Proteomic Analysis of carboxylate-free and NE-mimetic Rare-Earth-Based Nanoprobes
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus Musculus
SUBMITTER: 
Yeteng Zhong
PROVIDER: PXD080114 | iProX | Tue Jun 23 00:00:00 BST 2026
REPOSITORIES: iProX
Similar Datasets
Project description:Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone. Intravenous immunoglobulin (IVIG) treatment-resistant patients are high risk of developing coronary artery lesions (CALs) with Kawasaki disease (KD). The IVIG-responsive (Group A; n = 6) and -resistant patients (Group B) were predicted before starting the initial treatment using the Egami scoring system, and randomly allocated a single-IVIG treatment group (Group B1; n = 6) or a IVIG-plus-methylprednisolone (IVMP) combined therapy group (Group B2; n = 5). We investigated transcript abundance in the leukocytes of those patients using microarray analysis. Results: five patients in Group A and 1 patient in Group B1 responded to initial IVIG treatment. All Group B2 patients responded to IVIP-plus-IVMP combined therapy. Prior to performing these treatments, those transcripts related to IVIG-resistance and to the development of CALs, such as IL1R, IL18R, oncostatin M, suppressor of cytokine signaling-3, S100A12 protein, carcinoembryonic antigen-related cell adhesion molecule-1, matrix metallopeptidase-9 and polycythemia rubra vera-1 were more abundant in Group B patients in comparison to Group A patients. Moreover, those transcripts in Group B2 patients were more profoundly and broadly suppressed than Group B1 patients after treatment. Conclusion: this study elucidated the molecular mechanism of the effectiveness of IVIG-plus-IVMP combined therapy.
2010-06-17 | GSE16797 | GEO
Project description:Neurogenesis and gliogenesis continue in the Ventricular-Subventricular Zone (V-SVZ) of the adult rodent brain. B1 cells are radial glia-derived astroglial cells that function as primary progenitors or neural stem cells (NSCs) in the V-SVZ. B1 cells, which have an apical contact with the ventricle, decline during early postnatal life, yet neurogenesis continues into adulthood. We found that a second population of V-SVZ astroglial cells (B2 cells), that do not contact the ventricle, function as NSCs in the adult brain. B2 cell numbers increase postnatally, remain constant in 12-month-old mice, and decrease by 18 months. Transcriptomic analysis revealed differences between B1 and B2 cells and shows that like B1 cells, B2 cells can be quiescent or activated. Transplantation and lineage tracing of B2 cells demonstrate their function as primary progenitors for adult neurogenesis. This study reveals that NSC function is relayed from B1 to B2 progenitors to maintain adult neurogenesis.
2025-01-10 | GSE282956 | GEO
Project description:Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone. Intravenous immunoglobulin (IVIG) treatment-resistant patients are high risk of developing coronary artery lesions (CALs) with Kawasaki disease (KD). The IVIG-responsive (Group A; n = 6) and -resistant patients (Group B) were predicted before starting the initial treatment using the Egami scoring system, and randomly allocated a single-IVIG treatment group (Group B1; n = 6) or a IVIG-plus-methylprednisolone (IVMP) combined therapy group (Group B2; n = 5). We investigated transcript abundance in the leukocytes of those patients using microarray analysis. Results: five patients in Group A and 1 patient in Group B1 responded to initial IVIG treatment. All Group B2 patients responded to IVIP-plus-IVMP combined therapy. Prior to performing these treatments, those transcripts related to IVIG-resistance and to the development of CALs, such as IL1R, IL18R, oncostatin M, suppressor of cytokine signaling-3, S100A12 protein, carcinoembryonic antigen-related cell adhesion molecule-1, matrix metallopeptidase-9 and polycythemia rubra vera-1 were more abundant in Group B patients in comparison to Group A patients. Moreover, those transcripts in Group B2 patients were more profoundly and broadly suppressed than Group B1 patients after treatment. Conclusion: this study elucidated the molecular mechanism of the effectiveness of IVIG-plus-IVMP combined therapy. 34 samples of pre- and post-treatment in three groups consisting of predicted as IVIG-responsive patients, given single-IVIG treatment patients and IVIG-plus-IVMP combined therapy group in predicted as IVIG-resistant patients.
