Profiling phospho-signaling networks in breast cancer using reverse-phase protein arrays.

Measuring the states of cell signaling pathways in tumor samples promises to advance the understanding of oncogenesis and identify response biomarkers. Here, we describe the use of Reverse Phase Protein Arrays (RPPAs or RPLAs) to profile signaling proteins in 56 breast cancers and matched normal tissue. In RPPAs, hundreds to thousands of lysates are arrayed in dense regular grids and each grid is probed with a different antibody (100 in the current work, of which 71 yielded strong signals with breast tissue). Although RPPA technology is quite widely used, measuring changes in phosphorylation reflective of protein activation remains challenging. Using repeat deposition and well-validated antibodies, we show that diverse patterns of phosphorylation can be monitored in tumor samples and changes mapped onto signaling networks in a coherent fashion. The patterns are consistent with biomarker-based classification of breast cancers and known mechanisms of oncogenesis. We explore in detail one tumor-associated pattern that involves changes in the abundance of the Axl receptor tyrosine kinase (RTK) and phosphorylation of the cMet RTK. Both cMet and Axl have been implicated in breast cancer, or in resistance to anticancer drugs, but the two RTKs are not known to be linked functionally. Protein depletion and overexpression studies in a 'triple-negative' breast cell line reveal cross talk between Axl and cMet involving Axl-mediated modification of cMet, a requirement for cMet in efficient and timely signal transduction by the Axl ligand Gas6 and the potential for the two receptors to interact physically. These findings have potential therapeutic implications, as they imply that bi-specific receptor inhibitors (for example, ATP-competitive small-kinase inhibitors such as GSK1363089, BMS-777607 or MP470) may be more efficacious than the mono-specific therapeutic antibodies currently in development (for example, Onartuzumab).

Assessing the risk of venous thromboembolic events in women taking progestin-only contraception: a meta-analysis.

OBJECTIVES: To evaluate the risk of venous thromboembolic events associated with the use of progestin-only contraception and whether that risk differs with the mode of drug delivery (oral, intrauterine, or depot injection). DESIGN: Systematic review and meta-analysis of randomised controlled trials and observational studies. DATA SOURCES: Pubmed, Embase, Cochrane Library, and reference lists of relevant reviews. STUDY SELECTION: Randomised controlled trials and case-control, cohort, and cross sectional studies with venous thromboembolic outcome for progestin-only contraception reported relative to a non-hormone comparator group. DATA EXTRACTION: Data were extracted by two independent investigators, and consensus for inclusion was reached after assessment by additional investigators. RESULTS: Among the 2022 unique references identified by all searches, eight observational studies fulfilled inclusion criteria. A total of 147 women across all studies were diagnosed with a venous thromboembolic event while taking progestin-only contraception, and the summary measure for the adjusted relative risk of a venous thromboembolic episode for users versus non-users of a progestin-only contraceptive was, based on the random effects model, 1.03 (95% CI 0.76 to 1.39). Subgroup analysis confirmed there was no association between venous thromboembolic risk and progestin-only pills (relative risk 0.90 (0.57 to 1.45)) or a progestin intrauterine device (0.61 (0.24 to 1.53)). The relative risk of a venous thromboembolic event for users of an injectable progestin versus non-users was 2.67 (1.29 to 5.53). CONCLUSIONS: Published data assessing the risk of venous thromboembolism in women prescribed progestin-only contraception are limited. In this meta-analysis of eight observational studies, the use of progestin-only contraception was not associated with an increased risk of venous thromboembolism compared with non-users of hormonal contraception. The potential association between injectable progestins and thrombosis requires further study.

An inhibitor of methionine aminopeptidase type-2, PPI-2458, ameliorates the pathophysiological disease processes of rheumatoid arthritis.

