Human genetic defects in SRP19 and SRPRA cause severe congenital neutropenia with distinctive proteome changes.

The mechanisms of coordinated changes in proteome composition and their relevance for the differentiation of neutrophil granulocytes are not well studied. Here, we discover 2 novel human genetic defects in signal recognition particle receptor alpha (SRPRA) and SRP19, constituents of the mammalian cotranslational targeting machinery, and characterize their roles in neutrophil granulocyte differentiation. We systematically study the proteome of neutrophil granulocytes from patients with variants in the SRP genes, HAX1, and ELANE, and identify global as well as specific proteome aberrations. Using in vitro differentiation of human induced pluripotent stem cells and in vivo zebrafish models, we study the effects of SRP deficiency on neutrophil granulocyte development. In a heterologous cell-based inducible protein expression system, we validate the effects conferred by SRP dysfunction for selected proteins that we identified in our proteome screen. Thus, SRP-dependent protein processing, intracellular trafficking, and homeostasis are critically important for the differentiation of neutrophil granulocytes.

The Reaction NCN + H2: Quantum Chemical Calculations, Role of 1NCN Chemistry, and 3NCN Absorption Cross Section.

The NCN radical plays a key role for modeling prompt-NO formation in hydrocarbon flames. Recently, in a combined shock tube and flame modeling study, the so far neglected reaction NCN + H2 and the related chemistry of the main product HNCN turned out to be significant for NO modeling under fuel-rich conditions. In this study, the reaction has been thoroughly revisited by detailed quantum chemical rate constant calculations both for the singlet 1NCN and triplet 3NCN pathways. Optimized geometries and vibrational frequencies of reactants, products, and transition states were calculated on B3LYP/aug-cc-pVQZ level with single-point energy calculations carried out against the optimized structures using CASPT2/aug-cc-pVQZ. The determined rate constants for the 1NCN + H2 reaction as well as the newly measured high temperature absorption cross section of 3NCN made a reevaluation of the shock tube data of the previous work necessary, finally revealing quantitative agreement between experiment and theory. Moreover, the new directly measured Doppler-limited absorption cross section data, σ(3NCN, λ = 329.1302 nm) = 2.63 × 109 × exp(-1.96 × 10-3 × T/K) cm2/mol (±23%, p = 0 bar, T = 870-1700 K), are in agreement with previously reported values based on detailed spectroscopic simulations. Hence, a long-standing debate about a reliable high temperature 3NCN absorption cross section has been resolved. Whereas 3NCN + H2 resembles a simple abstraction type reaction with the exclusive products HNCN + H, the singlet radical reaction is initiated by the insertion into the H-H bond. Up to pressures of 100 bar, the main products of the subsequent decomposition of the H2NCN intermediate are HNCN + H as well, with minor contributions of CN + NH2 toward higher temperatures. Although much faster than the triplet reaction, the singlet radical insertion is actually rather slow, due to the necessary reorganization of the HOMO electron density in 1NCN that is equally distributed over the two N atom sites. In general, the distinct reactivity differences call for a separate treatment of 1NCN and 3NCN chemistry. However, as the main reaction products in case of the H2 reaction are the same and as the population of the 1NCN in thermal equilibrium remains low, a properly weighted effective rate constant k(NCN + H2 → HNCN + H) = 2.62 × 104 × (T/K)2.78 × exp(-97.6 kJ/mol/RT) cm3 mol-1s-1(±30%, 800 K < T < 3000 K, p < 100 bar) is recommended for inclusion into flame models that, as yet, do not explicitly account for 1NCN chemistry.

A novel machine learning algorithm to predict disease free survival after resection of hepatocellular carcinoma.

BACKGROUND: Due to organ shortage, liver transplantation (LT) in hepatocellular carcinoma (HCC) patients can only be offered subsidiary to other curative treatments, including liver resection (LR). We aimed at developing and validating a machine-learning algorithm (ML) to predict which patients are sufficiently treated by LR. METHODS: Twenty-six preoperatively available routine laboratory values along with standard clinical-pathological parameters [including the modified Glascow Prognostic Score (mGPS), the Kings Score (KS) and the Model of Endstage Liver Disease (MELD)] were retrieved from 181 patients who underwent partial LR due to HCC in non-cirrhosis or compensated cirrhosis from January 2007 through March 2018 at our institution. These data were processed using a Random Forest (RF)-based workflow, which included preprocessing, recursive feature elimination (RFE), resampling, training and cross-validation of the RF model. A subset of untouched patient data was used as a test cohort. Basing on the RF prediction, test data could be stratified according to high (HR) or low risk (LR) profile characteristics. RESULTS: RFE analysis provided 6 relevant outcome predictors: mGPS, aPTT, CRP, largest tumor size, number of lesions and age at time of operation. After down-sampling, the predictive value of our model was 0.788 (0.658-0.919) for early DFS. 16.7% of HR and 74.2% of LR patients survived 2 years of follow-up (P<0.001). CONCLUSIONS: Our RF model, based solely on clinical parameters, proved to be a powerful predictor of DFS. These results warrant a prospective study to improve the model for selection of suitable candidates for LR as alternative to transplantation. The predictive model is available online: tiny.cc/hcc_model.

