Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.

DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites

The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.

Glycated haemoglobin and the association with long-term survival among patients evaluated for stable angina – a prospective Norwegian cohort

Background and methods

Recent guidelines have included glycated haemoglobin (HbA1c) ≥48 mmol/L as a diagnostic criterion for diabetes mellitus (DM) in addition to plasma glucose (PG) concentrations, mainly based on the relationship between hyperglycemia and microvascular disease [1]. However, increased HbA1c may stem not only from hyperglycemia, and the risk association between HbA1c and long-term survival in patients with stable coronary heart disease and HbA1c ≥48 mmol/L but no previous DM according to PG is uncertain. We explored the relationship between HbA1c and survival among patients with and without DM who were evaluated for stable angina in the period 2000–2004. Endpoints were obtained from the Norwegian Cause of Death Registry.

Results

In total, 4164 patients were evaluated by cardiac cathetherization, of whom 576 patients (13.8%) had DM (median HbA1c 55 mmol/L) according to self-report and/or baseline PG concentrations. Of the remaining 3588 patients 1026 had HbA1c ≥48 mmol/L; however, HbA1c did not correlate with the HOMA2 insulin resistance index or fasting PG in these patients. During median (25–75 percentile) follow-up time of 14.0 (12.1–15.4) years a total of 1328 patients (31.9%) died, of whom 582 from cardiovascular causes. In patients with DM according to PG, HbA1c trended towards positive associations with all-cause and CVD mortality when adjusted for age and gender (HRs (95% CIs) 1.13 (0.99–1.28) and 1.16 (0.98–1.39) per 1SD, respectively). However, HbA1c was not associated with survival in either the group of patients without DM and HbA1c <48 mmol/L (median HbA1c 38 mmol/L) (HRs (95% CIs) 0.99 (0.92–1.06) and 0.96 (0.86–1.08) for all-cause and CVD mortality, respectively) or patients without DM but having HbA1c ≥48 mmol/L (median HbA1c 53 mmol/L) (HRs (95% CIs) 0.99 (0.88–1.12) and 1.04 (0.88–1.22)).

Conclusion

In patients evaluated for stable angina pectoris about two decades ago, almost a third of patients with no history of DM according to PG still had HbA1c concentrations indicating DM according to current guidelines. Including these patients in the DM category yielded similar percentages of patients with DM as observed in recent populations with stable coronary disease [2]. However, as opposed to what we observed in patients with DM, HbA1c did not show any association with very long-term survival among patients without DM. Our findings therefore question the use of HbA1c in the diagnosis of DM, especially in terms of risk assessment for longevity among patients with chronic coronary syndrome.

Funding Acknowledgement

Type of funding sources: None.

Inflammation and cardiorespiratory fitness in overweight women and men: the FATCOR study

Background

Women have more body fat compared to men, and adipose tissue is associated with chronic inflammation. Cardiorespiratory fitness has on the other hand been postulated to lower chronic inflammation. However, sex-specific associations of inflammation with cardiorespiratory fitness is less studied.

Purpose

To assess inflammatory markers in overweight and obese women and men according to cardiorespiratory fitness in the FAT associated CardiOvasculaR dysfunction (FATCOR) study.

Methods

Cardiorespiratory fitness was assessed by maximal oxygen uptake (VO2max) by cardiopulmonary exercise testing in 566 subjects (mean age was 48±9 years, 60% women) with body mass index (BMI) >27.0 kg/m2. Participants were grouped according to sex, and fitness status identified from sex and age specific VO2max thresholds. C-reactive protein (CRP) and serum amyloid A (SAA) were analysed using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry. Serum levels of the kynurenine:tryptophan ratio (KTR) and pyriodoxic acid ratio (PAr) were measured by liquid chromatography tandem mass spectrometry. All inflammatory markers were log transformed before inclusion in linear regression analyses.

