Effects of genetic severity on glucose homeostasis in Friedreich ataxia

Introduction: Friedreich ataxia (FRDA) leads to increased risk of diabetes. Less is known regarding the dynamics of glucose homeostasis in FRDA, the influence of disease features, and the utility of oral‐based metrics for capturing metabolic dysfunction. Methods: To examine these dynamics, we analyzed oral and intravenous glucose tolerance test data in 42 non‐diabetic patients with FRDA. Results: Patients showed high insulin responsiveness to glucose and low insulin sensitivity. Genetic severity predicted overall metabolic impairment: individuals with longer guanine–adenine–adenine (GAA) repeats on the shorter allele showed a lower disposition index. Genetic severity did not predict any other variables. Measures of disposition index from intravenous and oral glucose tolerance testing did not correlate well, possibly reflecting divergent responses to oral and intravenous glucose loads. Conclusions: FRDA patients demonstrate abnormal compensatory activity for managing glucose. Genetic severity impacts the global homeostatic profile, whereas relative contributions of insulin secretion and action vary from patient to patient. Muscle Nerve 54 : 887–894, 2016     

Coronaviral Infection and Interferon Response: The Virus-Host Arms Race and COVID-19

The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in unprecedented morbidity and mortality worldwide. The host cells use a number of pattern recognition receptors (PRRs) for early detection of coronavirus infection, and timely interferon secretion is highly effective against SARS-CoV-2 infection. However, the virus has developed many strategies to delay interferon secretion and disarm cellular defense by intervening in interferon-associated signaling pathways on multiple levels. As a result, some COVID-19 patients suffered dramatic susceptibility to SARS-CoV-2 infection, while another part of the population showed only mild or no symptoms. One hypothesis suggests that functional differences in innate immune integrity could be the key to such variability. This review tries to decipher possible interactions between SARS-CoV-2 proteins and human antiviral interferon sensors. We found that SARS-CoV-2 actively interacts with PRR sensors and antiviral pathways by avoiding interferon suppression, which could result in severe COVID-19 pathogenesis. Finally, we summarize data on available antiviral pharmaceutical options that have shown potential to reduce COVID-19 morbidity and mortality in recent clinical trials.     

Is there utility for fluorine-18-fluorodeoxyglucose positron-emission tomography scan before surgery in breast cancer? A 15-year overall survival analysis

BACKGROUNDThe prognostic value of preoperative fluorine-18-fluorodeoxyglucose positron-emission tomography (¹⁸F-FDG PET) scan for determining overall survival (OS) in breast cancer (BC) patients is controversial. AIMTo evaluate the OS predictive value of preoperative PET positivity after 15 years.METHODSWe performed a retrospective search of the Universitair Ziekenhuis Brussel patient database for nonmetastatic patients who underwent preoperative PET between 2002-2008. PET positivity was determined by anatomical region of interest (AROI) findings for breast and axillary, sternal, and distant sites. The prognostic role of PET was examined as a qualitative binary factor (positive vs negative status) and as a continuous variable [maximum standard uptake value (SUVmax)] in multivariate survival analyses using Cox proportional hazards models. Among the 104 identified patients who received PET, 36 were further analyzed for the SUVmax in the AROI. RESULTSPoor OS within the 15-year study period was predicted by PET-positive status for axillary (P = 0.033), sternal (P = 0.033), and combined PET-axillary/sternal (P = 0.008) nodes. Poor disease-free survival was associated with PET-positive axillary status (P = 0.040) and combined axillary/sternal status (P = 0.023). Cox models confirmed the long-term prognostic value of combined PET-axillary/sternal status [hazard ratio (HR): 3.08, 95% confidence interval: 1.42-6.69]. SUVmax of ipsilateral breast and axilla as continuous covariates were significant predictors of long-term OS with HRs of 1.25 (P = 0.048) and 1.54 (P = 0.029), corresponding to relative increase in the risk of death of 25% and 54% per SUVmax unit, respectively. In addition, the ratio of the ipsilateral axillary SUVmax over the contralateral axillary SUVmax was the most significant OS predictor (P = 0.027), with 1.94 HR, indicating a two-fold relative increase of mortality risk.CONCLUSIONPreoperative PET is valuable for prediction of long-term survival. Ipsilateral axillary SUVmax ratio over the uninvolved side represents a new prognostic finding that warrants further investigation.     

Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Heme is an oxygen carrier and a cofactor of both industrial enzymes and food additives. The intracellular level of free heme is low, which limits the synthesis of heme proteins. Therefore, increasing heme synthesis allows an increased production of heme proteins. Using the genome-scale metabolic model (GEM) Yeast8 for the yeast Saccharomyces cerevisiae, we identified fluxes potentially important to heme synthesis. With this model, in silico simulations highlighted 84 gene targets for balancing biomass and increasing heme production. Of those identified, 76 genes were individually deleted or overexpressed in experiments. Empirically, 40 genes individually increased heme production (up to threefold). Heme was increased by modifying target genes, which not only included the genes involved in heme biosynthesis, but also those involved in glycolysis, pyruvate, Fe-S clusters, glycine, and succinyl-coenzyme A (CoA) metabolism. Next, we developed an algorithmic method for predicting an optimal combination of these genes by using the enzyme-constrained extension of the Yeast8 model, ecYeast8. The computationally identified combination for enhanced heme production was evaluated using the heme ligand-binding biosensor (Heme-LBB). The positive targets were combined using CRISPR-Cas9 in the yeast strain (IMX581-HEM15-HEM14-HEM3-Δshm1-HEM2-Δhmx1-FET4-Δgcv2-HEM1-Δgcv1-HEM13), which produces 70-fold-higher levels of intracellular heme.

Heme is a cofactor of essential enzymes for aerobic life within the three domains of life (archaea, bacteria, and eukarya). The heme molecule consists of a porphyrin ring that surrounds an iron atom, which alternates between its ferric and ferrous states in the oxidation and reduction reactions. Heme-containing proteins (HCPs) have several functions. For example, HCPs transport electrons in the respiratory chain in mitochondria and are crucial for energy production, transport molecular oxygen in globin proteins (e.g., hemoglobin in humans), and protect cells from oxidative damage (1–4). The heme biosynthetic pathway is conserved and tightly regulated to supply heme at levels to meet cellular demands. The cotranslational incorporation of heme into heme proteins governs their folding process (5, 6). The intracellular availability of heme is crucial for the production of heme proteins, which denature and lose their function without heme.Because of their biological importance, heme and HCPs are a central topic in molecular cell biology, with basic research occurring together with applications in medicine and technology. The production of heme and heme proteins has been a focus of research in microbial metabolic engineering. For example, research on blood substitutes focuses on human hemoglobin (7, 8), and plant-derived hemoglobin provides vegetarian protein (artificial meat with a lower carbon footprint) (9). Heme was used to improve charging of lithium batteries (10) and in the bioremediation of sulfite waste (11). Cytochromes and their new mutant forms catalyze novel chemical reactions with silicon (12) and were evolved to perform novel chemical reactions (13). The heterologous production of heme proteins is, however, challenging due to the limited amount of free heme and the complexity of the metabolic network in the cell.While a heme-biosynthesis pathway is conserved in nature, the precursor 5-aminolevulinic acid (5-ALA) is synthesized distinctly in different organisms. In the C4 pathway, the precursor 5-ALA is produced from glycine and from succinyl-coenzyme A (CoA) (the C4 intermediate of the tricarboxylic acid [TCA] cycle) in yeast, birds, mammals, and purple nonsulfur photosynthetic bacteria. In contrast, in the C5 pathway, the precursor 5-ALA is produced from alpha-ketoglutarate (the C5 intermediate of the TCA cycle) in algae, plants, and bacteria such as Escherichia coli (14).In E. coli, heme production has been increased by metabolic engineering of the pathways for 5-ALA synthesis, both native (C5) and heterologous (C4). The metabolic engineering studies using the C4 pathway increased heme production by overexpression of the Rhodobacter sphaeroides hemA gene (encoding ALA synthase), which produces the 5-ALA precursor; by overexpressing the native coaA gene (encoding pantothenate kinase), which produces CoA; and by overexpression of genes for heme biosynthesis. This engineering strategy yielded 3.3 μmol/L (15) and 9.1 μmol/g_cell (16) of heme. By overexpressing genes for heme production via the C5 pathway and by deleting genes of competing pathways, 51.5 mg/L total heme was produced (17). In the same strain, metabolic engineering of a heme-secretory pathway and feed-control optimization of substrates in fed-batch cultivation increased the production of total heme to 239 mg/L (17).In the unicellular eukaryote and established yeast cell-factory Saccharomyces cerevisiae, heme is synthesized through the C4 pathway (14). To improve the production of heme and heme proteins in S. cerevisiae, metabolic engineering studies have overexpressed genes encoding the known rate-limiting enzymes for heme biosynthesis (18–21) and have engineered oxygen sensing involved in heme biosynthesis regulation (22). To increase the production of the first intermediate of the heme pathway, 5-ALA, the HEM1 and ACO2 genes were overexpressed (23). However, the contribution of overall metabolism to heme production has not been analyzed.The impressive development of heme production in E. coli, however, has had some limitations, such as weak tolerance to acidic pH and phage sensitivity. As E. coli produces endotoxins, it is difficult to use E. coli directly in food production. In contrast, the S. cerevisiae yeast has greater tolerance for acidic pH and has been used for food production for millennia.The S. cerevisiae has been analyzed with genome-scale metabolic models (GEMs) (24). For S. cerevisiae, GEM analysis has guided the construction of strains with optimized yields of industrial molecules (e.g., bioethanol, sesquiterpenes, vanillin, 2,3-butanediol, fumaric acid, succinate, amorphadiene, 3-hydroxypropionate, β-farnesene, and dihydroxyacetone phosphate [DHAP]) (24, 25). The measurement of metabolic compounds in screening has facilitated the development of new biosensors that can be used for novel applications in other organisms (26).For S. cerevisiae, the consensus GEM (version 7.6) informed the engineering of strains with increased production of acetyl-CoA and malonyl-CoA in 2019 (27). The updated consensus Yeast8 model was followed by ecYeast8, which has additional constraints on the metabolic fluxes, representing enzymatic abundances. Enzyme-constrained GEMs improved the prediction of specific phenotypes (28, 29).Studies of heme production have explored the modification of genes and their expression, improving our knowledge of particular pathways. Using metabolic GEMs to maximize the production of heme is the focus of this study. We used the 2019 enzyme-constrained ecYeast8 (29) to identify metabolic fluxes that are important for heme biosynthesis. Our systems-biology analysis and modification of the gene expression guided the optimization of a heme strain with 58 genes in silico. The sequential strain engineering increased intracellular heme production 70-fold. In optimization of sequentially accumulated gene modifications, we developed a heme biosensor, which detects heme availability and the incorporation of heme into hemoglobin protein. This heme ligand-binding biosensor (Heme-LBB), like earlier genetically encoded ratiometric heme sensors (30), is likely useful for heme detection in other organisms.Our results are striking in terms of the dramatic increase in heme production and as a showcase of model-assisted synthetic biology. More importantly, our case study is one of the most rigorous in terms of evaluation of model-predicted targets for the widely used cell factory S. cerevisiae. As several of the model-predicted targets resulted in improved production, our paper represents a significant milestone in terms of a wider use of model-based design of yeast cell factories.     

