Prospective Metabolomic Studies in Precision Medicine: The AKRIBEA Project.

For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship with diabetes), ultimately offering incomplete diagnostic value. Nowadays, precision medicine emerges as an option to improve the prevention and/or treatment of numerous pathologies, focusing on the molecular mechanisms, acting in a patient-specific dimension, and leveraging multiple contributing factors such as genetic, environmental, or lifestyle. Metabolomics grasps the required subcellular complexity while being sensitive to all these factors, which results in a most suitable technique for precision medicine. The aim of this chapter is to describe how NMR-based metabolomics can be integrated in the design of a precision medicine strategy, using the Precision Medicine Initiative of the Basque Country (the AKRIBEA project) as a case study. To that end, we will illustrate the procedures to be followed when conducting an NMR-based metabolomics study with a large cohort of individuals, emphasizing the critical points. The chapter will conclude with the discussion of some relevant biomedical applications.

ALAD Inhibition by Porphobilinogen Rationalizes the Accumulation of δ-Aminolevulinate in Acute Porphyrias.

Patients with major forms of acute hepatic porphyria present acute neurological attacks with overproduction of porphobilinogen (PBG) and δ-aminolevulinic acid (ALA). Even if ALA is considered the most likely agent inducing the acute symptoms, the mechanism of its accumulation has not been experimentally demonstrated. In the most frequent form, acute intermittent porphyria (AIP), inherited gene mutations induce a deficiency in PBG deaminase; thus, accumulation of the substrate PBG is biochemically obligated but not that of ALA. A similar scenario is observed in other forms of acute hepatic porphyria (i.e., porphyria variegate, VP) in which PBG deaminase is inhibited by metabolic intermediates. Here, we have investigated the molecular basis of δ-aminolevulinate accumulation using in vitro fluxomics monitored by NMR spectroscopy and other biophysical techniques. Our results show that porphobilinogen, the natural product of δ-aminolevulinate deaminase, effectively inhibits its anabolic enzyme at abnormally low concentrations. Structurally, this high affinity can be explained by the interactions that porphobilinogen generates with the active site, most of them shared with the substrate. Enzymatically, our flux analysis of an altered heme pathway demonstrates that a minimum accumulation of porphobilinogen will immediately trigger the accumulation of δ-aminolevulinate, a long-lasting observation in patients suffering from acute porphyrias.

Uneven metabolic and lipidomic profiles in recovered COVID-19 patients as investigated by plasma NMR metabolomics.

COVID-19 is a systemic infectious disease that may affect many organs, accompanied by a measurable metabolic dysregulation. The disease is also associated with significant mortality, particularly among the elderly, patients with comorbidities, and solid organ transplant recipients. Yet, the largest segment of the patient population is asymptomatic, and most other patients develop mild to moderate symptoms after SARS-CoV-2 infection. Here, we have used NMR metabolomics to characterize plasma samples from a cohort of the abovementioned group of COVID-19 patients (n = 69), between 3 and 10 months after diagnosis, and compared them with a set of reference samples from individuals never infected by the virus (n = 71). Our results indicate that half of the patient population show abnormal metabolism including porphyrin levels and altered lipoprotein profiles six months after the infection, while the other half show little molecular record of the disease. Remarkably, most of these patients are asymptomatic or mild COVID-19 patients, and we hypothesize that this is due to a metabolic reflection of the immune response stress.

A molecular signature for the metabolic syndrome by urine metabolomics.

