∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis.

Deletion of phenylalanine 508 of the cystic fibrosis transmembrane conductance regulator (∆F508 CFTR) is the major cause of cystic fibrosis, one of the most common inherited childhood diseases. The mutated CFTR anion channel is not fully glycosylated and shows minimal activity in bronchial epithelial cells of patients with cystic fibrosis. Low temperature or inhibition of histone deacetylases can partly rescue ∆F508 CFTR cellular processing defects and function. A favourable change of ∆F508 CFTR protein-protein interactions was proposed as a mechanism of rescue; however, CFTR interactome dynamics during temperature shift and inhibition of histone deacetylases are unknown. Here we report the first comprehensive analysis of the CFTR and ∆F508 CFTR interactome and its dynamics during temperature shift and inhibition of histone deacetylases. By using a novel deep proteomic analysis method, we identify 638 individual high-confidence CFTR interactors and discover a ∆F508 deletion-specific interactome, which is extensively remodelled upon rescue. Detailed analysis of the interactome remodelling identifies key novel interactors, whose loss promote ∆F508 CFTR channel function in primary cystic fibrosis epithelia or which are critical for CFTR biogenesis. Our results demonstrate that global remodelling of ∆F508 CFTR interactions is crucial for rescue, and provide comprehensive insight into the molecular disease mechanisms of cystic fibrosis caused by deletion of F508.

Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers.

Palmitoylation involves the reversible posttranslational addition of palmitate to cysteines and promotes membrane binding and subcellular localization. Recent advancements in the detection and identification of palmitoylated proteins have led to multiple palmitoylation proteomics studies but these datasets are contained within large supplemental tables, making downstream analysis and data mining time-consuming and difficult. Consequently, we curated the data from 15 palmitoylation proteomics studies into one compendium containing 1,838 genes encoding palmitoylated proteins; representing approximately 10% of the genome. Enrichment analysis revealed highly significant enrichments for Gene Ontology biological processes, pathway maps, and process networks related to the nervous system. Strikingly, 41% of synaptic genes encode a palmitoylated protein in the compendium. The top disease associations included cancers and diseases and disorders of the nervous system, with Schizophrenia, HD, and pancreatic ductal carcinoma among the top five, suggesting that aberrant palmitoylation may play a pivotal role in the balance of cell death and survival. This compendium provides a much-needed resource for cell biologists and the palmitoylation field, providing new perspectives for cancer and neurodegeneration.

Secretome of the biocontrol agent metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection.

Metarhizium anisopliae is an entomopathogenic fungus that has evolved specialized strategies to infect insect hosts. Here we analyzed secreted proteins related to Dysdercus peruvianus infection. Using shotgun proteomics, abundance changes in 71 proteins were identified after exposure to host cuticle. Among these proteins were classical fungal effectors secreted by pathogens to degrade physical barriers and alter host physiology. These include lipolytic enzymes, Pr1A, B, C, I, and J proteases, ROS-related proteins, oxidorreductases, and signaling proteins. Protein interaction networks were generated postulating interesting candidates for further studies, including Pr1C, based on possible functional interactions. On the basis of these results, we propose that M. anisopliae is degrading host components and actively secreting proteins to manage the physiology of the host. Interestingly, the secretion of these factors occurs in the absence of a host response. The findings presented here are an important step in understanding the host-pathogen interaction and developing more efficient biocontrol of D. peruvianus by M. anisopliae.

Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes.

Cryptococcus neoformans, a pathogenic yeast, causes meningoencephalitis, especially in immunocompromised patients, leading in some cases to death. Microbes in biofilms can cause persistent infections, which are harder to treat. Cryptococcal biofilms are becoming common due to the growing use of brain valves and other medical devices. Using shotgun proteomics we determine the differences in protein abundance between biofilm and planktonic cells. Applying bioinformatic tools, we also evaluated the metabolic pathways involved in biofilm maintenance and protein interactions. Our proteomic data suggest general changes in metabolism, protein turnover, and global stress responses. Biofilm cells show an increase in proteins related to oxidation-reduction, proteolysis, and response to stress and a reduction in proteins related to metabolic process, transport, and translation. An increase in pyruvate-utilizing enzymes was detected, suggesting a shift from the TCA cycle to fermentation-derived energy acquisition. Additionally, we assign putative roles to 33 proteins previously categorized as hypothetical. Many changes in metabolic enzymes were identified in studies of bacterial biofilm, potentially revealing a conserved strategy in biofilm lifestyle.

