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Zhou X, Wang ZJ, Camps J, Tomek J, Santiago A, Quintanas A, Vazquez M, Vaseghi M, Rodriguez B. Clinical phenotypes in acute and chronic infarction explained through human ventricular electromechanical modelling and simulations. eLife 2024; 13:RP93002. [PMID: 39711335 DOI: 10.7554/elife.93002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2024] Open
Abstract
Sudden death after myocardial infarction (MI) is associated with electrophysiological heterogeneities and ionic current remodelling. Low ejection fraction (EF) is used in risk stratification, but its mechanistic links with pro-arrhythmic heterogeneities are unknown. We aim to provide mechanistic explanations of clinical phenotypes in acute and chronic MI, from ionic current remodelling to ECG and EF, using human electromechanical modelling and simulation to augment experimental and clinical investigations. A human ventricular electromechanical modelling and simulation framework is constructed and validated with rich experimental and clinical datasets, incorporating varying degrees of ionic current remodelling as reported in literature. In acute MI, T-wave inversion and Brugada phenocopy were explained by conduction abnormality and local action potential prolongation in the border zone. In chronic MI, upright tall T-waves highlight large repolarisation dispersion between the border and remote zones, which promoted ectopic propagation at fast pacing. Post-MI EF at resting heart rate was not sensitive to the extent of repolarisation heterogeneity and the risk of repolarisation abnormalities at fast pacing. T-wave and QT abnormalities are better indicators of repolarisation heterogeneities than EF in post-MI.
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Choi YJ, Park HJ, Kim CY, Choi A, Cho JH, Byun MK. Dynamic microbial changes in exacerbation of chronic obstructive pulmonary disease. Front Microbiol 2024; 15:1507090. [PMID: 39712895 PMCID: PMC11659282 DOI: 10.3389/fmicb.2024.1507090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 11/13/2024] [Indexed: 12/24/2024] Open
Abstract
Background Microbial profiles in patients with chronic obstructive pulmonary disease (COPD) provide insights for predicting, preventing, and treating exacerbations. This study aimed to analyze the impact of microbial diversity and spectrum on COPD exacerbation. Methods From November 1, 2018, to May 31, 2023, we prospectively enrolled patients with stable disease (SD) and exacerbation of COPD (ECOPD). Sputum samples were collected for microbiome DNA sequencing, and amplicon sequence variants were analyzed. Results We collected sputum samples from 38 patients: 17 samples from patients with SD and samples from patients with ECOPD at two time points-during exacerbation (AE-1: 21 samples) and again during stabilization after 2 weeks of treatment (AE-2: 17 samples). Alpha diversity indices, specifically observed feature count and Fisher's alpha index, were significantly higher in SD (133.0 [98.0-145.0]; 17.1 [12.7-19.6]) compared to AE-1 (88.0 [72.0-125.0], p = 0.025; 10.9 [8.5-16.1], p = 0.031). The SD showed significantly higher abundances of Neisseria (linear discriminant analysis [LDA] 4.996, adj.p = 0.021), Fusobacterium (LDA 3.688, adj.p = 0.047), and Peptostreptococcus (LDA 3.379, adj.p = 0.039) at the genus level compared to AE-1. At the species level, N. perflava (LDA 5.074, adj.p = 0.010) and H. parainfluenzae (LDA 4.467, adj. p = 0.011) were more abundant in SD. Hub genera in the microbial network included Haemophilus, Granulicatella, Neisseria, Lactobacillus, and Butyrivibrio in SD and Streptococcus, Gemella, Actinomyces, Klebsiella, and Staphylococcus in AE-1. Conclusion COPD exacerbations are linked to changes in specific strains of normal flora. Maintaining microbial diversity and balance within the microbial network is critical for preventing and managing COPD exacerbations.
