Characterization of functional protein complexes from Alzheimer's disease and healthy brain by mass spectrometry-based proteome analysis

Alzheimer's disease (AD) is a complex neurodegenerative disorder with impaired protein activities. Proteins in the form of complexes have a ubiquitous role in diverse range of cellular functions. The key challenge is to identify novel disease associated protein complexes and their potential role in the progression of AD pathology. Protein complexes were obtained from AD brain prefrontal cortex and age matched controls by Blue Native-Polyacrylamide Gel Electrophoresis. A proteomic analysis was performed using second dimension SDS-PAGE followed by nano LC-MS/MS. Differentially expressed proteins were mapped to existing biological networks by Ingenuity Pathway Analysis (IPA). A total of 13 protein complexes with their interacting proteins were resolved on SDS-PAGE. We identified 34 protein spots and found significant abundance difference between the two experimental samples. IPA analysis revealed degeneration of neurons and cell death as a major consequence of protein dysregulation. Furthermore, focused network analysis suggested an integrated regulation of the identified proteins through APP and MAPT dependent mechanisms. The interacting differentially expressed proteins in AD were found to be part of concomitant signaling cascades terminating in neuronal cell death. The identified protein networks and pathways warrant further research to study their actual contribution to AD pathology.

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development

Nephrogenesis is driven by complex signaling pathways that control cell growth and differentiation. The endoplasmic reticulum chaperone calreticulin (Calr) is well known for its function in calcium storage and in the folding of glycoproteins. Its role in kidney development is still not understood. We provide evidence for a pivotal role of Calr in nephrogenesis in this investigation. We show that Calr deficiency results in the disrupted formation of an intact nephrogenic zone and in retardation of nephrogenesis, as evidenced by the disturbance in the formation of comma-shaped and s-shaped bodies. Using proteomics and transcriptomics approaches, we demonstrated that in addition to an alteration in Wnt-signaling key proteins, embryonic kidneys from Calr-/- showed an overall impairment in expression of ribosomal proteins which reveals disturbances in protein synthesis and nephrogenesis. CRISPR/cas9 mediated knockout confirmed that Calr deficiency is associated with a deficiency of several ribosomal proteins and key proteins in ribosome biogenesis. Our data highlights a direct link between Calr expression and the ribosome biogenesis.

Final results from the EU focal impulse and rotor modulation (E-FIRM) registry

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Abbott

Background

The exact pathophysiology of how pulmonary vein (PV) triggers initiate or maintain episodes of atrial fibrillation (AF) has been elusive. Catheter ablation at relatively circumscribed areas of rapidly spinning rotors or very rapid focal impulse formation can significantly affect AF. Targeted ablation of these sources using Focal Impulse and Rotor Modulation (FIRM™) shows promise.

Purpose

To assess the safety and effectiveness of FIRM-guided procedures for the treatment of any type of symptomatic atrial fibrillation (AF).

Methods

Two hundred and ninety-nine subjects were enrolled in the E-FIRM Registry at 9 clinical sites in Germany and the Netherlands. Subjects were eligible if they had reported incidence of at least 2 documented episodes of symptomatic AF during the preceding 3 months and had failed at least Class I or III anti-arrhythmia drug. Data was collected at enrollment/baseline, procedure, and at 3-, 6-, and 12-month follow-up visits.

Results

A majority (59.5%, 178/299) had a history of previous ablation, 81.1% (133/164) in the left side, with an average of 1.5 ± 0.8 [range 0, 5] prior ablations. The primary safety endpoint was defined as freedom from procedure related Serious Adverse Events (SAEs) through 7-days and at 12-months. At 7-days, freedom from procedure related SAEs was 94.8% (257/271). At 12-months, freedom from procedure related SAEs was 84.4% (184/218). There were no deaths. Acute effectiveness success, defined as the elimination of all identified rotors, occurred in 64.0% (165/258) of treated patients. All patients for which data was reported had at least 1 rotor identified. The most common regions to find rotors were the lateral wall of the right atrium, the anterior/septal wall of the left atrium, and the posterior inferior region of the left atrium. 75.2% (194/258) of patients had at least one rotor identified in the right atrium, and 84.1% (217/258) of patients had at least one rotor identified in the left atrium. Success was defined as two sequential endpoints: single procedure freedom from AF recurrence at 3-months and single procedure freedom from AF recurrence. At 12-months, success was achieved in 46.4% (13/28) Paroxysmal, 42.9% (87/203) Persistent, and 0% (0/9) Long Standing AF subjects. Conclusions: Since acute success was reported as being achieved in only ∼2/3 of the treated subjects, it is possible that the full potential benefit of the FIRM-guided ablation was hidden in this evaluation of the full cohort. Considering the previous ablation and disease history of subjects, a single-procedure success rate at 12-months over 40% was considered a positive result. Based on these results, FIRM-guided RF ablation in conjunction with conventional RF ablation practices is both a safe and effective treatment strategy for patients with symptomatic AF.