Characterization of a novel angiogenic model based on stable, fluorescently labelled endothelial cell lines amenable to scale-up for high content screening.

BACKGROUND: Blood vessel formation is important for many physiological and pathological processes and is therefore a critical target for drug development. Inhibiting angiogenesis to starve a tumour or promoting 'normalization' of tumour vasculature in order to facilitate delivery of anticancer drugs are both areas of active research. Recapitulation of vessel formation by human cells in vitro allows the investigation of cell-cell and cell-matrix interactions in a controlled environment and is therefore a crucial step in developing HCS (high content screening) and HTS (high throughput screening) assays to search for modulators of blood vessel formation. HUVECs (human umbilical-vein endothelial cells) exemplify primary cells used in angiogenesis assays. However, primary cells have significant limitations that include phenotypic decay and/or senescence by six to eight passages in culture, making stable integration of fluorescent markers and large-scale expansion for HTS problematic. To overcome these limitations for HTS, we developed a novel angiogenic model system that employs stable fluorescent endothelial cell lines based on immortalized HMECs (human microvascular endothelial cell). We then evaluated HMEC cultures, both alone and co-cultured with an EMC (epicardial mesothelial cell) line that contributes vascular smooth muscle cells, to determine the suitability for HTS or HCS. RESULTS: The endothelial and epicardial lines were engineered to express a panel of nuclear- and cytoplasm-localized fluorescent proteins to be mixed and matched to suit particular experimental goals. HMECs retained their angiogenic potential and stably expressed fluorescent proteins for at least 13 passages after transduction. Within 8 h after plating on Matrigel, the cells migrated and coalesced into networks of vessel-like structures. If co-cultured with EMCs, the branches formed cylindrical-shaped structures of HMECs surrounded by EMC derivatives reminiscent of vessels. Network formation measurements revealed responsiveness to media composition and control compounds. CONCLUSIONS: HMEC-based lines retain most of the angiogenic features of primary endothelial cells and yet possess long-term stability and ease of culture, making them intriguing candidates for large-scale primary HCS and HTS (of ~10000-1000000 molecules). Furthermore, inclusion of EMCs demonstrates the feasibility of using epicardial-derived cells, which normally contribute to smooth muscle, to model large vessel formation. In summary, the immortalized fluorescent HMEC and EMC lines and straightforward culture conditions will enable assay development for HCS of angiogenesis.

Safety and Feasibility of Transcatheter Aortic Valve Replacement in COVID-19 Patients: A Case Series.

In 2020, the coronavirus disease 2019 (COVID-19) pandemic has led to a decrease in interventional treatment for structural heart disease worldwide. In this context, the management of patients with symptomatic severe aortic stenosis (AS) or bioprosthetic valve dysfunction (BVD) represents a clinical challenge, as a delay in aortic valve replacement procedures may increase short-term morbidity and mortality. We report four cases of TAVR performed in patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. All of them were discharged in good clinical conditions and no adverse events were reported at 30 days follow-up. Our experience suggests that in selected patients with mild SARS-CoV-2 infection and symptomatic native AS or BVD, TAVR has a favorable short-term outcome.

Search algorithms as a framework for the optimization of drug combinations.

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms -- originally developed for digital communication -- modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs using only one-third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6-9 interventions in 80-90% of tests, compared with 15-30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.

Quantitative In Vivo Proteomics of Metformin Response in Liver Reveals AMPK-Dependent and -Independent Signaling Networks.

