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At least 1,189 records · Page 66Linked to original sources
PubMed1994

Instrumented examination of knee laxity in patients with anterior cruciate deficiency: a comparison of the KT-2000, Knee Signature System, and Genucom.

Knee ligament arthrometers are used during rehabilitation to assess changes in knee laxity after anterior cruciate ligament injury. This study investigated the reliability and error associated with measurements of knee laxity using three different instrumented devices: the KT-2000, the Knee Signature System (KSS), and the Genucom Knee Analysis System to aid in the interpretation of instrumented laxity measurements during rehabilitation. Ten subjects with unilateral anterior cruciate deficiency were examined by two testers on two separate days. Measurement error was calculated as the minimum difference required to assume a true change in laxity between two measurements (p < 0.05). Between-day reliability was relatively high for both the KSS and the KT-2000 (.95 and .83, respectively) but substantially lower for the Genucom (.22). Intertester reliability was slightly lower for the KT-2000 and the KSS (.92 and .78, respectively) and slightly higher but still low for the Genucom (.27). When monitoring changes in anterior laxity of an anterior-cruciate-deficient knee, the following error values were determined to be needed in order to assume a true difference between successive measurements: KT-2000, 2.0 mm; KSS, 4.2 mm; and Genucom, 5.9 mm. The results of this study suggest that measurements of anterior laxity taken by a single examiner using the KT-2000 provide the most reliable measurements.

Adult↗
PubMedDate not supplied

An application of laser Raman spectroscopy to the study of a hereditary cataractous lens; on the Raman band for a diagnostic marker of cataractous signatures.

Raman spectra were measured for cac-strain mouse (Nakano mouse) lenses in the various stages of cataract formation. The spectra were compared with those of normal mouse lenses of the corresponding ages. A significant difference was observed in the intensity of the Raman band due to an OH stretching mode of lens water (3390 cm-1) between the spectra of cataractous lenses and those of normal lenses. The difference was already obvious in the very incipient stage of hereditary cataract and became more pronounced with cataract development. These observations clearly show that changes in lens water occur during cataractogenesis. We propose in this communication that the intensity change of the Raman band at 3390 cm-1 may be very useful for the diagnostic marker of cataractous signatures.

Animals↗
PubMed2024

Developing a machine learning-based prognosis and immunotherapeutic response signature in colorectal cancer: insights from ferroptosis, fatty acid dynamics, and the tumor microenvironment.

INSTRUCTION: Colorectal cancer (CRC) poses a challenge to public health and is characterized by a high incidence rate. This study explored the relationship between ferroptosis and fatty acid metabolism in the tumor microenvironment (TME) of patients with CRC to identify how these interactions impact the prognosis and effectiveness of immunotherapy, focusing on patient outcomes and the potential for predicting treatment response. METHODS: Using datasets from multiple cohorts, including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we conducted an in-depth multi-omics study to uncover the relationship between ferroptosis regulators and fatty acid metabolism in CRC. Through unsupervised clustering, we discovered unique patterns that link ferroptosis and fatty acid metabolism, and further investigated them in the context of immune cell infiltration and pathway analysis. We developed the FeFAMscore, a prognostic model created using a combination of machine learning algorithms, and assessed its predictive power for patient outcomes and responsiveness to treatment. The FeFAMscore signature expression level was confirmed using RT-PCR, and ACAA2 progression in cancer was further verified. RESULTS: This study revealed significant correlations between ferroptosis regulators and fatty acid metabolism-related genes with respect to tumor progression. Three distinct patient clusters with varied prognoses and immune cell infiltration were identified. The FeFAMscore demonstrated superior prognostic accuracy over existing models, with a C-index of 0.689 in the training cohort and values ranging from 0.648 to 0.720 in four independent validation cohorts. It also responses to immunotherapy and chemotherapy, indicating a sensitive response of special therapies (e.g., anti-PD-1, anti-CTLA4, osimertinib) in high FeFAMscore patients. CONCLUSION: Ferroptosis regulators and fatty acid metabolism-related genes not only enhance immune activation, but also contribute to immune escape. Thus, the FeFAMscore, a novel prognostic tool, is promising for predicting both the prognosis and efficacy of immunotherapeutic strategies in patients with CRC.

Ferroptosis↗
PubMed2026

Transcriptomic and proteomic signatures following AS03-adjuvanted Influenza A/H7N9 vaccine.