OBJECTIVE: To elucidate the role of methionine aminopeptidase type-2 (MetAP-2) in the clinical pathology of rheumatoid arthritis, arthritis was induced in rats by administration of peptidoglycan-polysaccharide (PG-PS). DESIGN: The inhibitor of MetAP-2, PPI-2458, was administered orally at 5 mg/kg every other day during 3 distinct phases of the disease. In vitro studies were performed to clarify in vivo findings. RESULTS: Ankle swelling was completely alleviated by MetAP-2 inhibition. Inhibition of MetAP-2 in blood and tissues correlated with protection against PG-PS-induced arthritis. Histopathology of the tarsal joints improved following PPI-2458 administration, including a significant improvement of bone structure. In in vitro studies, osteoclast formation and activity were inhibited by PPI-2458, a mechanism not previously attributed to MetAP-2 inhibition. CONCLUSIONS: The important role that MetAP-2 has in the pathophysiological disease processes of PG-PS arthritis provides a strong rationale for evaluating PPI-2458 as a disease modifying antirheumatic treatment for rheumatoid arthritis.

Reconstructing chain functions in genetic networks.

Deciphering the mechanisms that control gene expression in the cell is a fundamental question in molecular biology. This task is complicated by the large number of possible regulation relations in the cell, and the relatively small amount of available experimental data. Recently, a new class of regulation functions called chain functions was suggested. Many signal transduction pathways can be accurately modeled by chain functions, and the restriction to chain functions greatly reduces the vast search space of regulation relations. In this paper we study the computational problem of reconstructing a chain function using a minimum number of experiments, in each of which only few genes are perturbed. We give optimal reconstruction schemes for several scenarios and show their application in reconstructing the regulation of galactose utilization in yeast.

Detecting protein sequence conservation via metric embeddings.

MOTIVATION: Comparing two protein databases is a fundamental task in biosequence annotation. Given two databases, one must find all pairs of proteins that align with high score under a biologically meaningful substitution score matrix, such as a BLOSUM matrix (Henikoff and Henikoff, 1992). Distance-based approaches to this problem map each peptide in the database to a point in a metric space, such that peptides aligning with higher scores are mapped to closer points. Many techniques exist to discover close pairs of points in a metric space efficiently, but the challenge in applying this work to proteomic comparison is to find a distance mapping that accurately encodes all the distinctions among residue pairs made by a proteomic score matrix. Buhler (2002) proposed one such mapping but found that it led to a relatively inefficient algorithm for protein-protein comparison. RESULTS: This work proposes a new distance mapping for peptides under the BLOSUM matrices that permits more efficient similarity search. We first propose a new distance function on peptides derived from a given score matrix. We then show how to map peptides to bit vectors such that the distance between any two peptides is closely approximated by the Hamming distance (i.e. number of mismatches) between their corresponding bit vectors. We combine these two results with the LSH-ALL-PAIRS-SIM algorithm of Buhler (2002) to produce an improved distance-based algorithm for proteomic comparison. An initial implementation of the improved algorithm exhibits sensitivity within 5% of that of the original LSH-ALL-PAIRS-SIM, while running up to eight times faster.

CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts.

We present CLIFF, an algorithm for clustering biological samples using gene expression microarray data. This clustering problem is difficult for several reasons, in particular the sparsity of the data, the high dimensionality of the feature (gene) space, and the fact that many features are irrelevant or redundant. Our algorithm iterates between two computational processes, feature filtering and clustering. Given a reference partition that approximates the correct clustering of the samples, our feature filtering procedure ranks the features according to their intrinsic discriminability, relevance to the reference partition, and irredundancy to other relevant features, and uses this ranking to select the features to be used in the following round of clustering. Our clustering algorithm, which is based on the concept of a normalized cut, clusters the samples into a new reference partition on the basis of the selected features. On a well-studied problem involving 72 leukemia samples and 7130 genes, we demonstrate that CLIFF outperforms standard clustering approaches that do not consider the feature selection issue, and produces a result that is very close to the original expert labeling of the sample set.

Should we screen for lead poisoning after 36 months of age? Experience in the inner city.

