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PubMed2006

Comparison of antibiotic susceptibility profiles and molecular typing patterns of clinical and environmental Salmonella enterica serotype Newport.

The genus Salmonella is composed of more than 2,400 serotypes, many of which cause enteric diseases in humans and animals. Several Salmonella serotypes are multidrug resistant, and there is evidence of the clonal spread of these strains from animals to humans. Salmonella enterica serotype Newport is one of the serotypes that increasingly present a multidrug-resistant phenotype. Source tracking and antibiotic resistance testing are important considerations for identifying the outbreak strain. The first goal of this study was to examine the antibiotic susceptibility patterns of clinical and environmental Salmonella Newport isolates from various geographic locations and to compare the discriminatory ability of two DNA fingerprinting techniques. The second goal was to determine whether the antibiotic resistance profiles and typing patterns correlated. Thirty Salmonella Newport isolates, including environmental and human clinical strains, were subjected to pulsed-field gel electrophoresis (PFGE), ribotyping, and antibiotic susceptibility testing. Eighty percent of the isolates showed total or intermediate resistance to one or more drugs; 75% of the isolates were multidrug resistant. Ribotyping with the EcoRI enzyme and PFGE with the XbaI enzyme each divided the isolates into 14 groups. Cluster analysis based on antibiotic susceptibility patterns generated 23 profiles. The susceptible and resistant isolates were not differentiated on the basis of either of the molecular typing techniques. Hence, no correlation was observed between the antibiotic resistance profiles and the DNA subtyping patterns. In conclusion, ribotyping is as discriminatory as PFGE and, when used in combination with antibiotic resistance profiles, provides a powerful tool for the source tracking of Salmonella Newport.

Animals↗

PubMed1981

Tumor-associated antigens in spent medium of human melanoma cells: immunochemical characterization with xenoantisera.

Xenoantisera to human melanoma cells and to partially purified melanoma-associated antigens were coupled to protein A-bearing Staphylococcus Aureus or protein A-Sepharose and used as immunoadsorbents for the indirect immunoprecipitation of intrinsically radiolabeled proteins released into culture medium from various cultured human tumor and nontumor cell lines. These radiolabeled immunoprecipitates when analyzed by SDS-PAGE revealed highly reproducible molecular profiles of proteins and glycoproteins released by various cultured tumor lines and control cells into their spent culture media. A comparison of molecular profiles together with data indicating the binding specificity of known xenoantisera produced against human melanoma cells or their extracts led to the discovery of 2 macromolecules that are associated with human melanoma cells; a glycoprotein with a subunit m.w. of 240,000 (240K) and a single-chain glycoprotein of 94,000 (94K) m.w. also found in association with human carcinoma cells are described in this report.

Animals↗

PubMed2004

High throughput gene expression profiling: a molecular approach to integrative physiology.

Integrative physiology emphasizes the importance of understanding multiple pathways with overlapping, complementary, or opposing effects and their interactions in the context of intact organisms. The DNA microarray technology, the most commonly used method for high-throughput gene expression profiling, has been touted as an integrative tool that provides insights into regulatory pathways. However, the physiology community has been slow in acceptance of these techniques because of early failure in generating useful data and the lack of a cohesive theoretical framework in which experiments can be analysed. With recent advances in both technology and analysis, we propose a concept of multidimensional integration of physiology that incorporates data generated by DNA microarray and other functional, genomic, and proteomic approaches to achieve a truly integrative understanding of physiology. Analysis of several studies performed in simpler organisms or in mammalian model animals supports the feasibility of such multidimensional integration and demonstrates the power of DNA microarray as an indispensable molecular tool for such integration. Evaluation of DNA microarray techniques indicates that these techniques, despite limitations, have advanced to a point where the question-driven profiling research has become a feasible complement to the conventional, hypothesis-driven research. With a keen sense of homeostasis, global regulation, and quantitative analysis, integrative physiologists are uniquely positioned to apply these techniques to enhance the understanding of complex physiological functions.

