Abstract 1277: Discovery of novel CDC7 inhibitors that disrupt cell cycle dynamics and show anti-proliferative effects in cancer cells

Introduction: CDC7 is a serine/threonine protein kinase that phosphorylates the MCM2-7 helicase complex, a required step in DNA replication initiation. CDC7 has emerged as an attractive target for cancer treatment because of high expression in a number of tumors (e.g. ovarian, lung, and oral) which is thought to be linked to their proliferative capacity and ability to bypass DNA damage responses. Consistent with this, disruption of CDC7 activity in cancer cells results in delayed DNA replication, mitotic abnormalities and cell death whereas non-transformed, p53 wildtype cells are protected from cytotoxicity due to G1 cell cycle arrest. Due to the low ATP Km of CDC7, very potent inhibitor molecules are required to effectively block CDC7 activity and drive cancer cells into apoptosis. We have identified novel potent and selective CDC7 inhibitors targeting the ATP binding site that are active in biophysical, biochemical and cellular assays as well as in vivo CDX models.

Results: Our lead compounds show potent picomolar (pM) inhibition of CDC7 in a biochemical kinase activity assay, pM affinity in SPR assay and complete inhibition of MCM2 (S53) phosphorylation in COLO205, A427, MV-4-11 and SW48 cancer cell lines. In a broad kinase selectivity panel, the novel inhibitors showed good selectivity for CDC7 kinase. Mechanistic studies show that our CDC7 inhibitors induced apoptosis, disrupted DNA replication and cell cycle dynamics with accumulation of polyploid cells after 48 h of treatment of cancer cells with minimal effects on human fibroblast cell lines. Our compounds have shown potent anti-proliferative and cytotoxic effects in a panel of more than a 100 cancer cell lines of varying origin including COLO205, SW48, A427, MOLM-13, and SUM149. Comparison of CDC7 inhibitors with other oncology drugs in a panel of cancer cell lines revealed a unique mechanism of action. In vivo, our compounds reduced tumor cell MCM2 (S53) phosphorylation in the mouse COLO205 xenograft model and showed strong tumor growth inhibition. We have also examined the effect of CDC7 inhibitors on cancer cell proliferation in combination with other anti-cancer agents, including other DNA damage response (DDR) targeting agents.

Conclusions: We have identified novel potent ATP-competitive CDC7 inhibitors that show target engagement in cells and CDX tumors and have shown strong inhibition of cancer cell proliferation in vitro and tumor growth in vivo. CDC7 inhibitors show promise for use in combination with other targeted therapies for the treatment of cancers of varying origin.

Citation Format: Lyuben Tsvetkov, Adam Levinson, Xianhai Huang, Sayan Mondal, Jeff Bell, Lin Tang, Robert Pelletier, Karen Dingley, Nick Boyles, Jackson Chief Elk, Leah Frye, Alan Futran, Phani Ghanakota, Jeremy Greenwood, George Lai, Sarah Silvergleid, Wu Yin, Hamish Wright, Karen Akinsanya, Wayne Tang, Kristian Jensen. Discovery of novel CDC7 inhibitors that disrupt cell cycle dynamics and show anti-proliferative effects in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1277.

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis

Lactococcus lactis cheese starter cultures typically contain a mix of many strains and may include variants that produce and/or tolerate the antimicrobial bacteriocin nisin. Nisin is well-established as an effective agent against several undesirable Gram-positive bacteria in cheese and various other foods. In the current study, we have examined the effect of nisin on 710 individual L. lactis strains during milk fermentations. Changes in milk acidification profiles with and without nisin exposure, ranging from unaltered acidification to loss of acidification, could be largely explained by the type(s) and variants of nisin immunity and nisin degradation genes present, but surprisingly, also by genotypic lineage (L. lactis ssp. cremoris vs. ssp. lactis). Importantly, we identify that nisin degradation by NSR is frequent among L. lactis and therefore likely the main mechanism by which dairy-associated L. lactis strains tolerate nisin. Insights from this study on the strain-specific effect of nisin tolerance and degradation during milk acidification is expected to aid in the design of nisin-compatible cheese starter cultures.

