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PubMed2025

Differential expression of plasma proteins and pathway enrichments in pediatric diabetic ketoacidosis.

BACKGROUND: In children with type 1 diabetes (T1D), diabetic ketoacidosis (DKA) triggers a significant inflammatory response; however, the specific effector proteins and signaling pathways involved remain largely unexplored. This pediatric case-control study utilized plasma proteomics to explore protein alterations associated with severe DKA and to identify signaling pathways that associate with clinical variables. METHODS: We conducted a proteome analysis of plasma samples from 17 matched pairs of pediatric patients with T1D; one cohort with severe DKA and another with insulin-controlled diabetes. Proximity extension assays were used to quantify 3072 plasma proteins. Data analysis was performed using multivariate statistics, machine learning, and bioinformatics. RESULTS: This study identified 214 differentially expressed proteins (162 upregulated, 52 downregulated; adj P < 0.05 and a fold change > 2), reflecting cellular dysfunction and metabolic stress in severe DKA. We characterized protein expression across various organ systems and cell types, with notable alterations observed in white blood cells. Elevated inflammatory pathways suggest an enhanced inflammatory response, which may contribute to the complications of severe DKA. Additionally, upregulated pathways related to hormone signaling and nitrogen metabolism were identified, consistent with increased hormone release and associated metabolic processes, such as glycogenolysis and lipolysis. Changes in lipid and fatty acid metabolism were also observed, aligning with the lipolysis and ketosis characteristic of severe DKA. Finally, several signaling pathways were associated with clinical biochemical variables. CONCLUSIONS: Our findings highlight differentially expressed plasma proteins and enriched signaling pathways that were associated with clinical features, offering insights into the pathophysiology of severe DKA.

Humans↗

PubMed2003

Differential expression, localization and activity of two alternatively spliced isoforms of human APC regulator CDH1.

The timely destruction of key regulators through ubiquitin-mediated proteolysis ensures the orderly progression of the cell cycle. The APC (anaphase-promoting complex) is a major component of this degradation machinery and its activation is required for the execution of critical events. Recent studies have just begun to reveal the complex control of the APC through a regulatory network involving WD40 repeat proteins CDC20 and CDH1. In the present paper, we report on the identification and characterization of human CDH1beta, a novel alternatively spliced isoform of CDH1. Both CDH1alpha and CDH1beta can bind to the APC and stimulate the degradation of cyclin B1, but they are differentially expressed in human tissues and cells. CDH1alpha contains a nuclear localization signal which is absent in CDH1beta. Intracellularly, CDH1alpha appears in the nucleus whereas CDH1beta is a predominantly cytoplasmic protein. The forced overexpression of CDH1alpha in cultured cells correlates with the reduction of nuclear cyclin A, but the steady-state amount of cyclin A does not change noticeably in CDH1beta-overexpressed cells. In Xenopus embryos, ectopic overexpression of human CDH1alpha, but not of CDH1beta, induces cell-cycle arrest during the first G(1) phase at the mid-blastula transition. Taken together, our findings document the differential expression, subcellular localization and cell-cycle-regulatory activity of human CDH1 isoforms.

Alternative Splicing↗

PubMed2003

Cloning of a gene encoding an Alt a 1 isoallergen differentially expressed by the necrotrophic fungus Alternaria brassicicola during Arabidopsis infection.

Alternaria species are considered some of the most important fungi responsible for allergenic morbidity in humans. The Alternaria protein that elicits the most intense allergic reaction in humans is Alt a 1, yet no biological function has been identified for this protein. In this study, suppression subtractive hybridization and virtual Northern blots were used to identify and characterize an Alt a 1 homolog in the phytopathogenic fungus Alternaria brassicicola. RNA was extracted from A. brassicicola spores germinated in water and on leaf surfaces of the Arabidopsis ecotype Landsberg for 24 h and used to create cDNA by PCR. Double-stranded cDNA was then used in suppression subtractive hybridization to identify differentially expressed genes. mRNA transcript levels were assessed by virtual Northern blotting. A sequence with significant homology (90% amino acid, 92% cDNA) to the Alt a 1 subunit from Alternaria alternata was identified. Virtual Northern blots demonstrated that this homolog, designated Alt b 1 precursor, was highly up-regulated during the infection process of A. brassicicola on Arabidopsis: The full-length cDNA sequence of Alt b 1 was 815 bp, with an open reading frame of 477 bp. In this preliminary study, we identified a homolog of the major Alternaria allergen precursor, Alt a 1, in A. brassicicola, designated Alt b 1. This isoallergen is differentially expressed during fungal pathogenesis on Arabidopsis, suggesting a possible biological role in pathogenesis.