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Oliveira D, Nishimura AL. Editorial: Mechanisms of neurodegeneration in amyotrophic lateral sclerosis and related disorders. Front Cell Neurosci 2024; 18:1531449. [PMID: 39703459 PMCID: PMC11655186 DOI: 10.3389/fncel.2024.1531449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 12/21/2024] Open
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Du C, Liu J, Liu S, Xiao P, Chen Z, Chen H, Huang W, Lei Y. Bone and Joint-on-Chip Platforms: Construction Strategies and Applications. SMALL METHODS 2024; 8:e2400436. [PMID: 38763918 DOI: 10.1002/smtd.202400436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/28/2024] [Indexed: 05/21/2024]
Abstract
Organ-on-a-chip, also known as "tissue chip," is an advanced platform based on microfluidic systems for constructing miniature organ models in vitro. They can replicate the complex physiological and pathological responses of human organs. In recent years, the development of bone and joint-on-chip platforms aims to simulate the complex physiological and pathological processes occurring in human bones and joints, including cell-cell interactions, the interplay of various biochemical factors, the effects of mechanical stimuli, and the intricate connections between multiple organs. In the future, bone and joint-on-chip platforms will integrate the advantages of multiple disciplines, bringing more possibilities for exploring disease mechanisms, drug screening, and personalized medicine. This review explores the construction and application of Organ-on-a-chip technology in bone and joint disease research, proposes a modular construction concept, and discusses the new opportunities and future challenges in the construction and application of bone and joint-on-chip platforms.
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de Weerd HA, Guala D, Gustafsson M, Synnergren J, Tegnér J, Lubovac-Pilav Z, Magnusson R. Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules. PATTERNS (NEW YORK, N.Y.) 2024; 5:101093. [PMID: 39568475 PMCID: PMC11573900 DOI: 10.1016/j.patter.2024.101093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/26/2024] [Accepted: 10/11/2024] [Indexed: 11/22/2024]
Abstract
Computational analyses of transcriptomic data have dramatically improved our understanding of complex diseases. However, such approaches are limited by small sample sets of disease-affected material. We asked if a variational autoencoder trained on large groups of healthy human RNA sequencing (RNA-seq) data can capture the fundamental gene regulation system and generalize to unseen disease changes. Importantly, we found this model to successfully compress unseen transcriptomic changes from 25 independent disease datasets. We decoded disease-specific signals from the latent space and found them to contain more disease-specific genes than the corresponding differential expression analysis in 20 of 25 cases. Finally, we matched these disease signals with known drug targets and extracted sets of known and potential pharmaceutical candidates. In summary, our study demonstrates how data-driven representation learning enables the arithmetic deconstruction of the latent space, facilitating the dissection of disease mechanisms and drug targets.
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Xiong Y, Yu J. LRRK2 in Parkinson's disease: upstream regulation and therapeutic targeting. Trends Mol Med 2024; 30:982-996. [PMID: 39153957 PMCID: PMC11466701 DOI: 10.1016/j.molmed.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 08/19/2024]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common causes of Parkinson's disease (PD) to date. Dysfunction in LRRK2 enzymatic activities and elevated protein levels are associated with the disease. How is LRRK2 activated, and what downstream molecular and cellular processes does LRRK2 regulate? Addressing these questions is crucial to decipher the disease mechanisms. In this review we focus on the upstream regulations and briefly discuss downstream substrates of LRRK2 as well as the cellular consequences caused by these regulations. Building on these basic findings, we discuss therapeutic strategies targeting LRRK2 and highlight the challenges in clinical trials. We further highlight the important questions that remains to be answered in the LRRK2 field.
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Tasoula A, Szewczyk N. Astronaut proteomics: Japan leads the way for transformative studies in space. Proteomics 2024; 24:e2300645. [PMID: 39388383 DOI: 10.1002/pmic.202300645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/17/2024] [Indexed: 10/12/2024]
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Du J, Shui H, Chen R, Dong Y, Xiao C, Hu Y, Wong NK. Neuraminidase-1 (NEU1): Biological Roles and Therapeutic Relevance in Human Disease. Curr Issues Mol Biol 2024; 46:8031-8052. [PMID: 39194692 DOI: 10.3390/cimb46080475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024] Open
Abstract
Neuraminidases catalyze the desialylation of cell-surface glycoconjugates and play crucial roles in the development and function of tissues and organs. In both physiological and pathophysiological contexts, neuraminidases mediate diverse biological activities via the catalytic hydrolysis of terminal neuraminic, or sialic acid residues in glycolipid and glycoprotein substrates. The selective modulation of neuraminidase activity constitutes a promising strategy for treating a broad spectrum of human pathologies, including sialidosis and galactosialidosis, neurodegenerative disorders, cancer, cardiovascular diseases, diabetes, and pulmonary disorders. Structurally distinct as a large family of mammalian proteins, neuraminidases (NEU1 through NEU4) possess dissimilar yet overlapping profiles of tissue expression, cellular/subcellular localization, and substrate specificity. NEU1 is well characterized for its lysosomal catabolic functions, with ubiquitous and abundant expression across such tissues as the kidney, pancreas, skeletal muscle, liver, lungs, placenta, and brain. NEU1 also exhibits a broad substrate range on the cell surface, where it plays hitherto underappreciated roles in modulating the structure and function of cellular receptors, providing a basis for it to be a potential drug target in various human diseases. This review seeks to summarize the recent progress in the research on NEU1-associated diseases and highlight the mechanistic implications of NEU1 in disease pathogenesis. An improved understanding of NEU1-associated diseases should help accelerate translational initiatives to develop novel or better therapeutics.
