Discovery Of Novel Therapeutic Interventions Research Articles

Clonal evolution of the 3D chromatin landscape in patients with relapsed pediatric B-cell acute lymphoblastic leukemia

Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. We performed Hi-C, ATAC-seq, and RNA-seq on 12 matched diagnosis/relapse pediatric leukemia specimens to uncover dynamic structural variants (SVs) and 3D chromatin rewiring that may contribute to relapse. While translocations are assumed to occur early in leukemogenesis and be maintained throughout progression, we discovered novel, dynamic translocations and confirmed several fusion transcripts, suggesting functional and therapeutic relevance. Genome-wide chromatin remodeling was observed at all organizational levels: A/B compartments, TAD interactivity, and chromatin loops, including some loci shared by 25% of patients. Shared changes were found to drive the expression of genes/pathways previously implicated in resistance as well as novel therapeutic candidates, two of which (ATXN1 and MN1) we functionally validated. Overall, these results demonstrate chromatin reorganization under the selective pressure of therapy and offer the potential for discovery of novel therapeutic interventions.

Elucidating the antidiabetic potential of Chrysophyllum albidum: An integrative approach combining in vitro and in silico studies on dipeptidyl peptidase IV and adenosine deaminase inhibition

Diabetes mellitus remains a significant global health challenge, necessitating the discovery of novel therapeutic interventions. This study elucidated the inhibitory potential of phytochemicals derived from the African star apple (Chrysophyllum albidum (C. albidum)) against two critical enzymes implicated in diabetes pathogenesis: dipeptidyl peptidase IV (DPP-IV) and adenosine deaminase (ADA). A multi-pronged approach integrating in vitro enzyme inhibition assays and in silico molecular docking simulations was employed. Aqueous extracts from various C. albidum fruit parts were evaluated for enzyme inhibition using colorimetric assays. Molecular docking studies were performed using the crystal structures of DPP-IV (PDB ID: 2ONC) and ADA (PDB ID: 3IAR) to investigate binding interactions and identify potential hit compounds using autodock-vina. In vitro assays revealed potent, dose-dependent inhibition of both DPP-IV and ADA by the aqueous extracts, with the fruit's seed coat extract exhibiting the most promising activity (IC50 = 4.88 μg/mL and 18.25 μg/mL against DPP-IV and ADA, respectively). Molecular docking unveiled several C. albidum hits, including CIDs 562,128 (-9.569), 6,430,793 (-9.501), and 23,647,311 (-8.286), and 73,530 (-6.936) exhibiting favorable drug-like properties and binding geometries. This integrative study unveiled the inhibitory potential of C. albidum phytochemicals against DPP-IV and ADA, with a notable correlation between in vitro and in silico data, underscoring the therapeutic promise of this indigenous African plant source for developing novel antidiabetic agents, most importantly the seedcoat.

Improving obesity research: Unveiling metabolic pathways through a 3D In vitro model of adipocytes using 3T3-L1 cells.

Obesity, a burgeoning global health crisis, has tripled in prevalence over the past 45 years, necessitating innovative research methodologies. Adipocytes, which are responsible for energy storage, play a central role in obesity. However, most studies in this field rely on animal models or adipocyte monolayer cell cultures, which are limited in their ability to fully mimic the complex physiology of a living organism, or pose challenges in terms of cost, time consumption, and ethical considerations. These limitations prompt a shift towards alternative methodologies. In response, here we show a 3D in vitro model utilizing the 3T3-L1 cell line, aimed at faithfully replicating the metabolic intricacies of adipocytes in vivo. Using a workable cell line (3T3-L1), we produced adipocyte spheroids and differentiated them in presence and absence of TNF-α. Through a meticulous proteomic analysis, we compared the molecular profile of our adipose spheroids with that of adipose tissue from lean and obese C57BL/6J mice. This comparison demonstrated the model's efficacy in studying metabolic conditions, with TNF-α treated spheroids displaying a notable resemblance to obese white adipose tissue. Our findings underscore the model's simplicity, reproducibility, and cost-effectiveness, positioning it as a robust tool for authentically mimicking in vitro metabolic features of real adipose tissue. Notably, our model encapsulates key aspects of obesity, including insulin resistance and an obesity profile. This innovative approach has the potential to significantly impact the discovery of novel therapeutic interventions for metabolic syndrome and obesity. By providing a nuanced understanding of metabolic conditions, our 3D model stands as a transformative contribution to in vitro research, offering a pathway for the development of small molecules and biologics targeting these pervasive health issues in humans.

