Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals.

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope-labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study, we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first-order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.

Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size Exclusion Chromatography for Proteome-wide Cross-Linking Mass Spectrometry.

Ion-mobility spectrometry shows great promise to tackle analytically challenging research questions by adding another separation dimension to liquid chromatography-mass spectrometry. The understanding of how analyte properties influence ion mobility has increased through recent studies, but no clear rationale for the design of customized experimental settings has emerged. Here, we leverage machine learning to deepen our understanding of field asymmetric waveform ion-mobility spectrometry for the analysis of cross-linked peptides. Knowing that predominantly m/z and then the size and charge state of an analyte influence the separation, we found ideal compensation voltages correlating with the size exclusion chromatography fraction number. The effect of this relationship on the analytical depth can be substantial as exploiting it allowed us to almost double unique residue pair detections in a proteome-wide cross-linking experiment. Other applications involving liquid- and gas-phase separation may also benefit from considering such parameter dependencies.

Improved Peptide Backbone Fragmentation Is the Primary Advantage of MS-Cleavable Crosslinkers.

Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of mass spectrometry (MS)-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently, such studies have also been published with noncleavable crosslinkers, suggesting that MS-cleavability is not essential. We therefore examined in detail the advantages and disadvantages of using the commonly used MS-cleavable crosslinker, disuccinimidyl sulfoxide (DSSO). Indeed, DSSO gave rise to signature peptide fragments with a distinct mass difference (doublet) for nearly all identified crosslinked peptides. Surprisingly, we could show that it was not these peptide masses that proved the main advantage of MS cleavability of the crosslinker, but improved peptide backbone fragmentation which reduces the ambiguity of peptide identifications. This also holds true for another commonly used MS-cleavable crosslinker, DSBU. We show furthermore that the more intricate MS3-based data acquisition approaches lack sensitivity and specificity, causing them to be outperformed by the simpler and faster stepped higher-energy collisional dissociation (HCD) method. This understanding will guide future developments and applications of proteome-wide crosslinking mass spectrometry.

Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging.

The risks of heart diseases are significantly modulated by age and sex, but how these factors influence baseline cardiac gene expression remains incompletely understood. Here, we used RNA sequencing and mass spectrometry to compare gene expression in female and male young adult (4 mo) and early aging (20 mo) mouse hearts, identifying thousands of age- and sex-dependent gene expression signatures. Sexually dimorphic cardiac genes are broadly distributed, functioning in mitochondrial metabolism, translation, and other processes. In parallel, we found over 800 genes with differential aging response between male and female, including genes in cAMP and PKA signaling. Analysis of the sex-adjusted aging cardiac transcriptome revealed a widespread remodeling of exon usage patterns that is largely independent from differential gene expression, concomitant with upstream changes in RNA-binding protein and splice factor transcripts. To evaluate the impact of the splicing events on cardiac proteoform composition, we applied an RNA-guided proteomics computational pipeline to analyze the mass spectrometry data and detected hundreds of putative splice variant proteins that have the potential to rewire the cardiac proteome. Taken together, the results here suggest that cardiac aging is associated with 1) widespread sex-biased aging genes and 2) a rewiring of RNA splicing programs, including sex- and age-dependent changes in exon usages and splice patterns that have the potential to influence cardiac protein structure and function. These changes contribute to the emerging evidence for considerable sexual dimorphism in the cardiac aging process that should be considered in the search for disease mechanisms.NEW & NOTEWORTHY Han et al. used proteogenomics to compare male and female mouse hearts at 4 and 20 mo. Sex-biased cardiac genes function in mitochondrial metabolism, translation, autophagy, and other processes. Hundreds of cardiac genes show sex-by-age interactions, that is, sex-biased aging genes. Cardiac aging is accompanied with a remodeling of exon usage in functionally coordinated genes, concomitant with differential expression of RNA-binding proteins and splice factors. These features represent an underinvestigated aspect of cardiac aging that may be relevant to the search for disease mechanisms.

Annular plaques on the back.

Annular lichen planus is a rare clinical variant of the lichen planus presenting with round-oval, red to brown macules and plaques with no central atrophy and slightly raised, nonscaly borders. Histopathological features are indistinguishable from typical lichen planus. Given that the accurate diagnosis relies on both the clinical presentation and typical histological features, it is important to be aware of the clinical spectrum of lichen planus. Click https://wileyhealthlearning.com/#/online-courses/6be3b20c-e9c3-40e9-8f36-bfcda6718a73 for the corresponding questions to this CME article.

