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PubMed2025

How Does Tendon Region, Donor, and the Presence of Disease Affect Protein Composition of the Achilles Tendon?

BACKGROUND: Response to treatment for tendinopathy is variable, which may reflect variability in underlying etiology and capacity for the tendon to respond to treatment. Understanding variability in tendon protein composition may help improve our understanding of the mechanistic underpinnings of painful tendon degeneration and inform treatment targets. QUESTIONS/PURPOSES: (1) What factors (tendon region, individual characteristics, presence of disease) contribute to protein compositional (proteomic) and structural variation in human Achilles tendons? (2) What compositional changes characterize tendinopathy, and what protein interactions might contribute to tendon degeneration? (3) How does diabetes influence tendon composition, and what mechanisms might underlie tendon dysfunction in individuals with diabetes? METHODS: In this exploratory, cross-sectional study, human Achilles tendon specimens were obtained from individuals with (diabetes group, n = 5) or without diabetes (control group, n = 5) undergoing lower extremity amputation and from individuals undergoing tendon debridement surgeries for tendinopathy (tendinopathy group, n = 8). Specimens were collected between 2019 and 2023. Protein abundances were quantified and analyzed using mass spectrometry, hierarchical clustering, and principal component analysis. To evaluate the role of tendon region and donor on tendon protein compositional variability, we assessed proteomic differences between three regions in nontendinopathic tendons from three individuals. To identify the contribution of disease (that is, presence of tendinopathy or diabetes) on protein composition, we compared tendons from the tendinopathy (n = 8 [2 males, 6 females], mean ± SD age 48 ± 11 years), diabetes (n = 5 [3 males, 2 females], age 54 ± 9 years), and control (n = 5 [3 males, 2 females], age 42 ± 12 years) groups. Proteomic differences associated with tendinopathy and diabetes were further examined using functional enrichment and protein-protein interaction network analysis. RESULTS: Variability in tendon protein composition was primarily from presence of disease, followed by donor and then tendon region. Protein composition distinguished tendons with tendinopathy from controls, with 311 proteins differentially expressed (152 overexpressed and 159 underexpressed; fold change ≥ 1.5, p < 0.05) and higher Bonar scores indicating greater degeneration (mean ± SD Bonar score tendinopathy group 8.6 ± 1.2 versus control group 2.1 ± 0.7; p = 0.01). Pathway analysis identified dysregulation in extracellular matrix remodeling (TIMP1, MMP3, MMP10), inflammatory response (TNF-α, EGFR1), and metabolic reprogramming. Tendons from individuals with diabetes exhibited minimal proteomic changes compared with the control group, with 66 differentially expressed proteins (31 overexpressed and 35 underexpressed; fold change ≥ 1.5, p < 0.05) with no histopathologic differences between diabetes and control group tendons (mean ± SD Bonar score diabetes group 3.4 ± 1.0 versus control group 2.1 ± 0.7; p = 0.19). Tendons in the diabetes group showed reductions in Type I collagen, enrichment of pathways associated with fibrosis and metabolic dysfunction, and inflammatory pathways associated with α 6 β 4 integrin. CONCLUSION: Our findings indicate that Achilles tendon composition primarily differs based on disease etiology, with tendinopathy showing extensive extracellular matrix disruption and inflammatory activity, whereas tendons from individuals with diabetes exhibit more subtle compositional changes. This distinction suggests that tendinopathy may require targeted interventions addressing tissue remodeling and inflammation, whereas diabetes may predispose tendons to injury but not directly result in degeneration. Understanding these protein compositional variations can help refine hypotheses about disease progression, treatment response, and potential therapeutic targets. CLINICAL RELEVANCE: While proteomic analysis is not currently a part of routine clinical assessment, these findings provide a framework for identifying protein markers that may aid in early diagnosis or patient stratification to improve treatment alignment. Future studies could determine whether these proteomic changes correlate with treatment response and further inform our understanding of early-stage degeneration from chronic disease. By bridging molecular findings with clinical presentation, this study lays the groundwork for future research on precision medicine approaches for tendon disorders, with the long-term goal of tailoring treatment based on both biological and symptomatic characteristics.

