs are being identified, and may be promising and effective strategies to eliminate cancer. MicroRNAs (miRNAs, miRs), small noncoding RNAs regulating gene expression in a post-transcriptional manner, are dysregulated in most malignancies and are identified as important regulators of CSCs. However, limited knowledge exists for biological and molecular mechanism by which miRNAs regulate CSCs. In this article, we review CSCs, miRNAs and the interactions between miRNA regulation and CSCs, with a specific focus on the molecular mechanisms and clinical applications. This review will help us to know in detail how CSCs are regulated by miRNAs networks and also help to develop more effective and secure miRNA-based clinical therapies.

Transcriptome profiling of the whitefly Bemisia tabaci reveals stage-specific gene expression signatures for thiamethoxam resistance

Bemisia tabaci has developed high levels of resistance to many insecticides including the neonicotinoids and there is strong evidence that for some compounds resistance is stage-specific. To investigate the molecular basis of B. tabaci resistance to the neonicotinoid thiamethoxam we used a custom whitefly microarray to compare gene expression in the egg, nymph and adult stages of a thiamethoxam-resistant strain (TH-R) with a susceptible strain (TH-S). Gene ontology and bioinformatic analyses revealed that in all life stages many of the differentially expressed transcripts encoded enzymes involved in metabolic processes and/or metabolism of xenobiotics. Several of these are candidate resistance genes and include the cytochrome P450 CYP6CM1, which has been shown to confer resistance to several neonicotinoids previously, a P450 belonging to the Cytochrome P450s 4 family and a glutathione S-transferase (GST) belonging to the sigma class. Finally several ATP-binding cassette transporters of the ABCG subfamily were highly over-expressed in the adult stage of the TH-R strain and may play a role in resistance by active efflux. Here, we evaluated both common and stage-specific gene expression signatures and identified several candidate resistance genes that may underlie B. tabaci resistance to thiamethoxam.

APP/PS1 Transgenic Mice Treated with Aluminum: An Update of Alzheimer's Disease Model

There is still no animal model available that can mimic all the cognitive, behavioral, biochemical, and histopathological abnormalities observed in patients with Alzheimer's disease (AD). We undertook to consider the interaction between genetic factors, including amyloid precursor protein (APP) and presenilin-1 (PS1), and environmental factors, such as Aluminum (Al) in determining susceptibility outcomes when studying the pathogenesis of AD. In this article, we provide an AD model in APP/PS1 transgenic mice triggered by Al. The animal model was established via intracerebral ventricular microinjection of aluminum chloride once a day for 5 days in APP/PS1 transgenic mice. Twenty wild type (WT) mice and 20 APP/PS1 transgenic (TG) mice were separately divided into 2 groups (control and Al group), and a stainless steel injector with stopper was used for microinjection into the left-lateral cerebral ventricle of each mouse. The Morris water maze task was used to evaluate behavioral function of learning and memory ability on the 20th day after the last injection. This AD model's brain was analyzed by: (1) amyloid β immunohistochemical staining; (2) Tunnel staining; (3) apoptotic rates; (4) caspase-3 gene expression. Here, decrease of cognitive ability and neural cells loss were shown in APP/PS1 transgenic mice exposed to Al, which were more extensive than those in APP/PS1 TG alone and WT mice exposed to Al alone. These findings indicate that there is a close relationship between over-expression of APP and PS1 genes and Al overload. It is also suggested that APP/PS1 TG mice exposed to Al have potential value for improving AD models.

Application of multifocal visual evoked potentials in the assessment of visual dysfunction in macular diseases

PURPOSE

To evaluate the use of AccuMap multifocal visual evoked potentials (mfVEP) in visual dysfunction caused by macular diseases.

METHODS

Forty-eight eyes with known macular diseases underwent AccuMap mfVEP and microperimetry 1 (MP1) assessments. Evaluation of mfVEP abnormality was based on an amplitude deviation probability plot and the AccuMap Severity Index (ASI). Correlation analyses of the mean mfVEP amplitude corresponding to a radius of 2°, 5°, and 10° of the central visual field, minimum angle of resolution best-corrected visual acuity (BCVA), and MP1 mean sensitivity of the corresponding areas were performed.

RESULTS

Among the 48 affected eyes, AccuMap mfVEP detected an abnormality of the central visual field in 45 eyes, with a sensitivity of 93.8%. The mean mfVEP amplitudes within a radius of 2°, 5°, and 10° of the central visual field were found to be positively correlated with BCVA (P<0.01 for all groups). The mean amplitudes also positively correlated with the MP1 mean sensitivity value of the corresponding visual field (P<0.01 for all groups). In the group with stable fixation or predominantly central fixation, the mean mfVEP amplitudes did not correlate with the BCVA or the MP1 mean sensitivity value. Regardless of the fixation status, the ASI was found to correlate with both the BCVA and the total MP1 mean defect value.