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Smith NJ, May LT, Grimsey NL. Highlights and hot topics in GPCR research from 'Down Under'. Br J Pharmacol 2024; 181:2091-2094. [PMID: 38798136 DOI: 10.1111/bph.16419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
LINKED ARTICLES This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
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Gehrke EJ, Pandey A, Thompson J, Bhattarai S, Gurung P, Hsu Y, Drack AV. Investigating the role of Caspase-1 in a mouse model of Juvenile X-linked Retinoschisis. Front Med (Lausanne) 2024; 11:1347599. [PMID: 38938378 PMCID: PMC11208328 DOI: 10.3389/fmed.2024.1347599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 06/29/2024] Open
Abstract
Purpose Previous studies have reported Caspase-1 (Casp1) is upregulated in mouse models of Juvenile X-linked Retinoschisis (XLRS), however no functional role for Casp1 in disease progression has been identified. We performed electroretinogram (ERG) and standardized optical coherence tomography (OCT) in mice deficient in the Retinoschisin-1 (Rs1) and Casp1 and Caspase-11 (Casp11) genes (Rs1-KO;Casp1/11-/- ) to test the hypothesis that Casp1 may play a role in disease evolution and or severity of disease. Currently, no studies have ventured to investigate the longer-term effects of Casp1 on phenotypic severity and disease progression over time in XLRS, and specifically the effect on electroretinogram. Methods Rs1-KO;Casp1/11-/- mice were generated by breeding Rs1-KO mice with Casp1/11-/- mice. OCT imaging was analyzed at 2-, 4-, and 15-16 months of age. Outer nuclear layer (ONL) thickness and adapted standardized cyst severity score were measured and averaged from 4 locations 500 μm from the optic nerve. Adapted standardized cyst severity score was 1: absent cysts, 2: <30 μm, 3: 30-49 μm, 4: 50-69 μm, 5: 70-99 μm, 6: >99 μm. Electroretinograms (ERG) were recorded in dark-adapted and light-adapted conditions at 2 and 4 months. Results obtained from Rs1-KO and Rs1-KO;Casp1/11-/- eyes were compared with age matched WT control eyes at 2 months. Results Intraretinal schisis was not observed on OCT in WT eyes, while schisis was apparent in most Rs1-KO and Rs1-KO;Casp1/11-/- eyes at 2 and 4 months of age. There was no difference in the cyst severity score from 2 to 4 months of age, or ONL thickness from 2 to 16 months of age between Rs1-KO and Rs1-KO;Casp1/11-/- eyes. ERG amplitudes were similarly reduced in Rs1-KO and Rs1-KO;Casp1/11-/- compared to WT controls at 2 months of age, and there was no difference between Rs1-KO and Rs1-KO;Casp1/11-/- eyes at 2 or 4 months of age, suggesting no impact on the electrical function of photoreceptors over time in the absence of Casp1. Conclusion Although Casp1 has been reported to be significantly upregulated in Rs1-KO mice, our preliminary data suggest that removing Casp1/11 does not modulate photoreceptor electrical function or alter the trajectory of the retinal architecture over time.