BACKGROUND: Metabolic syndrome (MetS) is a multimorbid long-term condition without consensual medical definition and a diagnostic based on compatible symptomatology. Here we have investigated the molecular signature of MetS in urine. METHODS: We used NMR-based metabolomics to investigate a European cohort including urine samples from 11,754 individuals (18-75 years old, 41% females), designed to populate all the intermediate conditions in MetS, from subjects without any risk factor up to individuals with developed MetS (4-5%, depending on the definition). A set of quantified metabolites were integrated from the urine spectra to obtain metabolic models (one for each definition), to discriminate between individuals with MetS. RESULTS: MetS progression produces a continuous and monotonic variation of the urine metabolome, characterized by up- or down-regulation of the pertinent metabolites (17 in total, including glucose, lipids, aromatic amino acids, salicyluric acid, maltitol, trimethylamine N-oxide, and p-cresol sulfate) with some of the metabolites associated to MetS for the first time. This metabolic signature, based solely on information extracted from the urine spectrum, adds a molecular dimension to MetS definition and it was used to generate models that can identify subjects with MetS (AUROC values between 0.83 and 0.87). This signature is particularly suitable to add meaning to the conditions that are in the interface between healthy subjects and MetS patients. Aging and non-alcoholic fatty liver disease are also risk factors that may enhance MetS probability, but they do not directly interfere with the metabolic discrimination of the syndrome. CONCLUSIONS: Urine metabolomics, studied by NMR spectroscopy, unravelled a set of metabolites that concomitantly evolve with MetS progression, that were used to derive and validate a molecular definition of MetS and to discriminate the conditions that are in the interface between healthy individuals and the metabolic syndrome.

Therapeutic Targeting of Fumaryl Acetoacetate Hydrolase in Hereditary Tyrosinemia Type I.

Fumarylacetoacetate hydrolase (FAH) is the fifth enzyme in the tyrosine catabolism pathway. A deficiency in human FAH leads to hereditary tyrosinemia type I (HT1), an autosomal recessive disorder that results in the accumulation of toxic metabolites such as succinylacetone, maleylacetoacetate, and fumarylacetoacetate in the liver and kidney, among other tissues. The disease is severe and, when untreated, it can lead to death. A low tyrosine diet combined with the herbicidal nitisinone constitutes the only available therapy, but this treatment is not devoid of secondary effects and long-term complications. In this study, we targeted FAH for the first-time to discover new chemical modulators that act as pharmacological chaperones, directly associating with this enzyme. After screening several thousand compounds and subsequent chemical redesign, we found a set of reversible inhibitors that associate with FAH close to the active site and stabilize the (active) dimeric species, as demonstrated by NMR spectroscopy. Importantly, the inhibitors are also able to partially restore the normal phenotype in a newly developed cellular model of HT1.

Hereditary tyrosinemia type I-associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate.

More than 100 mutations in the gene encoding fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1), a metabolic disorder characterized by elevated blood levels of tyrosine. Some of these mutations are known to decrease FAH catalytic activity, but the mechanisms of FAH mutation-induced pathogenicity remain poorly understood. Here, using diffusion ordered NMR spectroscopy, cryo-EM, and CD analyses, along with site-directed mutagenesis, enzymatic assays, and molecular dynamics simulations, we investigated the putative role of thermodynamic and kinetic stability in WT FAH and a representative set of 19 missense mutations identified in individuals with HT1. We found that at physiological temperatures and concentrations, WT FAH is in equilibrium between a catalytically active dimer and a monomeric species, with the latter being inactive and prone to oligomerization and aggregation. We also found that the majority of the deleterious mutations reduce the kinetic stability of the enzyme and always accelerate the FAH aggregation pathway. Depending mainly on the position of the amino acid in the structure, pathogenic mutations either reduced the dimer population or decreased the energy barrier that separates the monomer from the aggregate. The mechanistic insights reported here pave the way for the development of pharmacological chaperones that target FAH to tackle the severe disease HT1.

Tuning intracellular homeostasis of human uroporphyrinogen III synthase by enzyme engineering at a single hotspot of congenital erythropoietic porphyria.