A new face of old cells: An overview about the role of senescence and telomeres in inflammatory bowel diseases.

Cellular senescence is a pivotal factor contributing to aging and the pathophysiology of age-related diseases. Despite the presence of inflammation and abnormal immune system function in both inflammatory bowel diseases (IBD) and senescence, the relationship between the two remains largely unexplored. Therefore, our study aimed to investigate the intricate connection between cellular senescence, telomeres, and IBD. The review highlights the presence of senescence markers, particularly p16 and p21, in IBD patients, suggesting their potential association with disease progression and mucosal inflammation. We emphasize the critical role of macrophages in eliminating senescent cells and how disturbance in effective clearance may contribute to persistent senescence and inflammation in IBD. Additionally, we shed light on the involvement of telomeres in IBD, as their dysfunction impairs enterocyte function and disrupts colonic barrier integrity, potentially exacerbating the pathogenesis of the disease. Targeting senescence and telomere dysfunctions holds promise for the development of innovative therapeutic approaches to mitigate intestinal inflammation and alleviate symptoms in IBD patients. By unraveling the precise role of senescence in IBD, we can pave the way for the discovery of novel therapeutic interventions that effectively address the underlying mechanisms of intestinal inflammation, offering hope for improved management and treatment of IBD patients.

Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches.

During the course of a viral infection, virus–host protein–protein interactions (PPIs) play a critical role in allowing viruses to replicate and survive within the host. These interspecies molecular interactions can lead to viral-mediated perturbations of the human interactome causing the generation of various complex diseases. Evidences suggest that viral-mediated perturbations are a possible pathogenic etiology in several neurodegenerative diseases (NDs). These diseases are characterized by chronic progressive degeneration of neurons, and current therapeutic approaches provide only mild symptomatic relief; therefore, there is unmet need for the discovery of novel therapeutic interventions. In this paper, we initially review databases and tools that can be utilized to investigate viral-mediated perturbations in complex NDs using network-based analysis by examining the interaction between the ND-related PPI disease networks and the virus–host PPI network. Afterwards, we present our theoretical-driven integrative network-based bioinformatics approach that accounts for pathogen–genes–disease-related PPIs with the aim to identify viral-mediated pathogenic mechanisms focusing in multiple sclerosis (MS) disease. We identified seven high centrality nodes that can act as disease communicator nodes and exert systemic effects in the MS-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways network. In addition, we identified 12 KEGG pathways, 5 Reactome pathways and 52 Gene Ontology Immune System Processes by which 80 viral proteins from eight viral species might exert viral-mediated pathogenic mechanisms in MS. Finally, our analysis highlighted the Th17 differentiation pathway, a disease communicator node and part of the 12 underlined KEGG pathways, as a key viral-mediated pathogenic mechanism and a possible therapeutic target for MS disease.