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Honoré B, Hajari JN, Pedersen TT, Ilginis T, Al-Abaiji HA, Lønkvist CS, Saunte JP, Olsen DA, Brandslund I, Vorum H, Slidsborg C. Proteomic analysis of diabetic retinopathy identifies potential plasma-protein biomarkers for diagnosis and prognosis. Clin Chem Lab Med 2024; 62:1177-1197. [PMID: 38332693 DOI: 10.1515/cclm-2023-1128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/10/2024]
Abstract
OBJECTIVES To identify molecular pathways and prognostic- and diagnostic plasma-protein biomarkers for diabetic retinopathy at various stages. METHODS This exploratory, cross-sectional proteomics study involved plasma from 68 adults, including 15 healthy controls and 53 diabetes patients for various stages of diabetic retinopathy: non-diabetic retinopathy, non-proliferative diabetic retinopathy, proliferative diabetic retinopathy and diabetic macular edema. Plasma was incubated with peptide library beads and eluted proteins were tryptic digested, analyzed by liquid chromatography-tandem mass-spectrometry followed by bioinformatics. RESULTS In the 68 samples, 248 of the 731 identified plasma-proteins were present in all samples. Analysis of variance showed differential expression of 58 proteins across the five disease subgroups. Protein-Protein Interaction network (STRING) showed enrichment of various pathways during the diabetic stages. In addition, stage-specific driver proteins were detected for early and advanced diabetic retinopathy. Hierarchical clustering showed distinct protein profiles according to disease severity and disease type. CONCLUSIONS Molecular pathways in the cholesterol metabolism, complement system, and coagulation cascade were enriched in patients at various stages of diabetic retinopathy. The peroxisome proliferator-activated receptor signaling pathway and systemic lupus erythematosus pathways were enriched in early diabetic retinopathy. Stage-specific proteins for early - and advanced diabetic retinopathy as determined herein could be 'key' players in driving disease development and potential 'target' proteins for future therapies. For type 1 and 2 diabetes mellitus, the proteomic profiles were especially distinct during the early disease stage. Validation studies should aim to clarify the role of the detected molecular pathways, potential biomarkers, and potential 'target' proteins for future therapies in diabetic retinopathy.
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Nguyen L. Updates on Disease Mechanisms and Therapeutics for Amyotrophic Lateral Sclerosis. Cells 2024; 13:888. [PMID: 38891021 PMCID: PMC11172142 DOI: 10.3390/cells13110888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is a motor neuron disease. In ALS, upper and lower motor neurons in the brain and spinal cord progressively degenerate during the course of the disease, leading to the loss of the voluntary movement of the arms and legs. Since its first description in 1869 by a French neurologist Jean-Martin Charcot, the scientific discoveries on ALS have increased our understanding of ALS genetics, pathology and mechanisms and provided novel therapeutic strategies. The goal of this review article is to provide a comprehensive summary of the recent findings on ALS mechanisms and related therapeutic strategies to the scientific audience. Several highlighted ALS research topics discussed in this article include the 2023 FDA approved drug for SOD1 ALS, the updated C9orf72 GGGGCC repeat-expansion-related mechanisms and therapeutic targets, TDP-43-mediated cryptic splicing and disease markers and diagnostic and therapeutic options offered by these recent discoveries.
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Hu Y, Chen W, Wei C, Jiang S, Li S, Wang X, Xu R. Pathological mechanisms of amyotrophic lateral Sclerosis. Neural Regen Res 2024; 19:1036-1044. [PMID: 37862206 PMCID: PMC10749610 DOI: 10.4103/1673-5374.382985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 10/22/2023] Open
Abstract
Amyotrophic lateral sclerosis refers to a neurodegenerative disease involving the motor system, the cause of which remains unexplained despite several years of research. Thus, the journey to understanding or treating amyotrophic lateral sclerosis is still a long one. According to current research, amyotrophic lateral sclerosis is likely not due to a single factor but rather to a combination of mechanisms mediated by complex interactions between molecular and genetic pathways. The progression of the disease involves multiple cellular processes and the interaction between different complex mechanisms makes it difficult to identify the causative factors of amyotrophic lateral sclerosis. Here, we review the most common amyotrophic lateral sclerosis-associated pathogenic genes and the pathways involved in amyotrophic lateral sclerosis, as well as summarize currently proposed potential mechanisms responsible for amyotrophic lateral sclerosis disease and their evidence for involvement in amyotrophic lateral sclerosis. In addition, we discuss current emerging strategies for the treatment of amyotrophic lateral sclerosis. Studying the emergence of these new therapies may help to further our understanding of the pathogenic mechanisms of the disease.