Allergens↗

PubMed2004

Differential expression of mitochondrial electron transport chain proteins in cardiac tissues of broilers from pulmonary hypertension syndrome-resistant and -susceptible lines.

Pulmonary hypertension syndrome (PHS) is a metabolic disease associated with the rapid growth rate of modern broilers. Broilers susceptible to PHS experience sustained elevation of pulmonary arterial pressure leading to right ventricular hypertrophy and ultimately heart failure. Previous studies have shown that mitochondrial function is defective in broilers with PHS; they use oxygen less efficiently than broilers without PHS. In this study mitochondrial electron transport chain (ETC) protein levels were compared in cardiac tissues from PHS resistant and susceptible line broilers using quantitative immunoblots. Seven of 9 anti-mammalian mitochondrial ETC protein antibodies tested exhibited cross-species reactivity. Six ETC proteins were differentially expressed in the right ventricles of broilers raised under simulated high altitude conditions (2,900 m above sea level). Four ETC proteins were present at higher levels in resistant line birds without PHS than in resistant line birds with PHS or in susceptible line birds with or without PHS. One ETC protein was present at higher levels in broilers without PHS than in broilers with PHS in both lines, and one ETC protein was present at lower levels in susceptible line birds without PHS than in susceptible line birds with PHS or in resistant line birds with or without PHS. Interestingly, differential expression of mitochondrial ETC proteins was not observed in the right ventricles of broilers raised at local altitude (390 m above sea level) nor was it observed in the left ventricles of broilers exposed to simulated high altitude. These results suggest that higher levels of mitochondrial ETC proteins in right ventricle cardiac muscle may be correlated with resistance to PHS in broilers.

Animals↗

PubMed2001

Differential expression of CXCR3 targeting chemokines CXCL10, CXCL9, and CXCL11 in different types of skin inflammation.

Recruitment of activated T-cells to the skin is a common feature in a wide variety of inflammatory skin diseases. As CXCR3 activating chemokines CXCL10 (IP-10), CXCL9 (Mig), and CXCL11 (IP-9/I-TAC) specifically attract activated T-cells, this study addressed the question of whether differences in the expression of these chemokines correlate with the site and cellular composition of the skin infiltrates in different types of inflammatory skin disease. Skin biopsies from lichen planus, chronic discoid lupus erythematosus, allergic patch test reactions, psoriasis, and Jessner's lymphocytic infiltration of the skin were investigated for chemokine expression using RNA in situ hybridization, and for the expression of CXCR3 using immunohistochemistry. The results showed differential expression of CXCL10, CXCL9, and CXCL11, which correlated with differences in the localization and cellular composition of the infiltrates. Whereas CXCL10 and CXCL11 were mainly expressed by basal keratinoctyes, CXCL9 mRNA expression was located predominantly in the dermal infiltrates. Correlation with immunohistochemical data suggested that macrophages and activated keratinocytes were the main producers of these chemokines. CXCR3 was expressed by a majority of both CD4+ and CD8+ infiltrating T-cells, suggesting a functional interaction between locally produced chemokines and CXCR3-expressing T-cells. In conclusion, these findings indicate that these CXCR3 activating chemokines play a significant role in the recruitment and maintenance of T-cell infiltrates in the inflammatory skin diseases studied.

Chemokine CXCL10↗

PubMed1995

Differential expression of HLA-DQB1 alleles in a heterozygous cell line.