Congenital erythropoietic porphyria (CEP) results from a deficiency in uroporphyrinogen III synthase enzyme (UROIIIS) activity that ultimately stems from deleterious mutations in the uroS gene. C73 is a hotspot for these mutations and a C73R substitution, which drastically reduces the enzyme activity and stability, is found in almost one-third of all reported CEP cases. Here, we have studied the structural basis, by which mutations in this hotspot lead to UROIIIS destabilization. First, a strong interdependency is observed between the volume of the side chain at position 73 and the folded protein. Moreover, there is a correlation between the in vitro half-life of the mutated proteins and their expression levels in eukaryotic cell lines. Molecular modelling was used to rationalize the results, showing that the mutation site is coupled to the hinge region separating the two domains. Namely, mutations at position 73 modulate the inter-domain closure and ultimately affect protein stability. By incorporating residues capable of interacting with R73 to stabilize the hinge region, catalytic activity was fully restored and a moderate increase in the kinetic stability of the enzyme was observed. These results provide an unprecedented rationale for a destabilizing missense mutation and pave the way for the effective design of molecular chaperones as a therapy against CEP.

Therapeutic potential of proteasome inhibitors in congenital erythropoietic porphyria.

Congenital erythropoietic porphyria (CEP) is a rare autosomal recessive disorder characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in massive porphyrin accumulation in blood cells, which is responsible for hemolytic anemia and skin photosensitivity. Among the missense mutations actually described up to now in CEP patients, the C73R and the P248Q mutations lead to a profound UROS deficiency and are usually associated with a severe clinical phenotype. We previously demonstrated that the UROS(C73R) mutant protein conserves intrinsic enzymatic activity but triggers premature degradation in cellular systems that could be prevented by proteasome inhibitors. We show evidence that the reduced kinetic stability of the UROS(P248Q) mutant is also responsible for increased protein turnover in human erythroid cells. Through the analysis of EGFP-tagged versions of UROS enzyme, we demonstrate that both UROS(C73R) and UROS(P248Q) are equally destabilized in mammalian cells and targeted to the proteasomal pathway for degradation. We show that a treatment with proteasomal inhibitors, but not with lysosomal inhibitors, could rescue the expression of both EGFP-UROS mutants. Finally, in CEP mice (Uros(P248Q/P248Q)) treated with bortezomib (Velcade), a clinically approved proteasome inhibitor, we observed reduced porphyrin accumulation in circulating RBCs and urine, as well as reversion of skin photosensitivity on bortezomib treatment. These results of medical importance pave the way for pharmacologic treatment of CEP disease by preventing certain enzymatically active UROS mutants from early degradation by using proteasome inhibitors or chemical chaperones.

Percutaneous Endoscopic Gastrostomy with T-Fasteners versus "Pull Technique": Analysis of Complications.

INTRODUCTION: The T-fasteners gastrostomy (T-PEG) has become increasingly popular over recent years as an alternative to the "pull-technique" gastrostomy (P-PEG). This study aimed to compare P-PEG and T-PEG complications. MATERIALS AND METHODS: A retrospective observational study of pediatric patients who underwent percutaneous endoscopic gastrostomy (PEG) placement. P-PEG was performed using the standard Ponsky technique and was replaced after 6 months by a balloon gastrostomy under sedation. T-PEG was performed using three percutaneous T-fasteners (that allow a primary insertion of a balloon gastrostomy). The balloon was replaced by a new one after 6 months without sedation. Complications were recorded. RESULTS: In total, 146 patients underwent PEG placement, 70 P-PEG and 76 T-PEG. The mean follow-up was 3.9 years (standard deviation = 9.6). Age, weight, and associated comorbidities were comparable (p > 0.05). The overall complications were 17 (24.2%) in the P-PEG group and 16 (21.0%) in the T-PEG group (p > 0.05). P-PEG was associated with more sedation for button replacement (97 vs. 2.6% [p < 0.05]). P-PEG was associated with more early tube dislodgement during the first replacement (7.2 vs. 1.4% [p = 0.092]). Two of the five dislodged gastrostomies in the P-PEG group underwent laparotomy due to peritonitis, whereas the only dislodged gastrostomy in the T-PEG group was solved endoscopically. Altogether, P-PEG was associated with more complications that required urgent endoscopy, laparotomy, or laparoscopy (18.6 vs. 6.6% [p < 0.05]). CONCLUSIONS: P-PEG was associated with more sedation, complications during first button replacement, and complications requiring urgent endoscopy, laparotomy, or laparoscopy compared with T-PEG.