Metformin is the front-line treatment for type 2 diabetes worldwide. It acts via effects on glucose and lipid metabolism in metabolic tissues, leading to enhanced insulin sensitivity. Despite significant effort, the molecular basis for metformin response remains poorly understood, with a limited number of specific biochemical pathways studied to date. To broaden our understanding of hepatic metformin response, we combine phospho-protein enrichment in tissue from genetically engineered mice with a quantitative proteomics platform to enable the discovery and quantification of basophilic kinase substrates in vivo. We define proteins whose binding to 14-3-3 are acutely regulated by metformin treatment and/or loss of the serine/threonine kinase, LKB1. Inducible binding of 250 proteins following metformin treatment is observed, 44% of which proteins bind in a manner requiring LKB1. Beyond AMPK, metformin activates protein kinase D and MAPKAPK2 in an LKB1-independent manner, revealing additional kinases that may mediate aspects of metformin response. Deeper analysis uncovered substrates of AMPK in endocytosis and calcium homeostasis.

Transfemoral transcatheter aortic valve implantation for treatment of severe aortic regurgitation in a patient with previous aortic valve-sparing operation according to David.

The regurgitation of the native aortic valve in patient with previous David operation may represent a clinical challenge because the morbidity and mortality risk of re-operation is not negligible. Here we describe the case of a patient suffering from late severe aortic regurgitation, many years after David operation, efficaciously treated with transfemoral transcatheter aortic valve implantation. To the best of our knowledge, this is the first description of such treatment in a patient with aortic regurgitation and previous David operation.

Deep interactome profiling of membrane proteins by co-interacting protein identification technology.

Affinity purification coupled to mass spectrometry (AP-MS) is the method of choice for analyzing protein-protein interactions, but common protocols frequently recover only the most stable interactions and tend to result in low bait yield for membrane proteins. Here, we present a novel, deep interactome sequencing approach called CoPIT (co-interacting protein identification technology), which allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based workflow from sample preparation for mass spectrometric analysis to visualization of protein-protein interaction networks. The approach particularly improves the results for membrane protein interactomes, which have proven to be difficult to identify and analyze. CoPIT was used successfully to identify the interactome of the cystic fibrosis transmembrane conductance regulator (CFTR), demonstrating its validity and performance. The experimental step in this case achieved up to 100-fold-higher bait yield than previous methods by optimizing lysis, elution, sample clean-up and detection of interacting proteins by multidimensional protein identification technology (MudPIT). Here, we further provide evidence that CoPIT is applicable to other types of proteins as well, and that it can be successfully used as a general Co-IP method. The protocol describes all steps, ranging from considerations for experimental design, Co-IP, preparation of the sample for mass spectrometric analysis, and data analysis steps, to the final visualization of interaction networks. Although the experimental part can be performed in <3 d, data analysis may take up to a few weeks.

Registro Absorb Italiano (BVS-RAI): an investigators-owned and -directed, open, prospective registry of consecutive patients treated with the Absorb™ BVS: study design.

BACKGROUND: The Absorb™ BVS is a bioresorbable, everolimus-eluting scaffold approved and marketed for coronary use. Published data on long-term results after treatment are limited to a small number of patients, most of them with elective PCI of simple lesions. The importance of scaffold resorption is variably appreciated among cardiologists, and indications for use from health technology assessment bodies or guidelines are missing. Instruments are needed to collect, share and assess the experience being accumulated with this new device in several centres. METHODS/DESIGN: The BVS-RAI Registry is a spontaneous initiative of a group of Italian interventional cardiologists in cooperation with Centro di Ricerche Farmacologiche e Biomediche "Mario Negri" Institute, and is not recipient of funding or benefits originating from the BVS manufacturer. It is a prospective registry with 5-year follow-up of all consecutive patients who have undergone successful implantation of 1 or more coronary BVS following the indications, techniques and protocols used in each of the participating institutions. Outcome measures are BVS target lesion failure within one year and device-oriented major adverse cardiac events within 5years. The registry started in October 2012 and will extend enrolment throughout 2015, with the aim to include about 1000 patients. ClinicalTrials.gov identifier is CT02298413. CONCLUSIONS: The BVS-RAI Registry will contribute observational knowledge on the long-term safety and efficacy of the Absorb™ BVS as used in a number of Italian interventional centres in a broad spectrum of settings. Unrewarded and undirected consecutive patient enrolments are key-features of this observation, which is therefore likely to reflect common clinical practice in those centres.

Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes.

BACKGROUND: Developmental, physiological and tissue engineering studies critical to the development of successful myocardial regeneration therapies require new ways to effectively visualize and isolate large numbers of fluorescently labeled, functional cardiomyocytes. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe methods for the clonal expansion of engineered hESCs and make available a suite of lentiviral vectors for that combine Blasticidin, Neomycin and Puromycin resistance based drug selection of pure populations of stem cells and cardiomyocytes with ubiquitous or lineage-specific promoters that direct expression of fluorescent proteins to visualize and track cardiomyocytes and their progenitors. The phospho-glycerate kinase (PGK) promoter was used to ubiquitously direct expression of histone-2B fused eGFP and mCherry proteins to the nucleus to monitor DNA content and enable tracking of cell migration and lineage. Vectors with T/Brachyury and alpha-myosin heavy chain (alphaMHC) promoters targeted fluorescent or drug-resistance proteins to early mesoderm and cardiomyocytes. The drug selection protocol yielded 96% pure cardiomyocytes that could be cultured for over 4 months. Puromycin-selected cardiomyocytes exhibited a gene expression profile similar to that of adult human cardiomyocytes and generated force and action potentials consistent with normal fetal cardiomyocytes, documenting these parameters in hESC-derived cardiomyocytes and validating that the selected cells retained normal differentiation and function. CONCLUSION/SIGNIFICANCE: The protocols, vectors and gene expression data comprise tools to enhance cardiomyocyte production for large-scale applications.

Strut fracture: a further concern with drug-eluting stents.

A potential cause of drug-eluting stent restenosis is strut fracture. To date, few cases have been reported in the available literature and a best treatment method has not been established. We describe two cases of sirolimus-eluting stent fracture combined with focal restenosis and also review those previously reported.

Selective control of the apoptosis signaling network in heterogeneous cell populations.

BACKGROUND: Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is developed using cell death or apoptosis in heterogeneous cell populations as an example. Control of apoptosis is essential in a variety of therapeutic environments, including cancer where cancer cell death is a desired outcome and Alzheimer's disease where neuron survival is the desired outcome. However, in both cases these responses must occur with minimal response in other cells exposed to treatment; that is, the response must be selective. METHODOLOGY AND PRINCIPAL FINDINGS: Apoptosis signaling in heterogeneous cells is described by an ensemble of gene networks with identical topology but different link strengths. Selective control depends on the statistics of signaling in the ensemble of networks, and we analyze the effects of superposition, non-linearity and feedback on these statistics. Parallel pathways promote normal statistics while series pathways promote skew distributions, which in the most extreme cases become log-normal. We also show that feedback and non-linearity can produce bimodal signaling statistics, as can discreteness and non-linearity. Two methods for optimizing selective control are presented. The first is an exhaustive search method and the second is a linear programming based approach. Though control of a single gene in the signaling network yields little selectivity, control of a few genes typically yields higher levels of selectivity. The statistics of gene combinations susceptible to selective control in heterogeneous apoptosis networks is studied and is used to identify general control strategies. CONCLUSIONS AND SIGNIFICANCE: We have explored two methods for the study of selectivity in cell populations. The first is an exhaustive search method limited to three node perturbations. The second is an effective linear model, based on interpolation of single node sensitivity, in which the selective combinations can be found by linear programming optimization. We found that selectivity is promoted by acting on the least sensitive nodes in the case of weak populations, while selective control of robust populations is optimized through perturbations of more sensitive nodes. High throughput experiments with heterogeneous cell lines could be designed in an analogous manner, with the further possibility of incorporating the selectivity optimization process into a closed-loop control system.