INTRODUCTION: Vaccines targeting avian influenza virus A/H7N9 are poorly immunogenic. While the immune responses can be improved with oil-in-water emulsion adjuvants such as Adjuvant System 03 (AS03), the cellular mechanisms underpinning the adjuvant effect are incompletely characterized and poorly understood. METHODS: We enrolled 30 healthy adult participants and used RNA sequencing and quantitative proteomics to characterize the response to two doses of the influenza A/H7N9 vaccine, with and without AS03, in six immune cell types. These responses were compared to those seen after administration of an unadjuvanted seasonal in uenza A/H3N2 variant vaccine to identify signatures unique to adjuvanted influenza vaccines and correlated with later antibody responses. Transcriptomic and proteomic analyses revealed that. RESULTS: AS03-adjuvanted vaccine was associated with upregulation of immune pathways in innate immune cells within 24h following vaccination for phagocytosis, antigen presentation and processing, inflammasome activation, NK-cell mediated cytotoxicity, IgA production, and interferon-response pathways. Moreover, while major histocompatibility complex (MHC I and II) upregulation was observed across multiple immune cell types, MHCII gene transcription was also increased in the neutrophil compartment, generating the hypothesis that neutrophils may play a more important role in antigen presentation than previously understood. DISCUSSION: Taken together, these data provide a more complete mechanistic understanding of oil-in-water adjuvants and their role in enhancing the immune response for pandemic influenza preparedness. CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT02921997?term=NCT02921997&viewType, idientifier NCT02921997.

Adult↗
PubMed2026

Urine-Derived Cells in Kidney Transplantation: Linking Cellular Phenotypes, Secretome Signatures and Multi-Omic Technologies.

Kidney transplant monitoring and early identification of graft dysfunction are central needs for long-term graft survival. Although kidney biopsy represents the gold standard in diagnostic procedures, its invasiveness may limit frequent longitudinal evaluation, highlighting the necessity of non-invasive diagnostic tools. Urine has emerged over the years as an easily obtainable source of cellular and molecular components derived from transplanted kidneys. Particularly, exfoliated cells and extracellular vesicles (EVs) represent complementary and interconnected markers able to reflect tissue injury, inflammatory signals, immune cell infiltration, and regenerative processes occurring in the graft. Also, recent advances in transcriptomics, proteomics, metabolomics, and single-cell technologies have expanded the diagnostic and mechanistic value of urinary liquid biopsy, enabling the identification of disease-specific molecular signatures associated with rejection, delayed graft function, fibrosis, and graft loss. This review discusses the emerging concept of an integrated urinary cell-EV ecosystem and highlights how integrated multi-omic approaches may transform non-invasive graft surveillance and advance precision medicine in kidney transplantation.

Humans↗
PubMed2025

Cell-Free DNA Bisulfite Sequencing Reveals Epithelial-Mesenchymal Transition Signatures for Breast Cancer.

Cell-free DNA (cfDNA), shed by malignant tumor cells into extracellular fluid, provides valuable epigenetic information indicative of cancer status. Nipple aspirate fluid (NAF), a noninvasive liquid biopsy from at-risk women, contains nucleic acid and protein biomarkers from adjacent cancer cells, showing promise for breast cancer (BrC) detection. However, despite its potential, the application of cfDNA in NAF for BrC screening is still underexplored. Here, we report a proof-of-concept study for using cfDNA bisulfite sequencing (cfBS) to assess tumor DNA methylation signatures from NAF samples. For four healthy individuals and three BrC patients, cfBS achieved greater than 20&#xd7; sequencing depth with an average coverage of 26.5&#xd7; on the genome. A total of 7471 differentially methylated regions were identified, with significant hypermethylation in BrC samples compared to healthy controls. Gene set enrichment analysis indicated that the differentially methylated genes (DMGs) were significantly associated with epithelial-mesenchymal transition (EMT). By developing a novel EMT scoring metric, we found that BrC samples had more of a mesenchymal phenotype than samples from healthy individuals. CDH1, WNT2, and TRIM29 were hypermethylated near the promoter region, while COL5A2 was hypermethylated in the coding region. The DNA methylation and EMT changes were validated through The Cancer Genome Atlas Breast Invasive Carcinoma study, which confirmed that DMGs were associated with gene expression change and that our methylation-based EMT score reliably distinguished tumors from healthy controls. Our findings support the utilization of the NAF cfDNA cfBS methylation profile for noninvasive BrC screening and pave the way for enhanced early detection of this disease.

Humans↗
PubMed2003

Molecular signatures of anti-nuclear antibodies: contributions of specific light chain residues and a novel New Zealand Black V kappa 1 germline gene.