Esophageal Atresia and Gastric Ectopic Pancreas: Is There a Real Association?

OBJECTIVE: Heterotopic pancreas (HP) is a condition in which there is well-differentiated pancreatic tissue that lacks any anatomic or vascular contact with the pancreatic gland. It normally arises from the stomach but can be found in other locations. Although it is usually asymptomatic, obstructive symptoms, bleeding, or malignant degeneration can occur. The incidence is very low, but it is significantly more common in patients with esophageal atresia (EA). The aim of this study is to evaluate the incidence of HP in patients with and without EA and to compare the results in both groups. MATERIAL AND METHODS: We conducted a 2-year prospective study in pediatric patients who benefited from an upper gastrointestinal endoscopy. Patients were divided into two groups: group "A" comprised patients with EA and group "B" those without EA. The variables analyzed were the clinical presentation, presence of HP, location, associated malformations, genetic disorders, and management. RESULTS: A total of 192 consecutive patients were included in the study: 51 (26.6%) in group A and 141 (73.4%) in group B. Indications for endoscopy in group B were eosinophilic esophagitis in 37 (19.2%) patients, celiac disease in 23 (11.95%) patients, and other disorders in 81 (42.2%) patients. Gastric HP was found in seven patients, all of them in group A. All lesions were hosted in the prepyloric antrum. The prevalence of HP in groups A and B was 13.7 and 0%, respectively (p < 0.05). Female gender was predominant in patients with AE and HP, this result being statistically significant (p = 0.044). No other associated malformation or genetic syndrome studied showed association with HP. Only one patient debuted with upper gastrointestinal (GI) bleeding and required excision, while six patients were asymptomatic. The mean follow-up was 54 months (range: 45-78 months). CONCLUSION: The incidence of gastric HP is more common in patients with EA, with the female gender being a risk factor for their association. Active search and follow-up is recommended as it may become symptomatic anytime and need resection.

Structural basis for the aminoacid composition of proteins from halophilic archea.

Proteins from halophilic organisms, which live in extreme saline conditions, have evolved to remain folded at very high ionic strengths. The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids, a low frequency of lysine, and a high occurrence of amino acids with a low hydrophobic character. Using extensive mutational studies on the protein surfaces, we show that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form. NMR studies demonstrate complete preservation of the three-dimensional structure of extreme mutants and confirm that salt dependency is conferred exclusively by surface residues. In spite of the statistically established fact that most halophilic proteins are strongly acidic, analysis of a very large number of mutants showed that the effect of salt on protein stability is largely independent of the total protein charge. Conversely, we quantitatively demonstrate that halophilicity is directly related to a decrease in the accessible surface area.

An NMR-Based Model to Investigate the Metabolic Phenoreversion of COVID-19 Patients throughout a Longitudinal Study.

After SARS-CoV-2 infection, the molecular phenoreversion of the immunological response and its associated metabolic dysregulation are required for a full recovery of the patient. This process is patient-dependent due to the manifold possibilities induced by virus severity, its phylogenic evolution and the vaccination status of the population. We have here investigated the natural history of COVID-19 disease at the molecular level, characterizing the metabolic and immunological phenoreversion over time in large cohorts of hospitalized severe patients (n = 886) and non-hospitalized recovered patients that self-reported having passed the disease (n = 513). Non-hospitalized recovered patients do not show any metabolic fingerprint associated with the disease or immune alterations. Acute patients are characterized by the metabolic and lipidomic dysregulation that accompanies the exacerbated immunological response, resulting in a slow recovery time with a maximum probability of around 62 days. As a manifestation of the heterogeneity in the metabolic phenoreversion, age and severity become factors that modulate their normalization time which, in turn, correlates with changes in the atherogenesis-associated chemokine MCP-1. Our results are consistent with a model where the slow metabolic normalization in acute patients results in enhanced atherosclerotic risk, in line with the recent observation of an elevated number of cardiovascular episodes found in post-COVID-19 cohorts.

