Ponatinib Drives Cardiotoxicity by S100A8/A9-NLRP3-IL-1ß Mediated Inflammation.

BACKGROUND: The tyrosine kinase inhibitor ponatinib is the only treatment option for chronic myelogenous leukemia patients with T315I (gatekeeper) mutation. Pharmacovigilance analysis of Food and Drug Administration and World Health Organization datasets has revealed that ponatinib is the most cardiotoxic agent among all Food and Drug Administration-approved tyrosine kinase inhibitors in a real-world scenario. However, the mechanism of ponatinib-induced cardiotoxicity is unknown. METHODS: The lack of well-optimized mouse models has hampered the in vivo cardio-oncology studies. Here, we show that cardiovascular comorbidity mouse models evidence a robust cardiac pathological phenotype upon ponatinib treatment. A combination of multiple in vitro and in vivo models was employed to delineate the underlying molecular mechanisms. RESULTS: An unbiased RNA sequencing analysis identified the enrichment of dysregulated inflammatory genes, including a multifold upregulation of alarmins S100A8/A9, as a top hit in ponatinib-treated hearts. Mechanistically, we demonstrate that ponatinib activates the S100A8/A9-TLR4 (Toll-like receptor 4)-NLRP3 (NLR family pyrin domain-containing 3)-IL (interleukin)-1ß signaling pathway in cardiac and systemic myeloid cells, in vitro and in vivo, thereby leading to excessive myocardial and systemic inflammation. Excessive inflammation was central to the cardiac pathology because interventions with broad-spectrum immunosuppressive glucocorticoid dexamethasone or specific inhibitors of NLRP3 (CY-09) or S100A9 (paquinimod) nearly abolished the ponatinib-induced cardiac dysfunction. CONCLUSIONS: Taken together, these findings uncover a novel mechanism of ponatinib-induced cardiac inflammation leading to cardiac dysfunction. From a translational perspective, our results provide critical preclinical data and rationale for a clinical investigation into immunosuppressive interventions for managing ponatinib-induced cardiotoxicity.

Fibroblast GSK-3α Promotes Fibrosis via RAF-MEK-ERK Pathway in the Injured Heart.

BACKGROUND: Heart failure is the leading cause of mortality, morbidity, and health care expenditures worldwide. Numerous studies have implicated GSK-3 (glycogen synthase kinase-3) as a promising therapeutic target for cardiovascular diseases. GSK-3 isoforms seem to play overlapping, unique and even opposing functions in the heart. Previously, we have shown that of the 2 isoforms of GSK-3, cardiac fibroblast GSK-3ß acts as a negative regulator of myocardial fibrosis in the ischemic heart. However, the role of cardiac fibroblast-GSK-3α in the pathogenesis of cardiac diseases is completely unknown. METHODS: To define the role of cardiac fibroblast-GSK-3α in myocardial fibrosis and heart failure, GSK-3α was deleted from fibroblasts or myofibroblasts with tamoxifen-inducible Tcf21- or Postn-promoter-driven Cre recombinase. Control and GSK-3α KO mice were subjected to cardiac injury and heart parameters were evaluated. The fibroblast kinome mapping was carried out to delineate molecular mechanism followed by in vivo and in vitro analysis. RESULTS: Fibroblast-specific GSK-3α deletion restricted fibrotic remodeling and preserved function of the injured heart. We observed reductions in cell migration, collagen gel contraction, α-SMA protein levels, and expression of ECM genes in TGFß1-treated KO fibroblasts, indicating that GSK-3α is required for myofibroblast transformation. Surprisingly, GSK-3α deletion did not affect SMAD3 activation, suggesting the profibrotic role of GSK-3α is SMAD3 independent. The molecular studies confirmed decreased ERK signaling in GSK-3α-KO CFs. Conversely, adenovirus-mediated expression of a constitutively active form of GSK-3α (Ad-GSK-3αS21A) in fibroblasts increased ERK activation and expression of fibrogenic proteins. Importantly, this effect was abolished by ERK inhibition. CONCLUSIONS: GSK-3α-mediated MEK-ERK activation is a critical profibrotic signaling circuit in the injured heart, which operates independently of the canonical TGF-ß1-SMAD3 pathway. Therefore, strategies to inhibit the GSK-3α-MEK-ERK signaling circuit could prevent adverse fibrosis in diseased hearts.