Animals↗

PubMed2006

Point-of-care biosensor systems for cancer diagnostics/prognostics.

With the growing number of fatalities resulting from the 100 or so cancer-related diseases, new enabling tools are required to provide extensive molecular profiles of patients to guide the clinician in making viable diagnosis and prognosis. Unfortunately with cancer-related diseases, there is not one molecular marker that can provide sufficient information to assist the clinician in making effective prognoses or even diagnoses. Indeed, large panels of markers must typically be evaluated that cut across several different classes (mutations in certain gene fragments--DNA; over/under-expression of gene activity as monitored by messenger RNAs; the amount of proteins present in serum or circulating tumor cells). The classical biosensor format (dipstick approach for monitoring the presence of a single element) is viewed as a valuable tool in many bioassays, but possesses numerous limitations in cancer due primarily to the single element nature of these sensing platforms. As such, if biosensors are to become valuable tools in the arsenal of the clinician to manage cancer patients, new formats are required. This review seeks to provide an overview of the current thinking on molecular profiling for diagnosis and prognosis of cancers and also, provide insight into the current state-of-the-art in the biosensor field and new strategies that must be considered to bring this important technology into the cancer field.

Biomarkers, Tumor↗

PubMed1998

Antagonist profile and molecular dynamic simulation of a Drosophila melanogaster muscarinic acetylcholine receptor.

A stably-transfected, Drosophila cell line (S2-DMl-1) expressing the Drosophila DMl muscarinic acetylcholine receptor (mAChR) exhibits high-affinity, saturable, specific binding of the radiolabelled muscarinic antagonist [3H]-N-methyl scopolamine ([3H]-NMS) with an equilibrium dissociation constant (Kd) of 0.67 +/- 0.02 and a Bmax of 1.53 +/- 0.3 pmol/mg protein. Displacement of [3H]-NMS by mAChR antagonists results in the pharmacological profile: 4-diphenylacetoxy-N-methylpiperidine methiodide (4-DAMP) > hexahydrosiladifenidol > p-fluorohexahydrosiladifenidol > nitrocaramiphen > pirenzepine > methoctramine > AFDX-116. This antagonist profile most closely resembles that of the vertebrate M3 mAChR subtype. In this study, however, we have demonstrated that the antagonist profile of DM1 is distinct from those of vertebrate mAChR subtypes. Molecular dynamic simulations of the Drosophila muscarinic receptor are presented in the free, carbamylcholine-bound and NMS-bound forms. Theoretical, quantitative structure-activity relationship models have been developed; a good correlation is observed between the interaction energies of the minimized ligand-receptor complexes and the pharmacological affinities of the antagonists tested.

Animals↗

PubMed1995

Carbohydrate molecular weight profiling, sequence, linkage, and branching data: ES-MS and CID.

This section summarizes several strategies for a more complete understanding of carbohydrate structure with a focus on glycolipids and glycoprotein glycans. The techniques include periodate oxidation to impart greater molecular specificity to isomeric glycans, methylation to improve sensitivity and the information content within CID spectra, electrospray for "soft" and efficient ionization, and CID to obtain structural detail. The lipophilicity of the products following derivatization contributes to product cleanup by solvent extraction and enhances sensitivity during ES. When combined with CID information, this yields sequence, linkage, and branching information. Oxidation and reduction preceding methylation augments CID analysis with an altered structure that can be profiled at the same sensitivity. Within the context of established motifs, these contrasting profiles corroborate glycan structure and specifically identify isobaric elements transparent in the initial profile. An earlier report indicating ring-opening fragments were essentially absent in low-energy collisions of methylated and natriated oligosaccharides contrasts our observations. However, as this report used a methylated oligomer containing an internal N-acetylhexose as an illustration, the conclusion is plausible (cf., Figure 9). The poor ionization efficiency of FAB and the high matrix background limit the dynamic range in the CID spectrum and, thereby, the ability to unambiguously identify weaker peaks. It would be expected that high-energy CID affords a broader range of fragment types, including ring-opening fragments. In terms of a structural methodology, this is ambivalent since the increase in fragmentation pathways also applies to small molecule eliminations which are usually less informative. In ES-CID-MS, the carbohydrate chemist has a powerful new tool in hand for structural elucidations that can be conducted at the low-picomole level. Parallel developments can be expected to continue for other ionization methods, in particular matrix-assisted desorption/ionization on linear and reflectron time of flight mass spectrometers, and improvement in the performance and sensitivity of high-resolution mass analyzers through the use of focal plane detectors and more sophisticated hardware and software for Fourier transform ion cyclotron resonance mass measurements. These have, as yet, only begun to be applied to carbohydrate structural analysis but should add still more versatility to experimental design in the future.