Humans↗

PubMed2026

Metabolomics Reveals Metabolic Characteristics of Functional Cure in Chronic Hepatitis B Treated With Entecavir Combined With Pegylated Interferon Alpha.

BACKGROUND: Entecavir (ETV) combined with pegylated interferon alpha (PEG-IFNα) improves chronic hepatitis B (CHB) functional cure rates, but therapeutic heterogeneity and underlying metabolic mechanisms remain unclear. This study used untargeted metabolomics to identify metabolic signatures, mechanisms, and predictive biomarkers of functional cure with ETV-PEG-IFNα. METHODS: Thirty-eight CHB patients were grouped into ETV monotherapy (Group E, n = 12) and ETV-PEG-IFNα combination therapy (Group Z, n = 26); Group Z was subdivided into cured (Group A, n = 13) and noncured (Group B, n = 13). Serum metabolomic profiling, multivariate statistics, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified differential metabolites. A random forest model was built using key metabolites. RESULTS: Three hundred eighty-eight metabolites were identified. Four differential metabolites distinguished Group A and B (upregulated guanidinoacetic acid, uracil 5-carboxylate; downregulated L-methionine S-oxide, oleamide), enriching amino acid metabolism pathways. Nine differential metabolites between Group E and Z implicated amino acid, immune, and fatty acid pathways. The random forest model based on the four Group A/B metabolites showed 88.5% cross-validation accuracy (AUC = 0.920), with L-methionine S-oxide and oleamide as key predictors. CONCLUSIONS: This study reveals metabolic rewiring in CHB functional cure via ETV-PEG-IFNα therapy, involving energy metabolism, oxidative stress, and immunomodulation, based on which we propose a tentative metabolism-immunity synergy model to guide future research. Key metabolites, especially L-methionine S-oxide and oleamide, show exploratory predictive potential for functional cure that warrants further validation in independent cohorts.

Humans↗

PubMed2003

GeneMerge--post-genomic analysis, data mining, and hypothesis testing.

SUMMARY: GeneMerge is a web-based and standalone program written in PERL that returns a range of functional and genomic data for a given set of study genes and provides statistical rank scores for over-representation of particular functions or categories in the data set. Functional or categorical data of all kinds can be analyzed with GeneMerge, facilitating regulatory and metabolic pathway analysis, tests of population genetic hypotheses, cross-experiment comparisons, and tests of chromosomal clustering, among others. GeneMerge can perform analyses on a wide variety of genomic data quickly and easily and facilitates both data mining and hypothesis testing. AVAILABILITY: GeneMerge is available free of charge for academic use over the web and for download from: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html.

Algorithms↗

PubMed2005

Shear stress-stimulated endothelial cells induce smooth muscle cell chemotaxis via platelet-derived growth factor-BB and interleukin-1alpha.

OBJECTIVE: Vascular smooth muscle cell (SMC) migration is critical to the development of atherosclerosis and neointimal hyperplasia. Hemodynamic forces such as shear stress and cyclic strain stimulate endothelial cell signal-transduction pathways, resulting in the secretion of several factors, including SMC chemoattractants such as platelet-derived growth factor (PDGF). We hypothesized that mechanical forces stimulate endothelial cells to secrete SMC chemoattractants to induce migration via the mitogen-activated protein kinase (MAPK) pathway. METHODS: Bovine aortic endothelial cells were exposed to shear stress, cyclic strain, or static conditions for 16 hours. The resulting conditioned medium was used as a SMC chemoattractant in a Boyden chamber. Activation of SMC extracellular signal-regulated protein kinase 1/2 (ERK1/2) was assessed by Western blot analysis. Pathways were inhibited with anti-PDGF-BB or anti-interleukin-1alpha (IL-1alpha) antibodies, or the ERK1/2 upstream pathway inhibitor PD98059. RESULTS: Conditioned medium from endothelial cells exposed to shear stress corresponding to arterial levels of shear stress stimulated SMC migration but lower levels of shear stress or cyclic strain did not. Both PDGF-BB and IL-1alpha were secreted into the conditioned medium by endothelial cells stimulated with shear stress. Both PDGF-BB and IL-1alpha stimulated SMC chemotaxis but were not synergistic, and both stimulated SMC ERK1/2 phosphorylation. Inhibition of PDGF-BB or IL-1alpha inhibited SMC chemotaxis and ERK1/2 phosphorylation. CONCLUSION: Shear stress stimulates endothelial cells to secrete several SMC chemoattractants, including PDGF-BB and IL-1alpha; both PDGF-BB and IL-1alpha stimulate SMC chemotaxis via the ERK1/2 signal-transduction pathway. These results suggest that the response to vascular injury may have a common pathway amenable to pharmacologic manipulation. CLINICAL RELEVANCE: One difficulty in the pharmacologic treatment of atherosclerosis or neointimal hyperplasia leading to restenosis is the multiplicity of activated pathways and thus potential treatment targets. This study demonstrates that shear stress, a hemodynamic force that may be a biologically relevant stimulus to induce vascular pathology, stimulates endothelial cells to secrete PDGF-BB and IL-1alpha. Both of these mediators stimulate the SMC ERK1/2 pathway to induce migration, a critical event in the pathogenesis of atherosclerosis and neointimal hyperplasia. Therefore, this study suggests a relevant common target pathway in SMC that is amenable to manipulation for clinical treatment.