Low risk of some common cancers in women with anorexia nervosa: Evidence from a national record-linkage study

Background

Some studies report that women with anorexia nervosa (AN) have lower risk than others of breast cancer, but increased risk of cancers of other sites. No work has been done to quantify the risk in the English population.

Methods

Retrospective cohort study using a national linked dataset of Hospital Episode Statistics for 1999–2021. We selected individuals with a hospital admission for AN, and compared their relative risk (RR) of developing site-specific cancers, with that in a reference cohort.

Results

We identified 75 cancers in 15,029 women hospitalised with AN. There was a low RR of all cancers combined at 0.75 (95%CI 0.59–0.94), and, notably, low RR for breast cancer 0.43 (0.20–0.81), cancers of secondary and ill-defined sites 0.52 (0.26–0.93). The RR for parotid gland cancer was 4.4 (1.4–10.6) within a year of first recorded diagnosis of AN. In men, we found 12 cancers in 1413 individuals hospitalised with AN, but no increased risks beyond the first year of diagnosis of AN.

Conclusions

This is the first report on the association between AN and cancers in the all-England population. The study showed low rates of breast cancer, and of all cancers combined, in women hospitalised with AN. It is possible that some of the metabolic or hormonal changes observed in AN could work as a protective factor for breast cancer. More experimental work is needed to identify and explain these factors. The new finding on the higher risk of salivary gland tumours could inform clinicians caring for patients with AN.     

Nephrobronchial fistula a case report and review of the literature

Nephrobronchial fistula is an extremely rare complications of renal infections. We present a case of nephrobronchial fistula in a middle age immunocompetent woman who complained cough and weight loss, with underlying asymptomatic nephrolithiasis. She underwent a chest X-ray that showed left lower lobe infiltrate and abdominal ultrasound. Abdominal ultrasound showed a complicated pyonephrosis ; CT of chest-abdomen-pelvis with intravenous contrast was performed in order to stage and define the extension of the pathology. At CT, a suspected diagnosis of stage III xanthogranulomatous pyelonephritis complicated with pyonephrosis and a nephrobronchial fistula was formulated. A nephrostomy tube was placed, and the patient was treated with antibiotics. Follow up CT, performed after 15 days, showed the healing of the fistulous connection between the perinephric abscess and bronchi; the patient underwent nephrectomy with no airway complication during intubation. Histopathological diagnosis confirmed the presence on complicated xanthogranulomatous pyelonephritis.     

