SEARCH · PubMed Health

Results for “molecular profiling”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

PubMed2005

Molecular profiling of bacterial species in the rabbit caecum.

The diversity of bacteria present in the caecum of the rabbit was investigated. Partial bacterial 16S rRNA genes from a digested sample collected from the caecum of an adult rabbit were amplified by PCR. Sequence analysis of the amplified fragments indicated highest similarity was to bacterial sequences previously described from other gut environments. However, only one sequence showed significant identity (97% threshold) to any previously described bacterial 16S rRNA genes. Furthermore, most of the sequences clustered together in groups lacking representatives from sequences already described, suggesting that the rabbit caecal flora contains organisms not previously described.

Animals↗

PubMed2026

Molecular profiling of coronary stent testenosis: A systematic review and functional analysis of implicated genes.

BACKGROUND: Coronary stent restenosis occurs in approximately 5% of patients treated with drug-eluting stents (DES) and is associated with adverse clinical outcomes. Elucidating the genetic mechanisms underlying restenosis may support precision medicine approaches to improve patient management.This systematic review aimed to synthesize evidence on genes and biological pathways associated with DES-related restenosis and to perform functional analysis of the implicated genes using bioinformatics tools. METHODS: The review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews guidelines. A systematic search of PubMed, Scopus, and Web of Science was performed for human studies investigating genetic or genomic factors in coronary restenosis, with the last search conducted in March 2024. Eligibility criteria included original studies reporting genetic associations with DES restenosis. Screening and data extraction were performed by a single reviewer. Identified genes underwent gene set enrichment analysis using Enrichr (Ma'ayan Laboratory, Computational Systems Biology) and ClueGo extension on Cytoscape (National Resource for Network Biology). RESULTS: Seventeen studies met the inclusion criteria. The studies highlighted multiple genes involved in extracellular matrix remodeling, inflammatory signaling, and the renin-angiotensin system. Gene enrichment analysis confirmed the overrepresentation of these biological pathways in DES-associated restenosis. CONCLUSIONS: This systematic review synthesizes the genetic and molecular contributors to DES-associated restenosis and identifies potential targets for future research and personalized therapies. No external funding was received, and the protocol was not registered.

Humans↗

PubMed1993

Molecular profile of an antibody response to HIV-1 as probed by combinatorial libraries.

A large number (33) of human Fab fragments reacting with HIV-1 surface glycoprotein gp120 have been generated by selection from a combinatorial IgG1 kappa library displayed on the surface of phage. The library was prepared from a long term asymptomatic HIV-seropositive donor. Analysis of the sequences from these Fabs shows the heavy chains can be placed in groups, many of which contain intraclonal variants, almost certainly corresponding to chains used in vivo. Further variants can be accessed via chain shuffling experiments in which a given light chain is recombined with a library of heavy chains. Heavy chain promiscuity, i.e. the ability of heavy chains to pair with different light chains with retention of antigen binding, is dependent on the particular heavy chain considered and probably excludes the identification of in vivo light chain partners. The antibodies examined here are primarily to the CD4 binding site on gp120 and broadly reflect the serum profile of the donor. The antibodies show evidence of extensive somatic modification indicative of an antigen-driven response. The heavy chain CDR3 regions of the antibodies show a remarkably conserved extended length. A number also show strong sequence conservation in CDR3 against a background of considerable diversity in the rest of the VH gene supporting a central role for this region in antigen recognition.

Amino Acid Sequence↗

PubMed1977

The immunologic and molecular profiles of HLA antigens isolated from urine.

Human urine was shown to be a good source for the isolation of immunologically functional HLA-A9 antigens. The use of complex solubilization procedures can be avoided since the antigens are present in soluble form and are not complexes with membrane fragements. Purification in excess of 400-fold could be achieved by the application of cellulose ion exchange chromatography, isoelectric focusing, and acrylamide gel electrophoresis. The purified HLA-A9 antigen is composed of a glycoprotein of m.w. 38,000 and beta2-microglobulin, a peptide of m.w. 12,000. HLA-A9 antigens isolated from urine proved to be immunologically functional since they not only reacted specifically with anti-HLA-A9 alloantibody but also elicited anti-HLA-A9 xenoantibodies. These antibodies when covalently attached to Sepharose 4B specifically bound HLA-A9 antigens isolated from both serum and urine.

Arginine↗

PubMedDate not supplied

Molecular profile and clinical variables in BRCA1-positive breast cancers. A population-based study.