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Roque A, Pereira SG. Bacteria: Potential Make-or-Break Determinants of Celiac Disease. Int J Mol Sci 2024; 25:2090. [PMID: 38396767 PMCID: PMC10889687 DOI: 10.3390/ijms25042090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 02/25/2024] Open
Abstract
Celiac disease is an autoimmune disease triggered by dietary gluten in genetically susceptible individuals that primarily affects the small intestinal mucosa. The sole treatment is a gluten-free diet that places a social and economic burden on patients and fails, in some, to lead to symptomatic or mucosal healing. Thus, an alternative treatment has long been sought after. Clinical studies on celiac disease have shown an association between the presence of certain microbes and disease outcomes. However, the mechanisms that underlie the effects of microbes in celiac disease remain unclear. Recent studies have employed disease models that have provided insights into disease mechanisms possibly mediated by bacteria in celiac disease. Here, we have reviewed the bacteria and related mechanisms identified so far that might protect from or incite the development of celiac disease. Evidence indicates bacteria play a role in celiac disease and it is worth continuing to explore this, particularly since few studies, to the best of our knowledge, have focused on establishing a mechanistic link between bacteria and celiac disease. Uncovering host-microbe interactions and their influence on host responses to gluten may enable the discovery of pathogenic targets and development of new therapeutic or preventive approaches.
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Schiopu A, Björkbacka H, Narasimhan G, Loong BJ, Engström G, Melander O, Orho-Melander M, Nilsson J. Elevated soluble LOX-1 predicts risk of first-time myocardial infarction. Ann Med 2023; 55:2296552. [PMID: 38134912 PMCID: PMC10763917 DOI: 10.1080/07853890.2023.2296552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND There is an unmet clinical need for novel therapies addressing the residual risk in patients receiving guideline preventive therapy for coronary heart disease. Experimental studies have identified a pro-atherogenic role of the oxidized LDL receptor LOX-1. We investigated the association between circulating soluble LOX-1 (sLOX-1) and the risk for development of myocardial infarction. METHODS The study subjects (n = 4658) were part of the Malmö Diet and Cancer study. The baseline investigation was carried out 1991-1994 and the incidence of cardiovascular events monitored through national registers during a of 19.5 ± 4.9 years follow-up. sLOX-1 and other biomarkers were analyzed by proximity extension assay and ELISA in baseline plasma. RESULTS Subjects in the highest tertile of sLOX-1 had an increased risk of myocardial infarction (hazard ratio (95% CI) 1.76 (1.40-2.21) as compared with those in the lowest tertile. The presence of cardiovascular risk factors was related to elevated sLOX-1, but the association between sLOX-1 and risk of myocardial infarction remained significant when adjusting for risk factors. CONCLUSIONS In this prospective population study we found an association between elevated sLOX-1, the presence of carotid disease and the risk for first-time myocardial infarction. Taken together with previous experimental findings of a pro-atherogenic role of LOX-1, this observation supports LOX-1 inhibition as a possible target for prevention of myocardial infarction.
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Mazein A, Acencio ML, Balaur I, Rougny A, Welter D, Niarakis A, Ramirez Ardila D, Dogrusoz U, Gawron P, Satagopam V, Gu W, Kremer A, Schneider R, Ostaszewski M. A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. FRONTIERS IN BIOINFORMATICS 2023; 3:1197310. [PMID: 37426048 PMCID: PMC10325725 DOI: 10.3389/fbinf.2023.1197310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.