Closed loop stimulation in heart failure patients with severe chronotropic incompetence: responder versus non-responders

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Biotronik SE & Co. KG Woermannkehre 1 12359 Berlin

Background

The prevalence of chronotropic incompetence (CI) in heart failure (HF) population is high and negatively impacts prognosis. Rate-adaptive pacing (RAP) is an important treatment option for CI. However, only a proportion of HF patients treated with cardiac resynchronisation therapy (CRT) devices benefit from accelerometer-based RAP in terms of exercise tolerance, functional capacity, and quality of life (QoL). Further research is needed to identify patient characteristics predicting positive response to RAP, and to evaluate performance of alternative sensors such as closed loop stimulation (CLS) driven by cardiac impedance measurements. An optimal outcome measure is represented by ventilatory efficiency (VE) slope during cardio-pulmonary exercise test (CPX) because of superior prognostic value.

Purpose

The purpose of the BIO|Create pilot study was to assess the benefit of CLS in CRT patients with CI. In this predefined subanalysis, we identify predictors of positive response to CLS (reduction of VE slope by ≥5%) and compare study outcomes in responders vs non-responders.

Methods

The study enrolled CRT patients with NYHA class II or III and severe CI (<75% of age-predicted maximum heart rate [HR] or <50% of HR reserve utilised at end-exercise). Patients were randomised to DDD-CLS mode or to DDD pacing at 40 beats/min for 1 month, followed by crossover for another month. At 1- and 2-month follow-ups, exercise tolerance was assessed by treadmill CPX, functional capacity by 6-min walk test, and QoL by the EQ-5D-5L and Minnesota Living with HF (MLHFQ) questionnaires.

Results

Among 17 patients with full follow-up datasets, 8 (47%) were responders to CLS. Compared to non-responders, responders had larger left ventricular (LV) ejection fraction at baseline (46 ± 3 vs 36 ± 9 %; p = 0.0070), smaller end-diastolic (121 ± 34 vs 181 ± 41 ml; p = 0.0085) and end-systolic (65 ± 23 vs 114 ± 39 ml; p = 0.0076) LV volumes, and were predominantly in NYHA class II (p = 0.0498). For study outcomes, the mean difference between DDD-CLS and DDD-40 modes in responders vs non-responders was - 6.1 (-16.4%) vs +2.7 (+6.8%) for VE slope (both p < 0.05), +0.5 vs -0.2 ml/min (O2 uptake efficiency slope), +1.3 vs -0.3 ml/kg/min (peak O2 uptake), +1.4 vs -0.75 mmHg (end-exercise end-tidal CO2), 16 vs 7 m (6-min walk distance), 0.08 vs 0.06 (EQ-5D-5L index), 1.9 vs 0 (EQ-5D-5L scale), and -2.5 vs +1.75 (MLHFQ).

Conclusions

For the first time, predictors for positive outcome of RAP in CRT patients have been identified. Patients with less advanced HF were responders to RAP driven by CLS principle. In addition, a consistent increase in exercise and functional capacity and QoL in these patients could be achieved. In contrast, patients with advanced HF experienced worse exercise capacity and QoL during RAP, suggesting caution if RAP is desirable due to CI. Further clinical research is needed to evaluate if positive response to RAP can improve hard clinical outcomes.

Caveolin3 Stabilizes McT1-Mediated Lactate/Proton Transport in Cardiomyocytes

[Figure: see text].

Creation of physiologic rhythm by closed loop stimulation in heart failure patients with severe chronotropic incompetence: worldwide first results of a pilot study

Background

The prevalence of chronotropic incompetence (CI) in heart failure (HF) population is high and negatively impacts prognosis. In HF patients with an implanted cardiac resynchronisation therapy (CRT) device and severe CI, the effect of rate adaptive pacing on patient outcomes is unclear. Closed loop stimulation (CLS) based on cardiac impedance measurement may be an optimal method of heart rate adaptation according to metabolic need in HF patients with severe CI.