2010-07-08 | E-GEOD-16797 | biostudies-arrayexpress
Project description:Myxomatous mitral valve disease (MMVD) in Cavalier King Charles Spaniels (CKCSs) can be diagnosed at a young age. Early and sensitive biomarkers related to the disease are currently lacking. MicroRNAs (miRNAs) are involved in the onset and progression of canine MMVD. This study aimed to profile the salivary miRNAs associated with MMVD severity in CKCSs and to identify their target genes. This was a pilot prospective, cross-sectional study. Saliva was collected from twenty-five CKCSs belonging to the American College of Veterinary Internal Medicine (ACVIM) stages A (n. 6), B1 (n. 13), and B2 (n. 6), and salivary miRNAs’ expression was profiled by Next Generation Sequencing. MiRNAs’ target genes were identified using bioinformatic tools. Results showed that 25 miRNAs were differentially expressed (DE) in the ACVIM A versus B1 group; 35 DE-miRNAs were identified in the ACVIM B2 versus B1 group; 4 miRNAs were up-regulated in ACVIM stage B1 patients compared to both ACVIM stages A and B2. The identified miRNAs impacted genes related to cell survival and functions. Results demonstrated that miRNAs can be extracted and quantified from canine saliva, and that their profile changes following disease progression. Validation studies are necessary to investigate their diagnostic value.
2026-01-27 | GSE307507 | GEO
Project description:Three innate (B1-B, NKT, CD8aaT cells) and adaptive (B2-B, CD4T, CD8abT cells) cell-types were sorted by FACS. Three biological replicates for NKT, CD4T, CD8aaT, CD8abT cells and two biological replicates for B1 and B2 cells were generated and the expression profiles were determined using Affymetrix Mu74Av2 chip. Comparisons between the sample groups allow the identification of genes differentially expressed between the innate and adaptive cell-types. Experiment Overall Design: 3 biological replicates for NKT, CD4T, CD8aaT, CD8abT cells and 2 biological replicates for B1, B2 cells were analyzed
2008-06-12 | E-GEOD-3039 | biostudies-arrayexpress
Project description:Humoral immunity in mammals relies on the function of two developmentally and functionally distinct B cell subsets - B1 and B2 cells. While B2 cells are responsible for the adaptive response to environmental antigens, B1 cells regulate the production of polyreactive and low affinity antibodies for innate humoral immunity. The molecular mechanism of B cell specification into different subsets is understudied. We identified lysine methyltransferase NSD2 (MMSET/WHSC1) as a critical regulator of B1 cell development. In contrast to its minor impact on B2 cells, deletion of the catalytic domain of NSD2 in primary B cells impairs the generation of B1 lineage. Thus, NSD2, a histone H3 K36 dimethylase, is the first-in-class epigenetic regulator of a B cell lineage in mice.
2020-09-30 | GSE155689 | GEO
Project description:Gene expression is regulated by chromatin DNA methylation and other features, including histone post-translational modifications (PTMs), chromatin remodelers, and transcription factor occupancy. A complete understanding of gene regulation will require the mapping of these chromatin features in small cell number samples. Here we describe a novel genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq). NEED-seq offers antibody-targeted controlled nicking by Nt.CviPII-pGL fusion to study specific protein-DNA complexes in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide profile of chromatin associated proteins and histone PTMs. Additionally, NEED-seq of lamin B1 and B2 demonstrated their association with heterochromatin. Lamin B1 and B2 associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1 and B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1 and B2 partitioning to facultative and constitutive heterochromatin respectively and were associated with neuronal development. Thus, lamin B1 and B2 show structural and functional partitioning in mammalian nucleus.
2025-01-16 | GSE261834 | GEO
Project description:Development and progression of myxomatous mitral valve disease (MMVD) in domestic dogs is unpredictable and pathobiology still unclear. The American College of Veterinary Internal Medicine (ACVIM) perceived that mayor improvement in management of diseased dogs would be timely diagnosis, especially detection of transition from MMVD stage B1 into B2. Thus, in this study we compared by tandem mass tag (TMT) protocol and mass spectrometry (MS) acquired quantitative proteome profiles of serum collected from healthy (control) (N=12) and dogs diagnosed with different stages of naturally occurring MMVD: B1 (N=13), B2 (N=12) and C (N=13). Prior to proteomic analysis dogs were distinguished into experimental categories based on echocardiography results. Serum biochemistry and concentrations of three cardiac biomarkers (galectin-3, suppression of tumorigenicity 2 and asymmetric dimethylarginine) were performed to obtain better characterization of healthy/control group and MMVD cases.