Carbohydrate Conformation↗

PubMedDate not supplied

Effect of enzyme inhibitors on profiles of IR-ACTH/beta-endorphin in brain and pituitary.

Processing of pro-opiomelanocortin (POMC) in brain and pituitary results in various proportions of multiple peptides appearing as immunoreactive (IR-) ACTH and IR-beta-endorphin. Because it is desirable that molecular profiles of POMC-related peptides reflect in vivo processing and not isolation artifact, inhibition of proteolytic activity during extraction is critical. Although enzyme inhibitors are frequently used during extraction of POMC-related peptides, their benefit or necessity has not been established. To determine the benefit of using enzyme inhibitors for studying molecular profiles of IR-ACTH and IR-beta-endorphin from rat brain and pituitary, chromatographic profiles were compared to assess the effect of each of several enzyme inhibitors. Results suggested that the enzyme inhibitors studied provided no additional benefit in terms of inhibition of extraction proteolysis over that provided by a strong acid and heat inactivation.

Adrenocorticotropic Hormone↗

PubMed2026

Worldwide Innovative Network Consortium: Building a Common Global Cancer Database.

This review shares the ongoing work of the global Worldwide Innovative Network (WIN) Consortium for Precision Medicine to synthesize emerging cancer treatment data and to define the requirements for a common global cancer database that can truly support precision oncology. We performed a narrative review of emerging cancer treatment data, molecular profiling technologies, and existing clinicogenomic databases, focusing on how tumors are characterized, how subgroups are defined, and how demographic, lifestyle, and environmental factors are captured. The growth in molecular profiling technologies and the development of new targeted therapies are transforming cancer care. Tumors, regardless of tissue origin, are increasingly defined as composites of multiple, often rare, subgroups, each with distinct biology and likely response to specific therapies, based on multidimensional profiling of the tumor and its microenvironment. The solution lies in building vast databases that capture racial and ethnic diversity, reflected in genomic data, as well as diet and lifestyle factors that may have epigenetic impact on gene expression and post-translational modifications. A truly inclusive and informative data set must reflect global diversity, and there are multiple examples of demography-dependent differences in genomic signals. With members caring for and studying patients with cancer across five continents, WIN is actively exploring pathways to create a global cancer database, rich in clinical and molecular detail, granular enough for precise analysis, and large enough to power artificial intelligence-driven insights, provided appropriate data quality, validation, and governance frameworks are in place. This review surveys the current landscape and outlines practical paths forward to achieve this goal.

Humans↗

PubMed1999

Comparative molecular genetic profiles of anaplastic astrocytomas/glioblastomas multiforme and their subsequent recurrences.

Malignant glial tumors (anaplastic astrocytomas and glioblastomas multiforme) arise mostly either from the progression of low grade precursor lesions or rapidly in a de novo fashion and contain distinct genetic alterations. There is, however, a third subset of malignant gliomas in which genetic lesions remain to be identified. Following surgical resection, all gliomas appear to have an inherent tendency to recur. Comparative molecular analysis of ten primary malignant gliomas (three anaplastic astrocytomas and seven glioblastomas multiforme) with their recurrences identified two distinct subgroups of recurrent tumors. In one group, primary tumors harbored genetic aberrations frequently associated with linear progression or de novo formation pathways of glial tumorigenesis and maintained their genetic profiles upon recurrence. In the other subset with no detectable known genetic mutations at first presentation, the recurrent tumors sustained specific abnormalities associated with pathways of linear progression or de novo formation. These included loss of genes on chromosomes 17 and 10, mutations in the p53 gene, homozygous deletion of the DMBTA1 and p16 and/ or p15 genes and amplification and/or overexpression of CDK4 and alpha form of the PDGF receptor. Recurrent tumors from both groups also displayed an abnormal expression profile of the metalloproteinase, gel A, and its inhibitor, TIMP-2, consistent with their highly invasive behavior. Delineation of the molecular differences between malignant glioblastomas and their subsequent recurrences may have important implications for the development of rational clinical approaches for this neoplasm that remains refractory to existing therapeutic modalities.