Results

In the total study population, 63% had obesity and 74% were cardiorespiratory unfit. Unfit women had the highest fat percentage and the highest serum levels of CRP and SAA compared to the other groups (p<0.05), while serum levels of KTR and PAr were higher only compared to fit men (p<0.05). In multivariable linear regression analyses in women, higher CRP (β −0.15, p=0.001), SAA (β −0.10, p=0.03) and PAr (β −0.09, p=0.03) were associated with lower VO2max after adjusting for age, fat percentage, hypertension and metabolic syndrome. In men, only higher PAr (β −0.14, p=0.02) was associated with lower VO2max in multivariable analyses adjusted for age, fat percentage and metabolic syndrome. In multivariable analyses in obese women only (n=213), higher CRP (β −0.15, p=0.01) and PAr (β −0.13, p=0.03) remained associated with lower VO2max, while in obese men (n=144) there was no significant associations between inflammatory markers and VO2max.

Conclusion

Among overweight subjects participating in the FATCOR study, cardiorespiratory unfit women had the highest serum levels of inflammatory markers. The association of inflammation with reduced cardiorespiratory fitness was more pronounced in women than men, in particular when obesity was present.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Western Regional Health Authority of Norway

Onasemnogene abeparvovec-xioi: a gene replacement strategy for the treatment of infants diagnosed with spinal muscular atrophy

In May of 2019, the adeno-associated virus (AAV)-based gene therapy onasemnogene abeparvovec-xioi (Zolgensma) became the second Food and Drug Administration (FDA)-approved gene therapy with designated use for infants diagnosed with spinal muscular atrophy (SMA). The decision came nearly 10 years after results of the first preclinical models were initially reported. While the journey was an arduous one, the approval was an indication of the remarkable success of the first in-human clinical trials. According to the traditional classification system of autosomal recessive SMA, of which there are multiple types with phenotypic variability, SMA type 1 is the most common and most severe and represents 45% of the SMA patient population. Children with SMA type 1 cannot lift their heads without assistance and do not live past their second birthday. With Zolgensma, the first treated children with SMA type 1 have reached 5 years of age and some of them achieved the ability to sit unassisted or even walk. In this article, we review the work that led to FDA approval with emphasis on the development of preclinical and clinical studies.

Fitness is associated with lower inflammatory markers in obesity: the FATCOR study

Background

Obesity is associated with chronic low-grade inflammation, but exercise has anti-inflammatory properties. It is unknown whether the anti-inflammatory effects of fitness may influence the obesity-associated inflammation.

Purpose

To assess levels of inflammatory markers in fit vs. unfit overweight and obese subjects without known cardiovascular disease.

Methods

Peak oxygen uptake (VO2max) was measured by treadmill cardiopulmonary exercise testing in 566 subjects (mean age 48±9 years, 60% women) with body mass index >27.0 kg/m2 in the FAT associated CardiOvasculaR dysfunction (FATCOR) study. Fitness was defined from age- and sex adjusted reference levels of VO2max. Serum levels of C-reactive protein (CRP), serum amyloid A (SAA) and calprotectin were assessed by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry and log transformed before inclusion in analyses.

Results

Fit subjects (n=147) were older and had less metabolic syndrome, obesity and hypertension compared to unfit subjects (n=419) (all p<0.05). Serum levels of CRP and SAA were lower in fit subjects vs. unfit (p<0.01), while serum calprotectin showed no difference (p=0.06). In multivariable logistic regression analyses, lower CRP (odds ratio [OR] 0.73, 95% confidence interval [CI] 0.61–0.87, p<0.001) and SAA (OR 0.61, 95% CI 0.40–0.93, p=0.02) remained associated with being fit after adjusting for age, sex, obesity, metabolic syndrome and hypertension. When looking at obese (n=357, fit n=53) and overweight subjects (n=209, fit n=94) separately, lower CRP (OR 0.60, 95% CI 0.46–0.78, p<0.001) and SAA (OR 0.44, 95% CI 0.24–0.83, p=0.01) remained associated with being fit in obese, but not in overweight subjects after adjustment for age, sex and metabolic syndrome.