2023-05-10 | PXD038475 | Pride
Project description:<p>Background: Parturition is a critical event in the reproductive cycle of dairy animals, accompanied by multiple physiological changes in sex hormones, metabolism, antioxidant capacity and immune function. However, the changes in the rectal microbiota and metabolic products of Jennies from late gestation to parturition affect serum antioxidant capacity and anti-inflammatory responses, but it is still unclear. The present study aimed to investigate the serum antioxidant capacity and anti-inflammatory responses of Dezhou donkeys from late gestation to parturition by analyzing rectal microbiomes and serum metabolomics.</p><p>Results: The results showed that from groups B1 to B2, serum activity of GSH-Px, IL-10 and GLU concentrations were decreased significantly. In contrast, the concentrations of MDA, IgG, LF, IL-1β, IL-2, IL-6, TNF-α and ROS increased significantly. From groups B2 to B3, serum activity of GSH-Px, CAT, SOD and T-AOC, as well as the concentrations of MDA, IgG, IL-2, AST, ALP and BHBA, were significantly increased, whereas the concentrations of IL-4, IL-10 and CRE decreased considerably. Therefore, from 35 days prepartum to parturition, Jennies experienced a gradually intensifying oxidative stress and inflammatory states, with the inflammatory response being the most severe at parturition, and with enhanced antioxidant capacity corresponding to increased oxidative damage. Microbiome analysis revealed that the group B1 significantly increased the relative abundance of Prevotella and Fibrobacteres. Group B2 significantly increased the relative abundance of Prevotellaceae_UCG-001, Streptococcus and Acetitomaculum. Group B3 showed a significant upregulation of the relative abundance of Norank_f__F082, Lachnospiraceae_UCG-009 and Prevotellaceae_UCG-004. At the same time, metabolomics analysis revealed that, compared with group B1, group B3 may alleviate inflammation and enhance the body's antioxidant function by upregulating the tryptophan and arginine metabolic pathways and enriching the differential metabolites (L-tryptophan, L-kynurenine, 3-Indoleacetonitrile, N-acetylglutamic acid). Concurrently, the elevation of these differential metabolites may be associated with the relative abundance of the beneficial bacterium Lachnospiraceae_UCG-009. However, the increase in LysoPC, a fatty acid oxidation product in glycerophospholipid metabolism, as well as the correlation between the sucrose content in the galactose metabolic pathway and the abundance of Paracoccus, indicate the reason why the Jennies are in a state of oxidative stress. Furthermore, group B1 may enhance the serum anti-inflammatory response in Jennies during late gestation by increasing the levels of estrogen in the steroid hormone biosynthesis metabolic pathway. These results could provide useful information for improving the health levels at the specific physiological stages and processes in Dezhou donkeys.</p>
2025-08-27 | MTBLS12897 | MetaboLights
Project description:miR-181a1/b1, miR-181a2/b2, and miR-181c/d belong to a highly conserved family of microRNA clusters, yet their role in vivo is poorly understood. Here we show that the miR-181a1/b1 cluster is absolutely essential for NKT development and is a critical determinant of thymocyte proliferation, survival and T-cell receptor α locus rearrangement. Furthermore, while individual ablation of miR-181a2/b2 and miR-181c/d revealed no overt phenotypes, compound mutant mice lacking both miR-181a1/b1 and miR-181a2/b2 display decreased survival, reduced body weight, and abnormal B cell development. Mechanistically, we reveal that miR-181 regulates PTEN, a key tumor suppressor whose abundance determines key metabolic adaptations required to meet the biosynthetic demands of highly proliferative tissues. These results provide important insights into the physiological function of this family of microRNAs in vivo; moreover, it places miR-181 as a central regulator of the PI3K signaling pathway and cellular metabolism. Three sorted populations of double positive (DP) thymocytes from each of two conditions (WT and miR181a1/b1 -/- mice)
2014-04-09 | E-GEOD-41090 | biostudies-arrayexpress