Regulation of HLA class II transcription is complex, with both locus-specific and allele-specific polymorphisms associated with consensus regulatory region promoter elements. In order to evaluate the potential function of allele-specific elements, HLA-DQB1 transcripts and in vivo footprinting of the DQB1 promoter were studied in human cell lines inducible for HLA class II expression. In the heterozygous melanoma cell line Me9229/18, differential expression was observed for two DQB1 alleles. This variation was reflected in both steady-state and inducible transcripts, although methylation patterns of the promoter elements were similar for both alleles. This in vivo allelic difference expression, which correlates with previous studies of in vitro reporter gene transcription, indicates the potential for functionally important differences in tissue-specific and inducible expression attributable to promoter region polymorphism in HLA genes.

Alleles↗

PubMed2005

Differential expression of p63 isotypes (DeltaN and TA) in salivary gland neoplasms: biological and diagnostic implications.

To determine the association between the expression of p63 gene isoforms (TA and DeltaN) and salivary gland tumorigenesis, we performed reverse transcription-polymerase chain reaction analysis of these markers in 71 benign and malignant salivary gland neoplasms. The results were correlated with the expression of Notch ligand JAG1 gene and the clinicopathologic features and the full-length p63 protein expression by immunohistochemistry. Both p63 isoforms were either negative or weakly expressed in normal salivary gland tissues. TAp63 was highly expressed in most benign tumors and was either negative or weakly positive in most carcinomas. Conversely, DeltaNp63 was negative or faintly positive in most benign neoplasms and was highly expressed in adenoid cystic, mucoepidermoid, and myoepithelial carcinomas. Immunohistochemical analysis using anti-full-length p63 protein showed ubiquitous nuclear staining in basal and myoepithelial cells in both benign and malignant neoplasms. JAG1 was expressed in most benign and malignant tumors and did not correlate with p63 isoforms expression. We conclude that (1) p63 isoforms are differentially expressed in most benign and malignant tumors and may play distinct biological roles in certain salivary gland neoplasms; (2) p63 immunostaining do not correlate with the isoforms expression; and (3) isoform-specific antibodies are required for better cellular localization and biological correlations.

Adenocarcinoma↗

PubMed2005

Differentially expressed cortical genes contribute to perivascular deposition in transgenic mice with inducible neuron-specific expression of TGF-beta1.

In the brain the expression of transforming growth factor beta1 (TGF-beta1) is involved both in neuroprotective and neurodegenerative processes. Recently, we have established a transgenic mouse model with inducible neuron-specific expression of TGF-beta1 based on the tetracycline-regulated gene expression system. A long-term expression of TGF-beta1 results in persisting perivascular thioflavin-positive depositions, which did not disappear even though the transgene synthesis was repressed completely by administration of doxycycline. Formation and composition of these depositions are hardly elucidated. The aim of this study was to identify TGF-beta1 responding genes potentially participating in forming these depositions. To address this problem we have compared the cortical mRNA expression pattern of TGF-beta1 expressing mice with mice impeded to express the transgenic protein using oligonucleotide microarray analysis. Differential gene expression was further characterized by quantitative real-time reverse transcription-polymerase chain reaction including animals, where the long-lasting TGF-beta1 expression was repressed. While no change of amyloid precursor protein RNA expression level was detected, various genes strongly involved in calcium homeostasis, tissue mineralization or vascular calcification were identified differentially expressed. It is suggested, that these genes might contribute to the perivascular depositions in the TGF-beta1 expressing mice.

Animals↗

PubMed2005

Differential expression of two RXR/ultraspiracle isoforms during the life cycle of the hemimetabolous insect Blattella germanica (Dictyoptera, Blattellidae).