Animals↗

PubMed2005

[Unequal genetic exchange in Escherichia coli tandem duplications may represent a special pathway of homologous recombination].

Heterozygous tandem duplications that appear in Escherichia coli conjugation matings segregate different types of haploid and diploid recombinants because of unequal crossing over between sister chromosomes. As shown previously, the frequency of segregants in the extended duplication D104 (approximately 150 kb or more than 3 min of the genetic map) heterozygous for E. coli deo-operon genes (deoA deoB::Tn5/deoC deoD) is not decreased in strains with defective RecBCD and RecF recombination pathways. Analysis of a shorter duplication of this type (approximately 46 kb) showed that the frequency of segregants in the strain recBC sbcBC recF was similar to that in a strain with undamaged system of recombination. Thus, genetic exchange between direct DNA repeats in tandem duplications may follow a special pathway of homologous recombination, which is independent of the recBC and recF genes.

Crossing Over, Genetic↗

PubMed1997

Liver ischemia/reperfusion induces an increase of microvascular leukocyte flux, but not heterogeneity of leukocyte trafficking.

Leukocytic response plays a major role in the manifestation of hepatic ischemia/reperfusion (I/R) injury. To clarify whether post-ischemic hepatic leukocyte accumulation is based on increased leukocyte flux to the hepatic tissue due to systemic inflammation or chemoattractant activities or whether it represents solely a local tissue response without changing overall leukocyte flux and trafficking characteristics through the microvasculature, we studied acinar and sinusoidal leukocyte flux and distribution in rat livers in vivo both under normal (sham, n = 8) and post-ischemic (60' ischemia/75' reperfusion) conditions (I/R, n = 8), using fluorescence epi-illumination microscopy (rhodamine-6G). Hepatic ischemia/reperfusion significantly (p < 0.05) increased acinar leukocyte flux (58.4 +/- 20.9 cells/min vs 36.4 +/- 12.8 cells/min in sham controls); however, it did not exhibit increased heterogeneity of acinar leukocyte distribution, as indicated by the unchanged coefficient of variance (CV) of 0.36 +/- 0.16 (sham controls: 0.31 +/- 0.14). In parallel, analysis of individual sinusoidal leukocyte flux demonstrated significantly (p < 0.05) higher values (8.9 +/- 3.7 cells/min) after ischemia/reperfusion when compared with sham controls (5.7 +/- 1.9 cells/min), which, however, was not associated with increased heterogeneity of sinusoidal leukocyte trafficking (CV: 0.85 +/- 0.15 vs 0.85 +/- 0.16 in sham controls) and manifestation of preferential pathways. Analysis of blood cell count did not demonstrate an overall increase of total blood leukocyte count; however, an increased (p < 0.01) fraction of polymorphonuclear leukocytes (65.2 +/- 11.2%) and stab cells (9.5 +/- 7.9%) during post-ischemic reperfusion when compared with sham controls (8.8 +/- 3.5% and 0.2 +/- 0.4%) was demonstrated. Thus, the increase of hepatic leukocyte flux after ischemia/reperfusion may be the result of both the manifestation of a systemic inflammatory response and the increase of local chemoattractant activities, such as the production and release of the cytokine-induced neutrophil chemoattractant of the IL-8 family.

