bluuebunny/crossref_metadata_2025 huggingface dataset:
The spatial scale of habitat selection by red deer
Authors: Schaefer James A. , Morellet Nicolas , Pépin Dominique , Verheyden Hélène
Published: December 2008

Accounting for spatial scale is essential for understanding habitat selection, but few studies have used spatial statistics to reveal the characteristic scale at which organisms respond to their environment. We studied habitat selection by GPS-tracked red deer ( Cervus elaphus L., 1758) in the Pyrenees Mountains, France, by applying a geostatistical model that compares autocorrelation of a resource between used and available sites to uncover the scale at which animals assess habitat. Using an artificial landscape, we demonstrated that the model can handle discrete habitat classes. Based on conventional hierarchical analysis, deer selected for open habitat, especially meadow, and avoided coniferous forest, more strongly at the coarse level of the home range than GPS locations. Home ranges exhibited generally lower autocorrelation in elevation and meadow habitat than random locations within the population range, indicative of preference for high habitat heterogeneity. Mean maximum discrepancy in autocorrelation, which was more pronounced at the level of the home range than GPS locations, occurred at 830 m for meadow habitat and at 1511 m for elevation, suggesting that red deer responded to their environment at this scale. Our study demonstrates how spatial statistics can serve as an instructive complement to conventional approaches to habitat selection.
Acute phase nematode infection reduces resting metabolic rate in both protein-sufficient and protein-deficient mice
Authors: Tu T. , Phillips A. T. , Koski K. G. , Scott M. E.
Published: December 2008

The objective of this study was to investigate whether protein deficiency concurrent with the acute phase of infection with the murine nematode Heligmosomoides bakeri (Durette-Desset, Kinsella and Forrester, 1972; Tenora and Barus, 2001) affected the resting metabolic rate (RMR) in BALB/c mice, and whether deworming caused RMR to return to normal. Mice fed either a protein-sufficient (PS, 24%) or protein-deficient (PD, 3%) diet were infected with 100 larvae, and then treated with an anthelmintic drug on 9 and 14 days postinfection (dpi). RMR was measured on –2, 2, 7, and 19 dpi. The results showed that protein deficiency did not affect RMR at any of these times. RMR was unchanged immediately following infection (2 vs. –2 dpi) at the time when larvae are first embedded in the serosal musculture. Surprisingly, at 7 dpi when larvae migrate from the serosal musculture into the intestinal lumen, RMR was significantly lower in both diet groups compared with earlier time points. This reduced RMR persisted even after deworming. Possible reasons for these results are discussed.
Facilitative interactions between the Eurasian badger (Meles meles), the red fox (Vulpes vulpes), and the invasive raccoon dog (Nyctereutes procyonoides) in Białowieża Primeval Forest, Poland
Authors: Kowalczyk R. , Jędrzejewska B. , Zalewski A. , Jędrzejewski W.
Published: December 2008

Based on radio-tracking of Eurasian badgers ( Meles meles (L., 1758)), red foxes ( Vulpes vulpes (L., 1758)), and raccoon dogs ( Nyctereutes procyonoides (Gray, 1834)) and observations at burrows conducted in Białowieża Primeval Forest (eastern Poland) in 1996–2002, we addressed the hypothesis that facilitative interactions between a native (badger) and an alien (raccoon dog) species contributed to the invasion success of the latter. In winter, 88% of badger setts were occupied by both badgers and raccoon dogs, 4% by badgers and red foxes, and 4% by all three species. In summer, only 20% of badger setts were cohabited by other carnivore species (10% by raccoon dogs and 10% by foxes). Duration of occupation of badger setts by raccoon dogs averaged 117 days (SE = 21 days). Seasonal variation in raccoon dog use of badger setts was explained by changes in ambient temperature: the lower was the temperature, the higher was the rate of sett occupation by raccoon dogs. When wintering in the same sett, badgers and raccoon dogs used different parts of the sett. We conclude that facilitation by badgers (through habitat amelioration and refuge from cold and predation) makes the realized niche of raccoon dogs larger than predicted from their fundamental niche. The facilitating role of badger is stronger in winter, which is a critical period for raccoon dog survival in the temperate and boreal zone.
Reduced parasite infestation in urban Eurasian blackbirds (Turdus merula): a factor favoring urbanization?
Authors: Geue Dirk , Partecke Jesko
Published: December 2008