In insects, the molecular basis of ecdysteroid action has been analysed in great detail in flies and moths, but rarely in primitive orders. Using the primitive hemimetabolous insect Blattella germanica, the German cockroach, as a model, we isolated two cDNAs of RXR/USP, a component of the heterodimeric ecdysone receptor. These two cDNAs correspond to two isoforms, named BgRXR-S (short form) and BgRXR-L (long form). Both are identical except for a 23-amino acid deletion/insertion located in the loop between helices H1 and H3 of the ligand-binding domain. Pattern expression studies show that the two isoforms are differentially expressed throughout the life cycle of B. germanica. During embryogenesis, BgRXR-L occurs in early embryos, whereas BgRXR-S is highly expressed in middle and late embryogenesis. In the penultimate and last larval instars, BgRXR-S mRNA is the predominant form in the fat body and in the prothoracic gland. In the adult female, BgRXR-S mRNA predominates in the fat body, whereas BgRXR-L mRNA predominates in the ovary. Experiments performed with fat body and embryo cells incubated in vitro showed that the expression of BgRXR-S and BgRXR-L is not affected by 20-hydroxyecdysone or by juvenile hormone III.

Amino Acid Sequence↗

PubMed1997

Differential expression of nonmuscle myosin II isoforms in human atherosclerotic plaque.

Intimal proliferation and functional changes involving vascular smooth muscle cells are key events in the development of atherosclerosis, including restenosis after percutaneous transluminal angioplasty. Nonmuscle myosin (NMM) is required for cytokinesis and has been shown in cultures of vascular smooth muscle cells to undergo changes of isoform expression depending on the stage of proliferation and differentiation. The purpose of this study was to examine the differential expression of the two most recently identified nonmuscle myosin heavy chain isoform II (NMMHC-II) isoforms A and B in atherosclerotic plaque. Primary atherosclerotic and restenotic atherectomy specimens and non-atherosclerotic controls, were analyzed by Western Blot analysis, immunohistochemistry and in situ hybridization. Nonmuscle myosin heavy chain isoform IIA (NMMHC-IIA) was equally expressed in all types of tissue specimens both at the protein and mRNA levels. In contrast, NMMHC-IIB protein was found in restenotic specimens and normal artery but was at very low levels in primary atherosclerotic plaque. By in situ hybridization NMMHC-IIB mRNA levels were significantly greater in restenotic versus primary atherosclerotic lesions. NMMHC-IIB expression is associated with vascular restenosis but is downregulated in stable atherosclerotic lesions, whereas NMMHC-IIA is expressed in both. These results indicate that these new myosin isoforms have different functions and should be regarded separately with respect to smooth muscle proliferation and restenosis. They should prove to be useful molecular markers for the study of atherosclerosis and restenosis.

Aged↗

PubMed2001

The human intersectin genes and their spliced variants are differentially expressed.

Human intersectins (ITSN1 and ITSN2) are members of a conserved family of proteins involved in clathrin-mediated endocytosis. A short and a long isoform with different protein domain compositions have been described for both human intersectins. Here, we have resolved the exon/intron structure of the ITSN2 gene to explain the genomic origin of its alternatively spliced transcripts. Comparison of the two ITSN human genes shows a high level of conservation in their genomic organization, including the main alternative splicing events. An extensive tissue expression analysis of the two predominant transcripts as well as other minor variants shows that ITSN expression is under tissue and developmental controls. Their differential expression is made more evident when the expression of both intersectins is studied by in situ hybridization in mouse brain.

Adaptor Proteins, Vesicular Transport↗

PubMed2001

Identifying differentially expressed genes associated with metastasis of follicular thyroid cancer by cDNA expression array.

Patients with follicular thyroid carcinoma have a higher incidence of metastasis than papillary thyroid carcinoma when thyroid cancer is diagnosed. The cDNA expression array technology is utilized herein to profile differentially expressed genes from metastatic human follicular thyroid carcinoma and reveal new tumor markers as well as target genes for therapeutic intervention. Tissue samples were obtained during surgical resection of the thyroid follicular carcinoma and metastatic tissue in the brain of the same patient. Two identical Atlas human cDNA expression arrays were hybridized with 32P-labeled cDNA probes derived from RNA of either primary thyroid cancer or metastatic tissue. Parallel analysis of the hybridized signals allowed us to identify the alteration of gene expression in the metastasis process. Eighteen genes significantly overexpressed and 40 genes significantly underexpressed were identified in the metastatic thyroid cancer. Genes that displayed an altered expression were associated with the processes of cell cycle regulation, apoptosis, DNA damage response, angiogenesis, cell adhesion and mobility, invasion, and immune response. An expression profile of genes that are associated with metastasis process of follicular thyroid cancer was also discussed. Further investigation is required to understand the precise relationship between the altered expression of these genes and the metastasis process of follicular thyroid cancer.