Conclusion

Fitness was associated with lower circulatory inflammatory markers in obesity independent of cardiometabolic risk factors. Our results suggest that fitness may promote cardiovascular benefit through the anti-inflammatory properties of exercise also in obesity.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): The Western Norway Regional Health Authority

In vitro activity of oritavancin alone or in combination against vancomycin-susceptible and -resistant enterococci

OBJECTIVES

The optimal treatment for serious infections due to Enterococcus spp. is unknown although combination antimicrobial therapy is often recommended for invasive infections to achieve bactericidal activity and improve clinical outcomes. Oritavancin is a novel lipoglycopeptide agent with in vitro activity against enterococci, including vancomycin-resistant VanA-type Enterococcus faecium. Data on its activity in combination with other antibacterials are limited. The objective of this study was to evaluate the activity of oritavancin alone and in combination with ceftriaxone, daptomycin, gentamicin, linezolid and rifampicin against vancomycin-susceptible and -resistant enterococci in in vitro time-kill analyses.

METHODS

Five enterococcal strains were used for all experiments: three vancomycin-resistant VanA-type E. faecium clinical bloodstream isolates, vancomycin-resistant VanA-type E. faecium ATCC 700221 and vancomycin-susceptible Enterococcus faecalis ATCC 29212. Individual drugs were tested at ¼, ½, 1, 2 and 4× MIC. Oritavancin combination experiments were performed with each agent at ¼× MIC.

RESULTS

Daptomycin was the most active single agent and was bactericidal against all strains at 4× MIC, followed by oritavancin, which was bactericidal against all three clinical VRE strains at ≥2× MIC. In combination experiments at ¼× MIC, oritavancin was synergistic with gentamicin against strains not displaying high-level aminoglycoside resistance. No other synergy against VRE strains was observed in any experiment. Strain- and drug-dependent antagonism was observed for many combinations.

CONCLUSIONS

These in vitro data do not support the routine use of combination therapy with oritavancin in the treatment of infections due to VRE.

Peptide-based Interaction Proteomics

Protein-protein interactions are often mediated by short linear motifs (SLiMs) that are located in intrinsically disordered regions (IDRs) of proteins. Interactions mediated by SLiMs are notoriously difficult to study, and many functionally relevant interactions likely remain to be uncovered. Recently, pull-downs with synthetic peptides in combination with quantitative mass spectrometry emerged as a powerful screening approach to study protein-protein interactions mediated by SLiMs. Specifically, arrays of synthetic peptides immobilized on cellulose membranes provide a scalable means to identify the interaction partners of many peptides in parallel. In this minireview we briefly highlight the relevance of SLiMs for protein-protein interactions, outline existing screening technologies, discuss unique advantages of peptide-based interaction screens and provide practical suggestions for setting up such peptide-based screens.

Determination of Fumonisins B1 and B2 in Corn and Corn Flakes by Liquid Chromatography with Immunoaffinity Column Cleanup: Collaborative Study

A liquid chromatographic (LC) method for the determination of fumonisins B1 (FB1) and B2 (FB2) in corn and corn flakes was collaboratively studied by 23 laboratories, which analyzed 5 blind duplicate pairs of each matrix to establish the accuracy, repeatability, and reproducibility characteristics of the method. Fumonisin levels in the corn ranged from <0.05 (blank) to 1.41 μg/g for FB1 and from <0.05 to 0.56 μg/g for FB2, whereas in the corn flakes they ranged from <0.05 to 1.05 μg/g for FB1 and from <0.05 to 0.46 μg/g for FB2. The method involved double extraction with acetonitrile–methanol–water (25 + 25 + 50), cleanup through an immunoaffinity column, and LC determination of the fumonisins after derivatization with o-phthaldialdehyde. Relative standard deviations for the within-laboratory repeatability (RSDr) of the corn analyses ranged from 19 to 24% for FB1 and from 19 to 27% for FB2; for the corn flakes analyses, RSDr ranged from 9 to 21% for FB1 and from 8 to 22% for FB2. Relative standard deviations for the between-laboratories reproducibility (RSDR) of the corn analyses ranged from 22 to 28% for FB1 and from 22 to 30% for the FB2; for corn flakes analyses, RSDR ranged from 27 to 32% for FB1 and from 26 to 35% for FB2. Mean recoveries of FB1 and FB2 from corn spiked with FB1 at 0.80 μg/g and with FB2 at 0.40 μg/g were 76 and 72%, respectively; for corn flakes spiked at the same levels recoveries were 110 and 97% for FB1 and FB2, respectively. HORRAT ratios for the analyses of corn ranged from 1.44 to 1.53 for FB1 and from 0.96 to 1.48 for FB2, whereas for corn flakes they ranged from 1.60 to 1.82 for FB1 and from 1.39 to 1.68 for FB2.