Air variability in maxillary sinus during radiotherapy for sinonasal carcinoma

INTRODUCTION

The aim was to characterise patterns and predictability of aeration changes in the ipsilateral maxillary sinus during intensity-modulated radiotherapy (IMRT) for sinonasal cancer (SNC), and in a sample evaluate the dosimetric effects of aeration changes for both photon and proton therapy.

MATERIALS AND METHODS

The study included patients treated with IMRT for SNC in a single institution in 2009-2017. The volume of air in the ipsilateral maxillary sinus was recorded in 1578 daily cone beam computer tomography (CBCT) from 53 patients. Patterns of changing air volumes were categorised as 'stable', increasing', 'decreasing', or 'erratic'. For the prediction analysis, categorisation was performed based both on the entire treatment course and the first five fractions (F1-5). Photon and proton therapy plans were generated for four patients, the one from each category with the largest aeration variation. Synthetic CT images were generated for each CBCT and all plans were recalculated on the daily synthetic CTs.

RESULTS

The absolute volume of air varied considerably during the treatment course, ranging from 0 to 25.9 cm3. Changes within a single participant varied in the range of 0-18.7 cm3. In the categorisation of patterns, most patients had increasing aeration of the sinus. Generally, patterns of aeration could not be predicted from F1-5. Patients categorised as increasing in F1-5 had the best prediction, with 78% predicted correctly as increasing for the entire treatment course. The numeric correlation coefficients for target coverage and air volume were low for 3/4 scenarios (photons 0.03-0.23, protons 0.26-0.48). No straightforward correlation between the dosimetric effect and the volume changes could be detected in the sample test of four patients for neither photon nor proton therapy.

CONCLUSION

The variation of aeration was large and unpredictable. No clear dosimetric consequences of the aeration variation were evident for neither IMRT nor proton therapy for the patients investigated.

Thermographic visualization of facial vasoconstriction is associated with 30-day all-cause mortality in medical patients; prospective observational two-site cohort study

INTRODUCTION

Quick and reliable assessment of acute patients is required for accurate triage. The temperature gradient between core and peripheral temperature could possibly instantly provide information on circulatory status.

METHODS

Adult medical patients, who did not receive supplementary oxygen, attending two emergency departments, had a thermographic image taken on arrival. The association between 30-day mortality and gradients was tested using logistic regression.

RESULTS

726 patients were studied, median age was 64 years and 14 (1.9%) died within 30 days. There was a significant association between mortality and temperature gradient, comparable to vital signs, age, and clinical intuition.

CONCLUSION

Temperature gradient between nose and eye had an acceptable discriminatory power for 30-day all-cause mortality.

Hemoglobin level at stabilization is associated with long-term all-cause mortality in patients with left-sided endocarditis, a POET substudy

Background

Left-sided infectious endocarditis (IE) has a high 1-year mortality. Anemia is a common finding in patients with IE, yet little is known about frequency, severity, and associated outcomes in this setting.

Purpose

To examine the relationship between Hemoglobin (Hgb) level measured at IE stabilization (time of randomization) in the Partial Oral versus intravenous Antibiotic Treatment of Endocarditis (POET) trial - and long-term all-cause mortality.

Methods

In the POET trial, 400 patients with left-sided IE were randomized, after medical and/or surgical stabilization, to conventional antibiotic treatment or partial oral treatment. Only non-surgically treated patients were considered in this study. Patients were divided by quartiles into four groups based on Hgb level at randomization.

Results

We examined 248 patients with non-surgically treated IE. Median time from diagnosis of IE to randomization was 14 days (IQ 12–19). At long-term follow-up (median 3.2 years, IQ 2.18–4.60), 71 patients had died (28.6%). Patients in the lowest quantile (Hgb ≤6.0 mmol) had a HR of 4.17 (95% CI 1.81–9.61, p<0.001) for death compared to patients in the highest quantile (Hgb >7.5 mmol/L). This association remained significant after multivariable adjustment for age, sex, renal disease, C-Reactive Protein, and Prosthetic heart valve (HR 2.69, 95% CI 1.11–6.50); p=0.028).

Conclusion

Low Hemoglobin level at stabilization in patients with IE was associated with an increased risk of long-term mortality. Whether intensified treatment of anemia in patients with IE could improve long-term outcome requires investigation.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): The Danish Heart Foundation, The Capital Regions Research Council

Late toxicity in the brain after radiotherapy for sinonasal cancer: Neurocognitive functioning, MRI of the brain and quality of life

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Compared with matched normative data, impaired cognitive function was substantial.