Animal Models of Exercise From Rodents to Pythons.

Acute and chronic animal models of exercise are commonly used in research. Acute exercise testing is used, often in combination with genetic, pharmacological, or other manipulations, to study the impact of these manipulations on the cardiovascular response to exercise and to detect impairments or improvements in cardiovascular function that may not be evident at rest. Chronic exercise conditioning models are used to study the cardiac phenotypic response to regular exercise training and as a platform for discovery of novel pathways mediating cardiovascular benefits conferred by exercise conditioning that could be exploited therapeutically. The cardiovascular benefits of exercise are well established, and, frequently, molecular manipulations that mimic the pathway changes induced by exercise recapitulate at least some of its benefits. This review discusses approaches for assessing cardiovascular function during an acute exercise challenge in rodents, as well as practical and conceptual considerations in the use of common rodent exercise conditioning models. The case for studying feeding in the Burmese python as a model for exercise-like physiological adaptation is also explored.

Photocatalytic C2-trifluoroethylation and perfluoroalkylation of 3-substituted indoles using fluoroalkyl halides.

A photocatalytic reactivity platform for the C2-trifluoroethylation and perfluoroalkylation of 3-substituted indoles has been developed. A range of fluoroalkyl halides have been employed as radical precursors under mild, transition-metal-free conditions to access new (per)fluorinated chemical space featuring the indole substructure. This general protocol is also applicable to indole-containing peptides.

Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.

Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription.

Spatiotemporal dynamics of prey-predator model incorporating Holling-type II functional response with fear and its carryover effects.

The recent focus in the fields of biology and ecology has centered on the significant attention given to the mathematical modeling and analyzing the spatiotemporal population distribution among species engaged in interactions. This paper explores the dynamics of the temporal and spatiotemporal delayed Bazykin-type prey-predator model, incorporating fear and its carryover effect. In our model, we incorporated a functional response of the Holling-type II. In the temporal model, a detailed dynamic analysis was carried out, investigating the positivity and boundedness of solutions, establishing the uniqueness and existence of positive interior equilibria, and examining both local and global stability. Additionally, we explored the presence of saddle-node, transcritical, and Hopf bifurcations varying attack rate parameter. The delayed system shows highly periodic behavior. Additionally, for the spatiotemporal model, we provide a complete analysis of local and global stability, and we derive the conditions for the existence of Turing instability for both self-diffusion and cross-diffusion, respectively. The two-dimensional diffusive model is further discussed, highlighting various Turing patterns, including holes, stripes, and hot and cold spots, along with their biological significance. Numerical simulations are executed to validate the analytical findings in both temporal and spatiotemporal models.

Urban trees' potential for regulatory services in the urban environment: an exploration of carbon sequestration.

Urbanisation has emerged as a formidable challenge for urban policymakers, reaching unparalleled heights and unsettling the ecological equilibrium of the cities. Urban areas now grapple with many issues encompassing climate change, resource depletion, population surges and increased pollution levels. Many planned cities have planted trees and other vegetation within the urban sectors to enhance air quality, mitigate climate effects and provide valuable ecosystem services. This study assessed tree species diversity and their potential for carbon sequestration in Panjab University Campus, Chandigarh. We established 188 plots, each comprising randomly selected quadrats measuring 10 m × 10 m, encompassing areas with varying levels of vegetation, ranging from low to moderate and high density. We used four different allometric equations to estimate tree biomass and carbon stock. Our findings revealed that 92 tree species belong to 72 genera and 35 families, with a total tree density of 975 ha-1. The total CO2 sequestration in form of carbon stock was 18,769.46 Mg C ha-1, with Manilkara hexandra (1239.20 Mg C ha-1), Ficus benghalensis (1072.24 Mg C ha-1), Kigelia pinnata (989.89 Mg C ha-1) and Lagerstroemia floribunda (716.88 Mg C ha-1) being the top contributors. Specifically, the equation of Chave et al. (2005) without tree height yielded the highest biomass and carbon stock estimates than other equations. The present study underscores the vital role of trees on the campus as potent carbon reservoirs meet to maintain an aesthetic sense for biotic components and alleviate rising levels of CO2 in the atmospheric environment. By emphasising the role of urban trees as potent carbon reservoirs, the study underscores the importance of integrating green infrastructure into urban planning strategies. Furthermore, it offers valuable guidance for urban planners. It suggests that strategic tree planting and maintenance can enhance green spaces, regulate temperatures and ultimately support regional and global climate change mitigation goals. Incorporating these findings into urban planning processes can aid policymakers in developing resilient, ecologically sustainable cities worldwide.