P6373Serum amyloid A and left ventricular mass in psoriasis patients treated with infliximab

Background

Serum amyloid A (SAA) is an acute phase reactant associated with amyloid tissue deposition. Chronic skin inflammation in psoriasis could cause increased production of SAA in the liver and subsequent deposition in cardiac tissue.

Purpose

To assess if higher SAA is associated with higher left ventricular (LV) mass in psoriasis patients treated with infliximab

Methods

Data from 47 psoriasis patients treated with the tumour necrosis factor-α blocker infliximab (mean age 47±14 years, 66% men) was compared to 106 age and sex-matched control subjects (mean age 47±11 years, 70% men). LV mass was assessed by echocardiography and index to height m2.7. SAA was analysed by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry.

Results

Psoriasis patients were more likely to be smokers than controls (38% vs. 16%, p=0.005), while other cardiovascular risk factors and SAA levels were similar. Psoriasis patients had lower LV mass index than controls (35.6±9.6 g/m2.7 vs. 40.3±9.8 g/m2.7, p=0.008). In the total study population, higher SAA level (β=0.23, p=0.003) was associated with higher LV mass index independent of presence of psoriasis (Table). In psoriasis patients, higher SAA level (β=0.48, p<0.001) was associated with higher LV mass index after adjustment for age and body mass index in multivariable analysis (Table). No association between SAA and LV mass index was found in controls.

Table 1. Multivariable associations of LV mass index in the total study population and in psoriasis patients Total study population Psoriasis LV mass index LV mass index R2=0.33, p<0.001 R2=0.43, p<0.001 β P β P Psoriasis −0.21 0.006 na na SAA, μg/ml 0.23 0.003 0.48 <0.001 BMI, kg/m2 0.39 <0.001 0.50 <0.001 Age, years 0.18 0.03 0.11 0.35 Female gender −0.11 0.15 – – Hypertension 0.08 0.35 – – Smoking 0.03 0.75 – – BMI, body mass index; LV, left ventricular; SAA, serum amyloid A; na, not applicable.

Conclusion

In psoriasis patients on infliximab treatment, higher SAA level was associated with greater LV mass index, pointing to a potential role of chronic inflammation and SAA production in the development of subclinical cardiac disease in psoriasis.

Acknowledgement/Funding

Western Regional Health Authority of Norway, Hjertefondet

Therapeutic approach to chronic venous insufficiency - clinical benefits of red-vine-leaf-extract AS 195 (Antistax®)

Background: Chronic Venous Disorders or Diseases (CVD) of the lower extremities are a common finding affecting almost 90 % of an adult population. CVD includes varicose veins with a prevalence of approx. 25 %, overlapping with Chronic Venous Insufficiency (CVI) with a prevalence of approx. 17% in the adult population. CVI is characterized by venous pathology and objective signs like edema, skin changes or venous leg ulcers. Objective: To review and evaluate non-clinical and clinical data on a standardised herbal product containing flavonoids (AS195; Antistax^®) and to put them into a perspective with the pathophysiology of CVD. Methods: Literature available on non-clinical pharmacology and clinical studies with AS195 in CVI of the lower extremities was reviewed and described. Conclusion: Antistax^® is a well-described herbal product with standardised starting materials and manufacturing process. Its active ingredients accumulate in the venous intima, preserve the endothelial barrier function, and inhibit the inflammatory and prothrombotic cascade behind the progression of CVD. Its efficacy was analysed in adequately planned and executed clinical trials in patients with mild to moderately severe CVD (CEAP C1s to C4). AS195 showed a statistically significant and clinically relevant efficacy over placebo: in objective endpoints like volumetry of lower leg edema, but also in outcomes directly relevant for patients like tension and heaviness of the legs, tingling, and pain. Supportive studies confirmed and validated these results also for the broader population treated in daily practice. AS195 was well tolerated in studies and in everyday therapy. There are no known interactions with other medications. In the later stages, it can be used in combination with compression, complementing the beneficial haemodynamic effects of compression at a cellular level. AS195 is an addition to compression and closes a therapeutic gap especially in patients, who cannot use compression stockings, but still require CVD therapy.

