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Cystic fibrosis (CF) is caused by a mutation of the Cystic Fibrosis Transmembrane Conductance Regulator ( CFTR ) gene, which disrupts an ion channel involved in hydration maintenance via anion homeostasis. Nearly 5% of CF patients possess one or more copies of the G542X allele, which results in a stop codon at residue 542, preventing full-length CFTR protein synthesis. Identifying small-molecule modulators of mutant CFTR biosynthesis that affect the readthrough of this and other premature termination codons to synthesize a fully functional CFTR protein represents a novel target area of drug discovery. We describe the implementation and integration for large-scale screening of a homogeneous, 1536-well functional G542X-CFTR readthrough assay. The assay uses HEK 293 cells engineered to overexpress the G542X-CFTR mutant, whose functional activity is monitored with a membrane potential dye. Cells are co-incubated with a CFTR amplifier and CFTR corrector to maximize mRNA levels and trafficking of CFTR to the cell surface. Compounds that allow translational readthrough and synthesis of functional CFTR chloride channels are reflected by changes in membrane potential in response to cAMP stimulation with forskolin and CFTR channel potentiation with genistein. Assay statistics yielded Z' values of 0.69 ± 0.06. As further evidence of its suitability for high-throughput screening, we completed automated screening of approximately 666,000 compounds, identifying 7761 initial hits. Following secondary and tertiary assays, we identified 188 confirmed hit compounds with low and submicromolar potencies. Thus, this approach takes advantage of a phenotypic screen with high-throughput scalability to identify new small-molecule G542X-CFTR readthrough modulators.

Background: Cystic fibrosis (CF) is a recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We previously described a first-in-class CFTR modulator that functions as an amplifier to selectively increase CFTR expression and function. The amplifier mechanism is distinct from and complementary to corrector and potentiator classes of CFTR modulators. Here we characterize the mechanism by which amplifiers increase CFTR mRNA, protein, and activity., Methods: Biochemical studies elucidated the action of amplifiers on CFTR mRNA abundance and translation and defined the role of an amplifier-binding protein that was identified using chemical proteomics., Results: Amplifiers stabilize CFTR mRNA through a process that requires only the translated sequence of CFTR and involves translational elongation. Amplifiers enrich ER-associated CFTR mRNA and increase its translational efficiency through increasing the fraction of CFTR mRNA associated with polysomes. Pulldowns identified the poly(rC)-binding protein 1 (PCBP1) as directly binding to amplifier. A PCBP1 consensus element was identified within the CFTR open reading frame that binds PCBP1. This sequence proved necessary for amplifier responsiveness., Conclusions: Small molecule amplifiers co-translationally increase CFTR mRNA stability. They enhance translation through addressing the inherently inefficient membrane targeting of CFTR mRNA. Amplifiers bind directly to PCBP1, show enhanced affinity in the presence of bound RNA, and require a PCBP1 consensus element within CFTR mRNA to elicit translational effects. These modulators represent a promising new and mechanistically novel class of CFTR therapeutic. They may be useful as a monotherapy or in combination with other CFTR modulators., Competing Interests: Declaration of competing interest The authors are employees or scientific advisors of Proteostasis Therapeutics, Inc. and conducted this research as part of the company's drug discovery efforts., (Copyright © 2020. Published by Elsevier B.V.)

Cystic fibrosis (CF) is a lethal genetic disorder caused by mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Despite recent groundbreaking approval of genotype-specific small-molecule drugs, a significant portion of CF patients still lack effective therapeutic options that address the underlying cause of the disease. Through a phenotypic high-throughput screen of approximately 54,000 small molecules, we identified a novel class of CFTR modulators called amplifiers. The identified compound, the characteristics of which are represented here by PTI-CH, selectively increases the expression of immature CFTR protein across different CFTR mutations, including F508del-CFTR, by targeting the inefficiencies of early CFTR biosynthesis. PTI-CH also augments the activity of other CFTR modulators and was found to possess novel characteristics that distinguish it from CFTR potentiator and corrector moieties. The PTI-CH-mediated increase in F508del-CFTR did not elicit cytosolic or endoplasmic reticulum-associated cellular stress responses. Based on these data, amplifiers represent a promising new class of CFTR modulators for the treatment of CF that can be used synergistically with other CFTR modulators.