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Szabo L, McCracken C, Cooper J, Rider OJ, Vago H, Merkely B, Harvey NC, Neubauer S, Petersen SE, Raisi-Estabragh Z. The role of obesity-related cardiovascular remodelling in mediating incident cardiovascular outcomes: a population-based observational study. Eur Heart J Cardiovasc Imaging 2023; 24:921-929. [PMID: 36660920 PMCID: PMC10284050 DOI: 10.1093/ehjci/jeac270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/01/2022] [Indexed: 01/21/2023] Open
Abstract
AIMS We examined associations of obesity with incident cardiovascular outcomes and cardiovascular magnetic resonance (CMR) phenotypes, integrating information from body mass index (BMI) and waist-to-hip ratio (WHR). Then, we used multiple mediation to define the role of obesity-related cardiac remodelling in driving obesity-outcome associations, independent of cardiometabolic diseases. METHODS AND RESULTS In 491 606 UK Biobank participants, using Cox proportional hazard models, greater obesity (higher WHR, higher BMI) was linked to significantly greater risk of incident ischaemic heart disease, atrial fibrillation (AF), heart failure (HF), all-cause mortality, and cardiovascular disease (CVD) mortality. In combined stratification by BMI and WHR thresholds, elevated WHR was associated with greater risk of adverse outcomes at any BMI level. Individuals with overweight BMI but normal WHR had weaker disease associations. In the subset of participants with CMR (n = 31 107), using linear regression, greater obesity was associated with higher left ventricular (LV) mass, greater LV concentricity, poorer LV systolic function, lower myocardial native T1, larger left atrial (LA) volumes, poorer LA function, and lower aortic distensibility. Of note, higher BMI was linked to higher, whilst greater WHR was linked to lower LV end-diastolic volume (LVEDV). In Cox models, greater LVEDV and LV mass (LVM) were linked to increased risk of CVD, most importantly HF and an increased LA maximal volume was the key predictive measure of new-onset AF. In multiple mediation analyses, hypertension and adverse LV remodelling (higher LVM, greater concentricity) were major independent mediators of the obesity-outcome associations. Atrial remodelling and native T1 were additional mediators in the associations of obesity with AF and HF, respectively. CONCLUSIONS We demonstrate associations of obesity with adverse cardiovascular phenotypes and their significant independent role in mediating obesity-outcome relationships. In addition, our findings support the integrated use of BMI and WHR to evaluate obesity-related cardiovascular risk.
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Karnik I, Her Z, Neo SH, Liu WN, Chen Q. Emerging Preclinical Applications of Humanized Mouse Models in the Discovery and Validation of Novel Immunotherapeutics and Their Mechanisms of Action for Improved Cancer Treatment. Pharmaceutics 2023; 15:1600. [PMID: 37376049 DOI: 10.3390/pharmaceutics15061600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer therapeutics have undergone immense research over the past decade. While chemotherapies remain the mainstay treatments for many cancers, the advent of new molecular techniques has opened doors for more targeted modalities towards cancer cells. Although immune checkpoint inhibitors (ICIs) have demonstrated therapeutic efficacy in treating cancer, adverse side effects related to excessive inflammation are often reported. There is a lack of clinically relevant animal models to probe the human immune response towards ICI-based interventions. Humanized mouse models have emerged as valuable tools for pre-clinical research to evaluate the efficacy and safety of immunotherapy. This review focuses on the establishment of humanized mouse models, highlighting the challenges and recent advances in these models for targeted drug discovery and the validation of therapeutic strategies in cancer treatment. Furthermore, the potential of these models in the process of uncovering novel disease mechanisms is discussed.
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Gogia N, Tare M, Kannan R, Singh A. Editorial: Protein misfolding, altered mechanisms and neurodegeneration. Front Mol Neurosci 2023; 16:1134855. [PMID: 36818654 PMCID: PMC9930101 DOI: 10.3389/fnmol.2023.1134855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
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Rose TD, Köhler N, Falk L, Klischat L, Lazareva OE, Pauling JK. Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data. Brief Bioinform 2023; 24:bbac572. [PMID: 36592059 PMCID: PMC9851308 DOI: 10.1093/bib/bbac572] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 01/03/2023] Open
Abstract
Lipidomics is of growing importance for clinical and biomedical research due to many associations between lipid metabolism and diseases. The discovery of these associations is facilitated by improved lipid identification and quantification. Sophisticated computational methods are advantageous for interpreting such large-scale data for understanding metabolic processes and their underlying (patho)mechanisms. To generate hypothesis about these mechanisms, the combination of metabolic networks and graph algorithms is a powerful option to pinpoint molecular disease drivers and their interactions. Here we present lipid network explorer (LINEX$^2$), a lipid network analysis framework that fuels biological interpretation of alterations in lipid compositions. By integrating lipid-metabolic reactions from public databases, we generate dataset-specific lipid interaction networks. To aid interpretation of these networks, we present an enrichment graph algorithm that infers changes in enzymatic activity in the context of their multispecificity from lipidomics data. Our inference method successfully recovered the MBOAT7 enzyme from knock-out data. Furthermore, we mechanistically interpret lipidomic alterations of adipocytes in obesity by leveraging network enrichment and lipid moieties. We address the general lack of lipidomics data mining options to elucidate potential disease mechanisms and make lipidomics more clinically relevant.