Patients with bullous pemphigoid and comorbid psoriasis present with less blisters and lower serum levels of anti-BP180 autoantibodies.

BACKGROUND: Although the association of bullous pemphigoid (BP) and psoriasis is well-established, the clinical and immunological features of patients with coexisting BP and psoriasis are yet to be investigated. OBJECTIVE: We aimed to estimate the prevalence of psoriasis amongst patients with BP and to elucidate the clinical and immunological characteristics of BP patients with comorbid psoriasis. METHODS: A retrospective cohort study including all consecutive patients diagnosed with BP throughout the years 2009-2019 in a tertiary referral centre. RESULTS: The study encompassed 273 patients with BP, of whom 11 (4.0%; 95% CI, 2.3-7.1%) had comorbid psoriasis. The onset of psoriasis preceded that of BP in 81.8% of patients by a median (range) latency of 26.5 (5.0-34.0) years. Compared to BP patients without psoriasis, those with BP and comorbid psoriasis were significantly younger at the onset of BP [71.8 (9.3) vs. 79.4 (9.8) years; P = 0.023], had a milder erosive phenotype [erosion/blister BPDAI mean (SD)score; 5 (4.1) vs. 22.3 (15.2); P = 0.025], lower levels of anti-BP180 NC16A serum autoantibodies [236.6 (266.3) vs. 556.2 (1323.6) U/mL; P = 0.008] and a higher prevalence of isolated linear C3 deposits (36.4% vs. 14.1%; P = 0.043) and a lower prevalence of linear immunoglobulin G deposits (36.4% vs. 68.7%; P = 0.025) along the dermal-epidermal junction by direct immunofluorescence microscopy. CONCLUSIONS: Patients with BP and comorbid psoriasis present at a younger age with milder erosive phenotype and lower levels of pathogenic autoantibodies.

The impact of lesional inflammatory cellular infiltrate on the phenotype of bullous pemphigoid.

BACKGROUND: The influence of cutaneous cellular infiltration on the phenotype of bullous pemphigoid (BP) remains to be established. OBJECTIVES: To evaluate the main histopathological characteristics of patients with BP and to assess the association between the composition of lesional inflammatory infiltrate and the various clinical, immunological and immunopathological aspects of the disease. METHODS: Retrospective study encompassing patients diagnosed with BP throughout the years 2009-2020 in a specialized tertiary referral centre. RESULTS: The study encompassed 136 patients with BP, of whom 27 (19.9%) demonstrated a cell-poor inflammatory infiltrate in lesional skin specimens. Overall, 78 (57.4%), 71 (52.2%) and 5 (3.7%) specimens were found to include eosinophil-predominant, lymphocyte-predominant and neutrophil-predominant inflammatory infiltrates, respectively. Relative to the remaining patients with BP, those with an eosinophil-predominant inflammatory infiltrate had higher (90.8% vs. 77.2%; P = 0.030) whilst those with a cell-poor inflammatory infiltrate lower (70.3% vs. 88.7%; P = 0.017) seropositivity of anti-BP180 NC16A IgG. The latter subgroup presented with higher prevalence of mucosal involvement (25.9% vs. 8.3%; P = 0.011) and a non-inflammatory clinical phenotype (50.0% vs. 17.1%; P = 0.041). Patients with lymphocyte-predominant inflammatory infiltrate manifested with higher severity BPDAI scores and a lower frequency of the non-inflammatory subtype (11.1% vs. 36.4%; P = 0.035), whilst those with a neutrophilic infiltrate presented with lower mean (SD) levels of anti-BP180 NC16A IgG [269.3 (227.6) vs. 722.7 (1499.6) U/mL; P = 0.003]. CONCLUSIONS: Eosinophil-predominance and high cellularity in the lesional inflammatory infiltrate of BP skin are associated with increased seropositivity of anti-BP180 NC16A IgG. Lymphocyte-predominant infiltrates predict a more severe phenotype, pointing towards a pathogenic role of autoreactive lymphocytes.

Expression of PD-1 and Tim-3 is increased in skin of patients with bullous pemphigoid and pemphigus vulgaris.

