Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ.

PURPOSE: Prostate cancer is the second most common cancer diagnosed worldwide and the third most common cancer among men in India. This study's objective was to characterise the mutational landscape of Indian prostate cancer using whole-exome sequencing to identify population-specific polymorphisms. METHODS: Whole-exome sequencing was performed of 58 treatment-naive primary prostate tumors of Indian origin. Multiple computational and statistical analyses were used to profile the known common mutations, other deleterious mutations, driver genes, prognostic biomarkers, and gene signatures unique to each clinical parameter. Cox analysis was performed to validate survival-associated genes. McNemar test identified genes significant to recurrence and receiver-operating characteristic (ROC) analysis was conducted to determine its accuracy. OncodriveCLUSTL algorithm was used to deduce driver genes. The druggable target identified was modeled with its known inhibitor using Autodock. RESULTS: TP53 was the most commonly mutated gene in our cohort. Three novel deleterious variants unique to the Indian prostate cancer subtype were identified: POLQ, FTHL17, and OR8G1. COX regression analysis identified ACSM5, a mitochondrial gene responsible for survival. CYLC1 gene, which encodes for sperm head cytoskeletal protein, was identified as an unfavorable prognostic biomarker indicative of recurrence. The novel POLQ mutant, also identified as a driver gene, was evaluated as the druggable target in this study. POLQ, a DNA repair enzyme implicated in various cancer types, is overexpressed and is associated with a poor prognosis. The mutant POLQ was subjected to structural analysis and modeled with its known inhibitor novobiocin resulting in decreased binding efficiency necessitating the development of a better drug. CONCLUSION: In this pilot study, the molecular profiling using multiple computational and statistical analyses revealed distinct polymorphisms in the Indian prostate cancer cohort. The mutational signatures identified provide a valuable resource for prognostic stratification and targeted treatment strategies for Indian prostate cancer patients. The DNA repair enzyme, POLQ, was identified as the druggable target in this study.

Unfolding newer concepts in placental pathology of obstetric cholestasis-a cause for prematurity.

Intrahepatic cholestasis of pregnancy (ICP) has an increased predisposition to occur in the third trimester of pregnancy and has a varied population incidence rates due to genetic influences. Owing to the adverse and unpredictable fetal outcomes, it poses a serious therapeutic challenge to the clinician. A rise in the incidence of iatrogenic prematurity has been observed, raising concerns over the perinatal outcomes. Excess bile acids and altered placental transport mechanisms have been strongly implicated in the pathogenesis of ICP and its complications. The exact etiology is not known; yet major underlying risk factors that are thought to contribute to the disease process include genetic, environmental, hormonal, and immunological. Newer molecular processes acting at the placental level, apart from specific histopathological changes, have assumed significance in recent times. In this review, we attempt to highlight the recent understanding of the mechanisms that operate in the placenta in patients with obstetric cholestasis that lead to poor fetal outcomes, through various studies published in the literature. Despite these additions to the existing knowledge on the etiopathogenesis of obstetric cholestasis and its possible placental origin, further studies are needed to validate the newer concepts.

Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability.

Self-assembly of metallointercalators into DNA nanocages is a rapid and facile approach to synthesize discrete bioinorganic host/guest structures with a high load of metal complexes. Turberfield's DNA tetrahedron can accommodate one intercalator for every two base pairs, which corresponds to 48 metallointercalators per DNA tetrahedron. The affinity of the metallointercalator for the DNA tetrahedron is a function of both the structure of the intercalating ligand and the overall charge of the complex, with a trend in affinity [Ru(bpy)2(dppz)]2+ > [Tb-DOTAm-Phen]3+ ≫ Tb-DOTA-Phen. Intercalation of the metal complex stabilizes the DNA tetrahedron, resulting in an increase of its melting temperature and, importantly, a significant increase in its stability in the presence of serum. [Ru(bpy)2(dppz)]2+, which has a greater affinity for DNA than [Tb-DOTAm-Phen]3+, increases the melting point and decreases degradation in serum to a greater extent than the TbIII complex. In the presence of Lipofectamine, the metallointercalator@DNA nanocage assemblies substantially increase the cell uptake of their respective metal complex. Altogether, the facile incorporation of a large number of metal complexes per assembly, the higher stability in serum, and the increased cell penetration of metallointercalator@DNA make these self-assemblies well-suited as metallodrugs.

