Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.

TP53 mutations are strong predictors of poor survival and refractoriness in chronic lymphocytic leukemia (CLL) and have direct implications for disease management. Clinical information on TP53 mutations is limited to lesions represented in >20% leukemic cells. Here, we tested the clinical impact and prediction of chemorefractoriness of very small TP53 mutated subclones.

Supramolecular photochemistry of drugs in biomolecular environments.

In this tutorial review we illustrate how the interaction of photoactive drugs/potential drugs with proteins or DNA in supramolecular complexes can determine the course of the reactions initiated by the drug absorbed photons, evidencing the mechanistic differences with respect to the solution conditions. We focus on photoprocesses, independent of oxygen, that lead to chemical modification of the biomolecules, with formation of new covalent bonds or cleavage of existing bonds. Representative systems are mainly selected from the literature of the last decade.

Accuracy of chest radiography in predicting pulmonary hypertension: a case-control study.

Objective: To assess the accuracy of chest radiography (CXR) in predicting pulmonary hypertension (PH).

Methods: We studied 108 consecutive patients with suspected PH who underwent right heart catheterization (RHC). All were PH treatment naives.

The structural comparison between membrane-associated human carbonic anhydrases provides insights into drug design of selective inhibitors.

Carbonic anhydrase isoform XIV (CA XIV) is the last member of the human (h) CA family discovered so far, being localized in brain, kidneys, colon, small intestine, urinary bladder, liver, and spinal cord. It has recently been described as a possible drug target for treatment of epilepsy, some retinopathies as well as some skin tumors. Human carbonic anhydrase (hCA) XIV is a membrane-associated protein consisting of an N-terminal extracellular domain, a putative transmembrane region, and a small cytoplasmic tail.

Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.

Diffuse large B cell lymphoma (DLBCL) is a biologically heterogeneous and clinically aggressive disease. Here, we explore the role of bromodomain and extra-terminal domain (BET) proteins in DLBCL, using integrative chemical genetics and functional epigenomics. We observe highly asymmetric loading of bromodomain 4 (BRD4) at enhancers, with approximately 33% of all BRD4 localizing to enhancers at 1.

Educating translational researchers in research informatics principles and methods: an evaluation of a model online course and plans for its dissemination.

Translational research generates and/or uses very large amounts of diverse data. Informatics principles and methods address datasets that are large and complex, whereas few translational researchers know these principles and methods and many cannot design, carry out, or analyze the results of these studies optimally. With few exceptions, informatics education has not been directed to researchers, especially established researchers.

Induced pluripotent stem cell modeling of multisystemic, hereditary transthyretin amyloidosis.

Familial transthyretin amyloidosis (ATTR) is an autosomal-dominant protein-folding disorder caused by over 100 distinct mutations in the transthyretin (TTR) gene. In ATTR, protein secreted from the liver aggregates and forms fibrils in target organs, chiefly the heart and peripheral nervous system, highlighting the need for a model capable of recapitulating the multisystem complexity of this clinically variable disease. Here, we describe the directed differentiation of ATTR patient-specific iPSCs into hepatocytes that produce mutant TTR, and the cardiomyocytes and neurons normally targeted in the disease.

Prognostic value of alveolar volume in systolic heart failure: a prospective observational study.

Background: Ventilatory impairment is known to occur in patients with heart failure (HF). Alveolar volume (VA) is measured by the dilution of an inert gas during a single breath-hold maneuver. Such measurement is sensitive to ventilatory disturbances.

Rare variants in the TREX1 gene and susceptibility to autoimmune diseases.

TREX1 (DNase III) is an exonuclease involved in response to oxidative stress and apoptosis. Heterozygous mutations in TREX1 were previously observed in patients with systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS). We performed a mutational analysis of the TREX1 gene on three autoimmune diseases: SLE (210 patients) and SS (58 patients), to confirm a TREX1 involvement in the Italian population, and systemic sclerosis (SSc, 150 patients) because it shares similarities with SLE (presence of antinuclear antibodies and connective tissue damage).