BACKGROUND: Bullous pemphigoid (BP) and pemphigus vulgaris (PV) are common autoimmune bullous dermatoses (AIBD) characterized by blisters and erosions. Treatment options are limited and often insufficient. Immune checkpoint receptors play critical roles in immune homoeostasis and self- tolerance. Targeting checkpoint receptors is highly efficient in treatment of various cancers, but often also associated with autoimmune side effects. OBJECTIVES: We therefore aimed to investigate the expression of immune checkpoint receptors in patients with BP and PV. METHODS: We analysed expression of the checkpoint receptors programmed cell death protein 1 (PD-1), T-cell immunoglobulin and mucin domain 3 (Tim-3) and lymphocyte activation gene 3 (Lag-3) in lesional skin of patients with BP and PV compared to healthy control skin as well as the expression patterns of PD-1 and Tim-3 on various infiltrating immune cells in skin sections of AIBD by immunohistochemistry and immunofluorescence. We also measured serum levels of soluble PD-1, Tim-3 and Lag-3 in AIBD patients by ELISA. RESULTS: We report on increased expression of PD-1 and Tim-3, but not Lag-3, in lesional skin of patients with BP and PV. Investigating the expression pattern of PD-1 and Tim-3 on different cutaneous immune cells, we observed significant upregulation of PD-1 predominantly on infiltrating CD8 T cells and upregulation of Tim-3 on CD8 T cells as well as macrophages. CONCLUSIONS: Our results suggest exploring immune checkpoint receptors as novel therapeutic targets using an agonistic approach in autoimmune bullous diseases.

Coexistence of bullous pemphigoid with neuropsychiatric comorbidities is associated with anti-BP230 seropositivity.

BACKGROUND: While clustering of bullous pemphigoid (BP) with neuropsychiatric diseases is well-established, the clinical and immunological profile of BP patients with this comorbidity remains to be decisively determined. OBJECTIVES: To evaluate the burden of neurological and psychiatric comorbidities among patients with BP and to elucidate the clinical, immunological and immunopathological features of patients with BP and comorbid neuropsychiatric conditions. METHODS: We performed a retrospective study encompassing patients diagnosed with BP throughout the years 2009-2020 in a specialized tertiary referral centre. Multivariate logistic regression model was used to identify predictors of neuropsychiatric conditions among patients with BP. RESULTS: The study included 273 patients with BP, of whom 123 (45.1%) presented with comorbid neuropsychiatric disease. Compared to the remaining patients with BP (n = 150), those with pre-existing neuropsychiatric diseases demonstrated older mean [standard deviation (SD)] age [81.7 (9.1) vs. 76.9 (10.1); P < 0.001], female preponderance (65.0% vs. 49.3%; P = 0.009), higher seropositivity rate of anti-BP230 (67.7% vs. 36.5%; P = 0.006) and higher levels of anti-BP180 NC16A IgG [651.3 (1279.6) vs. 370.4 (818.6) U/mL; P = 0.039]. In multivariate analysis, anti-BP230 seropositivity was independently associated with coexistence of BP with neuropsychiatric conditions [adjusted odds ratio (OR), 3.43; 95% CI, 1.24-9.52; P = 0.018]. In a sensitivity analysis confined to patients with neurological diseases (n = 103), older age [82.1 (8.4) vs. 77.2 (10.3); P < 0.001] and increased anti-BP230 seropositivity (68.0% vs. 39.7%; P = 0.018) were identified. CONCLUSIONS: The coexistence of BP with neuropsychiatric diseases is independently associated with the generation of anti-BP230 antibodies.

Cyclic Octamer of Hydroxyl-functionalized Cations with Net Charge Q=+8e Kinetically Stabilized by a 'Molecular Island' of Cooperative Hydrogen Bonds.

The front cover artwork is provided by the group of Ralf Ludwig at the University of Rostock. The image shows the calculated cyclic octamer of hydroxyl-functionalized cations, being prominent constituents of ionic liquids. Strong cooperative hydrogen bonds overcome like-charge repulsion and prevent the cluster from Coulomb explosion. Read the full text of the Article at 10.1002/cphc.202000681.

Dissecting intermolecular interactions in the condensed phase of ibuprofen and related compounds: the specific role and quantification of hydrogen bonding and dispersion forces.

