Need For Molecular Markers Research Articles

Genetic Discrimination of Grade 3 and Grade 4 Gliomas by Artificial Neural Network.

Gliomas, including anaplastic gliomas (AG; grade 3) and glioblastomas (GBM; grade 4), are malignant brain tumors associated with poor prognosis and low survival rates. Current classification systems based on histopathology have limitations due to intratumoral heterogeneity. The treatment and prognosis are distinctly different between grade 3 and grade 4 gliomas patients. Therefore, there is a need for molecular markers to differentiate these tumors accurately. In this study, we aimed to identify a gene expression signature using an artificial neural network (ANN) in application to microarray and serial analysis of gene expression (SAGE) data for grade 3 (AG) and grade 4 (GBM) gliomas discrimination. We acquired gene expression data from publicly available datasets on glial tumors of grades 3 and 4-a total of 93 grade 3 gliomas and 224 grade 4 gliomas. To select genes for classification, we implemented an artificial neural network-based method using a combination of self-organized maps (SOM) and perceptron. In general, we implemented a multi-stage procedure that involved multiple runs of a genetic algorithm to identify genes that provided optimal clusterization on the SOM. We performed this procedure multiple times, resulting in different sets of genes each time. Eventually, we selected several genes that appeared most frequently in the reduced sets and performed classification using them. Our analysis identified a set of seven genes (BCAS4, GLUD2, KCNJ10, KCND2, AKR7A2, FOLR1, and KIAA0319). The classification accuracy using this gene set was 87.5%. These findings suggest the potential of this gene set as a molecular marker for distinguishing grade 3 (AG) from grade 4 (GBM) gliomas.

Analysis of Nuclear Encoded Mitochondrial Gene Networks in Cervical Cancer.

Background:Cervical cancer (CC) is one of the most common female cancers in many developing and underdeveloped countries. High incidence, late presentation, and mortality suggested the need for molecular markers. Mitochondrial defects due to abnormal expression of nuclear-encoded mitochondrial genes (NEMG) have been reported during cancer progression. Nevertheless, the application of NEMG for the prognosis of CC is still elusive. Herein, we aimed to investigate the associations between NEMG and CC prognosis. Materials and Methods:The differentially expressed genes (DEG) in the TCGA-CESC dataset and NEMGs were retrieved from TACCO and Mitocarta2.0 databases, respectively. The impact of methylation on NEMG expression were predicted using DNMIVD and UALCAN tools. HCMDB tool was used to predict genes having metastatic potential. The prognostic models were constructed using DNMIVD, TACCO, GEPIA2, and SurvExpress. The functional enrichment analysis (FEA) was performed using clusterProfiler. The protein-protein interaction network (PPIN) was constructed to identify the hub genes (HG) using String and CytoHubba tools. Independent validation of the HG was performed using Oncomine and Human Protein Atlas databases. The druggable genes were predicted using DGIdb.Results:Among the 52 differentially expressed NEMG, 15 were regulated by DNA methylation. The expression level of 16, 10, and 7 has the potential for CC staging, prediction of metastasis, and prognosis. Moreover, 1 driver gene and 16 druggable genes were also identified. The FEA identified the enrichment of cancer-related pathways, including AMPK and carbon metabolism in cancer. The combined expression of 10 HG has been shown to affect patient survival. Conclusion:Our findings suggest that the abnormal expression of NEMGs may play a critical role in CC development and progression. The genes identified in our study may serve as a prognostic indicator and therapeutic target in CC.

Lipidomic Profiling of the Epidermis in a Mouse Model of Dermatitis Reveals Sexual Dimorphism and Changes in Lipid Composition before the Onset of Clinical Disease.