Although the Ig H chains of anti-nuclear Abs (ANA) have been described to possess certain shared molecular signatures, it remains unclear whether the L chains of these Abs also possess distinctive molecular features. The present study examines this by generating and analyzing two comprehensive murine Ig L chain databases, one consisting of 264 monoclonal ANAs and the other consisting of 145 non-ANAs, drawn from previously published work. Importantly, clonal replicates were represented only once each, so as to minimize bias. ANAs and non-ANAs did not differ in Vkappa family or Jkappa gene usage, nor in their mutation frequencies. Interestingly, the L chains of ANAs exhibited differential usage of certain complementarity-determining region residues, arising almost entirely from the increased usage of certain Vkappa germline genes, notably, Vkappa ai4 among anti-dsDNA ANAs, Vkappa23-45 among anti-ssDNA ANAs, and Vkappa21-12 among non-ANAs. Finally, prompted by the increased prevalence of a particular Vkappa1 family sequence among ANAs, we proceeded to clone a novel New Zealand Black Vkappa1 germline gene, named bb1.1, which appears to be frequently used to encoded anti-ssDNA Abs. Collectively, these studies underline the potential contribution of particular Vkappa germline genes in promoting or thwarting DNA binding.

Animals↗
PubMed2005

Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets.

We used a comprehensive collection of Affymetrix microarray datasets to ascertain which genes or molecules distinguish the known major subsets of human T cells. Our strategy allowed us to identify the genes expressed in most T cell subsets: TCR alphabeta+ and gammadelta+, three effector subsets (Th1, Th2, and T follicular helper cells), T central memory, T effector memory, activated T cells, and others. Our genechip dataset also allowed for identification of genes preferentially or exclusively expressed by T cells, compared with numerous non-T cell leukocyte subsets profiled. Cross-comparisons between microarray datasets revealed important features of certain subsets. For instance, blood gammadelta T cells expressed no unique gene transcripts, but did differ from alphabeta T cells in numerous genes that were down-regulated. Hierarchical clustering of all the genes differentially expressed between T cell subsets enabled the identification of precise signatures. Moreover, the different T cell subsets could be distinguished at the level of gene expression by a smaller subset of predictor genes, most of which have not previously been associated directly with any of the individual subsets. T cell activation had the greatest influence on gene regulation, whereas central and effector memory T cells displayed surprisingly similar gene expression profiles. Knowledge of the patterns of gene expression that underlie fundamental T cell activities, such as activation, various effector functions, and immunological memory, provide the basis for a better understanding of T cells and their role in immune defense.

Cluster Analysis↗
PubMed2005

Molecular signatures distinguish human central memory from effector memory CD8 T cell subsets.

Memory T cells are heterogeneous in terms of their phenotype and functional properties. We investigated the molecular profiles of human CD8 naive central memory (T(CM)), effector memory (T(EM)), and effector memory RA (T(EMRA)) T cells using gene expression microarrays and phospho-protein-specific intracellular flow cytometry. We demonstrate that T(CM) have a gene expression and cytokine signaling signature that lies between that of naive and T(EM) or T(EMRA) cells, whereas T(EM) and T(EMRA) are closely related. Our data define the molecular basis for the different functional properties of central and effector memory subsets. We show that T(EM) and T(EMRA) cells strongly express genes with known importance in CD8 T cell effector function. In contrast, T(CM) are characterized by high basal and cytokine-induced STAT5 phosphorylation, reflecting their capacity for self-renewal. Altogether, our results distinguish T(CM) and T(EM)/T(EMRA) at the molecular level and are consistent with the concept that T(CM) represent memory stem cells.

CD8-Positive T-Lymphocytes↗
PubMed2005

Transcriptional activators of helper T cell fate are required for establishment but not maintenance of signature cytokine expression.

The stability of helper T cell fates is not well understood. Using conditional introduction of dominant-negative factors, we now show that T-bet and GATA-3 are far more critical in establishment than maintenance of IFN-gamma and IL-4 activity during Th1 and Th2 maturation, respectively. We also show that a genetic interaction between T-bet and its target Hlx seems to be required for Th1 maturation, but that Hlx may also be dispensable for maintenance of a transcriptionally permissive ifng gene. In parallel to progressive activator independence in the permissive lineage, the ifng gene becomes more recalcitrant to switching as the forbidden lineage matures. T-bet plus Hlx can disrupt ifng silencing when introduced into developing Th2 cells, but they fail to perturb ifng silencing in mature Th2 cells. In contrast, a hypermorphic allele of T-bet can reverse silencing of the ifng gene in mature Th2 cells. These results suggest that signature gene activity of helper T cells is initially plastic but later becomes epigenetically fixed and offer an initial strategy for inducing mature cells to switch their fate.