Purpose

This is the first study evaluating the effect of CLS on the established prognostic parameters assessed by the cardio-pulmonary exercise (CPX) testing and on quality of life (QoL) of the patients.

Methods

A randomised, controlled, double-blind and crossover pilot study has been performed in CRT patients with severe CI defined as the inability to achieve 70% of the age-predicted maximum heart rate (APMHR). After baseline assessment, patients were randomised to either DDD-CLS pacing (group 1) or DDD pacing at 40 bpm (group 2) for a 1-month period, followed by crossover for another month. At baseline and at 1- and 2-month follow-ups, a CPX was performed and QoL was assessed using the EQ-5D-5L questionnaire. The main endpoints were the effect of CLS on ventilatory efficiency (VE) slope (evaluated by an independent CPX expert), the responder rate defined as an improvement (decrease) of the VE slope by at least 5%, percentage of maximal predicted heart rate reserve (HRR) achieved, and QoL.

Results

Of the 36 patients enrolled in the study, 20 fulfilled the criterion for severe CI and entered the study follow-up (mean age 68.9±7.4 years, 70% men, LVEF=41.8±9.3%, 40%/60% NYHA class II/III). Full baseline and follow-up datasets were obtained in 17 patients. The mean VE slope and HRR at baseline were 34.4±4.4 and 49.6±23.8%, respectively, in group 1 (n=7) and 34.5±12.2 and 54.2±16.1% in group 2 (n=10). After completing the 2-month CPX, the mean difference between DDD-CLS and DDD-40 modes was −2.4±8.3 (group 1) and −1.2±3.5 (group 2) for VE slope, and 17.1±15.5% (group 1) and 8.7±18.8% (group 2) for HRR. Altogether, VE slope improved by −1.8±2.95 (p=0.31) in DDD-CLS versus DDD-40, and HRR improved by 12.9±8.8% (p=0.01). The VE slope decreased by ≥5% in 47% of patients (“responders to CLS”). The mean difference in the QoL between DDD-CLS and DDD-40 was 0.16±0.25 in group 1 and −0.01±0.05 in group 2, resulting in an overall increase by 0.08±0.08 in the DDD-CLS mode (p=0.13).

Conclusion

First results of the evaluation of the effectiveness of CLS in CRT patients with severe CI revealed that CLS generated an overall positive effect on well-established surrogate parameters for prognosis. About one half of the patients showed CLS response in terms of improved VE slope. In addition, CLS improved quality of life. Further clinical research is needed to identify predictors that can increase the responder rate and to confirm improvement in clinical outcomes.

Funding Acknowledgement

Type of funding source: Private company. Main funding source(s): Biotronik SE & Co. KG

Combination of cryothermy with radiofrequency energy sources during hybrid atrial fibrillation ablation- impact on lesion quality and outcomes

Background

Whereas pulmonary vein isolation lays the groundwork of endocardial atrial fibrillation (AF) ablation, it leaves patients undertreated. Additional substrate modification of the left atrium is often required, but lesion gaps and non-transmurality limit restoration of sinus rhythm. Moreover, some low voltage areas and conduction abnormalities are located exclusively on the epicardial aspect, and endocardial ablation alone does not address these issues. Our hybrid endo-/epicardial ablation strategy overcomes all these shortcomings.

Purpose

To test if the combination of epicardial cryo and radiofrequency (RF) ablation (dual) further improves the quality of ablation lines, and if the combined endo-/epicardial ablation can treat intractable cases of AF.

Methods

Twenty-six patients (13 paroxysmal, 13 long-persistent; 20 patients with 1–5 prior endocardial AF ablations) first underwent epicardial, total thoracoscopic beating heart ablation (TTA). Lesion sets included bilateral PVI, left atrial appendage closure, as well as superior (roof) and inferior (floor) interpulmonary vein lines. Roof and floor lines were alternatingly ablated by dual energy or RF only. Three months post TTA, endocardial mapping with optional gap closure completed this two-stage hybrid concept.