Cell Cycle Proteins↗

PubMed2003

Gene expression profiling identifies molecular subtypes of gliomas.

Identification of distinct molecular subtypes is a critical challenge for cancer biology. In this study, we used Affymetrix high-density oligonucleotide arrays to identify the global gene expression signatures associated with gliomas of different types and grades. Here, we show that the global transcriptional profiles of gliomas of different types and grades are distinct from each other and from the normal brain. To determine whether our data could be used to uncover molecular subtypes without prior knowledge of pathologic type and grade, we performed K-means clustering analysis and found evidence for three clusters with the aid of multidimensional scaling plots. These clusters corresponded to glioblastomas, lower grade astrocytomas and oligodendrogliomas (P<0.00001). A predictor constructed from the 170 genes that are most differentially expressed between the subsets correctly identified the type and grade of all samples, indicating that a relatively small number of genes can be used to distinguish between these molecular subtypes. These results further define molecular subsets of gliomas which may potentially be used for patient stratification, and suggest potential targets for treatment.

Astrocytoma↗

PubMed1996

PCR-RFLP analysis of the large subunit (23S) ribosomal RNA genes of Campylobacter jejuni.

Forty-seven strains of Campylobacter jejuni were examined by PCR-RFLP analysis of 23S rRNA genes. Seven different molecular profiles were detected by a combination of HpaII AluI and DdeI digest analysis. Most (83%) strains, including those with different Penner serotypes and from different hosts, had the same molecular profiles. The high level of conservation apparent within the 23S rDNA sequences confirmed their value as targets in species-specific PCR identification assays but not for subtypic discrimination within Camp. jejuni.

Campylobacter jejuni↗

PubMed2005

Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.

Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. We investigated global gene expression in surgical samples of brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower-grade oligodendroglial tumors. Extensive differences in gene expression were found among GBMs, particularly in genes involved in angiogenesis, immune cell infiltration, and extracellular matrix remodeling. We found that the gene expression patterns in paired specimens from the same GBM invariably were more closely related to each other than to any other tumor, even when the paired specimens had strikingly divergent histologies. Survival analyses revealed a set of approximately 70 genes more highly expressed in rapidly progressing tumors that stratified GBMs into two groups that differed by >4-fold in median duration of survival. We further investigated one gene from the group, FABP7, and confirmed its association with survival in two unrelated cohorts totaling 105 patients. Expression of FABP7 enhanced the motility of glioma-derived cells in vitro. Our analyses thus identify and validate a prognostic marker of both biologic and clinical significance and provide a series of putative markers for additional evaluation.

Brain Neoplasms↗

PubMed2025

Deep Learning on Histologic Slides Accurately Predicts Consensus Molecular Subtypes and Spatial Heterogeneity in Colon Cancer.