Compared to other aquaporins (AQPs), lens-specific AQP0 is a poor water channel, and its permeability was reported to be pH-dependent. To date, most water conduction studies on AQP0 were performed on protein expressed in Xenopus oocytes, and the results may therefore also reflect effects introduced by the oocytes themselves. Experiments with purified AQP0 reconstituted into liposomes are challenging because the water permeability of AQP0 is only slightly higher than that of pure lipid bilayers. By reconstituting high amounts of AQP0 and using high concentrations of cholesterol to reduce the permeability of the lipid bilayer, we improved the signal-to-noise ratio of water permeability measurements on AQP0 proteoliposomes. Our measurements show that mutation of two pore-lining tyrosine residues, Tyr-23 and Tyr-149 in sheep AQP0, to the corresponding residues in the high-permeability water channel AQP1 have additive effects and together increase the water permeability of AQP0 40-fold to a level comparable to that of AQP1. Molecular dynamics simulations qualitatively support these experimental findings and suggest that mutation of Tyr-23 changes the pore profile at the gate formed by residue Arg-187., (Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

We show here that the Saccharomyces cerevisiae GARP complex and the Cog1-4 subcomplex of the COG complex, both members of the complexes associated with tethering containing helical rods (CATCHR) family of multisubunit tethering complexes, share the same subunit organization. We also show that HOPS, a tethering complex acting in the endolysosomal pathway, shares a similar architecture, thus suggesting that multisubunit tethering complexes use related structural frameworks.

Introduction: The clinical course for patients with chronic lymphocytic leukaemia (CLL) is extremely heterogeneous; one of the most important challenges in the clinical management of these patients is the decision on initiating their treatment, but there is no available prognostic system that will resolve this issue. Usually, criteria for active disease are used to initiate therapy. Recently, some authors have proposed prognostic models, scoring systems involving a set of clinical and biological risk factors and estimates of individual patient survivals. Here, we report our initial results from a study designed to evaluate the statistical association of the distinct clinical and biological parameters with the prognosis and time to initiating treatment for patients with CLL., Material and Methods: Our study incorporated 100 consecutive, treatment naive CLL patients. In each patient all traditional laboratory, clinical and biological prognostic factors were evaluated at their first visit to our Institution. We then combined the following independent characteristics: age, β-2 microglobulin, absolute lymphocyte count, sex, Rai stage, and number of involved lymph node groups, which are included in some of the already published CLL prognostics index, in association with the CD38 expression and mutational status of the immunoglobulin heavy chain gene variable region (IGVH). Further, we correlated those factors by multivariable analysis with time to first treatment. This multivariable model was used to develop a nomogram-a weighted tool to calculate 5- and 10-year survival probability and estimate median time to first treatment (TFT)., Results: According to the prognostic index, a classification tree was built that identified three subsets of patients whose scores were 1-3 (low risk - 32 pts - 32%), 4-7 (intermediate risk - 48 pts - 48%) and > 8 (high risk - 20 pts - 20%). Estimated median survival in the low risk subset of patients is 141 years, and 10.7 and 4.6 years respectively in the intermediate and high risk subsets of patients. Projected survival in respectively low, intermediate and high-risk groups are 100%, 100%, 25%, and 43%, 34%, 25% at 5 years and 10 years, respectively. Also, statistical analyses showed that among other things CD38 expression and unmutated IGHV mutation status are associated with a shorter time to first treatment., Conclusion: Our prognostic model that combines and correlates the distinct clinical and biological markers of CLL patients enables identification of patients who are at high risk of progression. This prognostic model may facilitate the clinical decision for initiating treatment.