Results

Intraoperatively, 24 of 40 (60%) previous left or right endocardial PVIs were found incomplete. Apart from two post-TTA pacemaker insertions and one mini-thoracotomy for bleeding, respectively, no major morbidity was observed during follow up. The full protocol of the hybrid concept was applied in 24 patients. Forty-five of 47 (96%) epicardial PVIs were found gap-less during endocardial mapping, and the remaining 2 PVIs were readily re-ablated. In contrast, only 32 of 46 (70%) roof and floor lines were complete, and endocardial touch up was required in one of three patients. Of note, dual energy lines were more likely to be complete than RF only lines (17 of 22, 77%, vs. 15 of 24, 62%; p NS). Among 19 patients with continuous monitoring, only 4 (21%) had any AF burden including two patients within blanking period and before endocardial gap closure. The remaining 7 patients without continuous monitoring never experienced any symptoms related to recurrent AF, and serial Holter EKG were without pathology.

Conclusions

Hybrid ablation and dual energy provides a strong armamentarium for extra-pulmonary venous triggers of AF. Linear ablation lines were more likely to be gap-less and transmural, if dual energy sources were used. Dual energy TTA is highly efficient to restore sinus rhythm in patients with prior failed endocardial AF ablation. However, one of three patients will require endocardial gap closure to realize the full benefit of our two-stage hybrid concept. Further study will evaluate if dual energy lines outside the box can improve outcome in these challenging cases of intractable AF.

Funding Acknowledgement

Type of funding source: None

Identification of drivers of breast cancer invasion by secretome analysis: insight into CTGF signaling

An altered consistency of tumor microenvironment facilitates the progression of the tumor towards metastasis. Here we combine data from secretome and proteome analysis using mass spectrometry with microarray data from mesenchymal transformed breast cancer cells (MCF-7-EMT) to elucidate the drivers of epithelial-mesenchymal transition (EMT) and cell invasion. Suppression of connective tissue growth factor (CTGF) reduced invasion in 2D and 3D invasion assays and expression of transforming growth factor-beta-induced protein ig-h3 (TGFBI), Zinc finger E-box-binding homeobox 1 (ZEB1) and lysyl oxidase (LOX), while the adhesion of cell-extracellular matrix (ECM) in mesenchymal transformed breast cancer cells is increased. In contrast, an enhanced expression of CTGF leads to an increased 3D invasion, expression of fibronectin 1 (FN1), secreted protein acidic and cysteine rich (SPARC) and CD44 and a reduced cell ECM adhesion. Gonadotropin-releasing hormone (GnRH) agonist Triptorelin reduces CTGF expression in a Ras homolog family member A (RhoA)-dependent manner. Our results suggest that CTGF drives breast cancer cell invasion in vitro and therefore could be an attractive therapeutic target for drug development to prevent the spread of breast cancer.

14-3-3 binding creates a memory of kinase action by stabilizing the modified state of phospholamban

The cardiac membrane protein phospholamban (PLN) is targeted by protein kinase A (PKA) at Ser16and by Ca2+/calmodulin-dependent protein kinase II (CaMKII) at Thr17. β-Adrenergic stimulation and PKA-dependent phosphorylation of Ser16acutely stimulate the sarcoplasmic reticulum calcium pump (SERCA) by relieving its inhibition by PLN. CaMKII-dependent phosphorylation may lead to longer-lasting SERCA stimulation and may sustain maladaptive Ca2+handling. Here, we demonstrated that phosphorylation at either Ser16or Thr17converted PLN into a target for the phosphoadaptor protein 14-3-3 with different affinities. 14-3-3 proteins were localized within nanometers of PLN and endogenous 14-3-3 coimmunoprecipitated with pentameric PLN from cardiac membranes. Molecular dynamics simulations predicted different molecular contacts for peptides phosphorylated at Ser16or Thr17with the binding groove of 14-3-3, resulting in varied binding affinities. 14-3-3 binding protected either PLN phosphosite from dephosphorylation. β-Adrenergic stimulation of isolated adult cardiomyocytes resulted in the membrane recruitment of endogenous 14-3-3. The exogenous addition of 14-3-3 to β-adrenergic–stimulated cardiomyocytes led to prolonged SERCA activation, presumably because 14-3-3 protected PLN pentamers from dephosphorylation. Phosphorylation of Ser16was disrupted by the cardiomyopathy-associated ∆Arg14mutation, implying that phosphorylation of Thr17by CaMKII may become crucial for 14-3-3 recruitment to ∆Arg14PLN. Consistent with PLN acting as a dynamic hub in the control of Ca2+handling, our results identify 14-3-3 binding to PLN as a contractility-augmenting mechanism.