Cell-Matrix Interactions Regulate Functional Extracellular Vesicle Secretion from Mesenchymal Stromal Cells.

Extracellular vesicles (EVs) are cell-secreted particles with broad potential to treat tissue injuries by delivering cargo to program target cells. However, improving the yield of functional EVs on a per cell basis remains challenging due to an incomplete understanding of how microenvironmental cues regulate EV secretion at the nanoscale. We show that mesenchymal stromal cells (MSCs) seeded on engineered hydrogels that mimic the elasticity of soft tissues with a lower integrin ligand density secrete ∼10-fold more EVs per cell than MSCs seeded on a rigid plastic substrate, without compromising their therapeutic activity or cargo to resolve acute lung injury in mice. Mechanistically, intracellular CD63+ multivesicular bodies (MVBs) transport faster within MSCs on softer hydrogels, leading to an increased frequency of MVB fusion with the plasma membrane to secrete more EVs. Actin-related protein 2/3 complex but not myosin-II limits MVB transport and EV secretion from MSCs on hydrogels. The results provide a rational basis for biomaterial design to improve EV secretion while maintaining their functionality.

StackNet-DenVIS: a multi-layer perceptron stacked ensembling approach for COVID-19 detection using X-ray images.

The highly contagious nature of Coronavirus disease 2019 (Covid-19) resulted in a global pandemic. Due to the relatively slow and taxing nature of conventional testing for Covid-19, a faster method needs to be in place. The current researches have suggested that visible irregularities found in the chest X-ray of Covid-19 positive patients are indicative of the presence of the disease. Hence, Deep Learning and Image Classification techniques can be employed to learn from these irregularities, and classify accordingly with high accuracy. This research presents an approach to create a classifier model named StackNet-DenVIS which is designed to act as a screening process before conducting the existing swab tests. Using a novel approach, which incorporates Transfer Learning and Stacked Generalization, the model aims to lower the False Negative rate of classification compensating for the 30% False Negative rate of the swab tests. A dataset gathered from multiple reliable sources consisting of 9953 Chest X-rays (868 Covid and 9085 Non-Covid) was used. Also, this research demonstrates handling data imbalance using various techniques involving Generative Adversarial Networks and sampling techniques. The accuracy, sensitivity, and specificity obtained on our proposed model were 95.07%, 99.40% and 94.61% respectively. To the best of our knowledge, the combination of accuracy and false negative rate obtained by this paper outperforms the current implementations. We must also highlight that our proposed architecture also considers other types of viral pneumonia. Given the unprecedented sensitivity of our model we are optimistic it contributes to a better Covid-19 detection.

Fluorinated Paramagnetic Complexes: Sensitive and Responsive Probes for Magnetic Resonance Spectroscopy and Imaging.

Fluorine magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) of chemical and physiological processes is becoming more widespread. The strength of this technique comes from the negligible background signal in in vivo19F MRI and the large chemical shift window of 19F that enables it to image concomitantly more than one marker. These same advantages have also been successfully exploited in the design of responsive 19F probes. Part of the recent growth of this technique can be attributed to novel designs of 19F probes with improved imaging parameters due to the incorporation of paramagnetic metal ions. In this review, we provide a description of the theories and strategies that have been employed successfully to improve the sensitivity of 19F probes with paramagnetic metal ions. The Bloch-Wangsness-Redfield theory accurately predicts how molecular parameters such as internuclear distance, geometry, rotational correlation times, as well as the nature, oxidation state, and spin state of the metal ion affect the sensitivity of the fluorine-based probes. The principles governing the design of responsive 19F probes are subsequently described in a "how to" guide format. Examples of such probes and their advantages and disadvantages are highlighted through a synopsis of the literature.

Development of a Click-Chemistry Reagent Compatible with Mass Cytometry.