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Several correlations between radiation dose and cognitive impairment were present.

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Radiation-induced white matter hyperintensities were present in 2/27 participants.

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One participant displayed radiation-induced necrosis in the temporal lobe.

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The domains affecting quality of life the most were fatigue and quality of sleep.

Purpose

The aim of the study was to evaluate neurocognitive late effects, structural alterations and associations between cognitive impairment and radiation doses as well as cerebral tissue damage after radiotherapy for sinonasal cancer. Furthermore, the aim was to report quality of life (QoL) and self-reported cognitive capacity.

Materials and methods

Recurrence-free patients previously treated with intensity-modulated radiotherapy with a curative intent were eligible for the study. Study examinations comprised comprehensive neurocognitive testing, MRI of the brain, and self-reported outcomes.

Results

A total of 27 patients were included. Median age was 67 years (range 47–83). The majority of test outcomes were below normative values in any degree, and 37% of the participants had clinically significant neurocognitive impairment when compared with normative data. Correlations between absorbed doses to specific substructures of the brain and neurocognitive outcomes were present for Wechsler’s Adult Intelligence Scale-digit span and Controlled Oral Word Association Test-S. Structural MRI revealed macroscopic abnormalities in three patients; infarction (n = 1), diffuse white matter intensities (n = 2) and necrosis (n = 1). In the analysis of atrophy of cerebral tissue, no correlations were present with neither radiation dose to cerebral substructures nor neurocognitive impairment. The global QoL of the cohort was 75. The most affected outcomes were ‘fatigue’, ‘insomnia’, and ‘drowsiness’. A total of 59% of participants reported significantly impaired quality of sleep. Self-reported cognitive function revealed that ‘memory’ was the most affected cognitive domain. For the domains of ‘memory’ and ‘language’, self-reported functioning was associated with objectively measured neurocognitive outcomes.

Conclusion

Cerebral toxicity after radiotherapy for sinonasal cancer was substantial. Clinically significant cognitive impairment was present in more than one third of the participants, and several dose–response associations were present. Furthermore, the presence of macroscopic radiation sequelae indicated considerable impact of radiotherapy on brain tissue.

Grazing mediates soil microbial activity and litter decomposition in salt marshes

Salt marshes contribute to climate change mitigation because of their great capacity to store organic matter (OM) in soils. Most of the research regarding OM turnover in salt marshes in times of global change focuses on effects of rising temperature and accelerated sea-level rise, while effects of land-use change have gained little attention. The present work investigates the mechanisms by which livestock grazing can affect OM decomposition in salt marsh soils. In a grazing exclusion experiment at the mouth of the Yangtze estuary, China, we assessed soil microbial exo-enzyme activity (EEA) to gain insight into the microbial carbon (C) and nitrogen (N) demand. Additionally, we studied the decomposition of plant litter in soil using the Tea Bag Index (TBI), a widely used standardized litter bag assay to fingerprint soil decomposition dynamics. Based on EEAs, grazing markedly reduced microbial C acquisition, whereas microbial N acquisition was strongly increased. These opposing grazing effects were also evident in the decomposition of standardized plant litter: The decomposition rate constant (k) and the stabilization (S) of litter were not inversely related, as would be expected, but instead both were reduced by livestock grazing. Our data suggest that gazing effects on EEAs and litter decomposition can just partly be explained by grazing-driven soil compaction and resulting lower oxygen availability, which has previously been hypothesized as a main pathway by which grazing can reduce microbial activity in wetland soils. Instead, grazing effects on microbial nutrient demand occurs to be an at least equally important control on soil decomposition processes.

Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of "EC-Function;CAZy-Family" observations. These "Function;Family"-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of "Function;Family" enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme "Function;Family" profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by "shared presence" and "shared absence" of CAZyme "Function;Family" observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.