INTRODUCTION: Current lead screening guidelines recommend monitoring lead levels in children under 3 years of age. There are, however, a number of children between the ages of 3 and 6 years who have elevated blood lead levels. Whether these lead elevations are new or chronic has not been examined. OBJECTIVE: To determine the proportion of children with lead levels greater than or equal to 10 microg/dL after their third birthday when all prior testing had been normal. METHODS: Retrospective study based on 39000 venous lead tests obtained between 1993 and 1998. From this group, 2046 children were located who had blood lead levels of less than 10 microg/dL before 36 months and who had a follow-up lead level after 36 months. All lead assays were done by the City of New York laboratories, which had an intrasample variability of 13%. RESULTS: Sixty-six (3.2%) of the 2046 children showed an elevation in blood lead for the first time after their third birthday. The abnormal values ranged from 10 to 25 microg/dL. The majority (72%) of the screen-positive children, however, had lead levels of 10 to 12 microg/dL, and 63.3% of screen-positive children with repeat tests had lead levels that reverted to below 10 microg/dL. CONCLUSIONS: The data indicate that some new cases of lead level elevations did occur after 3 years of age in this 'high-risk' community; however, the current study provides evidence that universal screening for lead poisoning beyond 3 years of age is not warranted in this community as it is not likely to pick up clinically important exposure.

Universal DNA tag systems: a combinatorial design scheme.

Custom-designed DNA arrays offer the possibility of simultaneously monitoring thousands of hybridization reactions. These arrays show great potential for many medical and scientific applications, such as polymorphism analysis and genotyping. Relatively high costs are associated with the need to specifically design and synthesize problem-specific arrays. Recently, an alternative approach was suggested that utilizes fixed, universal arrays. This approach presents an interesting design problem-the arrays should contain as many probes as possible, while minimizing experimental errors caused by cross-hybridization. We use a simple thermodynamic model to cast this design problem in a formal mathematical framework. Employing new combinatorial ideas, we derive an efficient construction for the design problem and prove that our construction is near-optimal.

Estrogen receptor-beta expression in relation to the expression of luteinizing hormone receptor and cytochrome P450 enzymes in rat ovarian follicles.

Changes in mRNA expression for estrogen receptor (ER beta) in relation to mRNAs for LH receptor (LHr) and cytochrome P450 enzymes were examined in granulosa and theca cells from proestrous rat ovarian follicles. Of the 30 ovaries harvested from 15 adult rats, 24 were processed for in situ hybridization, and the remaining were used for reverse transcription-polymerase chain reaction. Messenger RNAs for ER beta, LHr, cytochrome P450 side-chain cleavage enzyme (P450(scc)), 17 alpha-hydroxylase (P450(c17)), aromatase (P450(arom)), and steroidogenic acute regulatory protein (StAR) were localized in cross sections of ovaries by in situ hybridization and quantified in granulosa and theca cell layers by a computer-image analyzing system. Ovarian follicles were classified as healthy or atretic. Healthy follicles were divided into four size groups: very small (40-100 microm), small (101-275 microm), medium (276-450 microm), and large (451-850 microm). Atretic follicles were divided into medium (276-450 microm) or large follicles (451-850 microm). A low level of ER beta mRNA expression was first detected in granulosa cells of very small healthy follicles, and the expression increased progressively up to medium-sized follicles. The expression of ER beta mRNA was highest (P < 0.01) in medium-sized follicles that was followed by a decrease (P < 0.01) in large follicles. Messenger RNAs for LHr, P450(scc), and P450(arom) were first detected in granulosa cells of medium-sized healthy follicles, while mRNAs for LHr, P450(scc), P450(c17), and StAR were first detected in theca cells associated with very small follicles. The highest expression of LHr, P450(scc), P450(c17), P450(arom), and StAR was seen in granulosa and/or theca cells of large healthy follicles. In atretic follicles, level of gene expression was relatively low in both granulosa and theca cells. In conclusion, stage-specific expression of ER beta mRNA was observed in granulosa cells during follicular development. The increased expression of ER beta and a concomitant initiation of LHr, P450(scc), and P450(arom) expression in granulosa cells of medium follicles may signify a role for estrogen in follicular development. Also, a strong correlation between ER beta mRNA expression in granulosa cells, and the expression of mRNAs for LHr, P450(scc), P450(c17), and StAR in theca cells associated with growing follicles suggests a possible role for estrogen in steroidogenesis.