Ibuprofen is a well-established non-steroidal anti-inflammatory drug, inhibiting the prostaglandin-endoperoxide synthase. One of the key features defining the ibuprofen structure is the doubly intermolecular O-HO[double bond, length as m-dash]C hydrogen bond in cyclic dimers as know from carboxylic acids and confirmed by X-ray analysis. Until now, there was neither information about the vaporization enthalpy of ibuprofen nor about how this thermal property is determined by the subtle balance between different types of intermolecular interaction. In this study we derive the vaporization enthalpy of ibuprofen from thermochemical experiments to be . We dissected the hydrogen bond energy, EHB = 45.0 kJ mol-1, exclusively from measured vaporization enthalpies of related aliphatic carboxylic acids, their homomorph methyl esters and alkyl acetates, respectively. This contribution from hydrogen bonding could be confirmed almost quantitatively from quantum chemical calculations of ibuprofen clusters, which also suggest dispersion interaction of similar order (Edisp = 47 kJ mol-1). Following the full analysis of the gas-vapor transition enthalpy, we studied the changing structural components from the solid to the liquid phase of ibuprofen by means of Attenuated Total Reflection Infrared (ATR-IR) spectroscopy. The cyclic dimers as observed in the X-ray patterns are essentially preserved in the liquid state just above the melting point. However, with increasing temperature the doubly hydrogen-bonded cyclic dimers are replaced by singly hydrogen-bonded linear dimers in the liquid ibuprofen. The transfer enthalpy from the temperature-dependent equilibria of both dimers as obtained from the IR intensity ratios of the vibrational bands quantifies for the first time the energy of the released, single hydrogen bond to be EHB = 21.0 kJ mol-1. Overall, we show that a combination of thermodynamics, infrared spectroscopy and quantum chemistry provides quantification and detailed understanding of structure and molecular interaction in ibuprofen and related compounds.

Updated S2K guidelines on the management of pemphigus vulgaris and foliaceus initiated by the european academy of dermatology and venereology (EADV).

BACKGROUND: Pemphigus encompasses a group of life-threatening autoimmune bullous diseases characterized by blisters and erosions of the mucous membranes and skin. Before the era of immunosuppressive treatment, pemphigus was almost always fatal. Due to its rarity, only few randomized controlled therapeutic trials are available. Recently, rituximab has been approved as first-line treatment for moderate and severe pemphigus vulgaris in Europe and the United States. OBJECTIVES: The Autoimmune blistering diseases Task Force of the European Academy of Dermatology and Venereology (EADV) has initiated a throughout update of the guideline for the management of patients with pemphigus. RESULTS: The guidelines for the management of pemphigus were updated, and the degree of consent among all task force members was included. The final version of the guideline was consented by the European Dermatology Forum (EDF) and several patient organizations.

When hydrogen bonding overcomes Coulomb repulsion: from kinetic to thermodynamic stability of cationic dimers.

Quantum chemical calculations have been employed to study the kinetic and thermodynamic stability of hydroxy-functionalized 1-(3-hydroxyalkyl)pyridinium cationic dimers. For [Py-(CH2)n-OH+]2 structures with n = 2-17 we have calculated the robust local minima with clear dissociation barriers preventing their "Coulomb explosion" into separated cations. For n = 15 hydrogen bonding and dispersion forces fully compensate for the repulsive Coulomb forces between the cations allowing for the quantification of the pure hydrogen bond in the order of 20 kJ mol-1. The increasing kinetic stability even turns to thermodynamic stability with further elongated hydroxyalkyl chains. Now, quantum-type short-range attraction wins over classical long-range electrostatic repulsion resulting in negative binding energies and providing the first thermodynamically stable cationic dimers. The electronic, structural and spectroscopic signatures of the cationic dimers could be correlated to NBO parameters, supporting the existence of anti-electrostatic hydrogen bonds (AEHB) as recently suggested by Weinhold. In principle, these pure cationic dimers should be detectable in gas-phase experiments at low temperatures without the need of mediating molecules or counteranions.

Simultaneous determination of deuteron quadrupole coupling constants and rotational correlation times: the model case of hydrogen bonded ionic liquids.

We show that deuteron quadrupole coupling constants (DQCCs), and reorientational correlation times of molecular bonds N-D that are involved in hydrogen bonding, can be determined from NMR T1 relaxation time experiments simultaneously. For this purpose, we used trialkylammonium-based protic ionic liquids (PILs) as model compounds. They exhibit high viscosities and wide liquid ranges that allow measurements far beyond the extreme narrowing region (ω0τc ≪ 1). The T1 minima already occur at temperatures significantly above room temperature. We obtain reasonable DQCCs for the liquid phase if anisotropic motion is considered. The DQCCs are very small due to attractive Coulomb interaction between the cation and anion, which is further enhanced by hydrogen bonding. The DQCCs strongly depend on the interaction strength of the anion but are independent of the alkyl chain length of the trialkyl ammonium cations pointing to the exclusive cation-anion interaction along the hydrogen bond.