Lavage lipidomics signatures in children with cystic fibrosis and protracted bacterial bronchitis.

BACKGROUND: Balanced composition of a well-functioning pulmonary surfactant is crucial and essential for normal breathing. Here, we explored whether the composition of lipids recovered by broncho-alveolar lavage (BAL) in children with cystic fibrosis (CF) differ from children with protracted bacterial bronchitis (PBB) and controls. We wanted to differentiate, if alterations are primarily caused by the disease process or secondary due to an increased amount of cell-membrane lipids derived from inflammatory cells. METHODS: Comprehensive lipidomics profiles of BAL fluid from children diagnosed with CF, PBB and controls were generated by electrospray ionization tandem mass spectrometry analysis. BAL cell differential and numbers were examined. RESULTS: 55 children (37 patients with CF, 8 children with PBB and 10 controls) were included in this study. Results showed comparable total quantities of lipids in all groups. Phospholipids were the major lipid fraction and similar in all groups, whereas the fractions of cholesteryl esters were less and of free cholesterol were increased in children with CF. Among the phospholipids, patients with CF had higher proportion of the non-surfactant membrane-lipids in the classes phosphatidylethanolamine based plasmalogens (PE P), phosphatidylethanolmine (PE) and phosphatidylserine (PS), but a lower proportion of phosphatidylcholine (PC) compared to healthy controls. No such changes were identified in the BAL fluid of children diagnosed with PBB. No differences were observed for the surfactant lipids dipalmitoyl-phosphatidylcholin (PC 32:0) and phosphatidylglycerol (PG). CONCLUSIONS: In CF patients with neutrophilic airway inflammation the lipid composition for surfactant phospholipid components were unchanged, whereas alteration in lipid profile were characteristic for those found in membranes of inflammatory cells. We suspect that the changes in CF were caused by the prolonged inflammation in contrast to a relatively short standing process in PBB.

Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition.

Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolated from fresh venous blood (purity >99%) and used to create a spectral library covering almost 8000 proteins using strong cation exchange fractionation. Patient neutrophil samples were then analyzed by data-independent acquisition proteomics, quantifying 4154 proteins in each sample. Neutrophils with mutations in the neutrophil elastase gene ELANE showed large proteome changes that suggest these mutations may affect maturation of neutrophil granulocytes and initiate misfolded protein response and cellular stress mechanisms. In contrast, only few proteins changed in patients with leukocyte adhesion deficiency (LAD) and chronic granulomatous disease (CGD). Strikingly, neutrophil transcriptome analysis showed no correlation with its proteome. In case of two patients with undetermined genetic causes, proteome analysis guided the targeted genetic diagnostics and uncovered the underlying genomic mutations. Data-independent acquisition proteomics may help to define novel pathomechanisms in neutrophil diseases and provide a clinically useful diagnostic dimension.

Poikiloderma with Neutropenia in Morocco: a Report of Four Cases.

PURPOSE: Poikiloderma with Neutropenia (PN) is inherited genodermatosis which results from a biallelic mutation in the USB1 gene (U Six Biogenesis 1). PN, first described in Navajo Native Americans, is characterized by early onset poikiloderma, pachyonychia, palmo-plantar hyperkeratosis, and permanent neutropenia. This condition results in frequent respiratory tract infections during infancy and childhood. From 2011 to 2013, four cases of PN were diagnosed in Morocco. In this paper, we report the first four cases of PN diagnosed in Morocco, out of three unrelated consanguinous families. METHODS: We investigated the genetic, immunological, and clinical features of four Moroccan patients with PN from three unrelated consanguinous families. RESULTS: Mean age at onset was 3 months and mean age at diagnosis was 7.5 years. The diagnosis of these PN patients was made based on clinical features and confirmed by molecular analysis for three cases. We identified two undescribed homozygous mutations in the USB1 gene: c.609 + 1G>A in two siblings and c.518 T>G(p.(Leu173Arg)) in the other case. CONCLUSION: This report confirms the clinical and genetic identity of Poikiloderma with Neutropenia syndrome.

Wnt4 and LAP2alpha as pacemakers of thymic epithelial senescence.