In this paper we present our results from a study designed in order to establish and standardize a diagnostic algorithm for acute myeloid leukaemia (AML) in the Republic of Macedonia. A total of 146 consecutive adult patients (>15 years) were enrolled in the study. First, we determined the correct lineage assignment of the blast cells and evaluated the incidence of the favourable PML/RARα, AML1/ETO, CBFβ/MYH11 genetic markers among the AML cases. Additionally, the obtained results were correlated with patients' age, comorbidities, and performance status, and each single AML patient was stratified to effective treatment strategy. Our results showed that morphology and cytochemistry established a lineage in 132 (89.1%) of the patients, but not in 16 cases that presented as acute leukaemia, of which 7 were assigned as myeloid, and in two a non-haematopoietic malignancy was indicated with immunophenotyping. Mulitparameter flow cytometry immunophenotyping also changed the assigned lineage based on morphology and cytochemistry in 5 (3.3%) of the patients from lymphoid to myeloid and improved diagnosis in 21 (14.1%) cases. By using a reverse transcriptase-polymerase chain reaction (RT-PCR) essay 28 (23.1%) patients were classified in the prognostically favourable AML genetic group; 8 patients expressed the fusion transcript PML/RARα AML1/ETO and 15 CBFβ/MYH11. Moreover, analyses of the age, performance status and comorbidities further strtified an additional 12.5% of the patients to a different risk-adapted therapy. The applied minimal screening-analysis-based diagnostic algorithm enabled improved and more precise diagnosis and clinical stratification in 37.2 % of AML patients from our study group.

Background: Proximal tubules of the kidney have a dominant function in the excretion of different enzymes in the urine. These enzymes can be used as markers for secondary renal damage under the action of different diseases, medicines, and toxins. The aim of this study was to evaluate the values of alanine aminopeptidase (AAP), gamma-glutamyl transferase (gamma-GT), and beta2 microglobulin (beta2m) in urine of patients with untreated rheumatoid arthritis (RA) and to define the possible association between untreated rheumatoid arthritis and tubular function at the brush border region., Methods: We used a kinetic assay for AAP, standard methods by the International Federation for Clinical Chemistry (IFCC) for gamma-GT and Microparticle Enzyme Immunoassay (MEIA), (Abbott A(x)SYM System) for the determination of beta2m in urine of 70 participants (35 untreated RA patients and 35 healthy volunteers (HC))., Results: From the total of 35 RA patients, AAP enzymuria was found in 24 patients with test sensitivity (68.57%), gamma-GT in 16 patients with test sensitivity (45.71%), while the presence of urinary beta2m was found in a very low percentage of cases. Out of 18 rheumatoid factor (RF) negative patients, 14 patients were AAP and 10 patients were gamma-GT positive, while the presence of beta2m in urine was not detected. Among 17 RF positive RA patients, the presence of AAP and gamma-GT was noticed in 10 and 6 patients, respectively, while the presence of beta2m in urine was not detected., Conclusions: In conclusion, AAP had a higher sensitivity than gamma-GT and beta2m in detection of asymptomatic renal lesions in untreated RA.

Affinity Grids are electron microscopy (EM) grids with a pre-deposited lipid monolayer containing functionalized nickel-nitrilotriacetic acid lipids. Affinity Grids can be used to prepare His-tagged proteins for single-particle EM from impure solutions or even directly from cell extracts. Here, we introduce the concept of His-tagged adaptor molecules, which eliminate the need for the target protein or complex to be His-tagged. The use of His-tagged protein A as adaptor molecule allows Affinity Grids to be used for the preparation of virtually any protein or complex provided that a specific antibody is available or can be raised against the target protein. The principle is that the Affinity Grid is coated with a specific antibody that is recruited to the grid by His-tagged protein A. The antibody-decorated Affinity Grid can then be used to isolate the target protein directly from a cell extract. We first established this approach by preparing negatively stained specimens of both native ribosomal complexes and ribosomal complexes carrying different purification tags directly from HEK-293T cell extract. We then used the His-tagged protein A/antibody strategy to isolate RNA polymerase II, still bound to native DNA, from HEK-293T cell extract, allowing us to calculate a 25-A-resolution density map by single-particle cryo-EM., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