Disturbance and vegetational structure in an urban forest of Indian Siwaliks: an ecological assessment.

Urban forests face multiple human-mediated pressures leading to compromised ecosystem structure and functioning. Therefore, understanding ecosystem structure in response to ongoing pressures is crucial for sustaining ecological integrity and human well-being. We aim to assess the disturbance and its effects on the vegetation structure of urban forests in Chandigarh using a combination of remote sensing techniques and vegetation surveys. The disturbance was evaluated as a change in NDVI (Normalised Difference Vegetation Index) from 2001 to 2021 by applying the BFAST (Breaks For Additive Season and Trend) algorithm to the MODIS satellite imagery data. A vegetation survey was conducted to compare the species composition, taxonomic and phylogenetic diversity as measures of forest vegetational structure. While signals of disturbance were evident, the changes in vegetation structure were not well established from our study. Further, this analysis indicated no significant differences in vegetation composition due to disturbance (F1,12 = 0.91, p = 0.575). However, the phylogenetic diversity was substantially lower for disturbed plots than undisturbed plots, though the taxonomic diversity was similar among the disturbed and undisturbed plots. Our results confirmed that disturbance effects are more prominent on the phylogenetic than taxonomic diversity. These findings can be considered early signals of disturbance and its impact on the vegetation structure of urban forests and contribute to the knowledge base on urban ecosystems. Our study has implications for facilitating evidence-based decision-making and the development of sustainable management strategies for urban forest ecosystems.

Visible Light-Mediated Carbamoylation of para-Quinone Methides.

We report a photocatalytic approach for the installation of the amide moiety onto para-quinone methides. This transformation features a net reductive approach for the generation of carbamoyl radicals from amide-substituted Hantzsch ester derivatives under transition metal-free conditions. This protocol exhibits wide scope and allows access to diarylacetamides employing a C-C bond formation approach.

Cascade Cyclizations Triggered by Photochemically Generated Carbamoyl Radicals Derived from Alkyl Amines.

We report on a visible light-mediated cascade carbamoylation/cyclization of acrylamides using dihydropyridyl carbamoyl donors derived from alkyl amines. Diversely selected acrylamides including 2-cyano-N-arylacrylamides, indolyl- and benzimidazolyl acrylamides, and 2-alkynyl-N-aryl acrylamides participate in this reaction, providing products in good yields. The highlights of this photochemical method include the application of alkyl amine-derived carbamoyl donors, peroxide-free reaction conditions, and a broad scope.

Pd-Catalyzed Photochemical Alkylative Functionalization of C═C and C═N Bonds.

The development of excited-state palladium-catalyzed alkylative cyclization of acrylamides and the alkylation of quinoxalinones is described. The application of a variety of primary, secondary, and tertiary unactivated alkyl halides as alkyl radical precursors and the use of a simple catalyst system are the highlights of this reactivity manifold. The reactions exhibit wide scope, occur under mild conditions, and furnish the products in excellent yields.

Annulation of quinone methides with 2-benzylidene dithiolanes: synthesis of spirochroman dithiolanes.