Humans nowadays dramatically alter environmental and ecological conditions worldwide. One of the most extreme forms of anthropogenic land-use alteration is urbanization. Animals thriving in urban areas are not only exposed to different environmental conditions compared with their nonurban conspecifics, but prevalence and impacts of wildlife diseases on urban populations may also be affected. In the present study, we tested whether blood-parasite prevalence differs between urban and forest habitats by comparing haematozoan infections of urban and forest-living Eurasian blackbirds ( Turdus merula L., 1758). In total, 76% of Eurasian blackbirds were infected with haematozoa and we detected five different blood parasite genera in both habitats. Blood-parasite prevalence varied both between years and between spring and summer in both urban and forest populations. Forest blackbirds had more parasite genera per individual than urban blackbirds, and in summer, forest blackbirds had higher blood-parasite prevalence than their urban conspecifics. These differences in blood-parasite prevalence between urban and forest blackbirds suggest a lower risk of haematozoan infections in urban than in forest habitats. The lower parasite prevalence could be one of the factors favoring the invasion of urban ecosystems.
Addressing uncertainty and remaining potential in a mature field. A case study from the Tertiary of Lake Maracaibo, Venezuela
Authors: Martin Charlotte A. L.
Published: December 2008

The Urdaneta West Field is located on the western margin of Lake Maracaibo in northern Venezuela. Biodegraded oil (12–15° API) is reservoired in Tertiary sandstones and produced through a series of lateral wells. The productive sandstones of the Icotea and Misoa Formations are thin, calculated as 0.5–4.5 m (1.5–15 ft) vertical thickness, and of limited lateral extent. This heterogeneity, coupled with heavy oil, results in poor fluid communication and low recovery efficiency. During 2004, a full field review was undertaken to address future development. Despite production from the Icotea and Misoa Formations, subsurface uncertainty was identified as a major issue due to the clustered nature of field development, complex depositional and structural environments, and reservoir fluid characteristics. In order to rank and mitigate reservoir uncertainties, a series of static models were built. The first phase of static modelling used a simple structural framework and reservoir interval averages to generate minimum, mid- and maximum volume cases. Dynamic simulation of these identified two major areas of uncertainty impacting oil-in-place and productivity – net sandbody connectivity and hydrocarbon contact. Two further phases of static and dynamic modelling concentrated on evaluating the full range of these uncertainties within a detailed structural framework.
Fault seal mapping – incorporating geometric and property uncertainty
Authors: Freeman S. R. , Harris S. D. , Knipe R. J.
Published: December 2008

In this paper, we present workflows, key relationships and results of multiple stochastic fault seal analyses conducted on geocellular geological or (static) reservoir grids. Ranges of uncertainties are computed from new and published datasets for the different input relationships (e.g. throw, VShale to VClay, fault clay prediction, fault rock clay content to permeability); these are used as input into stochastic modelling processes and the impact of each is assessed. The power of stochastic modelling to focus interpretation and risking effort is reviewed. Reducing the uncertainty distributions from the published data ranges has a massive impact on the range of predicted fault seal properties. Halving the uncertainties associated with the computation of the transmissibility multiplier, for instance, reduces this range from 7 to 1–1.5 orders of magnitude of the base‐case value (no uncertainty). Importantly, when combined together, the median predictions from each individual parameter do not lead to the median value for the final prediction; average relationships combined together will not therefore produce the average final prediction. This is a powerful result for two reasons: first, current geological modelling packages use global trends to define fault properties and so are likely to predict spurious results; and secondly, reducing the uncertainty on specific relationships by around 50% is an achievable goal. Locally calibrated datasets and relationships (field‐specific) based on carefully characterized samples should allow for this improvement in prediction accuracy. This paper presents a review of fault seal techniques, published data and the potential pitfalls associated with the analyses.
Realizing complex carbonate facies, diagenetic and fracture properties with standard reservoir modelling software
Authors: Pöppelreiter Michael C. , Balzarini Maria A. , Hansen Birger , Nelson Ronald
Published: December 2008