Transesophageal echocardiography during pectus excavatum correction in children: What happens to the heart?

OBJECTIVES: Cardiac compression in pectus excavatum remains difficult to evaluate. We describe the findings with intraoperative transesophageal echocardiography during pectus excavatum correction in pediatric patients. METHODS: We studied right heart changes during surgical correction of pectus excavatum by transesophageal echocardiograph. Four-D echo was associated to assess morphology of the tricuspid annulus. RESULTS: Twenty patients were included, mean age 13.5 (+/- 2.9). Mean preoperative Haller Index was 6.3 (+/- 2.63) and mean Correction Index 47.63% (+/- 12.4%). Preoperative transthoracic echocardiography at rest showed mild right heart compression in 6. Correction was gained by Nuss technique in 19, and Taulinoplasty in one. Initial transesophageal echocardiography showed compression of the right heart and deformation of the tricuspid annulus in all. During the sternal elevation, diameters of right atrium, ventricle and tricuspid annulus significantly improved: mean augmentation of right ventricle was 5.78 mm (+/- 3.56 p < 0.05), right atrium 6.64 mm (+/- 5.55 p < 0.05) and tricuspid annulus 6.02 mm (+/- 3.29 p < 0.05). The morphology of the tricuspid annulus in 4D normalized. CONCLUSIONS: Preoperative transthoracic echocardiography at rest underestimates right chamber compression in pediatric patients with pectus excavatum. Surgical correction improves diameters of the right ventricle, right atrium and tricuspid annulus and normalizes the morphology of the tricuspid annulus (4D). LEVEL OF EVIDENCE: Level III.

Thoracoscopic Bullectomy for Persistent Air Leak in a 14-Year-Old Child with COVID-19 Bilateral Pulmonary Disease.

Introduction: Thoracic surgery in children with coronavirus disease-19 (COVID-19) pulmonary disease is rare, as very limited virus-related lung lesions require intervention. However, some patients may suffer from other pulmonary abnormalities that can be worsened by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and they may consequently require lung surgery. COVID-19 affects the indications, surgical procedure, and postsurgical care of these patients. Background: We present a case of a 14-year-old girl with COVID-19 pulmonary disease and persistent air leak due to right apical bullae that required resection. Clinical, surgical, and safety implications are discussed. The role of thoracic minimally invasive surgery under COVID-19 conditions is also analyzed. Materials and Methods: The thoracoscopic procedure was scheduled earlier than normally expected. The surgery was performed in a COVID-19 reserved theatre with neutral pressure and only the necessary personnel was allowed inside. The use of the required personal protective equipment was supervised by an expert nurse before and after the intervention. Results: The surgeons used a three-port technique to resect the bullae with an endostapler and no mechanical pleural abrasion was added to the procedure. Electrocautery and CO2 insufflation were avoided, and a chest drain with a closed-circuit aspiration system was installed before removing the ports. The child was discharged home 3 days later after the removal of the chest drain. Conclusions: COVID-19 has an impact on the standard indications, surgical strategies and postoperative care of some conditions requiring intervention. Extra safety measures are needed in the operating room to limit the chance of transmission. Minimally invasive surgery for thoracic surgery remains safe if the current safety guidelines are followed closely.

Outcomes after Split Abdominal Wall Muscle Flap Repair for Large Congenital Diaphragmatic Hernias.