Atopic dermatitis (AD) is a multifactorial disease associated with alterations in lipid composition and organization in the epidermis. Multiple variants of AD exist with different outcomes in response to therapies. The evaluation of disease progression and response to treatment are observational assessments with poor inter-observer agreement highlighting the need for molecular markers. SHARPIN-deficient mice (Sharpincpdm) spontaneously develop chronic proliferative dermatitis with features similar to AD in humans. To study the changes in the epidermal lipid-content during disease progression, we tested 72 epidermis samples from three groups (5-, 7-, and 10-weeks old) of cpdm mice and their WT littermates. An agnostic mass-spectrometry strategy for biomarker discovery termed multiple-reaction monitoring (MRM)-profiling was used to detect and monitor 1,030 lipid ions present in the epidermis samples. In order to select the most relevant ions, we utilized a two-tiered filter/wrapper feature-selection strategy. Lipid categories were compressed, and an elastic-net classifier was used to rank and identify the most predictive lipid categories for sex, phenotype, and disease stages of cpdm mice. The model accurately classified the samples based on phospholipids, cholesteryl esters, acylcarnitines, and sphingolipids, demonstrating that disease progression cannot be defined by one single lipid or lipid category.

Development of EST-SSR markers for the Korean endemic species <i>Chrysosplenium aureobracteatum</i> (Saxifragaceae)

Chrysosplenium aureobracteatum Y. I. Kim & Y. D. Kim (Saxifragaceae) is a recently described endemic species growing in the central part of the Korean peninsula. It requires constant monitoring for conservation due to its limited distributions. There is also a need for molecular markers for proper assessments of the genetic differentiation of C. aureobracteatum from species morphologically similar to it. In this study, we developed microsatellite markers that can be used to evaluate the genetic diversity of this species, representing fundamental data with which to conserve the natural populations of the species. A total of 17 expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed by the Illumina pair-end sequencing of the transcriptomes of C. aureobracteatum. These markers were successfully applied to populations of C. aureobracteatum and to its most closely related species, C. barbatum, revealing high polymorphism in both species. The EST-SSR markers developed in this study were proven to be useful not only to monitor the population genetic structure of C. aureobracteatum for conservation purposes but also to study the genetic delimitation of the species from species closely related to it. Keywords: population genetics, endemic species, cross-amplification, conservation

Serum sHLA-G: Significant diagnostic biomarker with respect to therapy and immunosuppressive mediators in Head and Neck Squamous Cell Carcinoma

Head & Neck Squamous Cell Carcinoma is one of the highest mortality factors in the world due to the lack of potential biomarker for early detection of disease. There is an urgent need for molecular marker involved in disease progression which remains suppressed normally, required for specificity. HLA-G is highly expressed in cancers and creates immune-suppressive microenvironment. Cancerous cells secrete inflammatory cytokines like IL-10,IFN-γ which increase expression of immunosuppressive molecules, such as HLA-G. We evaluated sHLA-G protein level in serum of 120 HNSCC patients at diagnosis and after therapy and compared with 99 individuals by SPR, ELISA and determined its mRNA level by qRT-PCR. sHLA-G was correlated with serum IL-10 and IFN-γ of the patients. Significant elevated levels of sHLA-G were observed in patients (8.25 ± 1.74 ng/µl) than control (6.45 ± 1.31 ng/µl). Levels were declined in (8.09 ± 1.79 ng/µl to 6.64 ± 1.33 ng/µl) patients in response to therapy. sHLA-G levels with tumor burden (8.16 ± 1.91 to 6.63 ± 1.32 ng/µl), node (8.62 ± 1.45 to 6.66 ± 1.26 ng/µl), PDSCC (8.14 ± 0.62 to 5.65 ± 0.27 ng/µl) and oropharynx (7.90 ± 1.24 to 6.10 ± 1.33 ng/µl) showed a positive and significant response to therapy. Findings indicate that sHLA-G can be a potential diagnostic serum protein marker for HNSCC due to its suppressive function and over expression in diseased condition with the influence of cytokines.