Animals↗
PubMed2006

Microarrays reveal distinct gene signatures in the thymus of seropositive and seronegative myasthenia gravis patients and the role of CC chemokine ligand 21 in thymic hyperplasia.

Myasthenia gravis (MG) is an autoimmune disease mainly caused by antiacetylcholine receptor autoantibodies (seropositive (SP) disease) or by Abs against unknown autoantigenic target(s) (seronegative (SN) disease). Thymectomy is usually beneficial although thymic hyperplasia with ectopic germinal centers is mainly observed in SP MG. To understand the role of thymus in the disease process, we compared the thymic transcriptome of non-MG adults to those of SP patients with a low or high degree of hyperplasia or SN patients. Surprisingly, an overexpression of MHC class II, Ig, and B cell marker genes is observed in SP but also SN MG patients. Moreover, we demonstrate an overexpression of CXCL13 in all MG thymuses leading probably to the generalized B cell infiltration. However, we find different chemotactic properties for MG subgroups and, especially, a specific overexpression of CCL21 in hyperplastic thymuses triggering most likely ectopic germinal center development. Besides, SN patients present a peculiar signature with an abnormal expression of genes involved in muscle development and synaptic transmission, but also genes implicated in host response, suggesting that viral infection might be related to SN MG. Altogether, these results underline differential pathogenic mechanisms in the thymus of SP and SN MG and propose new research areas.

Adult↗
PubMed1999

A novel signature mutation for oxidative damage resembles a mutational pattern found commonly in human cancers.

To determine the types of mutations induced by oxidative damage, a kidney cell line with a heterozygous deficiency for the autosomal Aprt (adenine phosphoribosyltransferase) gene was tested for its mutagenic response to hydrogen peroxide. Aprt-deficient cells were selected and scored for loss of heterozygosity (LOH) for 11 microsatellite loci on mouse chromosome 8. On the basis of the LOH analysis, spontaneous mutants (n = 38) were distributed into four classes: apparent point mutation, mitotic recombination, chromosome loss, and large interstitial deletion. However, 9 of 20 (45%) hydrogen peroxide-induced mutants exhibited a novel class of mutations characterized by "discontinuous LOH" for one or more of the microsatellite loci. Interestingly, mutations resembling discontinuous LOH are commonly observed in a wide variety of human cancers. Our data suggest that discontinuous LOH is a signature mutational pattern for oxidative damage and further suggest that such genetic damage is widespread in cancer.

Adenine Phosphoribosyltransferase↗
PubMed2000

CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer.

CpG island hypermethylation is a frequent epigenetic event in cancer. We have recently developed an array-based method, called differential methylation hybridization (DMH), allowing for a genome-wide screening of CpG island hypermethylation in breast cancer cell lines (T. H-M. Huang et al., Hum. Mol. Genet., 8: 459-470, 1999). In the present study, DMH was applied to screen 28 paired primary breast tumor and normal samples and to determine whether patterns of specific epigenetic alterations correlate with pathological parameters in the patients analyzed. Amplicons, representing a pool of methylated CpG DNA derived from these samples, were used as hybridization probes in an array panel containing 1104 CpG island tags. Close to 9% of these tags exhibited extensive hypermethylation in the majority of breast tumors relative to their normal controls, whereas others had little or no detectable changes. Pattern analysis in a subset of CpG island tags revealed that CpG island hypermethylation is associated with histological grades of breast tumors. Poorly differentiated tumors appeared to exhibit more hypermethylated CpG islands than their moderately or well-differentiated counterparts (P = 0.041). This early finding lays the groundwork for a population-based DMH study and demonstrates the need to develop a database for examining large-scale methylation data and for associating specific epigenetic signatures with clinical parameters in breast cancer.

Adult↗
PubMed2000

A common molecular signature unifies the chitosanases belonging to families 46 and 80 of glycoside hydrolases.

The 3D structure-oriented alignment of the primary sequences of fourteen chitosanases, mainly of bacterial origin and belonging to families 46 and 80 of glycoside hydrolases, resulted in the identification of the following pattern common to all these enzymes: E-[DNQ]-x(8,17)-Y-x(7)-D-x-[RD]-[GP]-x-[TS]-x(3)-[AIVFLY]-G- x(5,11)-D. This pattern is proposed as the molecular signature of the chitosanases from families 46 and 80. It includes several amino acids essential for enzyme activity and (or) stability as shown by site-directed mutagenesis studies on the chitosanase from Streptomyces sp. N174. In particular, it includes two carboxylic residues directly involved in catalysis. We suggest that there is a continuum of sequence similarity between all the analyzed chitosanases, and that all these enzymes should probably be classified in one family.