A mini-fellowship in clinical nutrition for primary care physicians.

When the Regional Nutrition Center's (RNC's) mini-fellowship was being developed, physicians teaching in medical schools and residency programs had little formal training in nutrition, so it was difficult to identify faculty to serve as role models and clinical preceptors. Using funds provided by an NIH/NCI R-25 grant, the mini-fellowship in clinical nutrition was developed as a model to meet the nutrition education needs of senior residents and junior faculty in primary care disciplines. It provided a brief but broad exposure to clinical nutrition topics, with a focus on issues relevant to the practice of primary care and teaching skills. In four weeks, fellows completed didactic course work, a clinical preceptorship, and a teaching project. Tracking of the 55 physicians who completed the program by questionnaires has shown significant improvement in their nutrition-related patient care activities.

Algorithms for optical mapping.

Optical mapping is a novel technique for determining the restriction sites on a DNA molecule by directly observing a number of partially digested copies of the molecule under a light microscope. The problem is complicated by uncertainty as to the orientation of the molecules and by erroneous detection of cuts. In this paper we study the problem of constructing a restriction map based on optical mapping data. We give several variants of a polynomial reconstruction algorithm, as well as an algorithm that is exponential in the number of cut sites, and hence is appropriate only for small number of cut sites. We give a simple probabilistic model for data generation and for the errors and prove probabilistic upper and lower bounds on the number of molecules needed by each algorithm in order to obtain a correct map, expressed as a function of the number of cut sites and the error parameters. To the best of our knowledge, this is the first probabilistic analysis of algorithms for the problem. We also provide experimental results confirming that our algorithms are highly effective on simulated data.

Discovery of regulatory interactions through perturbation: inference and experimental design.

We present two methods to be used interactively to infer a genetic network from gene expression measurements. The predictor method determines the set of Boolean networks consistent with an observed set of steady-state gene expression profiles, each generated from a different perturbation to the genetic network. The chooser method uses an entropy-based approach to propose an additional perturbation experiment to discriminate among the set of hypothetical networks determined by the predictor. These methods may be used iteratively and interactively to successively refine the genetic network: at each iteration, the perturbation selected by the chooser is experimentally performed to generate a new gene expression profile, and the predictor is used to derive a refined set of hypothetical gene networks using the cumulative expression data. Performance of the predictor and chooser is evaluated on simulated networks with varying number of genes and number of interactions per gene.

The antigonadotropic action of testosterone but not 7alpha-methyl-19-nortestosterone is attenuated through the 5alpha-reductase pathway in the castrated male rat pituitary gland.