Animals↗

PubMed2000

Variance analysis in clinical pathways for total hip and knee joint arthroplasty.

Clinical pathways are being increasingly used for daily patient care. The pathways consist of a sequence of critical treatment events matched to the patient's recovery. Variance analysis identifies deviations from the pathway and can be used for quality improvement and clinical audit. The aim of this study is to analyse the variances from clinical pathways in two common elective orthopaedic operations. A prospective variance analysis was performed from the clinical pathways of all patients undergoing total hip and total knee arthroplasty over a 12 month period. Variances were categorised according to their source and then further divided into serious and non-serious variances. A total of 65 patients underwent total knee replacement during the study. Eleven serious variances were recorded in eight of these patients (12.3%) with a surprisingly high number of cardiac events. A total of 52 patients underwent total hip replacement with nine serious variances recorded in seven of these patients (13.5%). Clinical pathways can be used as a means of incorporating evidence-based medicine into clinical practice. Variance analysis of the pathways can be utilised as a process of quality control and to improve patient outcomes. Serious variances within this study were higher than anticipated.

Adult↗

PubMed2002

Analysis of signaling pathways using functional proteomics.

Advances in analytical methods for protein analysis by mass spectrometry provide new tools for global analysis of the expressed protein profile of cells (referred to as proteomics). Currently, available methodology samples only part of the proteome. This is sufficient for analysis of signal transduction, because signaling pathways contain enzymes, which modify high-abundance proteins other than those of the pathway. Thus, modulation of the signaling through a pathway will produce a "footprint" in the proteome that is characteristic of a specific cell phenotype. Comparison of different samples to identify these differences in posttranslational modification or protein expression is referred to as functional proteomics. This review surveys the methods in widest use in functional proteomics, as well as a few promising new ones. Although proteomic analyses were first conducted 26 years ago, a renewed interest is fueled by several recent advances. Most important are the availability of public genome and protein databases and the development of high-sensitivity, easy-to-use mass spectrometers and database search engines capable of exploiting these databases. Other important advances include improved two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), computer programs for analysis of the 2D-PAGE gel images, protocols for proteolytic digestion of proteins in excised gel pieces, and low-flow chromatography methods. Despite the limitations of these methods, they can distinguish subtle changes in the phenotype of cells, providing the basis for future studies in regulation of the phenotype.

Animals↗

PubMed2025

Metabolome analyses of mouse uteri two to four days post coitum.

To elucidate the temporal and dynamic changes in uterine metabolites in mice, uterine samples were collected on Day 2 (D2; n = 8), Day 3 (D3; n = 6), and Day 4 (D4; n = 7) postcoitum and subjected to an untargeted metabolomic analysis. The results revealed significant metabolic alterations across the time points. Compared to D2, D3 showed 124 differentially expressed metabolites (95 upregulated and 29 downregulated), whereas D4 exhibited 377 (262 upregulated and 115 downregulated). Between D4 and D3, 370 metabolites were altered (242 upregulated and 128 downregulated). K-means clustering identified five metabolite clusters, with Clusters 3 and 5 displaying the most pronounced temporal variations. Metabolites in cluster 3 remained stable from D2 to D3 but sharply increased by D4, whereas those in cluster 5 were stable from D2 to D3 and markedly decreased by D4. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that metabolites in Cluster 3 were primarily enriched in the tricarboxylic acid (TCA) cycle, arachidonic acid metabolism, and cholesterol and linoleic acid metabolism pathways. Cluster 5 metabolites were primarily enriched in pathways related to unsaturated fatty acids (linoleic acid, arachidonic acid, and α-linolenic acid) and amino acid metabolism (vitamin B6, taurine, and hypotaurine). Cluster 3 mainly comprised prostaglandins and related compounds, whereas Cluster 5 consisted largely of long-chain fatty acids. Notably, most lipid and lipid-like metabolites in these clusters were associated with embryonic development. These findings elucidate the dynamic metabolic changes in the uterus during the preimplantation stage and highlight the critical roles of amino acids, unsaturated fatty acids, prostaglandins, and lipid-related metabolites in modulating the uterine environment to support embryo implantation and early development.