Colon cancer (CC) is the third most prevalent cancer type. It is highly heterogeneous, particularly in terms of molecular profiles, which have both prognostic and predictive impacts on the treatment efficacy. However, CC treatment in adjuvant situations is currently guided solely by T and N staging. In this context, consensus molecular subtypes (CMSs) were introduced to stratify patients with CC based on molecular profiles. Recent studies have shown that CMS can be heterogeneous in CC, leading to a worse prognosis. This study focused on predicting CMS and its heterogeneity in CC using deep learning on digitized hematoxylin and eosin ± saffron-stained whole-slide images. Data and whole-slide images of 1996 patients from the PETACC-8, The Cancer Genome Atlas-COAD, and PRODIGE-13 cohorts were used. The model is trained to predict a 4-dimensional CMS vector, reflecting intratumor heterogeneity (ITH). It comprises a self-supervised model for embedding image patches into vectors and a weakly supervised model predicting CMS calls. Ground-truth CMS scores are obtained with the CMSclassifier package. Interpretability analyses are performed at the slide and patch levels. For homogeneous tumors, the model trained on PETACC-8 achieves 93.0% (±1.4%) macroaverage area under the curve in internal cross-validation and 94.4% macroaverage area under the curve in external validation over PRODIGE-13, whereas the The Cancer Genome Atlas-COAD model reaches 85.4% (±3.0%) in cross-validation and 92.4% over PRODIGE-13. The trained models also provide spatial distributions of CMS across tumor slides and associate specific histologic features with each CMS. Finally, the models are able to predict ITH. The results show that a deep learning model trained on routine histology slides is capable of providing an efficient and robust method for predicting CMS and characterizing a patient's ITH, paving the way for the routine consideration of CMS/ITH in clinical decision making in the adjuvant setting.

Humans↗

PubMed2004

Gene expression profiling for molecular staging and prognosis prediction in colorectal cancer.

A key issue for patients undergoing surgery for colorectal cancer is the accurate prediction of treatment outcome. Currently, classification of a tumor by histopathologic stage is the most accurate prognostic factor for the risk assessment of treatment failure. However, despite improved histologic techniques and the application of novel immunohistochemical and molecular techniques, it is still not possible to delineate the underlying biochemical and genetic events that predict clinical outcome for individual cancer patients. One reason for this lack of progress is that the factors which determine the metastatic potential of a primary tumor are still unknown. This reality, coupled to dramatic technological developments in the field of expression profiling, has started a paradigm shift in the staging of colorectal cancers. It has raised expectations that genetic and/or transcriptome profiling of the primary tumor will result in the identification of prognostic determinants relevant to the individual patient. In turn, this may allow a clinically relevant definition of patient subgroups based on individual molecular parameters for rational decision making regarding choice of therapy.

Biomarkers, Tumor↗

PubMed2004

Molecular diversity of Moraxella bovis isolated from Brazil, Argentina and Uruguay over a period of three decades.

The molecular profile of 30 Moraxella bovis strains, recovered from outbreaks of infectious bovine keratoconjunctivitis in Argentina, Brazil and Uruguay between 1974 and 2001, was determined through randomly applied polymorphic DNA (RAPD) analysis. Molecular profiles of nine strains recovered after 1990 varied from those recovered before 1990. The profiles of 13 strains (48%) differed from those of three vaccinal strains extensively used since 1984 in Argentina and Uruguay. Eight Argentinean strains, one from Brazil and two from Uruguay had identical RAPD profiles. Strains belonging to different serogroups had identical RAPD profiles, demonstrating that this technique was not able to discriminate among strains with low cross-reactivity indices. RAPD may be helpful in the primary characterization of M. bovis strains, but it does not replace serological characterization.

Animals↗

PubMed2004

Insights from the gene expression profiling of multiple myeloma.

Recent gene expression profiling using high throughput sequencing and microarray analysis of multiple myeloma has shed new light on this morphologically homogeneous yet clinically heterogeneous disease. The biology of the disease has been interrogated in studies, which reveal that patients have unique gene expression clusters that correlate with disease severity. These studies have also revealed that some myeloma cells have gene expression characteristics that resemble the molecular profile of late-stage B cells. Expression profiling can identify hallmark immunoglobulin translocations and other common structural genetic changes that impart prognostic significance. Molecular profiling has been demonstrated to be of value in pharmacogenomic studies predicting response to therapy and revealing novel therapeutic targets. These studies are providing insight into many previously unexplained features of this difficult disease.

Bone Marrow↗

PubMed2004

BRCA1-mediated repression of select X chromosome genes.