INTRODUCTION: Repair of large congenital diaphragmatic hernias (CDHs) is challenging. As primary repair is not always feasible, patches are commonly used. An alternative treatment is split abdominal wall muscle flap repair, which uses vascularized autologous tissue. The aim of this study was to analyze the long-term outcome of large CDH defects undergoing split abdominal wall muscle repair. MATERIALS AND METHODS: This is a retrospective review (2003-2016) of large CDH treated by split abdominal wall muscle flap repair. RESULTS: In a total of 107 CDH patients, the abdominal muscle flap technique was used in 10 (9.3%); 7 had been prenatally treated with tracheal occlusion. Two patients experienced recurrence at 2 months and 6 years, respectively. Only one patient required abdominoplasty due to abdominal wall muscle weakness. Two patients developed progressive scoliosis; one of them required orthopaedic treatment. Minor chest wall deformities were detected in seven, but only one required orthopaedic treatment. The lung-to-head ratio was 0.79 in patients developing musculoskeletal deformities, and 1.5 in those without this complication (p < 0.05). Median follow-up was 11.2 years (3.5-14.2), and all patients were alive at the time of writing this article. CONCLUSION: The split abdominal wall muscle flap technique is a valid option for repair of large CDH. Associated musculoskeletal deformities seem to be influenced not only by the repair technique used but also by the degree of pulmonary hypoplasia and inherent pathophysiological changes.

SARS-CoV-2 Infection Dysregulates the Metabolomic and Lipidomic Profiles of Serum.

COVID-19 is a systemic infection that exerts significant impact on the metabolism. Yet, there is little information on how SARS-CoV-2 affects metabolism. Using NMR spectroscopy, we measured the metabolomic and lipidomic serum profile from 263 (training cohort) + 135 (validation cohort) symptomatic patients hospitalized after positive PCR testing for SARS-CoV-2 infection. We also established the profiles of 280 persons collected before the coronavirus pandemic started. Principal-component analysis discriminated both cohorts, highlighting the impact that the infection has on overall metabolism. The lipidomic analysis unraveled a pathogenic redistribution of the lipoprotein particle size and composition to increase the atherosclerotic risk. In turn, metabolomic analysis reveals abnormally high levels of ketone bodies (acetoacetic acid, 3-hydroxybutyric acid, and acetone) and 2-hydroxybutyric acid, a readout of hepatic glutathione synthesis and marker of oxidative stress. Our results are consistent with a model in which SARS-CoV-2 infection induces liver damage associated with dyslipidemia and oxidative stress.

Uroporphyrinogen III synthase mutations related to congenital erythropoietic porphyria identify a key helix for protein stability.

In the present study we have investigated deleterious mutants in the uroporphyrinogen III synthase (UROIIIS) that are related to the congenital erythropoietic porphyria (CEP). The 25 missense mutants found in CEP patients have been cloned, expressed, and purified. Their enzymatic activities have been measured relative to wild-type UROIIIS activity. All mutants retain measurable activity, consistent with the recessive character of the disease. Most of the mutants with a significant decrease in activity involve residues likely associated in binding. However, other mutants are fully active, indicating that different mechanisms may contribute to enzyme missfunction. UROIIIS is a thermolabile enzyme undergoing irreversible denaturation. The unfolding kinetics of wild-type UROIIIS and the suite of mutants have been monitored by circular dichroism. This analysis allowed the identification of a helical region in the molecule, essential to retain the kinetic stability of the folded conformation. C73R is found in one-third of CEP patients, and Cys73 is part of this helix. The integrated analysis of the enzymatic activity and kinetic stability data is used to gain insight in the relationship between defects in UROIIIS sequence and CEP.

Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy.

Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.

Use of recombinant antigens for the diagnosis of invasive candidiasis.

Invasive candidiasis is a frequent and often fatal complication in immunocompromised and critically ill patients. Unfortunately, the diagnosis of invasive candidiasis remains difficult due to the lack of specific clinical symptoms and a definitive diagnostic method. The detection of antibodies against different Candida antigens may help in the diagnosis. However, the methods traditionally used for the detection of antibodies have been based on crude antigenic fungal extracts, which usually show low-reproducibility and cross-reactivity problems. The development of molecular biology techniques has allowed the production of recombinant antigens which may help to solve these problems. In this review we will discuss the usefulness of recombinant antigens in the diagnosis of invasive candidiasis.