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Łabaj PP, Dopazo J, Xiao W, Kreil DP. Editorial: Critical assessment of massive data analysis (CAMDA) annual conference 2021. Front Genet 2023; 14:1154398. [PMID: 36873943 PMCID: PMC9978925 DOI: 10.3389/fgene.2023.1154398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
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Zhang X, Flaws JA, Spinella MJ, Irudayaraj J. The Relationship between Typical Environmental Endocrine Disruptors and Kidney Disease. TOXICS 2022; 11:32. [PMID: 36668758 PMCID: PMC9863798 DOI: 10.3390/toxics11010032] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 05/12/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are exogenous substances that alter the endocrine function of an organism, to result in adverse effects on growth and development, metabolism, and reproductive function. The kidney is one of the most important organs in the urinary system and an accumulation point. Studies have shown that EDCs can cause proteinuria, affect glomeruli and renal tubules, and even lead to diabetes and renal fibrosis in animal and human studies. In this review, we discuss renal accumulation of select EDCs such as dioxins, per- and polyfluoroalkyl substances (PFAS), bisphenol A (BPA), and phthalates, and delineate how exposures to such EDCs cause renal lesions and diseases, including cancer. The regulation of typical EDCs with specific target genes and the activation of related pathways are summarized.
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Nold-Petry CA, Nold MF. Rationale for IL-37 as a novel therapeutic agent in inflammation. Expert Rev Clin Immunol 2022; 18:1203-1206. [PMID: 35916240 DOI: 10.1080/1744666x.2022.2108792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Induced Pluripotent Stem Cell (iPSC) Lines from a Family with Resistant Epileptic Encephalopathy Caused by Compound Heterozygous Mutations in SZT2 Gene. Int J Mol Sci 2022; 23:ijms232113095. [PMID: 36361881 PMCID: PMC9654488 DOI: 10.3390/ijms232113095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations in the SZT2 gene have been associated with developmental and epileptic encephalopathy-18, a rare severe autosomal recessive neurologic disorder, characterized by psychomotor impairment/intellectual disability, dysmorphic facial features and early onset of refractory seizures. Here we report the generation of the first induced pluripotent stem cell (iPSC) lines from a patient with treatment-resistant epilepsy, carrying compound heterozygous mutations in SZT2 (Mut1: c.498G>T and Mut2: c.6553C>T), and his healthy heterozygous parents. Peripheral blood mononuclear cells were reprogrammed by a non-integrating Sendai virus-based reprogramming system. The generated human iPSC lines exhibited expression of the main pluripotency markers, the potential to differentiate into all three germ layers and presented a normal karyotype. These lines represent a valuable resource to study neurodevelopmental alterations, and to obtain mature, pathology-relevant neuronal populations as an in vitro model to perform functional assays and test the patient’s responsiveness to novel antiepileptic treatments.
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Subtypes and Mechanisms of Hypertrophic Cardiomyopathy Proposed by Machine Learning Algorithms. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101566. [PMID: 36294999 PMCID: PMC9605444 DOI: 10.3390/life12101566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) is a relatively common inherited cardiac disease that results in left ventricular hypertrophy. Machine learning uses algorithms to study patterns in data and develop models able to make predictions. The aim of this study is to identify HCM subtypes and examine the mechanisms of HCM using machine learning algorithms. Clinical and laboratory findings of 143 adult patients with a confirmed diagnosis of nonobstructive HCM are analyzed; HCM subtypes are determined by clustering, while the presence of different HCM features is predicted in classification machine learning tasks. Four clusters are determined as the optimal number of clusters for this dataset. Models that can predict the presence of particular HCM features from other genotypic and phenotypic information are generated, and subsets of features sufficient to predict the presence of other features of HCM are determined. This research proposes four subtypes of HCM assessed by machine learning algorithms and based on the overall phenotypic expression of the participants of the study. The identified subsets of features sufficient to determine the presence of particular HCM aspects could provide deeper insights into the mechanisms of HCM.
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