Intronic CRISPR Repair in a Preclinical Model of Noonan Syndrome-Associated Cardiomyopathy

BACKGROUND

Noonan syndrome (NS) is a multisystemic developmental disorder characterized by common, clinically variable symptoms, such as typical facial dysmorphisms, short stature, developmental delay, intellectual disability as well as cardiac hypertrophy. The underlying mechanism is a gain-of-function of the RAS-mitogen-activated protein kinase signaling pathway. However, our understanding of the pathophysiological alterations and mechanisms, especially of the associated cardiomyopathy, remains limited and effective therapeutic options are lacking.

METHODS

Here, we present a family with two siblings displaying an autosomal recessive form of NS with massive hypertrophic cardiomyopathy as clinically the most prevalent symptom caused by biallelic mutations within the leucine zipper-like transcription regulator 1 (LZTR1). We generated induced pluripotent stem cell-derived cardiomyocytes of the affected siblings and investigated the patient-specific cardiomyocytes on the molecular and functional level.

RESULTS

Patients' induced pluripotent stem cell-derived cardiomyocytes recapitulated the hypertrophic phenotype and uncovered a so-far-not-described causal link between LZTR1 dysfunction, RAS-mitogen-activated protein kinase signaling hyperactivity, hypertrophic gene response and cellular hypertrophy. Calcium channel blockade and MEK inhibition could prevent some of the disease characteristics, providing a molecular underpinning for the clinical use of these drugs in patients with NS, but might not be a sustainable therapeutic option. In a proof-of-concept approach, we explored a clinically translatable intronic CRISPR (clustered regularly interspaced short palindromic repeats) repair and demonstrated a rescue of the hypertrophic phenotype.

CONCLUSIONS

Our study revealed the human cardiac pathogenesis in patient-specific induced pluripotent stem cell-derived cardiomyocytes from NS patients carrying biallelic variants in LZTR1 and identified a unique disease-specific proteome signature. In addition, we identified the intronic CRISPR repair as a personalized and in our view clinically translatable therapeutic strategy to treat NS-associated hypertrophic cardiomyopathy.

Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo, enhances translation, and modulates splicing

Axonal degeneration is a key and early pathological feature in traumatic and neurodegenerative disorders of the CNS. Following a focal lesion to axons, extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, the accumulation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we study the effect of ULK1 inhibition in different models of lesion-induced axonal degeneration in vitro and in vivo. Overexpression of a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons attenuates axotomy-induced AAD in vitro. Both ULK1.DN and the ULK1 inhibitor SBI-0206965 protect against AAD after rat optic nerve crush in vivo. ULK1.DN additionally attenuates long-term axonal degeneration after rat spinal cord injury in vivo. Mechanistically, ULK1.DN decreases autophagy and leads to an mTOR-mediated increase in translational proteins. Consistently, treatment with SBI-0206965 results in enhanced mTOR activation. ULK1.DN additionally modulates the differential splicing of the degeneration-associated genes Kif1b and Ddit3. These findings uncover ULK1 as an important mediator of axonal degeneration in vitro and in vivo, and elucidate its function in splicing, defining it as a putative therapeutic target.

How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells

Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and forming biofilms, allowing it to adjust to a range of growth conditions. We have recently shown that living in biofilms facilitates its survival under Cu²⁺ and Ni²⁺ stress, with specific rearrangements of the biofilm architecture observed following exposition. In this study, quantitative analyses were performed by SWATH mass spectrometry to determine the respective proteomes of planktonic and biofilm cells after exposition to Cu²⁺ and Ni²⁺.Quantitative data for 1180 proteins were obtained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 of 1180 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred in Cu²⁺ and Ni²⁺ treated samples. In biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms. Deletion strains were generated to assess the potential role of selected target genes. Strongest effects were observed for ΔOE5245F and ΔOE2816F strains which exhibited increased and decreased biofilm mass after Ni²⁺ exposure, respectively. Moreover, EPS obviously plays a crucial role in H. salinarum metal ion resistance. Further efforts are required to elucidate the molecular basis and interplay of additional resistance mechanisms.