Critical Role of the Maternal Immune System in the Pathogenesis of Autism Spectrum Disorder

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterised by impairments in communication, social interaction, and the presence of restrictive and repetitive behaviours. Over the past decade, most of the research in ASD has focused on the contribution of genetics, with the identification of a variety of different genes and mutations. However, the vast heterogeneity in clinical presentations associated with this disorder suggests that environmental factors may be involved, acting as a “second hit” in already genetically susceptible individuals. To this regard, emerging evidence points towards a role for maternal immune system dysfunctions. This literature review considered evidence from epidemiological studies and aimed to discuss the pathological relevance of the maternal immune system in ASD by looking at the proposed mechanisms by which it alters the prenatal environment. In particular, this review focuses on the effects of maternal immune activation (MIA) by looking at foetal brain-reactive antibodies, cytokines and the microbiome. Despite the arguments presented here that strongly implicate MIA in the pathophysiology of ASD, further research is needed to fully understand the precise mechanisms by which they alter brain structure and behaviour. Overall, this review has not only shown the importance of the maternal immune system as a risk factor for ASD, but more importantly, has highlighted new promising pathways to target for the discovery of novel therapeutic interventions for the treatment of such a life-changing disorder.

Differential Gene Expression Profile of Human Neutrophils Cultured with Plasmodium falciparum-Parasitized Erythrocytes.

Neutrophils (PMNs) are the most abundant cellular component of our innate immune system, where they play central roles in the pathogenesis of and resistance to a broad range of diseases. However, their roles in malarial infection remain poorly understood. Therefore, we examined the transcriptional gene profile of human PMNs in response to Plasmodium falciparum-parasitized erythrocytes (iRBCs) by using oligonucleotide microarrays. Results revealed that PMNs induced a broad and vigorous set of changes in gene expression in response to malarial parasites, represented by 118 upregulated and 216 downregulated genes. The transcriptional response was characterized by the upregulation of numerous genes encoding multiple surface receptors, proteins involved in signal transduction pathways, and defense response proteins. This response included a number of genes which are known to be involved in the pathogenesis of malaria and other inflammatory diseases. Gene enrichment analysis suggested that the biological pathways involved in the PMN responses to the iRBCs included insulin receptor, Jak-STAT signaling pathway, mitogen-activated protein kinase (MAPK), and interleukin and interferon-gamma (IFN-γ) signaling pathways. The current study provides fundamental knowledge on the molecular responses of neutrophils to malarial parasites, which may aid in the discovery of novel therapeutic interventions.

Epigenetic Impact on EBV Associated B-Cell Lymphomagenesis.

Epigenetic modifications leading to either transcriptional repression or activation, play an indispensable role in the development of human cancers. Epidemiological study revealed that approximately 20% of all human cancers are associated with tumor viruses. Epstein-Barr virus (EBV), the first human tumor virus, demonstrates frequent epigenetic alterations on both viral and host genomes in associated cancers—both of epithelial and lymphoid origin. The cell type-dependent different EBV latent gene expression patterns appear to be determined by the cellular epigenetic machinery and similarly viral oncoproteins recruit epigenetic regulators in order to deregulate the cellular gene expression profile resulting in several human cancers. This review elucidates the epigenetic consequences of EBV–host interactions during development of multiple EBV-induced B-cell lymphomas, which may lead to the discovery of novel therapeutic interventions against EBV-associated B-cell lymphomas by alteration of reversible patho-epigenetic markings.

GABA transmission via ATP-dependent K+channels regulates α-synuclein secretion in mouse striatum

α-Synuclein is readily released in human and mouse brain parenchyma, even though the normal function of the secreted protein has not been yet elucidated. Under pathological conditions, such as in Parkinson's disease, pathologically relevant species of α-synuclein have been shown to propagate between neurons in a prion-like manner, although the mechanism by which α-synuclein transfer induces degeneration remains to be identified. Due to this evidence extracellular α-synuclein is now considered a critical target to hinder disease progression in Parkinson's disease. Given the importance of extracellular α-synuclein levels, we have now investigated the molecular pathway of α-synuclein secretion in mouse brain. To this end, we have identified a novel synaptic network that regulates α-synuclein release in mouse striatum. In this brain area, the majority of α-synuclein is localized in corticostriatal glutamatergic terminals. Absence of α-synuclein from the lumen of brain-isolated synaptic vesicles suggested that they are unlikely to mediate its release. To dissect the mechanism of α-synuclein release, we have used reverse microdialysis to locally administer reagents that locally target specific cellular pathways. Using this approach, we show that α-synuclein secretion in vivo is a calcium-regulated process that depends on the activation of sulfonylurea receptor 1-sensitive ATP-regulated potassium channels. Sulfonylurea receptor 1 is distributed in the cytoplasm of GABAergic neurons from where the ATP-dependent channel regulates GABA release. Using a combination of specific agonists and antagonists, we were able to show that, in the striatum, modulation of GABA release through the sulfonylurea receptor 1-regulated ATP-dependent potassium channels located on GABAergic neurons controls α-synuclein release from the glutamatergic terminals through activation of the presynaptic GABAB receptors. Considering that sulfonylurea receptors can be selectively targeted, our study highlights the potential use of the key molecules in the α-synuclein secretory pathway to aid the discovery of novel therapeutic interventions for Parkinson's disease.