Four New Species of Paraorygmatobothrium (Eucestoda: Phyllobothriidea) From Sharks of the Gulf of Mexico and the Atlantic Ocean, with Comments on Their Host Specificity

Four new species of Paraorygmatobothrium are described from carcharhinid shark species from the Gulf of Mexico and the U.S. coast of the northwestern Atlantic Ocean. Paraorygmatobothrium bullardi n. sp. is described from Carcharhinus brevipinna as its type host, and from Carcharhinus acronotus and Carcharhinus limbatus. Paraorygmatobothrium campbelli n. sp. is described from Rhizoprionodon terraenovae. Paraorygmatobothrium deburonae n. sp. is described from Carcharhinus isodon as its type host, as well as from C. brevipinna, C. limbatus, and R. terraenovae. Paraorygmatobothrium mattisi n. sp. is described from R. terraenovae as its type host, and from C. brevipinna and C. limbatus. These 4 species differ from other species of Paraorygmatobothrium and from each other in bothridial microthrix shape, and in various combinations of features such as the total length of the worm, apical sucker size, bothridial musculature, proglottid number, testes number, and genital pore position. Difficulty in differentiating these 4 species from one another, and from other species of Paraorygmatobothrium, points to limitations in the use of morphology alone to recognize species diversity in this genus. A phylogenetic analysis of Paraorygmatobothrium and related genera, based on partial (D1-D3) 28S rDNA sequence data, confirms that the genus is not monophyletic. Genetic distances of COI revealed that sequence divergence between species of Paraorygmatobothrium is generally at least an order of magnitude larger than COI divergence within a species. Patterns of host use for 3 of the new species are consistent with previous findings that point to a lack of host specificity in Paraorygmatobothrium.

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

Interactive website for head and neck cancer patients: Adherence and coping program to prevent dysphagia after radiation

INTRODUCTION

Pharyngeal and laryngeal cancers are highly curable; however survivors are at high risk for long-term dysphagia after radiation. To address lack of access to preventive care in community settings, we developed a responsive web-based application to help patients adhere to preventive swallowing exercises and cope with radiation side effects. We conducted an interim study analysis to determine website usage characteristics and to examine the effect size for future trials.

METHODS

Pharyngeal and laryngeal cancer patients were recruited for enrollment by speech language pathologists before primary radiation and introduced to the interactive website. The program (English and Spanish) features tracking logs for preventive exercises, instructional videos, patient stories and search features. Patients' self-reported swallowing function was assessed with the MD Anderson Dysphagia Inventory (MDADI) at baseline and at 6 months. Adherence to preventive exercises was assessed during the 10 week intervention. Number of unique website visits, total duration of website exposure, and rankings of the most popular webpages were calculated. Preliminary regression models were run using adherence and MDADI as outcomes.

RESULTS

Of the 160 enrolled, 96 had 10-week adherence data and 61 had 6-month MDADI data. The average age was 63 (SD = 12.26), 49.4% were from rural counties, 44% had a high school education or lower, and 42% reported annual income of $30,000 or less. The average number of visits was 5.49 (SD = 9.96) and the average total time spent with the website was 41.09 min (SD =88.48). Preliminary analyses indicated that number of unique visits to the website was independently associated with increased adherence to preventive exercises (p = .001-.008).

CONCLUSION

Our website showed significant effects in promoting adherence to swallowing exercises. However, our return visit rate showed that the platform needs improvement in navigability and usability for this older population undergoing challenging treatment in community settings with low resources.

Temporal Changes in Effect Sizes of Studies Comparing Individuals With and Without Autism: A Meta-analysis

Importance

The definition and nature of autism have been highly debated, as exemplified by several revisions of the DSM (DSM-III, DSM-IIIR, DSM-IV, and DSM-5) criteria. There has recently been a move from a categorical view toward a spectrum-based view. These changes have been accompanied by a steady increase in the prevalence of the condition. Changes in the definition of autism that may increase heterogeneity could affect the results of autism research; specifically, a broadening of the population with autism could result in decreasing effect sizes of group comparison studies.

Objective

To examine the correlation between publication year and effect size of autism-control group comparisons across several domains of published autism neurocognitive research.

Data Sources

This meta-analysis investigated 11 meta-analyses obtained through a systematic search of PubMed for meta-analyses published from January 1, 1966, through January 27, 2019, using the search string autism AND (meta-analysis OR meta-analytic). The last search was conducted on January 27, 2019.

Study Selection

Meta-analyses were included if they tested the significance of group differences between individuals with autism and control individuals on a neurocognitive construct. Meta-analyses were only included if the tested group difference was significant and included data with a span of at least 15 years.

Data Extraction and Synthesis

Data were extracted and analyzed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline using fixed-effects models.