PURPOSE: To evaluate the clinical features of breast cancer patients with genetic susceptibility to this disease and to investigate the contribution of BRCA1 germline mutations to the phenotype of these tumors. PATIENTS AND METHODS: We reviewed the clinical and pathological records of 102 women with suspected inherited susceptibility to breast cancer consecutively seen at the Genetic Oncology Service of Parma, Italy. Sixty-two patients with a high probability of harboring a germline, cancer-predisposing mutation were tested for BRCA1 mutations. Exon 11 was screened using the protein truncation test and detected mutations were confirmed by direct sequencing (DS). All other exons were analyzed by DS. RESULTS: Among the 62 patients with a completed mutation analysis, 48 (77.4%) had wild-type BRCA1, six (9.6%) had variants of unclear significance, eight (13%) had deleterious mutations. BRCA1-associated breast cancers (BABC) were significantly less likely to be diagnosed at stage I than breast cancers in women without mutations (12.5% vs 51%; P = 0.045), more likely to have a high proliferation rate (100% vs 24%, P < 0.001), and more likely to be histological grade 3 (100% vs 14%, P < 0.001), estrogen and progesterone receptor negative (87.5% vs 13%, P < 0.001; 75% vs 23%, P = 0.004), and p53 positive (87.5% vs 30%, P = 0.023). All tumors with BRCA1 mutations were HER-2/neu negative compared with 57% of the non-BRCA1 tumors (P = 0.04). There were no significant differences between BABC and non-BABC in 20-year relapse-free survival, 20-year event-free survival, and 20-year overall survival. CONCLUSION: In this population-based study, BABC seems to present with adverse molecular features when compared with non-BABC, although the prognosis appears to be similar.

Adult↗

PubMed2006

Analysis of molecular alterations in left- and right-sided colorectal carcinomas reveals distinct pathways of carcinogenesis: proposal for new molecular profile of colorectal carcinomas.

To clarify distinct genetic profiles of colorectal cancers based on tumor location (left- and right-sided), we evaluated the status of loss of heterozygosity (LOH), CpG islands methylation phenotype (CIMP), microsatellite instability (MSI), and mutations of p53, Ki-ras, and APC genes in 119 colorectal cancers. Statuses of LOH (at 5q, 8p, 17p, 18q, and 22q), MSI, and CIMP (MINT1, MINT2, MINT31, MLH-1, MGMT, p14, p16, and RASSF1A) were determined using microsatellite polymerase chain reaction and methylation-specific polymerase chain reaction coupled with a crypt isolation method, respectively. In addition, mutations of p53, Ki-ras, and APC genes were also examined. LOH, MSI, and CIMP status allowed us to classify samples into two groups: low or negative and high or positive. Whereas the frequency of p53 mutations in the LOH-high status was significantly higher in left-sided cancers than in right-sided cancers, CIMP-high in the LOH-high status and MSI-positive status were more frequently found in right-sided cancers compared with left-sided cancers. Finally, location-specific methylated loci were seen in colorectal cancers: type I (dominant in right-sided cancer) and type II (common in both segments of cancer). Our data confirm that distinct molecular pathways to colorectal cancer dominate in the left and right sides of the bowel.

Aged↗

PubMed2005

Molecular profiling demonstrates limited diversity amongst geographically separate strains of Ustilago scitaminea.

Intraspecies diversity within Ustilago scitaminea isolates from South Africa, Reunion Island, Hawaii and Guadeloupe was assessed by RAPDs, bE mating-type gene detection, rDNA sequence analysis, microscopy and germination and morphological studies. Except for sequence data, the other analyses yielded no differences in the isolates that could be used in a phylogenetic separation. Mycelial DNA of the SA isolate shared 100% sequence identity with that of mycelial DNA cultured from in vitro produced teliospores of the parent cultivar. Overall the ITS1 and ITS2 regions were found to have 96.1% and 96.9% sequence identity with a total of 17 and 21 base changes, respectively, amongst the isolates. The Reunion Island isolate was shown to be most distantly related by 3.6% to the other isolates, indicating a single clonal lineage. The lack of germination in teliospores from Guadeloupe may be attributed to changes in temperature and humidity during transportation.

Base Sequence↗

PubMed1994

Similarity in the molecular profile of mutations induced by UV light in shuttle vector plasmids propagated in mouse and human cells.