A Drosophila model to investigate the neurotoxic side effects of radiation exposure.

ABSTRACTChildren undergoing cranial radiation therapy (CRT) for pediatric central nervous system malignancies are at increased risk for neurological deficits later in life. We have developed a model of neurotoxic damage in adult Drosophila following irradiation during the juvenile stages with the goal of elucidating underlying neuropathological mechanisms and of ultimately identifying potential therapeutic targets. Wild-type third-instar larvae were irradiated with single doses of γ-radiation, and the percentage that survived to adulthood was determined. Motor function of surviving adults was examined with a climbing assay, and longevity was assessed by measuring lifespan. Neuronal cell death was assayed by using immunohistochemistry in adult brains. We also tested the sensitivity at different developmental stages by irradiating larvae at various time points. Irradiating late third-instar larvae at a dose of 20 Gy or higher impaired the motor activity of surviving adults. A dose of 40 Gy or higher resulted in a precipitous reduction in the percentage of larvae that survive to adulthood. A dose-dependent decrease in adult longevity was paralleled by a dose-dependent increase in activated Death caspase-1 (Dcp1) in adult brains. Survival to adulthood and adult lifespan were more severely impaired with decreasing larval age at the time of irradiation. Our initial survey of the Drosophila Genetic Reference Panel demonstrated that differences in genotype can confer phenotypic differences in radio-sensitivity for developmental survival and motor function. This work demonstrates the usefulness of Drosophila to model the toxic effects of radiation during development, and has the potential to unravel underlying mechanisms and to facilitate the discovery of novel therapeutic interventions.

Lipid homeostasis and the formation of macrophage-derived foam cells in atherosclerosis

Atherosclerosis is a chronic, inflammatory disorder characterized by the deposition of excess lipids in the arterial intima. The formation of macrophage-derived foam cells in a plaque is a hallmark of the development of atherosclerosis. Lipid homeostasis, especially cholesterol homeostasis, plays a crucial role during the formation of foam cells. Recently, lipid droplet-associated proteins, including PAT and CIDE family proteins, have been shown to control the development of atherosclerosis by regulating the formation, growth, stabilization and functions of lipid droplets in macrophage-derived foam cells. This review focuses on the potential mechanisms of formation of macrophage-derived foam cells in atherosclerosis with particular emphasis on the role of lipid homeostasis and lipid droplet-associated proteins. Understanding the process of foam cell formation will aid in the future discovery of novel therapeutic interventions for atherosclerosis.

The Future of Primary Intraocular Lymphoma (Retinal Lymphoma)

Basic science and clinical investigations in cancer research have contributed to our understanding of the genetic causes of various neoplasms and discovery of novel therapeutic interventions to fight malignancies such as lymphoma. During this exciting time, we have witnessed the advent of new technologies to further characterize primary intraocular lymphoma (PIOL), or retinal lymphoma, which is selected as the first “Disease of the Year” by Ocular Immunology and Inflammation. Different comprehensive aspects of PIOL, including epidemiology, clinical manifestations, diagnosis, pathophysiology, therapy, and animal models are discussed. The future of PIOL holds an opportunity to really understand the unique cytologic, histopathologic, physiological and immunologic features, as well as the genotypic traits (gene expression, interaction, polymorphism, epigenetics, etc.) and epidemiology. This information will empower us to truly make a difference in patients’ managements with this devastating disease. While most of this technology already exists, much work still needs to be done to make translational therapy a reality for PIOL patients in the future.