An expeditious and regioselective approach towards the construction of a spiro-chroman motif is described. Quinone methides underwent a PTSA catalyzed annulation with 2-benzylidene dithiolanes to afford spiro-chroman dithiolanes in high yields. The synthetic versatility of the dithiolane motif was demonstrated by converting the adduct to coumarin, 3,4-dihydrocoumarin and chroman derivatives.

Visible-light mediated, oxygen-promoted regioselective cross-dehydrogenative coupling of coumarins and dimethylanilines.

Herein, we report a regioselective, photocatalytic C3 α-aminoalkylation of coumarins via a cross-dehydrogenative coupling of dimethylanilines and coumarins. Molecular oxygen was utilized as the oxidizing agent in this transformation, which exhibits a wide substrate scope and affords the products in good yields. It was established that 4-amino-substituted coumarin reacts via a different mechanism compared to coumarin derivatives that are unsubstituted at the 4-position.

The machine learning and geostatistical approach for assessment of arsenic contamination levels using physicochemical properties of water.

Arsenic contamination in groundwater due to natural or anthropogenic sources is responsible for carcinogenic and non-carcinogenic risks to humans and the ecosystem. The physicochemical properties of groundwater in the study area were determined in the laboratory using the samples collected across the Varanasi region of Uttar Pradesh, India. This paper analyses the physicochemical properties of water using machine learning, descriptive statistics, geostatistical and spatial analysis. Pearson correlation was used for feature selection and highly correlated features were selected for model creation. Hydrochemical facies of the study area were analyzed and the hyperparameters of machine learning models, i.e., multilayer perceptron, random forest (RF), naïve Bayes, and decision tree were optimized before training and testing the groundwater samples as high (1) or low (0) arsenic contamination levels based on the WHO 10 µg/L guideline value. The overall performance of the models was compared based on accuracy, sensitivity, and specificity value. Among all models, the RF algorithm outclasses other classifiers, as it has a high accuracy of 92.30%, a sensitivity of 100%, and a specificity of 75%. The accuracy result was compared to prior research, and the machine learning model may be used to continually monitor the amount of arsenic pollution in groundwater.

3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape.

The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01397-3.

Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer.

OBJECTIVE: Enhancer aberrations are beginning to emerge as a key epigenetic feature of colorectal cancers (CRC), however, a comprehensive knowledge of chromatin state patterns in tumour progression, heterogeneity of these patterns and imparted therapeutic opportunities remain poorly described. DESIGN: We performed comprehensive epigenomic characterisation by mapping 222 chromatin profiles from 69 samples (33 colorectal adenocarcinomas, 4 adenomas, 21 matched normal tissues and 11 colon cancer cell lines) for six histone modification marks: H3K4me3 for Pol II-bound and CpG-rich promoters, H3K4me1 for poised enhancers, H3K27ac for enhancers and transcriptionally active promoters, H3K79me2 for transcribed regions, H3K27me3 for polycomb repressed regions and H3K9me3 for heterochromatin. RESULTS: We demonstrate that H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumour-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was required for excessive proliferation. Consistently, combination of MEK plus bromodomain inhibition was found to have synergistic effects in CRC patient-derived xenograft models. Probing intertumour heterogeneity, we identified four distinct enhancer subtypes (EPIgenome-based Classification, EpiC), three of which correlate well with previously defined transcriptomic subtypes (consensus molecular subtypes, CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, TGFßi, mTORi and SRCi) for EpiC groups. CONCLUSION: Our data suggest that the dynamics of active enhancer underlies CRC progression and the patient-specific enhancer patterns can be leveraged for precision combination therapy.

Experimental models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor.