Amino Acid Sequence↗
PubMed2001

[Digital signature: new prospects for the information of the cardiologic clinical card].

In the last few years, remarkable improvements have been made in computerized database systems used in cardiology. However, they will not easily lead to further relevant improvements unless the weaknesses and the gaps deriving from the obligation of forming and storing case sheets, according to law, are faced and resolved in an original way. This article covers the topic of the digital signature and how it could form the basis for a new powerful impulse to the process of informatization of cardiology records. The proposal of elaborating a totally computerized case sheet involves the need of rationalizing the flow of clinical information and of implementing a management system integrated with the hospital information system. The elimination of paper support will probably lead to an advantageous cycle that will involve the entire hospital, both clinically as well as administratively.

Cardiology↗
PubMed2001

Electronic signature and certification models in health care.

Recently, Belgian legislation has enabled the practical use of electronic signatures. Several implementation options are still open and different models for deployment on a wide scale are possible. This document describes two models that can be applied to the healthcare domain and summarises the recommendations as issued by the Belgian Health Telematics Standards Committee

Belgium↗
PubMed2002

Tissue-specific deletion and discontinuous loss of heterozygosity are signatures for the mutagenic effects of ionizing radiation in solid tissues.

The mouse Aprt locus on chromosome 8 was used as the selectable target for the study of spontaneous and ionizing radiation-induced mutations in kidney epithelia and ear fibroblasts. Fifty-two Aprt heterozygous mice were exposed to 7.5 Gy of (137)Cs-gamma radiation on their right sides, and Aprt-deficient clones were isolated from enzymatically digested tissues at times ranging from 1 day to 14 months after irradiation. A statistically significant increase in the mutant frequencies for the irradiated tissues was observed when compared with the spontaneous mutant frequencies for the nonirradiated tissues. A molecular analysis of spontaneous mutations observed for the nonirradiated tissues revealed tissue-specific differences; apparent chromosome loss was common in kidney mutants but infrequent in the ear mutants, whereas apparent deletions were common in the ear mutants but not detected in the kidney mutants. For the irradiated kidneys, apparent deletions were observed commonly demonstrating that these events are markers for ionizing radiation mutagenesis in this tissue. All of the loss of heterozygosity (LOH) tracts observed in the spontaneous mutants were continuous, but discontinuous LOH patterns were observed in 6--8% of ionizing radiation-induced ear and kidney cell mutants. Work with kidney-derived cell lines showed that discontinuous LOH is a novel signature for delayed ionizing radiation mutagenesis. Considered together, these results suggest that ionizing radiation-induced mutations in vivo can result from both direct and delayed mutagenic effects.

Animals↗
PubMed2002

Mantle cell lymphomas express a distinct genetic signature affecting lymphocyte trafficking and growth regulation as compared with subpopulations of normal human B cells.

Differential gene expression analysis, using high-density microarray chips, demonstrated 300-400 genes to be deregulated in mantle cell lymphomas (MCLs) compared with normal B-cell populations. To investigate the significance of this genetic signature in lymphoma etiology and diagnostics, we selected 90 annotated genes involved in a number of cellular functions for further analysis. Our findings demonstrated a normal gene expression of CCR7, which indicated a normal homing to primary follicles, which was in contrast to other receptors for B-cell trafficking, such as a significant down-regulation for CXCR5 and CCR6, as well as down-regulation of IL4R involved in differentiation. This indicated that the malignant transformation of a normal B cell could have appeared during the transition of a primary follicle to a germinal center, i.e., after an initial B-cell activation. Genes involved in blockage of antiproliferative signals in normal cells were also deregulated, e.g., gene expression of TGF beta 2 and Smad3 was suppressed in MCLs. Furthermore, lymphoproliferative signal pathways were active in MCLs compared with normal B cells, because genes encoding, e.g., IL10R alpha and IL18 were up-regulated, as were oncogenes like Bcl-2 and MERTK. Genes encoding receptors for different neurotransmitters mediating B-cell stimulation, such as norepinephrine and cannabinoids were also up-regulated, again illustrating deregulation of a complex network of genes involved in growth and differentiation. Furthermore, hierarchical cluster analysis revealed two subpopulations of MCLs, which indicates that despite the homogeneous and strong overexpression of cyclin D1, further subtyping might be possible.

Apoptosis↗