Shuttle vector plasmids pYZ289 were irradiated with UV and transfected to mouse cells to permit repair of damage, mutation and replication in the cells. The frequency and types of mutations were compared with those of UV-irradiated shuttle vector plasmids pZ189 which were propagated in normal human and xeroderma pigmentosum (XP) patient cells defective in DNA repair. Both shuttle vector plasmids contain a bacterial suppressor tRNA gene supF as a common mutation target. pYZ289 propagated in the mouse cells showed survival and mutation frequency similar to pZ189 propagated in the normal human cells. All single base substitution mutations were induced in dipyrimidine sequences and G:C to A:T transition was most frequently observed (47%) in the mouse cells; however, the frequency was significantly lower than that in the XP cells. The frequency of the base substitution mutations at A:T base pairs was significantly higher in the mouse cells (29%) than in the normal human (12%) and the XP cells (6%). These results show that similar types of mutations are induced by UV in mouse and normal human cells, and that the A:T base pair is relatively more mutable in mouse than in normal human and XP cells.

Animals↗

PubMed2002

Molecular profiling of behavioural development: differential expression of mRNAs for inositol 1,4,5-trisphosphate 3-kinase isoforms in naive and experienced honeybees (Apis mellifera).

In seeking genetic factors that may control the extended behavioural maturation of adult honeybees we found that inositol 1,4,5-trisphosphate (IP(3)) 3-kinase, a key enzyme in the IP(3)-mediated signalling cascade, is differentially expressed in brains of naive, newly emerged bees and experienced foragers. DNA sequencing yielded a contig of 21.5 kb spanning the honeybee IP(3)K locus and a 3' flanking gene similar to a transcription factor NFR-kappa-B. The IP(3)K locus gives rise to three differentially expressed major transcripts produced by alternative splicing that encode proteins with identical, highly conserved C-termini and distinct, non-conserved N-terminal domains. The type A transcript is dominant in the adult brain and its level of expression increases threefold during the first 4 days of adult development. The type B message is expressed in brains of naive bees, but is also found in the thorax and abdomen, whereas transcript C is expressed largely in non-neural tissues and in the antenna. In contrast to type A message, the brain levels of transcript B decrease during the first 4 days of adult life. Our data are evaluated in the context of the contrasting behavioural phenotypes of immature and experienced worker honeybees.

Animals↗

PubMed2004

Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery.

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.

Bacteria↗

PubMed2004

Molecular profiles of Trypanosoma brucei, T. evansi and T. equiperdum stocks revealed by the random amplified polymorphic DNA method.

A total of 20 random primers (10-mers) were used to amplify RAPD markers from the genomic DNA of four Trypanosoma brucei stocks from East and West Africa, four T. evansi stocks from Africa, Asia and South America and one T. equiperdum stock from Asia. Between 65 and 88 reproducible fragments ranging from 0.25 to 2.15 kb were generated from these stocks depending on the stock/primer combination. The similarity coefficient (SC) among the stocks of T. brucei from Kenya, Nigeria, Tanzania and Zambia ranged from 62.9% to 74.0% (average: 67.6%). The SC among the stocks of T. evansi from Kenya, China and Brazil was 76.4%-95.5% (average: 86.4%), while the SC between T. evansi stock from China and Brazil was 95.5%. For T. evansi and T. equiperdum, the SC among the stocks ranged from 81.2% to 94.4% (average: 87.6%). As for the SC among the stocks of T. brucei and T. evansi, it was found to be from 54.7% to 80.3% (average: 68.0%) and the SC among stocks of T. brucei and T. equiperdum was from 59.4% to 76.9% (average: 68.1%). Our results indicate that the stocks of T. evansi from China and from Brazil are more closely related to the stock of T. equiperdum from China than to the stocks of T. evansi isolated from Kenya and to the stocks of T. brucei. In addition, our results further support the hypothesis that T. evansi stocks from China and Brazil could have arisen from a single lineage. The possible evolution of T. evansi and T. equiperdum is also discussed.

Animals↗

PubMed1992

Histopathologic and molecular profile of human cytomegalovirus infections in patients with heart transplants.