Lipid monolayers have traditionally been used in electron microscopy (EM) to form two-dimensional (2D) protein arrays for structural studies by electron crystallography. More recently, monolayers containing Nickel-nitrilotriacetic acid (Ni-NTA) lipids have been used to combine the purification and preparation of single-particle EM specimens of His-tagged proteins into a single, convenient step. This monolayer purification technique was further simplified by introducing the Affinity Grid, an EM grid that features a predeposited Ni-NTA lipid-containing monolayer. In this contribution, we provide a detailed description for the use of monolayer purification and Affinity Grids, discuss their advantages and limitations, and present examples to illustrate specific applications of the methods., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Transferrin (Tf) is an iron carrier protein that consists of two lobes, the N- and C-lobes, which can each bind a Fe(3+) ion. Tf binds to its receptor (TfR), which mediates iron delivery to cells through an endocytotic pathway. Receptor binding facilitates iron release from the Tf C-lobe, but impedes iron release from the N-lobe. An atomic model of the Tf-TfR complex based on single particle electron microscopy (EM) indicated that receptor binding is indeed likely to hinder opening of the N-lobe, thus interfering with its iron release. The atomic model also suggested that the TfR stalks could form additional contacts with the Tf N-lobes, thus potentially further slowing down its iron release. Here, we show that the TfR stalks are unlikely to make strong interactions with the Tf N-lobes and that the stalks have no effect on iron release from the N-lobes of receptor-bound Tf.

We have recently developed monolayer purification as a rapid and convenient technique to produce specimens of His-tagged proteins or macromolecular complexes for single-particle electron microscopy (EM) without biochemical purification. Here, we introduce the Affinity Grid, a pre-fabricated EM grid featuring a dried lipid monolayer that contains Ni-NTA lipids (lipids functionalized with a nickel-nitrilotriacetic acid group). The Affinity Grid, which can be stored for several months under ambient conditions, further simplifies and extends the use of monolayer purification. After characterizing the Affinity Grid, we used it to isolate, within minutes, ribosomal complexes from Escherichia coli cell extracts containing His-tagged rpl3, the human homolog of the E. coli 50 S subunit rplC. Ribosomal complexes with or without associated mRNA could be prepared depending on the way the sample was applied to the Affinity Grid . Vitrified Affinity Grid specimens could be used to calculate three-dimensional reconstructions of the 50 S ribosomal subunit as well as the 70 S ribosome and 30 S ribosomal subunit from images of the same sample. We established that Affinity Grids are stable for some time in the presence of glycerol and detergents, which allowed us to isolate His-tagged aquaporin-9 (AQP9) from detergent-solubilized membrane fractions of Sf9 insect cells. The Affinity Grid can thus be used to prepare single-particle EM specimens of soluble complexes and membrane proteins.

Visualizing macromolecular complexes by single-particle electron microscopy (EM) entails stringent biochemical purification, specimen preparation, low-dose imaging, and 3D image reconstruction. Here, we introduce the "monolayer purification" method, which employs nickel-nitrilotriacetic acid (Ni-NTA) functionalized lipids for simultaneously purifying His-tagged complexes directly from cell lysates while producing specimens suitable for single-particle EM. The method was established by using monolayers containing Ni-NTA lipid to specifically adsorb His-tagged transferrin-transferrin receptor (Tf-TfR) complexes from insect and mammalian cell extracts. The specificity and sensitivity of the method could be improved by adding imidazole to the extracts. The monolayer-purified Tf-TfR samples could be vitrified and used to calculate a 3D reconstruction of the complex. Monolayer purification was then used to rapidly isolate ribosomal complexes from bacteria by overexpressing a single His-tagged ribosomal subunit. The resulting monolayer samples allowed calculation of a cryo-EM 3D reconstruction of the Escherichia coli 50S ribosomal subunit.