[The skin and rheumatism]. / Haut und Rheuma.

The skin is commonly affected in chronic inflammatory disorders and may act as a visual marker for internal or systemic inflammation. Frequent inflammatory skin diseases, like psoriasis and atopic dermatitis (AD), are associated with rheumatic and inflammatory bowel diseases. Metabolic, mental and cardiovascular comorbidity are frequent consequences of chronic inflammation. Further intersections between skin and joints are connective tissue diseases (collagenoses) and can be observed in complex diseases, e.g. systemic lupus erythematosus. Clinically, these diseases range from predominant cutaneous to severe systemic implication of several organs. Localized scleroderma should be clinically distinguished from systemic sclerosis and treated sufficiently to avoid long-term damage and disability. Thus, interdisciplinary disease management is of crucial importance.

Low incidence of heparin-induced skin lesions in orthopedic surgery patients with low-molecular-weight heparins.

BACKGROUND: Heparins are widely prescribed for prevention and therapy of arterial and venous thromboembolic diseases. Heparin-induced skin lesions are the most frequent adverse effect of subcutaneous heparin treatment in non-surgical patients (7.5%-39.8%); no data exist on surgical patients. Commonly, they are due to a delayed-type hypersensitivity reaction (DTH), but may also be a manifestation of life-threatening heparin-induced thrombocytopenia (HIT). Lesions of both entities resemble initially. The risk of HIT is highest among heparin-anticoagulated orthopedic surgery patients. OBJECTIVE: To determine incidence and causes of heparin-induced skin lesions in major orthopedic surgery patients. METHODS: In a prospective cohort study, consecutive patients with subcutaneous low-molecular-weight heparin (LMWH) treatment were examined for cutaneous adverse effects. Further diagnostics (skin biopsy, clinical/laboratory assessment for thrombosis, bleeding, HIT, cross-allergies) were performed. RESULTS: Six of 316 enrolled patients (1.9%; 95% CI: 0.4%-3.4%) developed heparin-induced skin lesions. All were caused by a DTH reaction, and none was due to HIT or other rare heparin-associated skin diseases. Therapeutic use (dosage) of LMWH was identified as only risk factor (odds ratio: 3.1, 95% CI: 1.4-4.9; P = .00141). In addition to DTH, 5 thromboembolic, 4 major bleeding complications but no cases of HIT or cross-allergies were observed. CONCLUSIONS AND CLINICAL RELEVANCE: Orthopedic surgery patients have-unlike non-surgical patients-a low risk for heparin-induced skin lesions during LMWH treatment; all lesions were due to a DTH reaction. The risk for DTH differs considerably between individual patient cohorts. No association with HIT was observed. These data help to tailor anticoagulatory treatment individually and to increase patient safety.

Participative approach to elicit water quality monitoring needs from stakeholder groups - An application of integrated watershed management.

Water quality monitoring programs (WQMPs) must be based on monitoring objectives originating from the real knowledge needs of all stakeholders in a watershed and users of the resource. This paper proposes a participative approach to elicit knowledge needs and preferred modes of communication from citizens and representatives of organized stakeholders (ROS) on water quality and quantity issues. The participative approach includes six steps and is adaptable and transferable to different types of watersheds. These steps are: (1) perform a stakeholder analysis; (2) conduct an adaptable survey accompanied by a user-friendly public participation geographical information system (PPGIS); (3) hold workshops to meet with ROS to inform them of the results of the survey and PPGIS; discuss attainment of past monitoring objectives; exchange views on new knowledge needs and concerns on water quality and quantity; (4) meet with citizens to obtain the same type of input (as from ROS); (5) analyze the data and information collected to identify new knowledge needs and modes of communication and (6) identify, in collaboration with the individuals in charge of the WQMPs, the short-, medium- and long-term monitoring objectives and communication strategies to be pursued. The participative approach was tested on two distinct watersheds in the province of Quebec, Canada. It resulted in a series of optimization objectives of the existing WQMPs, new monitoring objectives and recommendations regarding communication strategies of the WQMPs' results. The results of this study show that the proposed methodology is appreciated by all parties and that the outcomes and monitoring objectives are acceptable. We also conclude that successful integrated watershed management is a question of scale, and that every aspect of integrated watershed management needs to be adapted to the surface watershed, the groundwater watershed (aquifers) and the human catchment area.