From November 1985 to December 1990, 2,552 endomyocardial biopsy specimens from 209 heart transplant patients were studied. Forty-four (21%) patients developed 45 episodes of major human cytomegalovirus infection (HCMV). Human cytomegalovirus infection was primary in 13 of 44 patients. Thirty-one patients developed episodes of recurrent major infection. One patient had both primary and recurrent infections. Conventional histopathologic and immunohistochemical study, in situ hybridization, and polymerase chain reaction were used to diagnose HCMV myocardial involvement on corresponding endomyocardial biopsy specimens performed during infection. Conventional morphologic study showed typical viral inclusion bodies in four biopsy specimens. Two cases had myocyte HCMV localization with necrotizing myocarditis, whereas two had endothelial cell involvement without any inflammatory reaction. In these four biopsy specimens, immunohistochemistry showed a higher number of infected cells than that recognized by conventional histopathologic study. In situ hybridization detected infected cells with no evidence of cytopathic effect. Polymerase chain reaction gave HCMV amplification products in two additional biopsy specimens otherwise interpreted as moderate and mild rejection, respectively. Therefore, 6 biopsies showed HCMV myocardial involvement (6 of 45; 13.3%): all were from patients with primary HCMV infection (6 of 13; 46%). None of 32 major recurrent infections showed any myocardial involvement. In conclusion, our study is the first to demonstrate that myocardial HCMV involvement preferentially occurs in primary infection and HCMV endothelial localization can be free from inflammatory reaction, whereas HCMV myocyte localization leads to necrotizing myocarditis. Polymerase chain reaction has a higher diagnostic sensitivity than in situ hybridization. However, polymerase chain reaction findings of HCMV DNA on otherwise negative endomyocardial biopsy specimens remains of questionable significance because polymerase chain reaction-positive biopsy samples do not necessarily indicate tissue infection. It is impossible to determine whether amplified sequences derive from circulating leukocytes or from tissue cells.

Antigens, Viral↗

PubMed2004

Molecular profiling and the identification of genes associated with metastatic oral cavity/pharynx squamous cell carcinoma.

OBJECTIVE: To investigate differences in gene expression profiles between oral cavity/oropharynx squamous cell carcinoma (OC/OP SCC) primary tumors that have metastasized to cervical lymph nodes and nonmetastatic OC/OP SCC tumors. DESIGN: Oligonucleotide microarray analysis of primary tumors was used to produce gene expression profiles. Profile comparisons between metastatic and nonmetastatic tumors were performed using principal component analysis, t test, and fold change differences. A similar comparison between metastatic tumors and noncancer oral mucosa samples was performed to ensure tumor origin. SUBJECTS: A prospective cohort of 20 patients with previously untreated OC/OP SCC who underwent pathologic staging following surgical resection and lymphadenectomy. RESULTS: Of the approximately 9600 genes profiled, 101 demonstrated significant expression differences between the metastatic and nonmetastatic tumors (fold change > or =1.5; P<.01). Among this subset, 57 genes also exhibited significant differences between metastatic tumors and normal mucosa samples (fold change > or =1.5; P<.05). This profile included genes related to the extracellular matrix, adhesion, motility, inflammation, and protease inhibition. Collagen type 11 alpha-1 (COL11A1) demonstrated the greatest differential expression between metastatic and nonmetastatic OC/OP SCC tumors (fold change=7.61; P=.002). Tissue inhibitor of metalloproteinase 1 (TIMP-1) also demonstrated increased expression in metastatic tumors (fold change=3.3; P=.003). CONCLUSIONS: Metastatic OC/OP SCC has a distinct gene expression profile compared with nonmetastatic OC/OP SCC and normal oral mucosa. This metastatic profile includes genes related to the extracellular matrix, adhesion, motility, and protease inhibition. Knowledge gained through tumor gene expression profiling may facilitate early detection of aggressive tumors and targeted therapeutic interventions.

Carcinoma, Squamous Cell↗

PubMed2005

Molecular profiling of tumor progression in head and neck cancer.

OBJECTIVE: To assess gene expression changes associated with tumor progression in patients with squamous cell carcinoma of the oral cavity. DESIGN: A microarray containing 17 840 complementary DNA clones was used to measure gene expression changes associated with tumor progression in 9 patients with squamous cell carcinoma of the oral cavity. Samples were taken for analysis from the primary tumor, nodal metastasis, and "normal" mucosa from the patients' oral cavity. SETTING: Tertiary care facility. Patients Nine patients with stage III or stage IV untreated oral cavity squamous cell carcinoma. RESULTS: Our analysis to categorize genes based on their expression patterns has identified 140 genes that consistently increased in expression during progression from normal tissue to invasive tumor and subsequently to metastatic node (in at least 4 of the 9 cases studied). A similar list of 94 genes has been identified that decreased in expression during tumor progression and metastasis. We validated this gene discovery approach by selecting moesin (a member of the ezrin/radixin/moesin [ERM] family of cytoskeletal proteins) and one of the genes that consistently increased in expression during tumor progression for subsequent immunohistochemical analysis using a head and neck squamous cell carcinoma tissue array. CONCLUSION: A distinct pattern of gene expression, with progressive up- or down-regulation of expression, is found during the progression from histologically normal tissue to primary carcinoma and to nodal metastasis.