Targeted amplicon sequencing of 40 nuclear genes supports a single introduction and rapid radiation of Hawaiian Metrosideros (Myrtaceae)

Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylogeny of genus Metrosideros (Myrtaceae), evaluate recent systematic revisions, and assess whether phylogenetic signal within the Hawaiian Archipelago is correlated with island biogeography or morphological diversification. We generated a final dataset of 40 nuclear genes for 187 specimens, used multiple search heuristics and species-tree analysis to estimate a phylogeny, and incorporated new fossils for the genus to estimate divergence times across the dataset. All analyses supported the monophyly of Metrosideros, including Carpolepis and Tepualia. Hawaiian Metrosideros were monophyletic and dated to 3.1 MYA using new fossils for the genus, which is intermediate to previous estimates based on nuclear ribosomal/chloroplast loci and calibrated with island ages. Within the Hawaiian Metrosideros clade, we observed short branch lengths and unresolved relationships, and phylogenetic patterns were not concordant with biogeographic hypotheses of island progression, or the delineation of taxa or morphotypes. Average nucleotide diversity was relatively consistent across the Hawaiian Islands with the exception of slightly lower diversity on Kauaʻi. These results provide a data-rich estimate of the timing of a single introduction of Metrosideros to Hawai‘i and highlight the need for molecular markers with higher evolutionary rates for resolution of relationships within this recent radiation.

VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement.

Genus Vigna represented by more than 100 species is a source of nutritious edible seeds and sprouts that are rich sources of protein and dietary supplements. It is further valuable because of therapeutic attributes due to its antioxidant and anti-diabetic properties. A highly diverse and an extremely ecological niche of different species can be valuable genomic resources for productivity enhancement. It is one of the most underutilized crops for food security and animal feeds. In spite of huge species diversity, only three species of Vigna have been sequenced; thus, there is a need for molecular markers for the remaining species. Computational approach of microsatellite marker discovery along with evaluation of polymorphism utilizing available genomic data of different genotypes can be a quick and an economical approach for genomic resource development. Cross-species transferability by e-PCR over available genomes can further prioritize the potential SSR markers, which could be used for genetic diversity and population differentiation of the remaining species saving cost and time. We present VigSatDB—the world’s first comprehensive microsatellite database of genus Vigna, containing >875 K putative microsatellite markers with 772 354 simple and 103 865 compound markers mined from six genome assemblies of three Vigna species, namely, Vigna radiata (Mung bean), Vigna angularis (Adzuki bean) and Vigna unguiculata (Cowpea). It also contains 1976 validated published markers. Markers can be selected on the basis of chromosomes/location specificity, and primers can be generated using Primer3core tool integrated at backend. Efficacy of VigSatDB for microsatellite loci genotyping has been evaluated by 15 markers over a panel of 10 diverse genotype of V. radiata. Our web genomic resources can be used in diversity analysis, population and varietal differentiation, discovery of quantitative trait loci/genes, marker-assisted varietal improvement in endeavor of Vigna crop productivity and management.

Utilization of Microsatellite Markers to Assess Hybridity and Genetic Identity of Canary seed (Phalaris canariensis L.) genotypes

Challenges in the emasculation of female parent panicles and limited morphological variation among canary seed (Phalaris canariensis L.) genotypes has resulted in a need for molecular markers to as...

Cell Line Phenotypic Enrichement based on Migration and Morphology

Cell Labeling via Photobleaching (CLaP) is an optical technique recently developed to cross-link fluorescent molecules to the surface of individual cells, by focusing a low-power laser on their membrane. Using CLaP, it is possible select single cells or a sub-population based on visual criteria without the need of molecular markers. This technology can also be exploited for inducing transient cell adhesion to culture substrates, which are resistant to dissociation agents such as EDTA or trypsin. Since only the illuminated cells remain attached to the dish surface, CLaP can be exploited to tailor the spatial distribution of cells in a culture dish, and also to enrich the proportion of a chosen phenotype within proliferating cells.Breast cancer cell line MDA-MB-231 is known for its potential to metastasize to secondary sites. Among the various factors influencing their metastatic ability, epithelial to mesenchymal transformation and its reverse, mesenchymal to epithelial transformation, are required for cells to leave the tumor primary site, migrate and establish metastases at secondary sites. Here we assess the heterogeneity in motility and morphology of these cancer cells via time-lapse microscopy, automated segmentation and tracking. We use CLaP as a way to select clones of proliferating cells based on morphological and behavioral characteristics, to enrich cell cultures of specific phenotypes. We validate which of these traits are preserved after cell division, and which ones are affected by exposure to different conditioned media promoting mesenchymal to epithelial transformation.