Main Outcomes and Measures

Estimated slope of the correlation between publication year and effect size, controlling for differences in methods, sample size, and study quality.

Results

The 11 meta-analyses included data from a total of 27 723 individuals. Demographic data such as sex and age were not available for the entire data set. Seven different psychological and neurologic constructs were analyzed based on data from these meta-analyses. Downward temporal trends for effect size were found for all constructs (slopes: -0.067 to -0.003), with the trend being significant in 5 of 7 cases: emotion recognition (slope: -0.028 [95% CI, -0.048 to -0.007]), theory of mind (-0.045 [95% CI, -0.066 to -0.024]), planning (-0.067 [95% CI, -0.125 to -0.009]), P3b amplitude (-0.048 [95% CI, -0.093 to -0.004]), and brain size (-0.047 [95% CI, -0.077 to -0.016]). In contrast, 3 analogous constructs in schizophrenia, a condition that is also heterogeneous but with no reported increase in prevalence, did not show a similar trend.

Conclusions and Relevance

The findings suggest that differences between individuals with autism and those without the diagnosis have decreased over time and that possible changes in the definition of autism from a narrowly defined and homogenous population toward an inclusive and heterogeneous population may reduce our capacity to build mechanistic models of the condition.

An opposite pattern of cognitive performance in autistic individuals with and without alexithymia

Oakley, Brewer, Bird, and Catmur (2016) investigated whether the Reading the Minds in the Eyes Test (RMET) measures emotion recognition rather than theory of mind (ToM). To explore this, 19 participants with autism and 23 controls, matched on alexithymia traits, were tested with the RMET, as well as the ToM Movie for Assessment of Social Cognition (MASC). The authors found a significant difference between the two groups on the MASC but not on the RMET, but dividing the groups based on alexithymia resulted in a significantly lower performance on the RMET but not on the MASC for the alexithymia group. Therefore, they conclude that difficulties on the RMET are associated with alexithymia, not autism, while difficulties on the MASC are associated with autism, not alexithymia. Here we investigated what seems to be opposite patterns of performance on the two cognitive tasks within the autism group, which modified the authors' interpretation of their data. This was examined by correlating the alexithymia scores with the RMET and a subscale of the MASC scores, referred to as the cognitive MASC. We found a negative correlation between the alexithymia score and the RMET score while also finding a positive correlation between the alexithymia score and the cognitive MASC score in the autism group. Such an opposite pattern of performance suggests the presence of distinct patterns of ToM difficulties within the autism group. This also indicates that, contrary to what is reported by Oakley et al., there is an association between alexithymia and the MASC within the autism group. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

NTCP model validation method for DAHANCA patient selection of protons versus photons in head and neck cancer radiotherapy

Introduction: Prediction models using logistic regression may perform poorly in external patient cohorts. However, there is a need to standardize and validate models for clinical use. The purpose of this project was to describe a method for validation of external NTCP models used for patient selection in the randomized trial of protons versus photons in head and neck cancer radiotherapy, DAHANCA 35. Material and methods: Organs at risk of 588 patients treated primarily with IMRT in the randomized controlled DAHANCA19 trial were retrospectively contoured according to recent international recommendations. Dose metrics were extracted using MatLab and all clinical parameters were retrieved from the DAHANCA database. The model proposed by Christianen et al. to predict physician-rated dysphagia was validated through the closed testing, where change of the model intercept, slope and individual beta's were tested for significant prediction improvements. Results: Six months prevalence of dysphagia in the validation cohort was 33%. The closed testing procedure for physician-rated dysphagia showed that the Christianen et al. model needed an intercept refitting for the best match for the Danish patients. The intercept update increased the risk of dysphagia for the validation cohort by 7.9 ± 2.5% point. For the raw model performance, the Brier score (mean squared residual) was 0.467, which improved significantly with a new intercept to 0.415. Conclusions: The previously published Dutch dysphagia model needed an intercept update to match the Danish patient cohort. The implementation of a closed testing procedure on the current validation cohort allows quick and efficient validation of external NTCP models for patient selection in the future.