LEF1 supports metastatic brain colonization by regulating glutathione metabolism and increasing ROS resistance in breast cancer

More than half of all brain metastases show infiltrating rather than displacing growth at the macro-metastasis/organ parenchyma interface (MMPI), a finding associated with shorter survival. The lymphoid enhancer-binding factor-1 (LEF1) is an epithelial-mesenchymal transition (EMT) transcription factor that is commonly overexpressed in brain-colonizing cancer cells. Here, we overexpressed LEF1 in an in vivo breast cancer brain colonization model. It shortened survival, albeit without engaging EMT at the MMPI. By differential proteome analysis, we identified a novel function of LEF1 as a regulator of the glutathione (GSH) system, the principal cellular redox buffer. LEF1 overexpression also conferred resistance against therapeutic GSH depletion during brain colonization and improved management of intracellular ROS. We conclude that besides EMT, LEF1 facilitates metastasis by improving the antioxidative capacity of epithelial breast cancer cells, in particular during colonization of the brain parenchyma.

Broad range of missense error frequencies in cellular proteins

Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with missense amino acid substitutions. By analyzing incorporation of near- and non-cognate amino acids in a model protein EF-Tu, we show that most of missense errors are too rare to detect by conventional methods, such as DDA, and are estimated to be between <10⁻⁷–10^-5 by QRAS. We also observe error hotspots of up to 10⁻³ for some types of mismatches, including the G-U mismatch. The error frequency depends on the expression level of EF-Tu and, surprisingly, the amino acid position in the protein. QRAS is not restricted to any particular miscoding event, organism, strain or model protein and is a reliable tool to analyze very rare proteogenomic events.

Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum)

Mass spectrometry-based proteomics methods are finding increasing use in structural biology research. Beyond simple interaction networks, information about stable protein-protein complexes or spatially proximal proteins helps to elucidate the biological functions of proteins in a wider cellular context. To shed light on new developments in this field, the Göttingen Proteomics Forum organized a one-day symposium focused on complexome profiling and proximity labeling, two emerging technologies that are gaining significant attention in biomolecular research. The symposium was held in Göttingen, Germany on 23 May, 2019, as part of a series of regular symposia organized by the Göttingen Proteomics Forum.

The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label-Free Mass Spectrometry

In-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii has been performed under standard, low/high salt, and low/high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high-pH/reversed-phase fractionated samples indicates 61.1% proteome coverage (2509 proteins), which is close to the maximum recorded values in archaea. Identified proteins match to the predicted proteome in their physicochemical properties, with only a small bias against low-molecular-weight and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress are quantitatively compared to standard cultures by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 2244 proteins, or 54.7% of the predicted proteome, are quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2034 are significantly regulated under at least one stress condition. KEGG pathway enrichment analysis shows that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, and tryptophan) are affected by temperature stress. The most strongly downregulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, are found oppositely regulated to their immediate genetic neighbors from the same operon.

The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates

Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.

Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane

Vesicle-associated membrane protein-associated protein B (VAPB) is a tail-anchored protein that is present at several contact sites of the endoplasmic reticulum (ER). We now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM. In combination with stable isotope labeling with amino acids in cell culture (SILAC), we confirmed many well-known interaction partners at the level of the ER with a clear distinction between specific and nonspecific hits. Furthermore, we identified emerin, TMEM43, and ELYS as potential interaction partners of VAPB at the INM and the nuclear pore complex, respectively.

A trap mutant reveals the physiological client spectrum of TRC40

The transmembrane recognition complex (TRC) pathway targets tail-anchored (TA) proteins to the membrane of the endoplasmic reticulum (ER). While many TA proteins are known to be able to use this pathway, it is essential for the targeting of only a few. Here, we uncover a large number of TA proteins that engage with TRC40 when other targeting machineries are fully operational. We use a dominant-negative ATPase-impaired mutant of TRC40 in which aspartate 74 was replaced by a glutamate residue to trap TA proteins in the cytoplasm. Manipulation of the hydrophobic TA-binding groove in TRC40 (also known as ASNA1) reduces interaction with most, but not all, substrates suggesting that co-purification may also reflect interactions unrelated to precursor protein targeting. We confirm known TRC40 substrates and identify many additional TA proteins interacting with TRC40. By using the trap approach in combination with quantitative mass spectrometry, we show that Golgi-resident TA proteins such as the golgins golgin-84, CASP and giantin as well as the vesicle-associated membrane-protein-associated proteins VAPA and VAPB interact with TRC40. Thus, our results provide new avenues to assess the essential role of TRC40 in metazoan organisms.

This article has an associated First Person interview with the first author of the paper.

Summary: A strategy to decipher which tail-anchored proteins do (as opposed to can or must) use the TRC pathway in intact cells generates a comprehensive list of human TRC40 clients.