Animals↗

PubMed1996

Structure/function of cytoplasmic vitamin A-binding proteins.

Two cytoplasmic retinol-binding proteins, CRBP and CRBP II, and two cytoplasmic retinoic acid-binding proteins, CRABP-I and CRABP-II, have been well characterized. There has been significant progress in the structural analysis of these four proteins with X-ray crystallography, nuclear magnetic resonance, mutagenesis, and binding studies. In contrast, the cellular functions of these cytoplasmic vitamin A-binding proteins are less well understood. Since these proteins bind their respective ligands with high affinity, they are likely to influence retinoid signaling pathways. Analysis of retinoid metabolism in the presence or absence of these proteins provides support for the hypothesis that these proteins are involved in modulating intracellular retinoid metabolism. Molecular genetic approaches to alteration of the levels of these proteins in tissue culture cells and in whole animals have provided a powerful means toward defining the physiological roles of the cytoplasmic vitamin A-binding proteins in vivo.

Amino Acid Sequence↗

PubMedDate not supplied

Benchmarking: a case report.

In mid 1993, administrators and physicians at Bristol Medical Center teams up with HCIA to perform clinical pathway analysis on five diagnosis related groups. The major goal of this project was to establish a partnership between the hospital administration and the medical staff to meet or beat existing benchmarks.

Critical Pathways↗

PubMed2005

The respiratory syncytial virus small hydrophobic protein is phosphorylated via a mitogen-activated protein kinase p38-dependent tyrosine kinase activity during virus infection.

The phosphorylation status of the small hydrophobic (SH) protein of respiratory syncytial virus (RSV) was examined in virus-infected Vero cells. The SH protein was isolated from [35S]methionine- and [33P]orthophosphate-labelled RSV-infected cells and analysed by SDS-PAGE. In each case, a protein product of the expected size for the SH protein was observed. Phosphoamino acid analysis and reactivity with the phosphotyrosine specific antibody PY20 showed that the SH protein was modified by tyrosine phosphorylation. The role of tyrosine kinase activity in SH protein phosphorylation was confirmed by the use of genistein, a broad-spectrum tyrosine kinase inhibitor, to inhibit SH protein phosphorylation. Further analysis showed that the different glycosylated forms of the SH protein were phosphorylated, as was the oligomeric form of the protein. Phosphorylation of the SH protein was specifically inhibited by the mitogen-activated protein kinase (MAPK) p38 inhibitor SB203580, suggesting that SH protein phosphorylation occurs via a MAPK p38-dependent pathway. Analysis of virus-infected cells using fluorescence microscopy showed that, although the SH protein was distributed throughout the cytoplasm, it appeared to accumulate, at low levels, in the endoplasmic reticulum/Golgi complex, confirming recent observations. However, in the presence of SB203580, an increased accumulation of the SH protein in the Golgi complex was observed, although other virus structures, such as virus filaments and inclusion bodies, remained largely unaffected. These results showed that during RSV infection, the SH protein is modified by an MAPK p38-dependent tyrosine kinase activity and that this modification influences its cellular distribution.

Amino Acid Sequence↗

PubMed2006

The role of initial trauma in the host's response to injury and hemorrhage: insights from a correlation of mathematical simulations and hepatic transcriptomic analysis.