Cover Picture: Preparation and Use of Microarrays Containing Synthetic Heparin Oligosaccharides for the Rapid Analysis of Heparin–Protein Interactions (Chem. Eur. J. 34/2006)

Heparin chips were employed to characterize the binding profiles of three heparin‐binding growth factors (FGF‐1, FGF‐2, and FGF‐4). The results, presented in the Full Paper by P. H. Seeberger et al. on page 8664 ff., demonstrate the potential of synthetic heparin‐oligosaccharide microarrays to elucidate the role of defined heparin sequences in biological processes, creating an opportunity for the discovery of novel therapeutic interventions for a variety of disease states. (The protein in the cover picture was taken from the RSCB Protein Databank (1FGA.pdb).)

Animal models of neurodegenerative dementing disorders other than Alzheimer's disease

Neurodegenerative dementias other than Alzheimer's disease (AD) are complex disorders with diverse causes. Recently, there has been tremendous progress in the pathobiology and genetics of several of these diseases, some of which are associated with pathological alterations in tau and α-synuclein. These findings have led to the generation of murine and invertebrate transgenic tau and α-synuclein animal models of these disorders to facilitate elucidation of mechanisms underlying these disorders and for discovery of novel therapeutic interventions to treat them. The focus of this review will be to provide an overview of diseases that have been modeled by these transgenic animals and to highlight the findings of these studies. Overall, transgenic models have supported the notion that tau and α-synuclein play central roles in the pathobiology of many non-AD dementias and have provided important insights into the mechanisms that lead to these disorders thereby setting the stage for identifying novel targets for pharmacological interventions as well as proof of concept studies of compounds with therapeutic potential in patients.

Animal models of neurodegenerative dementing disorders other than Alzheimer's disease

Neurodegenerative dementias other than Alzheimer's disease (AD) are complex disorders with diverse causes. Recently, there has been tremendous progress in the pathobiology and genetics of several of these diseases, some of which are associated with pathological alterations in tau and α-synuclein. These findings have led to the generation of murine and invertebrate transgenic tau and α-synuclein animal models of these disorders to facilitate elucidation of mechanisms underlying these disorders and for discovery of novel therapeutic interventions to treat them. The focus of this review will be to provide an overview of diseases that have been modeled by these transgenic animals and to highlight the findings of these studies. Overall, transgenic models have supported the notion that tau and α-synuclein play central roles in the pathobiology of many non-AD dementias and have provided important insights into the mechanisms that lead to these disorders thereby setting the stage for identifying novel targets for pharmacological interventions as well as proof of concept studies of compounds with therapeutic potential in patients.

Clinical Importance of Understanding Vascular Biology

A comprehensive understanding of the biology of the vessel wall has fostered the discovery of novel therapeutic interventions. The vascular endothelium, smooth muscle cells, and adventitial fibroblasts exist in a tightly regulated milieu in which extravascular stimuli produce coordinated physiologic actions in each cell type, which, in turn, modulate integrative responses in the vessel wall. When vascular injury occurs as a result of biochemical or mechanical forces, such as in hypertension, atherosclerosis, or restenosis, normal homeostatic mechanisms are perturbed, and if compensatory mechanisms are overwhelmed, the vessel becomes dysfunctional. These states are characterized by changes in regulatory molecules that stimulate aberrant responses. Recent advances in molecular biology, including gene transfer and antisense technology, have been used successfully to replete or diminish these factors and restore vascular homeostasis. We present an overview of basic vascular biology as it relates to relevant clinical vascular pathobiology and molecular therapeutics.