Adenocarcinoma, Follicular↗

PubMed2004

A novel B(var) allele (547 G>A) demonstrates differential expression depending on the co-inherited ABO allele.

BACKGROUND AND OBJECTIVES: Genetic analysis of group B donors in Korea was performed. MATERIALS AND METHODS: Exons 6 and 7 were sequenced in 12 phenotypically B3 donors 6 B3, 6 A1B3. RESULTS: Consensus sequences all B3 and 2/6 A1B3 donors were present. Four A1B3 donors demonstrated a novel B allele, B(var), in the context of A101/ or A102/B(var) genotypes. Family studies based on an A1B3 donor with the B(var) allele and on another unrelated subject with identical genotype and phenotype revealed B(var)/O01 genotypes with full B-antigen expression. CONCLUSIONS: B(var) allele is subject to differential expression, depending on the co-inherited ABO allele.

ABO Blood-Group System↗

PubMed1999

Differential expression of alpha1, alpha2, alpha3, and alpha5 GABAA receptor subunits in seizure-prone and seizure-resistant rat models of temporal lobe epilepsy.

Temporal lobe epilepsy remains one of the most widespread seizure disorders in man, the etiology of which is controversial. Using new rat models of temporal lobe epilepsy that are either prone or resistant to develop complex partial seizures, we provide evidence that this seizure susceptibility may arise from arrested development of the GABAA receptor system. In seizure-prone (Fast kindling) and seizure-resistant (Slow kindling) rat models, both the mRNA and protein levels of the major alpha subunit expressed in adult brain (alpha1), as well as those highly expressed during development (alpha2, alpha3, and alpha5), were differentially expressed in both models compared with normal controls. We found that alpha1 subunit mRNA expression in the Fast kindling strain was approximately half the abundance of control rats, whereas in the Slow kindling strain, it was approximately 70% greater than that of controls. However, Fast rats overexpressed the alpha2, alpha3, and alpha5 ("embryonic") subunits, having a density 50-70% greater than controls depending on brain area, whereas the converse was true of Slow rats. Using subunit-specific antibodies to alpha1 and alpha5 subunits, quantitative immunoblots and immunocytochemistry revealed a concordance with the mRNA levels. alpha1 protein expression was approximately 50% less than controls in the Fast strain, whereas it was 200% greater in the Slow strain. In contrast, alpha5 subunit protein expression was greater in the Fast strain than either the control or Slow strain. These data suggest that a major predispositional factor in the development of temporal lobe epilepsy could be a failure to complete the normal switch from the GABAA receptor alpha subunits highly expressed during development (alpha2, alpha3, and alpha5) to those highly expressed in adulthood (alpha1).

Animals↗

PubMed1992

Identification of genes differentially expressed in two types of v-myb-transformed avian myelomonocytic cells.