Geocellular modelling of diagenetically altered carbonates is challenging as geometries and pore systems often appear irregular. It has long been recognised, however, that tectonic evolution forms a framework that can influence patterns of carbonate facies, diagenesis and fracturing, the combination of which determines reservoir geometries and properties. Unravelling these processes can reveal trends that were not evident from well data alone. Such trends are useful in building geocellular models that extrapolate reservoir properties along them and can be used for economic screening of undrilled areas. This paper shows how standard reservoir modelling software can be used to model complex geology. In particular, it is shown how a carbonate reservoir model was constructed based on concepts of facies, burial diagenesis, hydrocarbon charge and fracturing. Workflows are discussed that were employed to distribute reservoir properties related to these processes.
Modelling of dipping clinoform barriers within deltaic outcrop analogues from the Cretaceous Western Interior Basin, USA
Authors: Howell John , Vassel Åsmund , Aune Tanja
Published: December 2008

Deltaic reservoirs typically contain seaward‐dipping surfaces termed clinoforms. Shale and carbonate cements covering clinoforms can frequently form a barrier or baffle to horizontal flow within reservoirs, However, clinoforms are not typically included in static or flow simulation models because they are often not identified in well data and little is known about their 3D geometry. High quality outcrops such as Cretaceous deposits of the US Western Interior Seaway provide an ideal opportunity to study clinoform geometry and shape, and to model their effects on flow. Within this study, two deltaic systems have been studied. The first is the Ferron Delta which crops out in the Wasatch Plateau, central Utah and is a highstand complex comprised of a number of small, overlapping lobes. Clinoforms are common and their 3D geometry is controlled by the position of the lobes. Large growth fault structures within the lobes add to the potential reservoir complexity. The forced regressive Panther Tongue Delta crops out in the Book Cliffs of Utah and is comprised of downstepping lobes with internal clinoforms. Data for modelling included traditional sedimentary logs, photomontages and calibrated photo logs. Models were built in IRAP RMS using a variety of modelling techniques from simple Truncated Gaussian Simulations on a regular grid to object modelling of shale barriers within a dipping grid designed to follow the clinoforms. The models were flow simulated as a means of comparing the different techniques for representing the heterogeneity results show that not modelling clinoforms explicitly in a dipping grid can lead to significant overestimates in the forecasted production; water injection in a down depositional dip position is optimum, and that there are only limited production differences between highstand and lowstand deltas.
Multiscale geological reservoir modelling in practice
Authors: Ringrose Philip S. , Martinius Allard W. , Alvestad Jostein
Published: December 2008

Geological systems exhibit variability and structure at a wide range of scales. Geological modelling of subsurface petroleum reservoirs has generally focused on the larger scales, driven by the types of measurement available and by computation limitations. Implementation of explicitly multiscale models of petroleum reservoirs is now realistically achievable and has proven value. This paper reviews the main approaches involved and discusses current limitations and challenges for routine implementation of multiscale modelling of petroleum-bearing rock systems. The main questions addressed are: (a) how many scales to model and upscale; (b) which scales to focus on; (c) how to best construct model grids; and (d) which heterogeneities matter most? The main future challenges identified are the need for improved handling of variance and more automated construction of geological and simulation grids.
Biological Research in the Evolution of Cancer Surgery: A Personal Perspective
Authors: Fisher Bernard
Published: December 2008