Loss of Protein Phosphatase 1 Regulatory Subunit PPP1R3A Promotes Atrial Fibrillation

BACKGROUND

Abnormal calcium (Ca²⁺) release from the sarcoplasmic reticulum (SR) contributes to the pathogenesis of atrial fibrillation (AF). Increased phosphorylation of 2 proteins essential for normal SR-Ca²⁺ cycling, the type-2 ryanodine receptor (RyR2) and phospholamban (PLN), enhances the susceptibility to AF, but the underlying mechanisms remain unclear. Protein phosphatase 1 (PP1) limits steady-state phosphorylation of both RyR2 and PLN. Proteomic analysis uncovered a novel PP1-regulatory subunit (PPP1R3A [PP1 regulatory subunit type 3A]) in the RyR2 macromolecular channel complex that has been previously shown to mediate PP1 targeting to PLN. We tested the hypothesis that reduced PPP1R3A levels contribute to AF pathogenesis by reducing PP1 binding to both RyR2 and PLN.

METHODS

Immunoprecipitation, mass spectrometry, and complexome profiling were performed from the atrial tissue of patients with AF and from cardiac lysates of wild-type and Pln-knockout mice. Ppp1r3a-knockout mice were generated by CRISPR-mediated deletion of exons 2 to 3. Ppp1r3a-knockout mice and wild-type littermates were subjected to in vivo programmed electrical stimulation to determine AF susceptibility. Isolated atrial cardiomyocytes were used for Stimulated Emission Depletion superresolution microscopy and confocal Ca²⁺ imaging.

RESULTS

Proteomics identified the PP1-regulatory subunit PPP1R3A as a novel RyR2-binding partner, and coimmunoprecipitation confirmed PPP1R3A binding to RyR2 and PLN. Complexome profiling and Stimulated Emission Depletion imaging revealed that PLN is present in the PPP1R3A-RyR2 interaction, suggesting the existence of a previously unknown SR nanodomain composed of both RyR2 and PLN/sarco/endoplasmic reticulum calcium ATPase-2a macromolecular complexes. This novel RyR2/PLN/sarco/endoplasmic reticulum calcium ATPase-2a complex was also identified in human atria. Genetic ablation of Ppp1r3a in mice impaired binding of PP1 to both RyR2 and PLN. Reduced PP1 targeting was associated with increased phosphorylation of RyR2 and PLN, aberrant SR-Ca²⁺ release in atrial cardiomyocytes, and enhanced susceptibility to pacing-induced AF. Finally, PPP1R3A was progressively downregulated in the atria of patients with paroxysmal and persistent (chronic) AF.

CONCLUSIONS

PPP1R3A is a novel PP1-regulatory subunit within the RyR2 channel complex. Reduced PPP1R3A levels impair PP1 targeting and increase phosphorylation of both RyR2 and PLN. PPP1R3A deficiency promotes abnormal SR-Ca²⁺ release and increases AF susceptibility in mice. Given that PPP1R3A is downregulated in patients with AF, this regulatory subunit may represent a new target for AF therapeutic strategies.

A MICOS-TIM22 Association Promotes Carrier Import into Human Mitochondria

Mitochondrial membrane proteins with internal targeting signals are inserted into the inner membrane by the carrier translocase (TIM22 complex). For this, precursors have to be initially directed from the TOM complex in the outer mitochondrial membrane across the intermembrane space toward the TIM22 complex. How these two translocation processes are topologically coordinated is still unresolved. Using proteomic approaches, we find that the human TIM22 complex associates with the mitochondrial contact site and cristae organizing system (MICOS) complex. This association does not appear to be conserved in yeast, whereby the yeast MICOS complex instead interacts with the presequence translocase. Using a yeast mic10Δ strain and a HEK293T MIC10 knockout cell line, we characterize the role of MICOS for protein import into the mitochondrial inner membrane and matrix. We find that a physiological cristae organization promotes efficient import via the presequence pathway in yeast, while in human mitochondria, the MICOS complex is dispensable for protein import along the presequence pathway. However, in human mitochondria, the MICOS complex is required for the efficient import of carrier proteins into the mitochondrial inner membrane. Our analyses suggest that in human mitochondria, positioning of the carrier translocase at the crista junction, and potentially in vicinity to the TOM complex, is required for efficient transport into the inner membrane.