Undifferentiated pleomorphic sarcoma (UPS) and malignant peripheral nerve sheath tumor (MPNST) are aggressive soft tissue sarcomas that do not respond well to current treatment modalities. The limited availability of UPS and MPNST cell lines makes it challenging to identify potential therapeutic targets in a laboratory setting. Understanding the urgent need for improved treatments for these tumors and the limited cellular models available, we generated additional cell lines to study these rare cancers. Patient-derived tumors were used to establish 4 new UPS models, including one radiation-associated UPS-UPS271.1, UPS511, UPS0103, and RIS620, one unclassified spindle cell sarcoma-USC060.1, and 3 new models of MPNST-MPNST007, MPNST3813E, and MPNST4970. This study examined the utility of the new cell lines as sarcoma models by assessing their tumorigenic potential and mutation status for known sarcoma-related genes. All the cell lines formed colonies and migrated in vitro. The in vivo tumorigenic potential of the cell lines and corresponding xenografts was determined by subcutaneous injection or xenograft re-passaging into immunocompromised mice. USC060.1 and UPS511 cells formed tumors in mice upon subcutaneous injection. UPS0103 and RIS620 tumor implants formed tumors in vivo, as did MPNST007 and MPNST3813E tumor implants. Targeted sequencing analysis of a panel of genes frequently mutated in sarcomas identified TP53, RB1, and ATRX mutations in a subset of the cell lines. These new cellular models provide the scientific community with powerful tools for detailed studies of tumorigenesis and for investigating novel therapies for UPS and MPNST.

Pancreatic hemorrhage contributes to late mortality in patients with acute necrotizing pancreatitis.

OBJECTIVES: The frequency, risk factors, and impact on survival of hemorrhage into (peri)pancreatic collections in patients with acute pancreatitis (AP) has not been well studied. The study was designed to evaluate the risk factors for hemorrhage, successful hemostasis and its effect on in-hospital mortality. METHODS: In a prospective cohort study for prediction of severity of AP, the incidence, risk factors, and outcomes of pancreatic hemorrhage were analyzed. Patients with significant hemorrhage were managed according to a predefined protocol including endovascular intervention. RESULTS: Out of 363 patients hospitalized during the study-period, 33(9%) patients developed hemorrhage. Median time from onset of AP to hemorrhage was 59(45-68) days. The cause of hemorrhage was arterial in 19(57.5%) patients and unlocalized in 14(42.5%) patients. Hemorrhage was managed by conservative approach in 7 (21.2%), radiographic angioembolisation in 16 (48.5%), radiographic angioembolisation followed by surgery in 3 (9.1%), and surgery in 7 (21.2%) patients. Persistent organ failure [aHR 2.3 (1.1-5.1), p = 0.03], use of large bore (>20 Fr) catheter for initial drainage [aHR 3.9 (1.7-9.1), p = 0.001] and extensive (>50%) necrosis [aHR 3.1 (1.4-6.9), p = 0.005] were significant risk factors for hemorrhage. Hemorrhage was an independent predictor of mortality [aHR 2.0 (1.2-3.4), p = 0.008] in addition to persistent organ failure (aHR 12.1 (5.7-25.8), p < 0.001). In-hospital mortality in patients with hemorrhage was 22/33 (66.7%) vs. 81/330 (25%) in no hemorrhage group [p <0.001]. CONCLUSION: Pancreatic hemorrhage occurs later in the course of acute pancreatitis in relatively sicker group of patients with organ failure and extensive necrosis, and is independently associated with a higher risk of in-hospital mortality.

Synthesis of Tritylones via Cascade Reaction of Arynes with 5-Ethoxyoxazoles.

A cascade reaction involving arynes and 5-ethoxyoxazoles has been developed toward the synthesis of 9-alkyl/aryl tritylones. 5-Ethoxyoxazoles undergo a [4 + 2] cycloaddition reaction with arynes followed by retro-[4 + 2] cycloaddition, a second intermolecular [4 + 2] cycloaddition reaction, and hydrolytic ring cleavage to generate substituted tritylones in good yields. The conversion of tritylone products to a series of spirocyclic anthrone derivatives has been demonstrated. The reaction is expeditious, exhibits wide scope, and employs readily available starting materials.

Brønsted acid catalyzed annulations of ketene dithioacetals: synthesis of 3-aryl coumarins and indenes.

PTSA-catalyzed divergent synthetic routes toward 3-aryl coumarins and indenes have been developed using ketene dithioacetals. These transformations are transition-metal and oxidant free, proceed under mild conditions, and provide expeditious access to these important structural motifs.