Integrated Phenotypic/Genotypic Analysis of Papillary Renal Cell Carcinoma Subtypes: Identification of Prognostic Markers, Cancer-related Pathways, and Implications for Therapy

BackgroundTwo histologic subtypes are recognized for papillary renal cell carcinoma (PRCC). Studies have shown that the subtypes differ in characteristic genetic alterations and clinical behavior. Clinically, the subtypes are managed similarly. ObjectivesTo analyze the biological differences between the two PRCC histological subtypes, in order to further guide their clinical management. Design, setting, and participantsPRCC cohort consisting of 317 patients from the Cancer Genome Atlas database and our institution. Patients were stratified according to histologic criteria as type 1, type 2, or not otherwise specified (NOS). Gene and miRNA expression data for the cohort were examined via unsupervised and supervised clustering. Outcome measurements and statistical analysisSignificant molecular signatures for each subtype were used to unravel the implicated molecular pathways via bioinformatics analysis. Survival was compared between the subtypes. Newly discovered biomarkers were used to further stratify survival of patients in the NOS category. Results and limitationsTumor genotyping revealed two distinct PRCC subtypes. The top molecular pathways enriched in PRCC1 were WNT, Hedgehog, and Notch signaling (p=0.001–0.01); highlighting an embryonic developmental theme to the pathogenesis of this subtype. PRCC2 showed enrichment in the mTOR, VEGF (p=7.49E−09) and HIF (p=7.63E−05) signaling pathways. Overall survival and disease-free survival significantly differed between the types. ABCC2 expression was identified as a significant prognostic biomarker for the NOS group in univariate (log rank p<0.0001; hazard ratio [HR] >11.63) and multivariate analysis (p=0.003; HR >2.12). ABCC2 expression and its effect on survival should be further validated at the protein level. ConclusionsThe classical PRCC types 1 and 2 have two distinct genotypes. We unraveled pathways that indicate that the two types could potentially respond differently to current therapies. We also identified biomarkers that stratify tumors within the PRCC NOS category into prognostic subgroups. Our findings highlight the need for molecular markers to accurately subtype PRCC and guide clinical management. Patient summaryThe two types of papillary renal cancer are treated similarly. We show that the two types have a different genetic makeup, and hence they should be considered two different tumors. There is a different biology underlying each tumor type that can potentially affect the way they respond to treatment. We uncovered genes that can be tested for to guide therapy in some problematic cases for which it hard to define the tumor type.

A review of current Antarctic limno-terrestrial microfauna

Antarctic arthropods (mites and springtails) have been the subject of numerous studies. However, by far, the most diverse and numerically dominant fauna in Antarctica are the limno-terrestrial microfauna (tardigrades, rotifers and nematodes). Although they have been the focus of several studies, there remains uncertainty of the actual number of species in Antarctica. Inadequate sampling and conserved morphology are the main cause of misclassification of species and underestimation of this diversity. Most species’ distributional records are dominated by proximity to research stations or limited opportunistic collections, and therefore, an absence of records for a species may also be a consequence of the limitations of sampling. Limitations in fundamental knowledge of how many species are present and how widespread they are prevents any meaningful analyses that have been applied more generally to the arthropods within Antarctica, such as exploring ancient origins (at least pre-last glacial maximum) and tracking colonisation routes from glacial refugia. In this review, we list published species names and where possible the distribution of microfaunal (tardigrade, rotifer and nematode) species reported for Antarctica. Our current state of knowledge of Antarctic records (south of 60°S) includes 28 bdelloid rotifers, 66 monogonont rotifers, 59 tardigrades and 68 nematodes. In the light of the difficulties in working with microfauna across such geographical scales, we emphasise the need for molecular markers to help understand the ‘true levels’ of diversity and suggest future directions for Antarctic biodiversity assessment and species discovery.