The multifaceted aspects of interstitial lung disease in rheumatoid arthritis.

Interstitial lung disease (ILD) is a relevant extra-articular manifestation of rheumatoid arthritis (RA) that may occur either in early stages or as a complication of long-standing disease. RA related ILD (RA-ILD) significantly influences the quoad vitam prognosis of these patients. Several histopathological patterns of RA-ILD have been described: usual interstitial pneumonia (UIP) is the most frequent one, followed by nonspecific interstitial pneumonia (NSIP); other patterns are less commonly observed.

Conformational analysis of Gly-Ala-NHMe in D(2)O and DMSO solutions: a two-dimensional infrared spectroscopy study.

A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy.

Thermal-stable carbonic anhydrases: a structural overview.

The potential of carbonic anhydrase (CA) family as target for the drug design of inhibitors with various medicinal chemistry applications has been recognized from long time, whereas the industrial interest in using these enzymes as biocatalysts for carbon dioxide sequestration and biofuel production is only recently emerging. However, an efficient utilization in these processes often requires stable enzymes, able to work in the harsh conditions typical of the CO2 capture process. In this context CAs active at very high temperatures are of extreme interest.

Structural basis for the rational design of new anti-Brucella agents: the crystal structure of the C366S mutant of L-histidinol dehydrogenase from Brucella suis.

L-Histidinol dehydrogenase from Brucella suis (BsHDH) is an enzyme involved in the histidine biosynthesis pathway which is absent in mammals, thus representing a very interesting target for the development of anti-Brucella agents. In this paper we report the crystallographic structure of a mutated form of BsHDH both in its unbound form and in complex with a nanomolar inhibitor. These studies provide the first structural background for the rational design of potent HDH inhibitors, thus offering new hints for clinical applications.

Hypoxia-targeting carbonic anhydrase IX inhibitors by a new series of nitroimidazole-sulfonamides/sulfamides/sulfamates.

A series of nitroimidazoles incorporating sulfonamide/sulfamide/sulfamate moieties were designed and synthesized as radio/chemosensitizing agent targeting the tumor-associated carbonic anhydrase (CA) isoforms IX and XII. Most of the new compounds were nanomolar inhibitors of these isoforms. Crystallographic studies on the complex of hCA II with the lead sulfamide derivative of this series clarified the binding mode of this type of inhibitors in the enzyme active site cavity.

Pathways of Toxicity.

Despite wide-spread consensus on the need to transform toxicology and risk assessment in order to keep pace with technological and computational changes that have revolutionized the life sciences, there remains much work to be done to achieve the vision of toxicology based on a mechanistic foundation. To this end, a workshop was organized to explore one key aspect of this transformation - the development of Pathways of Toxicity as a key tool for hazard identification based on systems biology. Several issues were discussed in depth in the workshop: The first was the challenge of formally defining the concept of a Pathway of Toxicity (PoT), as distinct from, but complementary to, other toxicological pathway concepts such as mode of action (MoA).

Absorption and Emission Spectra of a Flexible Dye in Solution: a Computational Time-Dependent Approach.

The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with a quantum mechanical description within the framework of the time-dependent density functional theory (TDDFT) approach. The atomistic simulations are based on an accurately parametrized force field, specifically designed to represent the conformational behavior of the molecule in its ground and bright excited states, whereas TDDFT calculations are performed through a selected combination of hybrid functionals and basis sets to obtain optical spectra closely matching the experimental findings. Solvent effects, crucial to obtain good accuracy, are taken into account through explicit molecules and polarizable continuum descriptions.

Clinical monoclonal B lymphocytosis versus Rai 0 chronic lymphocytic leukemia: A comparison of cellular, cytogenetic, molecular, and clinical features.

Purpose: To investigate the incidence and clinical relevance of classic and new prognostic markers, IGHV gene mutational status, and chromosomal abnormalities in clinical monoclonal B lymphocytosis (cMBL) compared with Rai stage 0 chronic lymphocytic leukemia (Rai0-CLL).