The recent development of mass cytometry has allowed simultaneous detection of 40 or more unique parameters from individual single cells. While similar to flow cytometry, which is based on detection of fluorophores, one key distinguishing feature of mass cytometry is the detection of atomic masses of lanthanides by mass spectrometry in a mass cytometer. Its superior mass resolution results in lack of signal overlap, thereby allowing multiparametric detection of molecular features in each single cell greater than that of flow cytometry, which is limited to 20 parameters. Unfortunately, most detection in mass cytometry relies on lanthanide-tagged antibodies, which is ideal to detect proteins, but not other types of molecular features. To further expand the repertoire of molecular features that are detectable by mass cytometry, we developed a lanthanide-chelated, azide-containing probe that allows click-chemistry mediated labeling of target molecules. Following incorporation of the thymidine analog 5-ethynyl-2'-deoxyuridine (EdU) during DNA synthesis in S-phase of the cell cycle, we demonstrate that the probe introduced here, tagged with Terbium-159 (159Tb), reacts via copper-catalyzed azide-alkyne Huisgen cycloaddition (click-chemistry) with Edu. Thus, detection of 159Tb makes it possible to measure DNA synthesis in single cells using mass cytometry. The approach introduced here shows similar sensitivity (true positive rate) to other methods used to measure DNA synthesis in single cells by mass cytometry and is compatible with the parallel antibody-based detection of other parameters in single cells. Due to its universal nature, the use of click-chemistry in mass cytometry expands the types of molecular targets that can be monitored by mass cytometry.

Eight-Coordinate, Stable Fe(II) Complex as a Dual 19F and CEST Contrast Agent for Ratiometric pH Imaging.

Accurate mapping of small changes in pH is essential to the diagnosis of diseases such as cancer. The difficulty in mapping pH accurately in vivo resides in the need for the probe to have a ratiometric response so as to be able to independently determine the concentration of the probe in the body independently from its response to pH. The complex FeII-DOTAm-F12 behaves as an MRI contrast agent with dual 19F and CEST modality. The magnitude of its CEST response is dependent both on the concentration of the complex and on the pH, with a significant increase in saturation transfer between pH 6.9 and 7.4, a pH range that is relevant to cancer diagnosis. The signal-to-noise ratio of the 19F signal of the probe, on the other hand, depends only on the concentration of the contrast agent and is independent of pH. As a result, the complex can ratiometrically map pH and accurately distinguish between pH 6.9 and 7.4. Moreover, the iron(II) complex is stable in air at room temperature and adopts a rare 8-coordinate geometry.

Piperine attenuates UV-R induced cell damage in human keratinocytes via NF-kB, Bax/Bcl-2 pathway: An application for photoprotection.

Chronic ultraviolet radiation (UV-R) exposure causes skin disorders like erythema, edema, hyperpigmentation, photoaging and photocarcinogenesis. Recent research trends of researchers have focused more attention on the identification and use of photo stable natural agents with photoprotective properties. Piperine (PIP), as a plant alkaloid, is an important constituent present in black pepper (Piper nigrum), used widely in ayurvedic and other traditional medicines and has broad pharmacological properties. The study was planned to photoprotective efficacy of PIP in human keratinocyte (HaCaT) cell line. We have assessed the UV-R induced activation of transcription factor NF-κB in coordination with cell death modulators (Bax/Bcl-2 and p21). The LC-MS/MS analysis revealed that PIP was photostable under UV-A/UV-B exposure. PIP (10µg/ml) attenuates the UV-R (A and B) induced phototoxicity of keratinocyte cell line through the restoration of cell viability, inhibition of ROS, and malondialdehyde generation. Further, PIP inhibited UV-R mediated DNA damage, prevented micronuclei formation, and reduced sub-G1 phase in cell cycle, which supported against photogenotoxicity. This study revealed that PIP pretreatment strongly suppressed UV-R induced photodamages. Molecular docking studies suggest that PIP binds at the active site of NF-κB, and thus, preventing its translocation to nucleus. In addition, transcriptional and translational analysis advocate the increased expression of NF-κB and concomitant decrease in IkB-α expression under UV-R exposed cells, favouring the apoptosis via Bax/Bcl-2 and p21 pathways. However, PIP induced expression of IkB-α suppress the NF-κB activity which resulted in suppression of apoptotic marker genes and proteins that involved in photoprotection. Therefore, we suggest the applicability of photostable PIP as photoprotective agent for human use.