During the 19th, and for most of the 20th century, malignant tumors were removed by mutilating radical anatomic dissection. Advances such as anesthesia, asepsis, and blood transfusion made possible increasingly more radical operations. There was no scientific rationale for the operations being performed. Surgery in the 20th century was dominated by the principles of William S. Halsted, who contended that the bloodstream was of little significance as a route of tumor cell dissemination; a tumor was autonomous of its host; and cancer was a local-regional disease that spread in an orderly fashion based on mechanical considerations. Halsted believed that both the extent and nuances of an operation influenced patient outcome and that inadequate surgical skill was responsible for the failure to cure. A new surgical era arose in 1957, when cancer surgery began to be influenced by laboratory and clinical research, with results contrary to Halstedian principles. A new hypothesis resulted in a scientific basis for cancer surgery. Clinical trials supported the thesis that operable cancer is a systemic disease and that variations in local-regional therapy are unlikely to substantially affect survival. Complex host-tumor relationships were shown to affect every aspect of cancer and, contrary to Halsted's thesis, the bloodstream is of considerable importance in tumor dissemination. Clinical trials also have shown that less radical surgery is justified. Studies have shown that improved survival can be achieved with systemic therapy after surgery. Such therapy can reduce both the incidence of distant disease and the tumor recurrence at the tumor site after minimal surgery. The use of systemic therapy in patients who have no identifiable metastatic disease is a drastic departure from previous strategies. New technological innovations resulting from engineering research have improved the quality of life of patients by eliminating the need for some surgical procedures. Because cancer is apt to be a systemic disease, however, clinical trials are necessary to determine the effect of these modalities on patient outcome. Although technological developments will continue to play a role in cancer therapy, research in molecular biology and genetics will dictate the future status of cancer treatment and, ultimately, the future of surgery. [Cancer Res 2008;68(24):10007–20]
Cancer Stem Cells Are Enriched in the Side Population Cells in a Mouse Model of Glioma
Authors: Harris Molly A. , Yang Hyuna , Low Benjamin E. , Mukherje Joydeep , Guha Abhijit , Bronson Roderick T. , Shultz Leonard D. , Israel Mark A. , Yun Kyuson
Published: December 2008

The recent identification of cancer stem cells (CSCs) in multiple human cancers provides a new inroad to understanding tumorigenesis at the cellular level. CSCs are defined by their characteristics of self-renewal, multipotentiality, and tumor initiation upon transplantation. By testing for these defining characteristics, we provide evidence for the existence of CSCs in a transgenic mouse model of glioma, S100β-verbB;Trp53. In this glioma model, CSCs are enriched in the side population (SP) cells. These SP cells have enhanced tumor-initiating capacity, self-renewal, and multipotentiality compared with non-SP cells from the same tumors. Furthermore, gene expression analysis comparing fluorescence-activated cell sorting–sorted cancer SP cells to non-SP cancer cells and normal neural SP cells identified 45 candidate genes that are differentially expressed in glioma stem cells. We validated the expression of two genes from this list (S100a4 and S100a6) in primary mouse gliomas and human glioma samples. Analyses of xenografted human glioblastoma multiforme cell lines and primary human glioma tissues show that S100A4 and S100A6 are expressed in a small subset of cancer cells and that their abundance is positively correlated to tumor grade. In conclusion, this study shows that CSCs exist in a mouse glioma model, suggesting that this model can be used to study the molecular and cellular characteristics of CSCs in vivo and to further test the CSC hypothesis. [Cancer Res 2008;68(24):10051–9]
Epithelial-Mesenchymal Transition Induced by Growth Suppressor p12CDK2-AP1 Promotes Tumor Cell Local Invasion but Suppresses Distant Colony Growth
Authors: Tsuji Takanori , Ibaragi Soichiro , Shima Kaori , Hu Miaofen G. , Katsurano Miki , Sasaki Akira , Hu Guo-fu
Published: December 2008

Epithelial-mesenchymal transition (EMT) has been considered essential for metastasis, a multistep process including local invasion, intravasation, extravasation, and proliferation at distant sites. However, controversy remains as to whether EMT truly happens and how important it is to metastasis. We studied the involvement of EMT in individual steps of metastasis and found that p12CDK2-AP1, a down-stream effector of transforming growth factor β, induced EMT of hamster cheek pouch carcinoma-1 cells by promoting the expression of Twist2. EMT cells have an increased invasive but decreased metastatic phenotype. When s.c. inoculated, both EMT and non-EMT cells established primary tumors, but only EMT cells invaded into the adjacent tissues and blood vessels; however, neither cells formed lung metastases. When i.v. inoculated, only non-EMT cells established lung metastases. Moreover, s.c. inoculation of a mixture of the two cell types resulted in intravasation of both cell types and formation of lung metastasis from non-EMT cells. Our results allowed us to propose a novel model for the role of EMT in cancer metastasis. We showed that EMT and non-EMT cells cooperate to complete the spontaneous metastasis process. We thus hypothesize that EMT cells are responsible for degrading the surrounding matrix to lead the way of invasion and intravasation. Non-EMT cells then enter the blood stream and reestablish colonies in the secondary sites. [Cancer Res 2008;68(24):10377–86]
Systemic Blockade of Transforming Growth Factor-β Signaling Augments the Efficacy of Immunogene Therapy
Authors: Kim Samuel , Buchlis George , Fridlender Zvi G. , Sun Jing , Kapoor Veena , Cheng Guanjun , Haas Andrew , Cheung Hung Kam , Zhang Xiamei , Corbley Michael , Kaiser Larry R. , Ling Leona , Albelda Steven M.
Published: December 2008