MARSI: metabolite analogues for rational strain improvement

Summary

Metabolite analogues (MAs) mimic the structure of native metabolites, can competitively inhibit their utilization in enzymatic reactions, and are commonly used as selection tools for isolating desirable mutants of industrial microorganisms. Genome-scale metabolic models representing all biochemical reactions in an organism can be used to predict effects of MAs on cellular phenotypes. Here, we present the metabolite analogues for rational strain improvement (MARSI) framework. MARSI provides a rational approach to strain improvement by searching for metabolites as targets instead of genes or reactions. The designs found by MARSI can be implemented by supplying MAs in the culture media, enabling metabolic rewiring without the use of recombinant DNA technologies that cannot always be used due to regulations. To facilitate experimental implementation, MARSI provides tools to identify candidate MAs to a target metabolite from a database of known drugs and analogues.

Availability and implementation

The code is freely available at https://github.com/biosustain/marsi under the Apache License V2. MARSI is implemented in Python.

Supplementary information

Supplementary data are available at Bioinformatics online.

Exercise-based cardiac rehabilitation in patients with reduced left ventricular ejection fraction: The Cardiac Rehabilitation Outcome Study in Heart Failure (CROS-HF): A systematic review and meta-analysis

Background

In heart failure with reduced left ventricular ejection fraction (HFrEF) patients the effects of exercise-based cardiac rehabilitation on top of state-of-the-art pharmacological and device therapy on mortality, hospitalization, exercise capacity and quality-of-life are not well established.

Design

The design of this study involved a structured review and meta-analysis.

Methods

Evaluation of randomised controlled trials of exercise-based cardiac rehabilitation in HFrEF-patients with left ventricular ejection fraction ≤40% of any aetiology with a follow-up of ≥6 months published in 1999 or later.

Results

Out of 12,229 abstracts, 25 randomised controlled trials including 4481 HFrEF-patients were included in the final evaluation. Heterogeneity in study population, study design and exercise-based cardiac rehabilitation-intervention was evident. No significant difference in the effect of exercise-based cardiac rehabilitation on mortality compared to control-group was found (hazard ratio 0.75, 95% confidence interval 0.39–1.41, four studies; 12-months follow-up: relative risk 1.29, 95% confidence interval 0.66–2.49, eight studies; six-months follow-up: relative risk 0.91, 95% confidence interval 0.26–3.16, seven studies). In addition there was no significant difference between the groups with respect to ‘hospitalization-for-any-reason’ (12-months follow-up: relative risk 0.79, 95% confidence interval 0.41–1.53, four studies), or ‘hospitalization-due-to-heart-failure’ (12-months follow-up: relative risk 0.59, 95% confidence interval 0.12–2.91, four studies; six-months follow-up: relative risk 0.84, 95% confidence interval 0.07–9.71, three studies). All studies show improvement of exercise capacity. Participation in exercise-based cardiac rehabilitation significantly improved quality-of-life as evaluated with the Kansas City Cardiomyopathy Questionnaire: (six-months follow-up: mean difference 1.94, 95% confidence interval 0.35–3.56, two studies), but no significant results emerged for quality-of-life measured by the Minnesota Living with Heart Failure Questionnaire (nine-months or more follow-up: mean difference –4.19, 95% confidence interval –10.51–2.12, seven studies; six-months follow-up: mean difference –5.97, 95% confidence interval –16.17–4.23, four studies).

Conclusion

No association between exercise-based cardiac rehabilitation and mortality or hospitalisation could be observed in HFrEF patients but exercise-based cardiac rehabilitation is likely to improve exercise capacity and quality of life.

OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Biological production of chemicals is an attractive alternative to petrochemical-based production, due to advantages in environmental impact and the spectrum of feasible targets. However, engineering microbial strains to overproduce a compound of interest can be a long, costly and painstaking process. If production can be coupled to cell growth it is possible to use adaptive laboratory evolution to increase the production rate. Strategies for coupling production to growth, however, are often not trivial to find. Here we present OptCouple, a constraint-based modeling algorithm to simultaneously identify combinations of gene knockouts, insertions and medium supplements that lead to growth-coupled production of a target compound. We validated the algorithm by showing that it can find novel strategies that are growth-coupled in silico for a compound that has not been coupled to growth previously, as well as reproduce known growth-coupled strain designs for two different target compounds. Furthermore, we used OptCouple to construct an alternative design with potential for higher production. We provide an efficient and easy-to-use implementation of the OptCouple algorithm in the cameo Python package for computational strain design.