B7‐H3 expression in colorectal cancer: Nuclear localization strongly predicts poor outcome in colon cancer

In colorectal cancer there is a need for molecular markers that can complement the histopathological staging in predicting the likelihood of disease recurrence following curatively intended surgery. B7-H3 is an immunoregulatory protein shown to be overexpressed in several cancer forms, often associated with more advanced disease and poor prognosis. We wanted to examine whether B7-H3 could be a potential prognostic marker in colorectal cancer. Paraffin-embedded samples from 277 colorectal cancer patients were immunostained with anti-B7-H3 antibody. B7-H3 was expressed in the tumor cell cytoplasm and cell membrane in 62% and 46% of the samples, respectively. Unexpectedly, B7-H3 was expressed in the nucleus in 30% of the tumors. The nuclear localization was confirmed by Western immunoblotting of subcellular fractions. Importantly, in colon cancer, nuclear B7-H3 expression was independently and significantly associated with reduced metastasis-free, disease-specific and overall survival. B7-H3 expression in tumor-associated vasculature and fibroblasts was observed in the majority of samples, and endothelial B7-H3 expression was also significantly associated with poor outcome in colon cancer. In rectal cancer patients, the only significant association was between fibroblast B7-H3 expression and shorter metastasis-free survival. Few significant associations to clinicopathological parameters were seen. The results indicate that nuclear B7-H3 might be involved in colon cancer progression and metastasis, and suggest that nuclear B7-H3 could become a useful prognostic marker in colon cancer.

Population genetics ofSchistosoma haematobium:development of novel microsatellite markers and their application to schistosomiasis control in Mali

The recent implementation of mass drug administration (MDA) for control of uro-genital schistosomiasis has identified an urgent need for molecular markers to both directly monitor the impact of MDA, for example to distinguish re-infections from uncleared infections, as well as understand aspects of parasite reproduction and gene flow which might predict evolutionary change, such as the development and spread of drug resistance. We report the development of a novel microsatellite tool-kit allowing, for the first time, robust genetic analysis of individual S. haematobium larvae collected directly from infected human hosts. We genotyped the parasite populations of 47 children from 2 schools in the Ségou region of Mali, the first microsatellite study of this highly neglected parasite. There was only limited evidence of population subdivision between individual children or between the two schools, suggesting that few barriers to gene flow exist in this population. Complex relationships between parasite reproductive success, infection intensity and host age and gender were identified. Older children and boys harboured more diverse infections, as measured by the number of unique adult genotypes present. Individual parasite genotypes had variable reproductive success both across hosts, a pre-requisite for evolutionary selection, and, phenotypically, in hosts of different ages and genders. These data serve as a baseline against which to measure the effect of treatment on parasite population genetics in this region of Mali, and the tools developed are suitable to further investigate this important pathogen, and its close relatives, throughout their range.

An update on the pathobiological relevance of nuclear receptors for cancers of the head and neck.

Cancers of the head and neck are among the most common neoplasms worldwide, characterized by local tumor aggressiveness, high rate of early recurrence, development of metastasis and second primary tumors. Although disease management of head and neck cancer has improved significantly, overall survival-rates remained largely unchanged over the last decades. Thus, in addition to modern chemo-radiation treatment strategies combined with sophisticated surgery, there is still a need for molecular markers and key regulatory factors exploitable for chemoprevention and targeted therapies. A critical event in carcinogenesis is the uncontrolled modulation of genetic programs, mediated by deregulated signaling cascades, together with downstream transcriptional modulators. Hence, nuclear receptors, belonging to a superfamily of transcription factors implicated in a broad spectrum of physiological and pathophysiological processes, have also been associated with HNC. Enhanced expression of several nuclear receptors has been shown in head and neck cancer cells, and strategies targeting these molecules have been developed and tested in the clinics. In particular, the effects of retinoids targeting nuclear receptors of the thyroid hormone receptor-like receptor subfamily have been vigorously examined in large clinical chemoprevention trials. This review seeks to provide a general overview of nuclear receptors' molecular functions and summarizes their prognostic/therapeutic relevance, as well as the (pre)clinical studies targeting nuclear receptors in HNC.