Trauma and hemorrhagic shock (HS) elicit severe physiological disturbances that predispose the victims to subsequent organ dysfunction and death. The general lack of effective therapeutic options for these patients is mainly due to the complex interplay of interacting inflammatory and physiological elements working at multiple levels. Systems biology has emerged as a new paradigm that allows the study of large portions of physiological networks simultaneously. Seeking a better understanding of the interplay among known inflammatory pathways, we constructed a mathematical model encompassing the dynamics of the acute inflammatory response that incorporates the intertwined effects of inflammation and global tissue damage. The model was calibrated using data from C57Bl/6 mice subjected to endotoxemia, sham operation (i.e., surgical trauma induced by cannulation [ST]) or ST + HS+ resuscitation (ST-HS-R). An in silico simulation, made at whole-organism level, suggested that similar pathways of different magnitudes were operant as the degree of total body damage increased. We sought to validate this hypothesis by subjecting mice to HS and comparing the models predictions to circulating markers of inflammation and tissue injury as well as the global transcriptomic response of the liver. C57Bl/6 mice were subjected to ST or ST-HS (without resuscitation). Liver gene expression was assessed using an Affymetrix DNA microarray (GeneChip Mouse Expression Set 430A, Affymetrix, Santa Clara, CA), which contains 22,621 probe sets and effectively interrogates 12,341 mouse genes. The microarray data sets were subjected to hierarchical clustering and pathway analysis. In agreement with model predictions, circulating levels of inflammation/tissue injury markers and the microarray analysis both demonstrated that ST alone accounts for a substantial proportion of the observed phenotypic and genetic/molecular changes versus untreated animals. The addition of HS further increased the magnitude of gene expression, but relatively few additional genes were recruited. Mathematical simulations and DNA microarrays, both systems biology tools, may provide valuable insight into the complex global physiological interactions that occur in response to trauma and hemorrhagic shock.

Animals↗

PubMed2005

Identification of an X-linked locus modifying mouse skin tumor susceptibility.

The enhancing effect of overexpression of an ornithine decarboxylase (Odc) transgene on skin tumor susceptibility can be modified by genetic loci present in several inbred mouse strains. The BALB/cJ strain is among the most resistant strains so far examined; tumor multiplicity following 7,12-dimethylbenz(a)anthracene (DMBA) treatment is reduced by 90% when the K6/ODC transgene is expressed on a BALB/cJ background versus the susceptible C57BL/6J background. Further, transgenic BALB/cJ males developed more tumors than females, indicating the presence of sex-dependent modifier pathway. Analysis of 263 F2 intercross mice revealed significant linkage of markers on the X chromosome to tumor multiplicity. This analyses as well as a similar genome-wide scan of 136 backcross mice found evidence for other modifier loci on chromosomes 4, 6, and 17. Identification of these modifier genes should reveal the effector pathways responsive to Odc overexpression that mediate susceptibility to skin tumorigenesis.

Animals↗

PubMed2006

Identification of early proteomic markers for hepatic steatosis.

The identification of biomarkers for disease state, drug efficacy, and toxicity is becoming increasingly important for drug discovery and development. We have used two-dimensional differential in-gel electrophoresis and mass spectrometry to identify proteomic markers associated with hepatocellular steatosis in rats after dosing with a compound (CDA) in preclinical development. Rats were dosed daily for up to 5 days with CDA for measurement of blood biochemical parameters, histological, and proteomic analysis. Alterations in plasma glucose and liver transaminases were detected from dosing day 3 onward, and livers showed trace levels of hepatocellular vacuolation from 6 h which increased in extent and severity over the 5 day time course. The number of significantly altered protein spots increased over the 5 day time course, and Ingenuity Pathway Analysis showed that the predominant functions altered by CDA treatment were cell death and cellular assembly and organization. This included alterations in secreted proteins, endoplasmic reticulum and mitochondrial chaperones, antioxidant proteins, and enzymes involved in fatty acid biosynthesis. Comparative in vitro dosing studies showed similar alterations to the proteome, neutral lipid accumulation, and mitochondrial dehydrogenase activity in response to CDA treatment of cultured rat hepatocytes. The finding that several proteins showed significant changes in abundance before the onset of overt toxicity in vivo suggested that these could serve as predictive biomarkers of compounds with a propensity to induce liver steatosis. These markers underwent further direct analysis in the in vitro hepatocyte toxicity model to determine their utility in the development of high throughput assays for drug-induced steatosis.

Animals↗

PubMed2025

Analysis of genomic traits of oral and laryngeal cancer: A comparative study.