Cross-sectional HIV and HCV cascades of care across the regions of Ukraine between 2019 and 2020: findings from the CARE cohort

Introduction

Eastern Europe is facing major HIV and hepatitis C (HCV) epidemics, with many people living with HIV (PLHIV) and HIV/HCV coinfection living in Ukraine. Despite the previous progress towards care quality improvement, the ongoing war in Ukraine is disrupting HIV and HCV care.

Methods

We described an HIV cascade of care (CoC) in PLHIV from two clinical sites and an HCV CoC for anti-HCV-positive PLHIV from six sites in Ukraine, enrolled in the CARE cohort between 1 January 2019 and 1 June 2020. The cross-sectional HIV CoC and HCV CoC are described at study enrolment.

Results

Of 1028 PLHIV, 1014 (98.6%, 95% confidence interval [CI] 97.7–99.3) were on antiretroviral therapy (ART), and 876 (86.4% of those on ART, 95% CI 84.1–88.4) were virologically suppressed. Of 894 participants on ART >6 months, 90.8% (95% CI 88.7–92.6) were virologically suppressed (HIV-RNA <200 copies/ml). Of 2040 anti-HCV-positive PLHIV, 417 (20.4%, 95% CI 18.7–22.3) were ever tested for HCV-RNA prior to enrolment, ranging from 4.9% to 54.4% across sites, and 13.5% were currently HCV-RNA positive. One hundred and eighteen persons (7.3% of ever chronically infected) had received HCV treatment, and 25 persons (1.6% of ever chronically infected) were cured, with variations across sites (0%–7.5%). The site diagnosing 54.4% of people with chronic HCV was the only one providing free RNA testing for all anti-HCV-positive persons, while the intra-country differences in treatment coverage were driven by the number of available direct-acting antiviral (DAA) courses.

Conclusions

Over 98% of PLHIV in care in both CARE sites in Ukraine were receiving ART, and the target of 90% virally suppressed was achieved in persons >6 months on ART. Only one of six HIV/HCV study sites tested over 50% anti-HCV-positive PLHIV for HCV-RNA and treated over 25% of eligible persons. While free HCV-RNA testing and DAA treatment are paramount to achieving HCV elimination targets, they remained a challenge in Ukraine in 2019–2020. The extent of the HIV and HCV care disruption during the war will be further assessed in the CARE cohort and compared with the pre-war findings.     

Distribution of lymphoma subtypes in Ukraine according to the WHO 2016 classification

The Ukrainian Lymphoma Registry (ULR) was established in 2019 with the aim of monitoring the quality of diagnosis, staging, and treatment of lymphoma in Ukraine. Between September 2019 and October 2021, 546 patients with newly diagnosed lymphoma were prospectively registered. All cases were diagnosed according to the 2016 updated WHO lymphoma classification. The male-to-female ratio (M/F) for the whole population was 0.7, with a median age of 46 years (range 18–95). The adoption of the 2016 WHO classification resulted in the identification of 36 different lymphoma subtypes, with 132 cases (24.2%) classified differently compared to the 2008 WHO classification. Only 12 cases (2.8%) were true new entities, including seven cases of high-grade B-cell lymphoma NOS, three of anaplastic large B-cell lymphoma, ALK-negative, 1 case of HHV8+ DLBCL NOS, and 1 of high-grade B-cell lymphoma with C-MYC and BCL2/BCL6 rearrangement. Moreover, 55 (61.1%) entities, including 37 defined by WHO 2008 and 18 defined by WHO 2016, were not represented at all. The analysis of cases registered in the ULR provides a comprehensive breakdown of the subtypes, stage distribution, and treatment of malignant lymphomas (ML) in Ukraine, supporting the usefulness of prospective data collection and timely reporting. We believe that this study is the first step toward a better understanding of the real-life outcomes of patients with ML.     

Machine-learning-derived heart and brain age are independently associated with cognition

Background and purpose

A heart age biomarker has been developed using deep neural networks applied to electrocardiograms. Whether this biomarker is associated with cognitive function was investigated.

Methods

Using 12-lead electrocardiograms, heart age was estimated for a population-based sample (N = 7779, age 40–85 years, 45.3% men). Associations between heart delta age (HDA) and cognitive test scores were studied adjusted for cardiovascular risk factors. In addition, the relationship between HDA, brain delta age (BDA) and cognitive test scores was investigated in mediation analysis.

Results

Significant associations between HDA and the Word test, Digit Symbol Coding Test and tapping test scores were found. HDA was correlated with BDA (Pearson's r = 0.12, p = 0.0001). Moreover, 13% (95% confidence interval 3–36) of the HDA effect on the tapping test score was mediated through BDA.

Discussion

Heart delta age, representing the cumulative effects of life-long exposures, was associated with brain age. HDA was associated with cognitive function that was minimally explained through BDA.