Fe- and Ln-DOTAm-F12 Are Effective Paramagnetic Fluorine Contrast Agents for MRI in Water and Blood.

A series of fluorinated macrocyclic complexes, M-DOTAm-F12, where M is LaIII, EuIII, GdIII, TbIII, DyIII, HoIII, ErIII, TmIII, YbIII, and FeII, was synthesized, and their potential as fluorine magnetic resonance imaging (MRI) contrast agents was evaluated. The high water solubility of these complexes and the presence of a single fluorine NMR signal, two necessary parameters for in vivo MRI, are substantial advantages over currently used organic polyfluorocarbons and other reported paramagnetic 19F probes. Importantly, the sensitivity of the paramagnetic probes on a per fluorine basis is at least 1 order of magnitude higher than that of diamagnetic organic probes. This increased sensitivity is due to a substantial-up to 100-fold-decrease in the longitudinal relaxation time (T1) of the fluorine nuclei. The shorter T1 allows for a greater number of scans to be obtained in an equivalent time frame. The sensitivity of the fluorine probes is proportional to the T2/T1 ratio. In water, the optimal metal complexes for imaging applications are those containing HoIII and FeII, and to a lesser extent TmIII and YbIII. Whereas T1 of the lanthanide complexes are little affected by blood, the T2 are notably shorter in blood than in water. The sensitivity of Ln-DOTAm-F12 complexes is lower in blood than in water, such that the most sensitive complex in water, HoIII-DOTAm-F12, could not be detected in blood. TmIII yielded the most sensitive lanthanide fluorine probe in blood. Notably, the relaxation times of the fluorine nuclei of FeII-DOTAm-F12 are similar in water and in blood. That complex has the highest T2/T1 ratio (0.57) and the lowest limit of detection (300 µM) in blood. The combination of high water solubility, single fluorine signal, and high T2/T1 of M-DOTAm-F12 facilitates the acquisition of three-dimensional magnetic resonance images.

Intramolecularly coordinated azobenzene selenium derivatives: effect of strength of the Se···N intramolecular interaction on luminescence.

A series of selenium derivatives (6-12) of 2-phenylazophenyl have been synthesized using o-lithiation route. The effect of the strength of the intramolecular Se···N interaction on the absorption spectra as well as emission spectra has been studied. The studies suggest that the secondary bonding Se···N interaction give rise to fluorescence, however, the strength of Se···N interaction cannot be directly correlated with the intensity of the fluorescence. TD-DFT calculations show that the main transition involved in the absorption spectra of the compound is the ligand based π-π* type.

Isolation and reactivity of an unusually stable organoselenenyl azide.

The stabilities of a series of isolated covalent selenium(II) azides such as [2-[1-(3,5-dimethylphenyl)-2-naphthyl]-4,5-dihydro-4,4-dimethyloxazole]selenium azide (2a), [2-(4,4-dimethyl-2-oxazolinyl)phenyl]selenenyl azide (3a), [o-(2,6-diisopropylphenyl-iminomethinyl)phenyl]selenenyl azide (4a), [o-(R)-(methylbenzyliminomethinyl)phenyl]selenenyl azide (5a) and o-formylphenylselenenyl azide (6a) are rationalized; also the reactivity of first room temperature stable azide (2a) toward 1,3-cycloaddition has been explored.

Hydrolysis of 2-phenylazophenyltellurium trihalides: isolation of an unprecedented homometallic, discrete heptanuclear organotellurium oxide cluster.

Alkaline hydrolysis of RTeBr(3) (R = 2-phenylazophenyl) gave intramolecularly stabilized homometallic, heptanuclear organotellurium oxide cluster R(6)Te(7)O(11) (4) in good yield.