Carcinoma, Squamous Cell↗

PubMed2000

Phenylketonuria and hyperphenylalaninemia in eastern Germany: a characteristic molecular profile and 15 novel mutations.

Phenylketonuria (PKU) is an important error of amino acid metabolism which results in most patients from phenylalanine hydroxylase (PAH) deficiency. PKU displays a marked genotypic heterogeneity both within and between different populations. The aim of this study was to establish the genotypic spectrum of PKU in eastern Germany, and to compare this to the distribution of mutations in western Germany. The study population included 302 patients in 290 families who were followed at treatment centers in Berlin, Leipzig and Jena. The study showed marked genotypic variability with a total of 75 mutations, including 15 that have so far not been described (eleven missense mutations, one splicing mutation, and three small deletions). One of these novel mutations, E183Q, occurred in cis to a R408W mutation. In the non-immigrant eastern German population, the frequency of R408W accounted for 40.1% of the PKU alleles. In the immigrant Turkish population of the former West Berlin, the most prevalent mutation was IVS10-11G>A (57%). There was a marked difference of the genotypic spectrum between the population studied here and the data reported from the western part of the country.

Amino Acid Substitution↗

PubMed2000

A New Self-Assembling System for Targeted Gene Delivery We thank the BBSRC Chiroptical Service for CD studies, Brian McManus (Optokem Instruments, Nercyws, Flintshire) for assistance with the light-scattering studies, Dr. Clive Roberts (Molecular Profiles Ltd.) for AFM studies, Professor J.-H. Fuhrhop for many discussions, Dr. I. S. Blagbrough for related synthetic work, the EPSRC for support, and the Royal Society for a Leverhulme Trust Senior Research Fellowship (D.P.).

Explore the source record for details and available documents.

Journal Article↗

PubMedDate not supplied

Molecular profiles of the cell membrane bound and cytoplasmic forms of the human MHC class-II associated invariant polypeptides.

Several sub-types of histocompatibility class-II molecules are known to exist, including DR, DQ and DP, each subset organized in alpha and beta heterodimers. These molecules play a central role in immunorecognition via direct noncovalent binding of degraded nonself immunogenic peptides followed by ligand-interaction with T cells. In the cytoplasm the class-II alpha and beta chains associate, in addition with a third backbone molecule known as the invariant chain. In this study we show that all class-II subsets associate with the invariant chain probably from the same pool and that a subset of invariant chain is expressed as a cell surface subunit. This sub-unit, whose function is still unknown, was detected by flow-cytometry and by two-dimensional gel analysis followed by antibody-mediated immunoprecipitations.

Antibodies, Monoclonal↗

PubMed2003

Two-dimensional molecular profiling of mantle cell lymphoma.

The present research establishes standard two-dimensional (2-D) maps for control, reactive lymph node and non-Hodgkin's lymphoma (mantle cell lymphoma, MCL). Medium sensitivity, mass spectrometry compatible colloidal Coomassie has revealed a total of ca. 750 spots in each of the maps. Comparison of 2-D maps by statistical packages, such as the PDQuest, established up- and downregulation of a total of ca. 145 spots, with positive variations of up to 10-folds and negative variations of up to 13-folds in both MCL biopsies' protein extracts. Qualitative and quantitative variations in the two lymphoma samples are consistent. More than 20 proteins have been so far identified by matrix assisted laser desorption/ionisation-time of flight (MALDI-TOF)-mass spectrometry, with an additional five spots, which gave very good spectra but could not be matched to any of the presently available databases. Some of the spots, such as the 78 kDa glucose-regulated protein precursor and the glutathione S-transferase P, appear to be in common with other tumors, such as lung adenocarcinoma. Others may simply reflect overall changes in cellular metabolism and growth rate that occur during malignancy and thus might turn out to be in common with any cell population receiving any kind of stress. Some (notably T-cell leukemia/lymphoma protein 1A, TCL1, found to be 10-fold overexpressed) appear to be specific of the non-Hodgkin's lymphoma here studied. Western blot and immunohistochemical analyses were applied to obtain further information about stathmin (Op18) and TCL1, respectively.

Biopsy↗