Locally produced transforming growth factor-β (TGF-β) promotes tumor-induced immunosuppression and contributes to resistance to immunotherapy. This article explores the potential for increased efficacy when combining immunotherapies with TGF-β suppression using the TGF-β type I receptor kinase inhibitor SM16. Adenovirus expressing IFN-β (Ad.IFN-β) was injected intratumorally once in established s.c. AB12 (mesothelioma) and LKR (lung cancer) tumors or intratracheally in a Kras orthotopic lung tumor model. Mice bearing TC1 (lung cancer) tumors were vaccinated with two injections of adenovirus expressing human papillomavirus-E7 (HPV-E7; Ad.E7). SM16 was administered orally in formulated chow. Tumor growth was assessed and cytokine expression and cell populations were measured in tumors and spleens by real-time PCR and flow cytometry. SM16 potentiated the efficacy of both immunotherapies in each of the models and caused changes in the tumor microenvironment. The combination of SM16 and Ad.IFN-β increased the number of intratumoral leukocytes (including macrophages, natural killer cells, and CD8+ cells) and increased the percentage of T cells expressing the activation marker CD25. SM16 also augmented the antitumor effects of Ad.E7 in the TC1 flank tumor model. The combination did not increase HPV-E7 tetramer-positive CD8+ T cells in the spleens but did induce a marked increase in the tumors. Tumors from SM16-treated mice showed increased mRNA and protein for immunostimulatory cytokines and chemokines, as well as endothelial adhesion molecules, suggesting a mechanism for the increased intratumoral leukocyte trafficking. Blockade of the TGF-β signaling pathway augments the antitumor effects of Ad.IFN-β immune-activating or Ad.E7 vaccination therapy. The addition of TGF-β blocking agents in clinical trials of immunotherapies may increase efficacy. [Cancer Res 2008;68(24):10247–56
The SWI/SNF ATPase Brm Is a Gatekeeper of Proliferative Control in Prostate Cancer
Authors: Shen Hui , Powers Nathan , Saini Nitin , Comstock Clay E.S. , Sharma Ankur , Weaver Katherine , Revelo Monica P. , Gerald William , Williams Erin , Jessen Walter J. , Aronow Bruce J. , Rosson Gary , Weissman Bernard , Muchardt Christian , Yaniv Moshe , Knudsen Karen E.
Published: December 2008

Factors that drive prostate cancer progression remain poorly defined, thus hindering the development of new therapeutic strategies. Disseminated tumors are treated through regimens that ablate androgen signaling, as prostate cancer cells require androgen for growth and survival. However, recurrent, incurable tumors that have bypassed the androgen requirement ultimately arise. This study reveals that the Brm ATPase, a component of selected SWI/SNF complexes, has significant antiproliferative functions in the prostate that protect against these transitions. First, we show that targeted ablation of Brm is causative for the development of prostatic hyperplasia in mice. Second, in vivo challenge revealed that Brm−/− epithelia acquire the capacity for lobe-specific, castration-resistant cellular proliferation. Third, investigation of human specimens revealed that Brm mRNA and protein levels are attenuated in prostate cancer. Fourth, Brm down-regulation was associated with an increased proliferative index, consistent with the mouse model. Lastly, gene expression profiling showed that Brm loss alters factors upstream of E2F1; this was confirmed in murine models, wherein Brm loss induced E2F1 deregulation in a tissue-specific manner. Combined, these data identify Brm as a major effector of serum androgen–induced proliferation in the prostate that is disrupted in human disease, and indicate that loss of Brm confers a proliferative advantage in prostate cancer. [Cancer Res 2008;68(24):10154–62]
Hypoxia-Inducible Factor 1α Mediates Anoikis Resistance via Suppression of α5 Integrin
Authors: Rohwer Nadine , Welzel Martina , Daskalow Katjana , Pfander David , Wiedenmann Bertram , Detjen Katharina , Cramer Thorsten
Published: December 2008