Age-associated thymic involution has considerable physiological impact by inhibiting de novo T-cell selection. This impaired T-cell production leads to weakened immune responses. Yet the molecular mechanisms of thymic stromal adipose involution are not clear. Age-related alterations also occur in the murine thymus providing an excellent model system. In the present work structural and molecular changes of the murine thymic stroma were investigated during aging. We show that thymic epithelial senescence correlates with significant destruction of epithelial network followed by adipose involution. We also show in purified thymic epithelial cells the age-related down-regulation of Wnt4 (and subsequently FoxN1), and the prominent increase in LAP2alpha expression. These senescence-related changes of gene expression are strikingly similar to those observed during mesenchymal to pre-adipocyte differentiation of fibroblast cells suggesting similar molecular background in epithelial cells. For molecular level proof-of-principle stable LAP2alpha and Wnt4-over-expressing thymic epithelial cell lines were established. LAP2alpha over-expression provoked a surge of PPARgamma expression, a transcription factor expressed in pre-adipocytes. In contrast, additional Wnt4 decreased the mRNA level of ADRP, a target gene of PPARgamma. Murine embryonic thymic lobes have also been transfected with LAP2alpha- or Wnt4-encoding lentiviral vectors. As expected LAP2alpha over-expression increased, while additional Wnt4 secretion suppressed PPARgamma expression. Based on these pioneer experiments we propose that decreased Wnt activity and increased LAP2alpha expression provide the molecular basis during thymic senescence. We suggest that these molecular changes trigger thymic epithelial senescence accompanied by adipose involution. This process may either occur directly where epithelium can trans-differentiate into pre-adipocytes; or indirectly where first epithelial to mesenchymal transition (EMT) occurs followed by subsequent pre-adipocyte differentiation. The latter version fits better with literature data and is supported by the observed histological and molecular level changes.

Molecular weight characteristics of humic substances from different environments as determined by size exclusion chromatography and their statistical evaluation.

Recorded molecular weights (MWs) for humic substances (HS) range from a few hundred to millions of daltons. For purposes of defining HS as a specific class of chemical compounds, it is of particular importance to ascertain if this broad range of MWs can be attributed to actual variability in molecular properties or is simply an artifact of the analytical techniques used to characterize HS. The main objectives of this study were (1)to establish if a preferential range of MWs exists for HS and (2) to determine any consistent MW properties of HS. To reach the goal, we have undertaken an approach to measure under standardized conditions the MW characteristics of a large set of HS from different natural environments. Seventy-seven humic materials were isolated from freshwater, soil, peat, and coal, such that each possessed a different fractional composition: humic acid (HA), fulvic acid (FA), and a nonfractionated mixture of HA and FA (HF). Size exclusion chromatography (SEC) was used as the analytical technique to determine molecular weight characteristics. The MW distributions were characterized by number (Mn) and weight (Mw) average MW, and by polydispersity. The complete range of Mw values varied within 4.7-30.4 kDa. The maximum Mw values were observed for peat HF and soil HA, whereas the smallest weights were measured for river water HF. Maximum values of polydispersity (3.5-4.4) were seen for peat HF and soil HA, while much lower values (1.6-3.1) were found for all preparations isolated with XAD-resins. Statistical evaluation showed consistent Mw and Mn variations with the HS source, while polydispersity was mostly a function of the isolation procedure used. A conclusion was made that HS have a preferential range of MW values that could characterize them as a specific class of chemical compounds.

Electron-beam treatment of aromatic hydrocarbons that can be air-stripped from contaminated groundwater. 2. Gas-phase studies.

The electron-beam (EB) degradation of volatile aromatics (benzene, toluene, ethylbenzene, xylenes: BTEX) in groundwater strip gas, which in the present work has been modeled by the introduction of the desired aromatic(s) to a stream of air or another gas, such as oxygen, is initiated essentially by the addition of *OH radicals to the aromatic ring, giving rise to hydroxycyclohexadienyl radicals, which form the corresponding peroxyl radicals upon addition of oxygen. As studied in some detail with benzene as a BTEX representative, various reactions of these lead to numerous oxidation products in a cascade of reactions, including the decomposition of products under the prevailing conditions of high turnover of the initial aromatic. Importantly, hydroxycyclohexadienylperoxyl radical formation is partly reversible, and the reactions of the hydroxycyclohexadienyl radicals, which thus have a significant presence in these systems, must therefore also be taken into consideration. In the gas phase, in contrast to the aqueous phase (see Part 1), the reactions of the hydroxycyclohexadienyl radicals lead to oligomeric products that appear to contribute, in addition to ionic clusters, to nucleation for the aerosols observed. Various nitrated products, among them nitrophenols, are observed when air is used for the stripping. However, these studies did not clear the pilot plant stage, since BTEX degradation using a bioreactor carried out in parallel was so successful that the EB technology was judged to be noncompetitive. As for the latter, expensive equipment consisting of a stripper, the EB machine, and an aerosol precipitator would be required. The condensed aerosols are biorefractory and would require further treatment for detoxification.