Experimental Design: A group of 136 patients with cMBL and a group of 216 Rai0-CLL cases were investigated prospectively.

Results: IGHV-mutated cases were significantly more frequent among cMBLs (P = 0.

Impact of phosphorylation on the encapsulation of nucleoside analogues within porous iron(iii) metal-organic framework MIL-100(Fe) nanoparticles.

Encapsulation of azidothymidine (AZT) or its phosphorylated derivatives (AZT-MP and AZT-TP) has been performed using nanoparticles of the porous crystalline iron(iii) trimesate metal-organic framework MIL-100(Fe). The number of phosphate groups per nucleoside analogue has a high impact on the drug loading capacity, and their interaction with the Lewis acid sites from the nanoMOFs is also discussed through a combination of techniques such as UV-vis absorption, circular dichroism, isothermal titration calorimetry, HPLC and molecular simulations. Finally, the effect of the differences in terms of host-guest interactions is discussed through the release in physiological buffers of AZT, AZT-MP and AZT-TP.

The role of the aryl hydrocarbon receptor in normal and malignant B cell development.

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor historically studied for its role in environmental chemical-mediated toxicity and carcinogenicity. In the last 5 years, however, it has become clear that the AhR, presumably activated by endogenous ligand(s), plays an important role in immune system development and function. Other articles in this edition summarize AhR function during T cell and antigen-presenting cell development and function, including the effects of AhR activation on dendritic cell function, T cell skewing, inflammation, and autoimmune disease.

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field.

In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector.

Interaction of collagen with chlorosulphonated paraffin tanning agents: Fourier transform infrared spectroscopic analysis and molecular dynamics simulations.

The binding of chlorosulphonated paraffins to collagen triple helices is studied by means of classical molecular dynamics simulations and experimental spectroscopic techniques in order to disclose the principal characteristics of their interaction during the leather fattening process. Indeed, collagen is the main target to develop new leather modifying agents with specific characteristics, and an accurate design of the collagen binders, supported by predictive computational strategies, could be a successful tool to obtain new effective eco-compatible compounds able to impart to the leather the required functionalities and distinctive mechanical properties. Possible effects caused by the tanning agents on the collagen matrix have been identified from both experimental and theoretical points of view.

Citric acid-γ-cyclodextrin crosslinked oligomers as carriers for doxorubicin delivery.

Two citric acid crosslinked γ-cyclodextrin oligomers (pγ-CyD) with a MW of 21-33 kDa and 10-15 γ-CyD units per molecule were prepared by following green chemistry methods and were fully characterized. The non-covalent association of doxorubicin (DOX) with these macromolecules was investigated in neutral aqueous medium by means of circular dichroism (CD), UV-vis absorption and fluorescence. Global analysis of multiwavelength spectroscopic CD and fluorescence titration data, taking into account the DOX monomer-dimer equilibrium, evidenced the formation of 1 : 1 and 1 : 2 pγ-CyD unit-DOX complexes.

Biochemical characterization of the chloroplastic β-carbonic anhydrase from Flaveria bidentis (L.) "Kuntze".

C3 and C4 plant carbonic anhydrases (CAs) are zinc-enzymes that catalyze the reversible hydration of CO2. They are sub-divided in three classes: α, β and γ, being distributed between both photosynthetic subtypes. The C4 dicotyledon species Flaveria bidentis (L.

A fluorine 1,2-migration via aryl cation/radical/radical anion/radical sequence.

Irradiation of a 7-piperazino-8-fluoroquinolone causes formal 1,2-fluorine migration, piperazine loss and reduction, or nucleophile addition in 8. Product study, laser flash photolysis, and computational modeling support F(-) detachment to yield a triplet 8-quinolyl cation that either inserts intramolecularly or is trapped by Cl(-), Br(-). However, iodide and pyrrole reduce it to the radical that continues the 'redox tour' (aryl cation→ radical→ radical anion→ radical and then again radical or radical anion) leading to the rearranged products.