CONCLUSION

Objective perimetry using AccuMap mfVEP might be applied in the assessment of macular function, with the ASI offering a potentially useful indicator for evaluating macular dysfunction.

Characterization of immune responses following intranasal immunization with the Mycobacterium bovis CFP-10 protein expressed by attenuated Salmonella typhimurium

Culture filtrate protein 10 (CFP-10) from Mycobacterium bovis or Mycobacterium tuberculosis (MTB) is an immunodominant T-cell antigen expressed during the early stages of infection. Because lungs are most commonly associated with primary M. bovis infections, specific immunity at this site is desirable for protection. Therefore, in this study, immune responses generated in mouse lung, spleen and Peyer's patches were examined following intranasal (i.n.) immunization with Salmonella typhimurium- expressing CFP-10. Cells harvested from the lungs and Peyer's patches of immunized mice and then stimulated with CFP-10 produced significant levels of IFN-γ and these mice developed elevated serum IgG and lung IgA anti-CFP-10 responses, suggesting that this approach induced potent anti-CFP-10 mucosal immunity. Our study demonstrates that i.n. administration of CFP-10 expressed by S. typhimurium represents an effective way to induce efficient immune response to M. bovis antigen.

Measurement of the interior structure of thin polymer films using grazing incidence diffuse x-ray scattering

A method is developed for calculating the small-angle x-ray scattering originating from within the interior of a thin film under grazing incidence illumination. This offers the possibility of using x-ray scattering to probe how the structure of polymers is modified by confinement. When the diffuse scattering from a thin film is measured over a range of incident angles, it is possible to separate the contributions to scattering from the interfaces and the contribution from the film interior. Using the distorted-wave Born approximation the structure factor, S(q), of the film interior can then be obtained. We apply this method to analyze density fluctuations from within the interior of a silicon supported molten polystyrene (PS) film. Measurements were made as a function of film thickness ranging from one to ten times the polymer radius of gyration (Rg). The compressibility, calculated by extrapolating the measured S(q) to q=0, agrees well with that of bulk PS for thick films, but thinner films exhibit a peak in S(q) near q=0. This peak, which grows with decreasing thickness, is attributed to a decreased interpenetration of chains and a consequent enhanced compressibility.

An Anisotropic Fluid-Solid Model of the Mouse Heart

A critical challenge in biomechanical simulations is the spatial discretization of complex fluid-solid geometries created from imaging. This is especially important when dealing with Lagrangian interfaces, as there must be at a minimum both geometric and topological compatibility between fluid and solid phases, with exact matching of the interfacial nodes being highly desirable. We have developed a solution to this problem and applied the approach to the creation of a 3D fluid-solid mesh of the mouse heart. First, a 50 micron isotropic MRI dataset of a perfusion-fixed mouse heart was segmented into blood, tissue, and background using a customized multimaterial connected fuzzy thresholding algorithm. Then, a multimaterial marching cubes algorithm was applied to produce two compatible isosurfaces, one for the blood-tissue boundary and one for the tissue-background boundary. A multimaterial smoothing algorithm that rigorously conserves volume for each phase simultaneously smoothed the isosurfaces. Next we applied novel automated meshing algorithms to generate anisotropic hybrid meshes with the number of layers and the desired element anisotropy for each material as the only input parameters. As the meshes are scale-invariant within a material and include boundary layer prisms, fluid-structure interaction computations would have a relative error equilibrated over the entire mesh. The resulting model is highly detailed mesh representation of the mouse heart, including features such as chordae and coronary vasculature, that is also maximally efficient to produce the best simulation results for the computational resources available.

Measurement of annexin V uptake and lactadherin labeling for the quantification of apoptosis in adherent Tca8113 and ACC-2 cells

Phosphatidylserine (PS) exposure occurs during the cell death program and fluorescein-labeled lactadherin permits the detection of PS exposure earlier than annexin V in suspended cell lines. Adherent cell lines were studied for this apoptosis-associated phenomenon to determine if PS probing methods are reliable because specific membrane damage may occur during harvesting. Apoptosis was induced in the human tongue squamous carcinoma cell line (Tca8113) and the adenoid cystic carcinoma cell line (ACC-2) by arsenic trioxide. Cells were harvested with a modified procedure and labeled with lactadherin and/or annexin V. PS exposure was localized by confocal microscopy and apoptosis was quantified by flow cytometry. The detachment procedure without trypsinization did not induce cell damage. In competition binding experiments, phospholipid vesicles competed for more than 95 and 90% of lactadherin but only about 75 and 70% of annexin V binding to Tca8113 and ACC-2 cells. These data indicate that PS exposure occurs in three stages during the cell death program and that fluorescein-labeled lactadherin permitted the detection of early PS exposure. A similar pattern of PS exposure has been observed in two malignant cell lines with different adherence, suggesting that this pattern of PS exposure is common in adherent cells. Both lactadherin and annexin V could be used in adherent Tca8113 and ACC-2 cell lines when an appropriate harvesting procedure was used. Lactadherin is more sensitive than annexin V for the detection of PS exposure as the physical structure of PS in these blebs and condensed apoptotic cell surface may be more conducive to binding lactadherin than annexin V.