In an earlier study we found that different forms of the v-myb oncogene transform myeloid cells which resemble either monoblasts [when v-myb of avian myeloblastosis virus (AMV) was used] or promyelocytes [when a point mutant in v-myb of AMV was used; Introna, M., Golay, J., Frampton J., Nakano, T., Ness, S.A. & Graf, T. (1990). Cell, 63, 1287-1297]. In the present study we have searched for genes expressed in AMV mutant-transformed promyelocytes that are not expressed in AMV-transformed monoblasts using a differential screening approach. Eight different genes were identified among more than 500 differentially expressed clones. The most abundant of these was the previously identified myb-regulated mim-1 gene. The others were found to encode a small calcium-binding (MRP-like) protein; the p20K protein; goose-type lysozyme; a ribonuclease A/angiogenin-related protein; and three non-identified proteins. Although these genes appear to be rather lineage restricted, their expression varied in different subtypes of transformed myelomonocytic cells, and only two of them (goose lysozyme and ribonuclease) showed a similar expression pattern in normal promyelocytes and macrophages, suggesting an aberrant gene regulation in the transformed cells. Co-transfection experiments of a reporter construct containing the promoter of the ribonuclease A-related gene indicated that this promoter is regulated by the v-Myb oncoprotein without the involvement of Myb-specific binding sequences.

Amino Acid Sequence↗

PubMed1989

Differential expression of cytokine mRNAs in human cell lines.

We investigated the expression of several cytokine genes known to be differentially expressed in human mononuclear cells depending on the way of stimulation. In order to investigate cytokine gene expression in cell lines we stimulated peripheral blood mononuclear cells, the human cell lines UBC 5637, Wil-2, K562, U937 and Jurkat with PHA or a phorbol ester. The patterns of cytokine expression were assessed at 8 and 20 hours after stimulation by Northern blot analysis. Our data show that after stimulation each cell line expressed its own pattern of cytokine mRNA levels. Additionally, superinduction with cycloheximide revealed no change of a stimulation dependent pattern. Furthermore, we found that each cytokine has its own kinetic suggesting that signal transduction may be followed by cell type specific intracellular mechanisms.

Biological Factors↗

PubMed2003

Use of a panel of congenic strains to evaluate differentially expressed genes as candidate genes for blood pressure quantitative trait loci.

Candidate gene(s) for multiple blood pressure (BP) quantitative trait loci (QTL) were sought by analysis of differential gene expression patterns in the kidneys of a panel of eight congenic strains, each of which carries a different low-BP QTL allele with a genetic composition that is otherwise similar to that of the hypertensive Dahl salt-sensitive (S) rat strain. First, genes differentially expressed in the kidneys of one-month-old Dahl S and salt-resistant (R) rats were identified. Then, Northern filter hybridization was used to examine the expression patterns of these genes in a panel of congenic strains. Finally, their chromosomal location was determined by radiation hybrid (RH) mapping. Seven out of 37 differentially expressed genes were mapped to congenic regions carrying BP QTLs, but only one of these genes, L-2 hydroxy acid oxidase (Hao2), showed the congenic strain-specific pattern of differential kidney gene expression predicted by its chromosomal location. This data suggests that Hao2 should be examined as a candidate gene for the rat chromosome 2 (RNO2) BP QTL.

Alcohol Oxidoreductases↗

PubMedDate not supplied

Differential expression of the alpha1 type VIII collagen gene by smooth muscle cells from atherosclerotic plaques of apolipoprotein-E-deficient mice.

We have investigated the morphology, growth and gene expression of smooth muscle cell (SMC) cultures derived from advanced atherosclerotic plaques and from non-plaque-containing aorta of individual apolipoprotein-E-deficient mice. The initial outgrowth of cells was faster from plaques (P) than from non-plaque segments (NP), but the cells in P cultures divided more slowly than NP cells in subcultures. By the 6th passage, the general growth pattern, morphology, ploidy and response to mitogenic factors of the cells were no longer consistently different in P and NP cultures. However, by the use of differential display, several transcripts were identified that were differentially expressed in three independent pairs of P and NP cultures. One of the transcripts, from a type VIII collagen gene, was elevated in all the P cultures compared to their NP counterparts even at the 40th passage. The alpha1 type VIII collagen transcripts were also readily detectable by RT-PCR in freshly dissected plaques, but not in the normal parts of aortas from the apolipoprotein-E-deficient mice. In situ hybridization showed that the transcripts were limited to the fibrous cap of plaques. Thus, SMCs from atherosclerotic plaques produce type VIII collagen and this differential expression continues when the cells are maintained in tissue culture.

Animals↗