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.

Breastfeeding and vitamin D supplementation reduce the risk of Kawasaki disease in a German population-based case-control study

Background

In Kawasaki disease (KD), a vasculitis of unknown etiology, the most serious complication is the development of coronary artery aneurysm (CAA). To date, the exact pathomechanism of KD is unknown. Both environmental and genetic factors seem to be associated with the development of the disease.

Methods

Data on KD patients recruited from the population-based German Pediatric Surveillance Study during 2012–2014 were used to evaluate the impact of various factors from the perinatal and infancy period on the development of KD. The study design was a matched case-control study with respect to age, sex and place of residence (n = 308 KD cases, n = 326 controls). All KD patients were individually re-evaluated; all fulfilled the international diagnostic KD criteria. A standardized questionnaire was used to review breastfeeding practices, vitamin D supplementation and birth characteristics. Logistic regression analyses were performed to obtain odds ratios (OR) for various risk factors among the case-control pairs. Simple measures of association were used to assess the impact of these factors on the clinical course.

Results

There was no difference in lengths of gestation, birth weight or parturition between KD patients and controls, but independently from each other vitamin D supplementation and breastfeeding were negatively associated with KD, even when adjusted for age, place of residence and sex. The duration of vitamin D was significantly shorter among children with KD than among children without KD (p = 0.039, OR = 0.964, 95% CI: 0.931–0.998), as was the duration of breastfeeding (p = 0.013, OR = 0.471, 95% CI: 0.260–0.853). Comparing KD patients with and without breastfeeding and/or vitamin D supplementation, there were no differences regarding developing CAA, being refractory to intravenous immunoglobulin treatment, age at onset of the disease and levels of inflammatory laboratory values.

Conclusion

Our findings indicate breastfeeding and vitamin D supplementation to have protective effects in association with KD in our study population; however, these seem not to influence the natural course of the disease. Although the overall effects were relatively small, they nevertheless underline the overall benefit of both interventions.

Trial registration

Clinical Trial Registration: German clinical trial registration, http://apps.who.int/trialsearch/Trial2.aspx?TrialID=DRKS00010071. Date of registration was 26. February 2016. The trial was registered retrospectively.

Electronic supplementary material

The online version of this article (10.1186/s12887-019-1438-2) contains supplementary material, which is available to authorized users.

The Association between Objectively Measured Physical Activity and the Gut Microbiome among Older Community Dwelling Men

OBJECTIVES

To determine the relationship between objectively measured physical activity (PA) and the gut microbiome among community-dwelling older men.

DESIGN

Cross-sectional study.

SETTING

Osteoporotic Fractures in Men (MrOS) cohort participants at Visit 4 (2014-16).

PARTICIPANTS

Eligible men (n=373, mean age 84 y) included participants with 5-day activity assessment with at least 90% wear time and analyzed stool samples.

MEASUREMENTS

PA was measured with the SenseWear Pro3 Armband and stool samples analyzed for 16S v4 rRNA marker genes using Illumina MiSeq technology. Armband data together with sex, height, and weight were used to estimate total steps, total energy expenditure, and level of activity. 16S data was analyzed using standard UPARSE workflow. Shannon and Inverse Simpson indices were measures of (within-participant) α-diversity. Weighted and unweighted Unifrac were measures of (between-participant) β-diversity. We used linear regression analysis, principal coordinate analysis, zero-inflated Gaussian models to assess association between PA and α-diversity, β-diversity, and specific taxa, respectively, with adjustments for age, race, BMI, clinical center, library size, and number of chronic conditions.

RESULTS

PA was not associated with α-diversity. There was a slight association between PA and β-diversity (in particular the second principal coordinate). Compared to those who were less active, those who had higher step counts had higher relative abundance of Cetobacterium and lower relative abundance of taxa from the genera Coprobacillus, Adlercreutzia, Erysipelotrichaceae CC-115 after multivariable adjustment including age, BMI, and chronic conditions. There was no consistent pattern by phylum.

CONCLUSION

There was a modest association between levels of PA and specific gut microbes among community-dwelling older men. The observed associations are consistent with the hypothesis that underlying health status and composition of the host microbiome are related.