Oral and laryngeal cancers exhibit overlapping clinical features but distinct genomic profiles. In a study of 60 Head and neck squamous cell carcinomas(HNSCC) cases (30 OSCC, 30 LSCC), NGS revealed TP53 mutations in 70% of oral squamous cell carcinoma (OSCC) and 83% of laryngeal squamous cell carcinoma (LSCC). CDKN2A alterations were more common in OSCC (40%) than LSCC (20%), while PIK3CA mutations were higher in LSCC (30%). NOTCH1 mutations were more frequent in OSCC (27%) than LSCC (10%). Pathway analysis showed disruptions in p53 and PI3K-Akt, with stronger enrichment in LSCC (ES: 3.42). The results suggest site-specific tumor biology influencing therapeutic targets. Molecular profiling is crucial for precision treatment in head and neck cancers.

Oral cancer↗

PubMed2006

Gene profiling of cathepsin K deficiency in atherogenesis: profibrotic but lipogenic.

Recently, we showed that cathepsin K deficiency reduces atherosclerotic plaque progression, induces plaque fibrosis, but aggravates macrophage foam cell formation in the ApoE -/- mouse. To obtain more insight into the molecular mechanisms by which cathepsin K disruption evokes the observed phenotypic changes, we used microarray analysis for gene expression profiling of aortic arches of CatK -/-/ApoE -/- and ApoE -/- mice on a mouse oligo microarray. Out of 20 280 reporters, 444 were significantly differentially expressed (p-value of < 0.05, fold change of > or = 1.4 or < or = - 1.4, and intensity value of > 2.5 times background in at least one channel). Ingenuity Pathway Analysis and GenMAPP revealed upregulation of genes involved in lipid uptake, trafficking, and intracellular storage, including caveolin - 1, - 2, - 3 and CD36, and profibrotic genes involved in transforming growth factor beta (TGFbeta) signalling, including TGFbeta2, latent TGFbeta binding protein-1 (LTBP1), and secreted protein, acidic and rich in cysteine (SPARC), in CatK -/-/ApoE -/- mice. Differential gene expression was confirmed at the mRNA and protein levels. In vitro modified low density lipoprotein (LDL) uptake assays, using bone marrow derived macrophages preincubated with caveolae and scavenger receptor inhibitors, confirmed the importance of caveolins and CD36 in increasing modified LDL uptake in the absence of cathepsin K. In conclusion, we suggest that cathepsin K deficiency alters plaque phenotype not only by decreasing proteolytic activity, but also by stimulating TGFbeta signalling. Besides this profibrotic effect, cathepsin K deficiency has a lipogenic effect owing to increased lipid uptake mediated by CD36 and caveolins.

Animals↗

PubMed2006

Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy.

Diabetic nephropathy (DN) is the leading cause of end-stage renal failure and a major risk factor for cardiovascular mortality in diabetic patients. To evaluate the multiple pathogenetic factors implicated in DN, unbiased mRNA expression screening of tubulointerstitial compartments of human renal biopsies was combined with hypothesis-driven pathway analysis. Expression fingerprints obtained from biopsies with histological diagnosis of DN (n = 13) and from control subjects (pretransplant kidney donors [n = 7] and minimal change disease [n = 4]) allowed us to segregate the biopsies by disease state and stage by the specific expression signatures. Functional categorization showed regulation of genes linked to inflammation in progressive DN. Pathway mapping of nuclear factor-kappaB (NF-kappaB), a master transcriptional switch in inflammation, segregated progressive from mild DN and control subjects by showing upregulation of 54 of 138 known NF-kappaB targets. The promoter regions of regulated NF-kappaB targets were analyzed using ModelInspector, and the NF-kappaB module NFKB_IRFF_01 was found to be specifically enriched in progressive disease. Using this module, the induction of eight NFKB_IRFF_01-dependant genes was correctly predicted in progressive DN (B2M, CCL5/RANTES, CXCL10/IP10, EDN1, HLA-A, HLA-B, IFNB1, and VCAM1). The identification of a specific NF-kappaB promoter module activated in the inflammatory stress response of progressive DN has helped to characterize upstream pathways as potential targets for the treatment of progressive renal diseases such as DN.

Biopsy↗