Thickness induced structural changes in polystyrene films

Changes to the structure of polystyrene melt films as measured through the spectrum of density fluctuations have been observed as a function of film thickness down to the polymer radius of gyration (Rg). Films thicker than 4Rg show bulklike density fluctuations. Thinner films exhibit a peak in S(q) near q=0 which grows with decreasing thickness. This peak is attributed to a decreased interpenetration of chains resulting in an enhanced compressibility. Measurements were made using small angle x-ray scattering in a standing wave geometry designed to enhance scattering from the interior of the film compared to interface scattering.

Second-harmonic emission from sub-wavelength apertures: Effects of aperture symmetry and lattice arrangement

We measure second-harmonic generation from arrays of sub-wavelength apertures in transmission using fundamental input at 800 nm. Lattice arrangements include disordered, Penrose (quasi-periodic or aperiodic), and square (periodic). Strong angular dependence of SHG is observed, with maxima located at angular positions that roughly correspond to incidence angles of extraordinary optical transmission (EOT) for the fundamental. In addition, even at incidence normal to the sample, strong secondary maxima are observed at off-normal scattering angles for the arrangements with higher degree of order. Breaking the inversion symmetry of the aperture allows second harmonic peaks at normal incidence and detection. These measurements help to resolve the role that symmetry plays in second-harmonic generation from arrays of apertures.

Clinical significance of pleural lavage cytology in non-small cell lung cancer: A meta-analysis

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Background: The clinical significance of pleural lavage cytology (PLC) in non-small-cell lung cancer (NSCLC) remains controversial. This study was performed to estimate the associations of positive PLC with the main clinicopathological characteristics, and its prognostic value. Methods: PLC studies were identified on Medline, supplemented by manual search of bibliographies and proceedings. Authors were contacted for updated information. The quality of the studies was evaluated, and the data were extracted. Pooled odds ratios (ORs) and pooled hazard ratios (HRs) with confidence intervals [95% CIs] were calculated to evaluate the association of positive PLC with clinico-pathological characteristics and survival respectively. Results: Nineteen articles assessing PLC in NSCLC were selected for this study after exclusion of repeated publications or reports with little clinical detail. Positive PLC was diagnosed in 10.2% (516) of a total of 5073 patients. Positive PLC was strongly associated with lymphatic permeation (OR 4.96 [3.29, 7.54]), pleural invasion (OR 4.38 [2.16, 8.89], and vascular involvement (OR 2.94 [1.99, 4.35]). It was also found to be associated with advanced T stage, N stage, and TNM stage. Positive PLC was more frequent in adenocarcinoma than in squamous cell carcinoma (OR 2.32, [1.51, 3.52]). It was relatively more common in moderately- and poorly-differentiated tumors than in well-differentiated tumors (OR 1.89 [0.86, 4.16]). No association was found between positive PLC and fine needle aspiration cytology (OR 1.04 [0.58, 1.81]). Positive PLC was associated with high overall recurrence (OR 2.51 [1.79, 3.53]), as well as high local recurrence (OR 3.85 [1.57, 9.44]) and distant recurrence (2.58 [1.76, 3.76]). In analysis of survival, the overall HR for mortality was 2.43 [1.87, 3.16], suggesting significantly poorer survival for patients with positive PLC. Conclusions: Positive PLC in NSCLC is strongly associated with several existing poor prognosticators including pleural invasion, lymphatic spread, and vascular involvement. It may indicate locally advanced disease with high risk of recurrence and poor survival. We recommend that the PLC test be included in future clinical trials of adjuvant therapy for patients with NSCLC.

No significant financial relationships to disclose.

Evidence for viscoelastic effects in surface capillary waves of molten polymer films

The surface dynamics of supported ultrathin polystyrene films with thickness comparable to the radius of gyration were investigated by surface sensitive x-ray photon correlation spectroscopy. We show for the first time that the conventional model of capillary waves on a viscous liquid has to be modified to include the effects of a shear modulus in order to explain both static and dynamic scattering data from ultrathin molten polymer films.