Imaging Mass Spectrometry of a Specific Fragment of Mitogen-Activated Protein Kinase/Extracellular Signal-Regulated Kinase Kinase Kinase 2 Discriminates Cancer from Uninvolved Prostate Tissue

Histopathology is the standard approach for tissue diagnostics and centerpiece of pathology. Although the current system provides prognostic information, there is need for molecular markers that enhance diagnosis and better predict clinical prognosis. The ability to localize disease-specific molecular changes in biopsy tissue would help improve critical pathology decision making. Direct profiling of proteins from tissue using matrix-assisted laser desorption/ionization imaging mass spectrometry has the potential to supplement morphology with underlying molecular detail. A discovery set of 11 prostate cancer (PCa)-containing and 10 benign prostate tissue sections was evaluated for protein expression differences. A separate validation set of 54 tissue sections (23 PCa and 31 benign) was used to verify the results. Cryosectioning was done to yield tissue sections analyzed by a pathologist to determine tissue morphology and mirror sections for imaging mass spectrometry. Spectra were acquired and the intensity of signals was plotted as a function of the location within the tissue. An expression profile was found that discriminates between PCa and normal tissue. The overexpression of a single ion at m/z 4,355 was able to discriminate cancer from uninvolved tissue. Tandem mass spectrometry identified this marker as a fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2 (MEKK2). The ability of MEKK2 to discriminate tumor from normal cells was orthogonally confirmed. This study highlights the potential of this approach to uncover molecular detail that can be correlated with pathology decision making. In addition, the identification of MEKK2 shows the ability to discover proteins of relevance to PCa biology.

Molecular marker based genetic diversity analysis of Curcuma species from India

Molecular genetic fingerprints of 15 Curcuma species were developed using Inter Simple Sequence Repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers to elucidate the genetic diversity/relatedness among the species. Thirty-nine RAPD primers yielded 376 bands of which 352 were polymorphic and out of the 91 bands produced by the 8 ISSR markers, 87 were polymorphic. Dendrograms were constructed based on the unweighted pair group method using arithmetic averages. Cluster analysis of data using UPGMA algorithm placed the 15 species into seven groups that are somewhat congruent with classification based on morphological characters proposed by the earlier works. However, the study also warrants the limitations of the conventional taxonomic tools for resolving the taxonomic confusion prevailing in the genus and suggests the need of molecular markers in conjunction with morpho-taxonomic and cytologic studies while revising the genus, which is currently in progress. The maximum molecular similarity observed between two of the Curcuma species namely Curcuma raktakanta and Curcuma montana is suggestive of the need for relooking the separate status given to these two species. Further, the status of C. montana and Curcuma pseudomontana, the two species mainly discriminated based on the presence of sessile tubers also need to be reassessed.

Microsatellite DNA marker-assisted selection ofSaccharum spontaneum cytoplasm-derived germplasm

New lines of Saccharum hybrids with an array of S. spontaneum cytoplasm backgrounds are reported. To expand the genetic base of sugarcane, we made eleven bi-parental crosses between ten S. spontaneum (S) and six commercial-type sugarcane (C) clones during the 2001 crossing season. Prior to crossing, all the maternal S. spontaneum inflorescences were emasculated by immersion in a 50°C circulating water bath for 5 minutes. Analysis of microsatellite fingerprints between parents and progeny allowed us to classify 1,952 progeny grown out from these crosses into four genotypic classes. Class H progeny inherited microsatellite alleles from both the S. spontaneum and the commercial-type parents and were, therefore, considered being F1 hybrids. Class S and Class C progeny inherited microsatellite alleles only from one parent and were considered to be either selfs of either parent or F1 hybrids that only inherited allele(s) from one parent. Class X progeny inherited non-parental microsatellite allele(s) in addition to the allele(s) from the maternal S. spontaneum parent and were considered to be contaminants. With the exception of one cross, eight to ten Class H progeny were pre-selected from each cross while still in seedling greenhouse and were backcrossed with commercial-type sugarcane clones. The remaining progeny were transplanted into a breeding nursery for phenotypic evaluation that concurred with the molecular classification. Pearson Correlation Coefficients between molecular and phenotypic classifications were inconsistent that justified the need of molecular markers in the selection process. This study demonstrated that the molecular approach of fingerprinting progeny to confirm parentage prior to field planting even with only one microsatellite marker might substantially increase selection efficiency.