The enzyme 5alpha-reductase plays a significant role in the prostate to amplify the action of testosterone (T) by converting it to a more potent androgen, dihydrotestosterone (DHT). The role of 5alpha-reductase in the testosterone feedback inhibition of gonadotropin secretion from the pituitary has not been elucidated. Therefore, we investigated the role of 5alpha-reductase on T action in in vitro and in vivo models. Castration has been reported to increase the 5alpha-reductase activity in pituitary glands. Hence, the effect of castration duration on the conversion of T to DHT by pituitary homogenates and the responsiveness of pituitary monolayer cell cultures to gonadotropin-releasing hormone (GnRH) challenge exposure were investigated. Incubation of [3H]-T with pituitary homogenates showed that the conversion of T to 5alpha-reduced metabolites was two- to threefold greater in pituitaries from rats who had been castrated for 14 days compared with those castrated for 1 day. In addition, the GnRH-stimulated release of LH from monolayer cell cultures of pituitaries from rats castrated for 1 day was twofold greater, whereas that from rats castrated for 2 weeks was six- to sevenfold greater compared with basal luteinizing hormone (LH) release. Hence we used rats castrated for 2 weeks to elucidate the role of 5alpha-reductase in T feedback inhibition. The inhibitory effects of the androgens T, 19-nortestosterone (19-NT), and 7alpha-methyl-19-nortestosterone (MENT) at 3 different concentrations (10(-9), 10(-7), and 10(-5) mol/L) on GnRH-stimulated LH release from monolayer cell cultures of pituitaries from rats castrated for 2 weeks were examined. All 3 androgens showed dose-dependent inhibition of LH release. MENT showed the greatest inhibition, followed by 19-NT and T. In the presence of finasteride (a 5alpha-reductase inhibitor), the inhibition of LH released by T and 19-NT were significantly greater. The inhibitory effect of MENT, which does not undergo 5alpha-reduction, was not altered by finasteride. In an in vivo study, rats castrated for 2 weeks received T with or without finasteride. There was a significantly greater suppression of serum LH in rats receiving T plus finasteride compared with those receiving T alone. These results suggested that 5alpha-reductase in the pituitary is not obligatory for the inhibitory action of T on gonadotropin secretion in the castrated rat. The action of MENT, a nonreducible androgen, on the pituitary is not affected by 5alpha-reductase.

An algorithm combining discrete and continuous methods for optical mapping.

Optical mapping is a novel technique for generating the restriction map of a DNA molecule by observing many single, partially digested copies of it, using fluorescence microscopy. The real-life problem is complicated by numerous factors: false positive and false negative cut observations, inaccurate location measurements, unknown orientations, and faulty molecules. We present an algorithm for solving the real-life problem. The algorithm combines continuous optimization and combinatorial algorithms applied to a nonuniform discretization of the data. We present encouraging results on real experimental data and on simulated data.

An algorithmic approach to multiple complete digest mapping.

Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many potential applications in DNA sequencing and genetics. In this work, we present a heuristic algorithm for fragment identification, a key step in the process of constructing an MCD map. Given measurements of the restriction fragment sizes from one or more complete digestions of each clone in a clone library covering the molecule to be mapped, the algorithm identifies groups of restriction fragments on different clones that correspond to the same region of the target DNA. Once these groups are correctly determined the desired map can be constructed by solving a system of simple linear inequalities. We demonstrate the effectiveness of our algorithm on real data provided by the Genome Center at the University of Washington.

Error checking and graphical representation of multiple-complete-digest (MCD) restriction-fragment maps.

Genetic and physical maps display the relative positions of objects or markers occurring within a target DNA molecule. In constructing maps, the primary objective is to determine the ordering of these objects. A further objective is to assign a coordinate to each object, indicating its distance from a reference end of the target molecule. This paper describes a computational method and a body of software for assigning coordinates to map objects, given a solution or partial solution to the ordering problem. We describe our method in the context of multiple-complete-digest (MCD) mapping, but it should be applicable to a variety of other mapping problems. Because of errors in the data or insufficient clone coverage to uniquely identify the true ordering of the map objects, a partial ordering is typically the best one can hope for. Once a partial ordering has been established, one often seeks to overlay a metric along the map to assess the distances between the map objects. This problem often proves intractable because of data errors such as erroneous local length measurements (e.g., large clone lengths on low-resolution physical maps). We present a solution to the coordinate assignment problem for MCD restriction-fragment mapping, in which a coordinated set of single-enzyme restriction maps are simultaneously constructed. We show that the coordinate assignment problem can be expressed as the solution of a system of linear constraints. If the linear system is free of inconsistencies, it can be solved using the standard Bellman-Ford algorithm. In the more typical case where the system is inconsistent, our program perturbs it to find a new consistent system of linear constraints, close to those of the given inconsistent system, using a modified Bellman-Ford algorithm. Examples are provided of simple map inconsistencies and the methods by which our program detects candidate data errors and directs the user to potential suspect regions of the map.