The transcription factor hypoxia-inducible factor 1 (HIF-1) α is abundantly expressed in the majority of human carcinomas and their metastases. HIF-1α controls central metastasis-associated pathways such as glycolysis, angiogenesis, and invasion. Functional inhibition of HIF-1α leads to impaired metastasis formation in murine tumor models. However, the precise molecular mechanisms underlying the metastasis-promoting role of HIF-1α have not been fully characterized. The ability of transformed epithelial cells to initiate the metastatic cascade relies on their ability to escape anoikis, a default program of apoptosis induction following loss of integrin anchoring to the extracellular matrix. Therefore, we addressed the function of HIF-1α in anoikis resistance and anchorage-independent growth. Inhibition of HIF-1α via RNA interference resulted in up-regulation of α5 integrin on the cell surface of human gastric cancer cells, whereas other integrins remained unaffected. Integrin α5 induction occurred at the level of transcription and was dependent on elevated intracellular superoxide in HIF-1α-knockdown cells. HIF-1α–deficient cells displayed significantly increased anoikis susceptibility due to up-regulated α5 integrin. Finally, colony formation in soft agar was shown to be dependent on HIF-1α as HIF-1α–deficient cells displayed a 70% reduction in anchorage-independent proliferation. Results obtained by RNA interference could be entirely confirmed by application of the pharmacologic HIF-1α-inhibitor 2-methoxyestradiol. Hence, our data argue for a pivotal role for HIF-1α in anoikis control via suppression of α5 integrin. HIF-1α–inhibiting drugs might therefore offer an innovative strategy for antimetastatic cancer therapy. [Cancer Res 2008;68(24):10113–20]
MicroRNAs Impair MET-Mediated Invasive Growth
Authors: Migliore Cristina , Petrelli Annalisa , Ghiso Elena , Corso Simona , Capparuccia Lorena , Eramo Adriana , Comoglio Paolo M. , Giordano Silvia
Published: December 2008

MicroRNAs (miRNA) are a recently identified class of noncoding, endogenous, small RNAs that regulate gene expression, mainly at the translational level. These molecules play critical roles in several biological processes, such as cell proliferation and differentiation, development, and aging. It is also known that miRNAs play a role in human cancers where they can act either as oncogenes, down-regulating tumor suppressor genes, or as onco-suppressors, targeting molecules critically involved in promotion of tumor growth. One of such molecules is the tyrosine kinase receptor for hepatocyte growth factor, encoded by the MET oncogene. The MET receptor promotes a complex biological program named “invasive growth” that results from stimulation of cell motility, invasion, and protection from apoptosis. This oncogene is deregulated in many human tumors, where its most frequent alteration is overexpression. In this work, we have identified three miRNAs (miR-34b, miR-34c, and miR-199a*) that negatively regulate MET expression. Inhibition of these endogenous miRNAs, by use of antagomiRs, resulted in increased expression of MET protein, whereas their exogenous expression in cancer cells blocked MET-induced signal transduction and the execution of the invasive growth program, both in cells expressing normal levels of MET and in cancer cells overexpressing a constitutively active MET. Moreover, we show that these same miRNAs play a role in regulating the MET-induced migratory ability of melanoma-derived primary cells. In conclusion, we have identified miRNAs that behave as oncosuppressors by negatively targeting MET and might thus provide an additional option to inhibit this oncogene in tumors displaying its deregulation. [Cancer Res 2008;68(24):10128–36]
Genetic Variants in Apoptosis and Immunoregulation-Related Genes Are Associated with Risk of Chronic Lymphocytic Leukemia
Authors: Enjuanes Anna , Benavente Yolanda , Bosch Francesc , Martín-Guerrero Idoia , Colomer Dolors , Pérez-Álvarez Susana , Reina Oscar , Ardanaz Maria T. , Jares Pedro , García-Orad Africa , Pujana Miguel A. , Montserrat Emili , de Sanjosé Silvia , Campo Elias
Published: December 2008