Recently BRCA1 has been implicated in the regulation of gene expression from the X chromosome. In this study the influence of BRCA1 on expression of X chromosome genes was investigated. Complementary DNA microarrays were used to compare the expression levels of X chromosome genes in 18 BRCA1-associated ovarian cancers to those of the 13 "BRCA1-like" and 14 "BRCA2-like" sporadic tumors (as defined by previously reported expression profiling). Significance was determined using parametric statistics with P < 0.005 as a cutoff. Forty of 178 total X-chromosome transcripts were differentially expressed between the BRCA1-associated tumors and sporadic cancers with a BRCA2-like molecular profile. Thirty of these 40 genes showed higher mean expression in the BRCA1-associated samples including all 11 transcripts that mapped to Xp11. In contrast, four of 178 total X chromosome transcripts showed significant differential expression between BRCA1-associated and sporadic tumors with a BRCA1-like molecular profile. All four mapped to Xp11 and showed higher mean expression in BRCA1-associated tumors. Re-expression of BRCA1 in HCC1937 BRCA1-deficient breast cancer cell resulted in the repression of 21 transcripts. Eleven of the 21 (54.5%) transcripts mapped to Xp11. However, there was no significant overlap between these Xp11 genes and those found to be differentially expressed between BRCA1-associated and sporadic ovarian cancer samples. These results demonstrate that BRCA1 mediates the repression of several X chromosome genes, many of which map to the Xp11 locus.

Journal Article↗

PubMedDate not supplied

Multiple forms of rat placental lactogen-II (rPL-II): purification and partial characterization of rPL-II.

The present study was designed to develop a procedure for purifying rPL-II and a homologous radioimmunoassay (RIA) for rPL-II. Molecular profiles of rPL-II were also investigated in tissue and plasma. rPL-II was purified 3,780-fold, based on its radioreceptor assay (RRA) activity compared to ovine prolactin (0PRL), from the placenta of day 18 pregnant rats using ammonium sulfate precipitation and chromatography on phenyl-Sepharose, DEAE-TOYOPEARL 650S, AF-chelate TOYOPEARL 650M and Sephadex G-100. Electrophoretic analysis on SDS gel revealed molecular weight heterogeneity of purified rPL-II, which consisted of three proteins; a major form with a molecular weight of 20.0 K and two minor forms with molecular weights of 20.6 K and 21.0 K under non-reducing conditions. One of the minor forms of rPL-II observed under non-reducing conditions disappeared with 2-mercaptoethanol treatment and the rest of the hormones migrated as 24.5 K and 25.0 K molecular weight species, suggesting that it is a cleaved form of rPL-II. Purified rPL-II displaced 125I-labelled oPRL from binding sites on rabbit mammary gland membranes in a dose-dependent manner. rPL-II and rPRL were, respectively, 21 and 2 per cent as effective as oPRL in the displacement. Antibody to purified rPL-II was raised in rabbits and a homologous RIA for rPL-II was developed. No displacement was observed with rPRL, rGH, oPRL, and other pituitary hormones up to 1,000 ng/ml. Molecular profiles of rPL-II in the placental tissue and plasma from day 18 pregnant rats were examined by gel chromatography on Sepharcryl S-300 HR and by Western blotting. Chromatography of the placental extracts revealed a single peak, which accounted for 86 per cent of the total RIA activity. Anti-rPL-II antiserum detected proteins of at least three molecular sizes as monomeric forms with molecular weights of 20.0, 20.6, and 21.0 K in the non-reducing placental extracts. One of them disappeared with 2-mercaptoethanol treatment and other two proteins had molecular weights of 24.5 and 25.0 K, indicating monomeric heterogeneity of rPL-II in the tissue. The elution profile of day 18 plasma in RIA activity gave two major peaks; the first, eluting just after the void volume (approximate molecular weight of 530 K) accounted for 35 per cent of the total RIA activity, and the second coinciding with the same elution volume as the monomeric form in the placental extract constituted about 26 per cent of the total RIA activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