High-risk percutaneous coronary intervention using the intracardiac microaxial pump 'Impella recover'.

Patients with multivessel coronary artery disease and severe left ventricular dysfunction are considered to be at high risk for percutaneous coronary intervention, and often are poor surgical candidates because of severe comorbidity. We report a case of high-risk percutaneous coronary intervention in a 67-year-old man with a severe left ventricular dysfunction and three-vessel coronary artery disease using a novel left ventricular assist device.

Abnormal total ejection isovolume index as early noninvasive marker of chronic rejection in heart transplantation.

Abnormally high myocardial performance index (MPI) is a Doppler-derived marker of combined systolic and diastolic left ventricular (LV) dysfunction. To identify early stage allograft dysfunction by MPI, we studied 154 long-term heart transplantation (HT) recipients (131 male, aged 51 +/- 13 years at HT, mean follow up 8.4 +/- 3.5 years), with normal left ventricular ejection fraction (LVEF) and free from acute rejection (AR), and 25 normals (13 male, aged 39 +/- 16 years). Rejection score (RS) on endomyocardial biopsy was calculated in the first year. MPI was prolonged (0.45 +/- 0.18 vs. 0.28 +/- 0.10, P = 0.0001) in patients and directly related with mean time from HT (P = 0.001), higher cumulative dosages of cyclosporine at 3 months (P = 0.01), 6 months (P = 0.03), 1 year (P = 0.02), 3 years (P = 0.04) and with cumulative dosage of methylprednisolone at 1 year (P = 0.002). The index was inversely related with mean age at HT (P = 0.002) and tended to be directly related with RS at 1 year (P = 0.05). Thus, MPI is abnormal in long-term HT recipients with normal LVEF. Its direct relation with time from HT as well as immunosuppressive load suggests an early stage of graft dysfunction because of chronic rejection. Extended prospective studies are warranted to clarify its potential role as a negative prognostic marker in HT.

C2 is superior to C0 as predictor of renal toxicity and rejection risk profile in stable heart transplant recipients.

To assess whether cyclosporine A (CsA) 2-h peak (C2) is superior to trough levels (C0) for Neoral dose monitoring in heart transplantation (HT), we studied 928 C0-C2 paired determinations from 313 stable HT patients (257 male, aged 50 +/- 14 years at HT, follow-up 6.9 +/- 4 years), on a C0-based regimen. Our target C0 levels (ng/ml) were 150-400 (first 3 months), 150-300 (4-12 months), 100-250 (>12 months). Mean C0 and C2 levels were 268 +/- 80 and 1031 +/- 386, respectively (first 3 months); 230 +/- 49 and 955 +/- 239 (4-12 months); 157 +/- 53 and 745 +/- 236 (>12 months). For patients within the target C0, the corresponding C2 were 600-1500 (first 3 months), 600-1300 (4-12 months), 400-1100 (>12 months). C2 correlated with C0 (r = 0.64, P = 0.0001). C2 correlated better with CsA dose than C0 (r = 0.41, P = 0.0001 vs. r = 0.33, P = 0.0001). Between patients, CsA dose varied by a factor of 9.3; the C/dose ratio varied by a factor of 8.5 for C2 and of 15.6 for C0. Patients with higher C2 (>740) had higher severe rejection score at 2 years (P = 0.02) than patients with lower C2. This did not apply to C0. Both C2 and C0 correlated with blood urea (r = -0.18, P = 0.0001; r = -0.12, P = 0.0002) and creatinine (r = -0.19, P = 0.0004; r = -0.19, P = 0.0001 respectively). By logistic regression higher C2 (>740) was associated with higher total severe rejection score at 2 years (P = 0.006). C2 showed better correlation with CsA dose, renal function, rejection profile and less variability between patients than C0. C2 may improve CsA-based immunosuppression in HT.