Comparative proteomics reveals a diagnostic signature for pulmonary head-and-neck cancer metastasis

Patients with head‐and‐neck cancer can develop both lung metastasis and primary lung cancer during the course of their disease. Despite the clinical importance of discrimination, reliable diagnostic biomarkers are still lacking. Here, we have characterised a cohort of squamous cell lung (SQCLC) and head‐and‐neck (HNSCC) carcinomas by quantitative proteomics. In a training cohort, we quantified 4,957 proteins in 44 SQCLC and 30 HNSCC tumours. A total of 518 proteins were found to be differentially expressed between SQCLC and HNSCC, and some of these were identified as genetic dependencies in either of the two tumour types. Using supervised machine learning, we inferred a proteomic signature for the classification of squamous cell carcinomas as either SQCLC or HNSCC, with diagnostic accuracies of 90.5% and 86.8% in cross‐ and independent validations, respectively. Furthermore, application of this signature to a cohort of pulmonary squamous cell carcinomas of unknown origin leads to a significant prognostic separation. This study not only provides a diagnostic proteomic signature for classification of secondary lung tumours in HNSCC patients, but also represents a proteomic resource for HNSCC and SQCLC.

Proteome Profiling by Label-Free Mass Spectrometry Reveals Differentiated Response of Campylobacter jejuni 81-176 to Sublethal Concentrations of Bile Acids

Purpose

Bile acids are crucial components of the intestinal antimicrobial defense and represent a significant stress factor for enteric pathogens. Adaptation processes of Campylobacter jejuni to this hostile environment are analyzed in this study by a proteomic approach.

Experimental design

Proteome profiling by label‐free mass spectrometry (SWATH‐MS) has been used to characterize the adaptation of C. jejuni to sublethal concentrations of seven bile acids.

Results

The bile acids with the lowest inhibitory concentration (IC₅₀), deoxycholic and chenodeoxycholic acid, induce the most significant proteome changes. Overall a downregulation of all basic biosynthetic pathways and a general decrease in the transcription machinery are found. Concurrently, an induction of factors involved in detoxification of reactive oxygen species, protein folding, and bile acid exporting efflux pumps is detected. Exposure to deoxycholic and chenodeoxycholic acid results in an increased expression of components of the more energy‐efficient aerobic respiration pathway, while the anaerobic branches of the electron transport chain are down‐expressed.

Conclusions and clinical relevance

The results show that C. jejuni has a differentiated system of adaptation to bile acid stresses. The findings enhance the understanding of the pathogenesis of campylobacteriosis, especially for survival of C. jejuni in the human intestine, and may provide clues to future medical treatment.

Crohn's disease patient serum changes protein expression in a human mesenchymal stem cell model in a linear relationship to patients' disease stage and to bone mineral density

BACKGROUND

Crohn's disease (CD) is associated with a higher prevalence of osteoporosis, a complication that is recognized as a significant cause of morbidity. Its pathogenesis is controversial, but the activity of CD is one contributing factor.

METHODS

We stimulated SCP-1 cells (mesenchymal stem cell line) under osteogenic conditions with serum from adult patients with CD in the symptomatic phase (SP) and in remission (R) and with control sera. Concentrations of IL-6, IL-1 beta, and TNF alpha in the sera were measured. Patients were classified as normal or osteopenic/osteoporotic based on bone mineral density (BMD) T-score measurements. After 14 days in culture, protein expression and gene ontology (GO) annotation analysis was performed.

RESULTS

Cytokine concentrations (IL-6, IL-1 beta, TNF alpha) varied within sera groups. None of the cytokines were significantly increased in the symptomatic phase compared to remission. Protein analysis revealed 17 proteins regulated by the SP versus R phase sera of disease. A linear relationship between CDAI (Crohn's disease activity index) and normalized protein expression of APOA1 and 2, TTR, CDKAL1 and TUBB6 could be determined. Eleven proteins were found to be differentially regulated comparing osteoporosis-positive and osteoporosis-negative sera. Gene annotation and further analysis identified these genes as part of heme and erythrocyte metabolism, as well as involved in hypoxia and in endocytosis. A significant linear relationship between bone mineral density and normalized protein expression could be determined for proteins FABP3 and TTR.

CONCLUSION

Our explorative results confirm our hypothesis that factors in serum from patients with CD change the protein expression pattern of human immortalized osteoblast like cells. We suggest, that these short time changes indeed influence factors of bone metabolism.