Expression of osteopontin and HGF/Met in adult soft tissue tumors

There is a need for molecular markers that predict biological behavior of adult soft tissue tumors. Elevated levels of osteopontin (OPN) a transformation-linked protein, have been associated with poor survival in many cancers. OPN induces cell migration in cancer cells, in part through activation of the hepatocyte growth factor (HGF) receptor (Met) and its signaling pathway. Met expression has been associated with a poor prognosis in some sarcomas. In a series of 15 patients with adult soft tissue tumors, we found that mRNA levels of OPN (p=0.015), Met (p=0.03) and HGF (p

A critical need for molecular markers of breast cancer risk and risk reduction

Carcinogenesis is a chronic disease process underlying the clonal evolution of cells progressing to the point of uncontrolled growth, metastatic potential, and molecular heterogeneity. By convention, chemoprevention drugs are developed from a molecular perspective with the goal of interrupting carcinogenesis before the occurrence of invasive lesions or extreme heterogeneity. The most successful demonstration of cancer chemoprevention to date has been an overall 49% reduction of invasive breast cancer, with a similar reduction in premalignant lesions by tamoxifen in the Breast Cancer Prevention Trial (BCPT) [1]. It is noteworthy that the main effect of tamoxifen is likely to be mediated through the estrogen receptor (ER), as reflected by a 70% reduction of lesions that are ER-positive in contrast to little or no effect on the incidence of ER-negative lesions. For interventions that are related to ER as a target, a number of drug development issues remain to be addressed including dose, schedule, and the comparative net clinical benefit of various selective ER modulators versus pure anti-estrogens, aromatase inhibitors, and combinations. In the BCPT there were 13,388 participants, and there were more than 22,000 in the STAR trial. The large sample size that may be needed for a randomized clinical trial to observe a prevention effect severely limits the opportunity to explore a multiplicity of important questions in clinical chemoprevention. Molecular studies have been helpful in classifying breast cancers according to categories of response to intervention. For instance, cytogenetic studies combined with molecular profiling suggest that ER-focused interventions are likely to address a particular subset of tumors arising from the luminal cell population [2]. As tumor subsets become better characterized, the need for additional prevention studies can be anticipated to address larger subsets (e.g. a combination of drugs for overlap) versus smaller subsets of individuals at risk. In order to reduce the sample size of future prevention trials, new molecular approaches are needed. One strategy would be to use non-invasive molecular tests to identify individuals at increased breast cancer risk so that populations for prevention trials could be further enriched according to that risk. Of the approaches currently under investigation, proteomic studies theoretically offer an opportunity to improve risk identification. Investigators who are performing proteomic studies for early detection are encouraged to expand their investigations to see whether it is possible to delineate according to ER status and between non-invasive conditions such as hyperplasia and DCIS versus invasive cancer. Another strategy for increasing the efficiency of breast cancer prevention trials is the validation of intermediate endpoint biomarkers [3] to secure validated intermediate endpoint biomarkers (VIEBs). If molecular entities in serum could be identified on the basis that they are predictably correlated with the future development of breast cancer, then a reduction in the VIEB level could serve as evidence of a preventive effect. Early work in this area suggests that nucleic acids in serum might be used to identify individuals with premalignant lesions [4]. Clinical correlation is needed for VIEBs and other molecular indicators of risk so that targets in addition to the ER can also be more efficiently studied. Targets of interest for breast cancer prevention include the EGFR family, RAR/RXR and mediators of inflammation or oxidative damage.

Polymorphic microsatellite loci from the western corn rootworm (Insecta: Coleoptera: Chrysomelidae) and cross‐amplification with other Diabrotica spp

AbstractCorn rootworms (Diabrotica spp.) make up the major insect pest complex of corn in the US and Europe, and there is a need for molecular markers for genetics studies. We used an enrichment strategy to develop microsatellite markers from the western corn rootworm (Diabrotica virgifera virgifera). Of 54 loci isolated, 25 were polymorphic, and of these, 17 were surveyed for variability in 59 wild individuals. In addition, the potential for cross‐amplification of these microsatellites was surveyed for Mexican, northern, and southern corn rootworms. Nine microsatellite loci showed Mendelian inheritance and are likely to be useful in population genetics studies.