To identify low-penetrance susceptibility alleles for chronic lymphocytic leukemia (CLL), we performed a case-control study genotyping 768 single-nucleotide polymorphisms (SNP) in 692 cases of CLL and 738 controls. We investigated nonsynonymous SNPs, SNPs with potential functional effect, and tag SNPs in regulatory gene regions in a total of 172 genes involved in cancer biology. After adjustment for multiple testing, we found a strong association between CLL risk and six genetic variants: CCNH (rs2266690, V270A), APAF1 (rs17028658, 3′region), IL16 (rs4505265, first intron), CASP8 (rs1045485, D302H), NOS2A (rs2779251, promoter), and CCR7 (rs3136687, intron 1). We found association with CLL susceptibility and 22 haplotypes in APAF1, IL6, TNFRSF13B, IL16, CASP3, CCR7, LTA/TNF, BAX, BCL2, CXCL12, CASP10/CASP8, CASP1, CCL2, BAK1, and IL1A candidate genes. Finally, we evaluated using public data sets the potential functional effect on gene expression levels of the CLL associated genetic variants detected in regulatory regions. Minor alleles for APAF1 and IL16 were associated with lower mRNA levels; no expression differences were observed for CCR7, whereas NOS2A could not be assessed. This study suggests that common genetic variation in apoptosis- and immunoregulation-related genes is associated with the CLL risk. [Cancer Res 2008;68(24):10178–86]
250K Single Nucleotide Polymorphism Array Karyotyping Identifies Acquired Uniparental Disomy and Homozygous Mutations, Including Novel Missense Substitutions of c-Cbl, in Myeloid Malignancies
Authors: Dunbar Andrew J. , Gondek Lukasz P. , O'Keefe Christine L. , Makishima Hideki , Rataul Manjot S. , Szpurka Hadrian , Sekeres Mikkael A. , Wang Xiao Fei , McDevitt Michael A. , Maciejewski Jaroslaw P.
Published: December 2008

Two types of acquired loss of heterozygosity are possible in cancer: deletions and copy-neutral uniparental disomy (UPD). Conventionally, copy number losses are identified using metaphase cytogenetics, whereas detection of UPD is accomplished by microsatellite and copy number analysis and as such, is not often used clinically. Recently, introduction of single nucleotide polymorphism (SNP) microarrays has allowed for the systematic and sensitive detection of UPD in hematologic malignancies and other cancers. In this study, we have applied 250K SNP array technology to detect previously cryptic chromosomal changes, particularly UPD, in a cohort of 301 patients with myelodysplastic syndromes (MDS), overlap MDS/myeloproliferative disorders (MPD), MPD, and acute myeloid leukemia. We show that UPD is a common chromosomal defect in myeloid malignancies, particularly in chronic myelomonocytic leukemia (CMML; 48%) and MDS/MPD-unclassifiable (38%). Furthermore, we show that mapping minimally overlapping segmental UPD regions can help target the search for both known and unknown pathogenic mutations, including newly identified missense mutations in the proto-oncogene c-Cbl in 7 of 12 patients with UPD11q. Acquired mutations of c-Cbl E3 ubiquitin ligase may explain the pathogenesis of a clonal process in a subset of MDS/MPD, including CMML. [Cancer Res 2008;68(24):10349–57]
Wnt1 Expression Induces Short-Range and Long-Range Cell Recruitments That Modify Mammary Tumor Development and Are Not Induced by a Cell-Autonomous β-Catenin Effector
Authors: Kim Young Chul , Clark Rod J. , Ranheim Erik A. , Alexander Caroline M.
Published: December 2008

Xenograft model studies have shown that tumor-associated, or genetically modified, activated stromal cells can promote tumor cell growth. Here, we examined mammary tumors arising in response to two different transgene-mediated Wnt signaling effectors: Wnt1 (a ligand with cell-nonautonomous effects) and ΔNβ-catenin (a constitutively active form of the intracellular effector). Although the route of tumor development has been shown to be similar for these two models, histologic analysis shows that Wnt1-induced tumors are associated with tracts of activated stroma, whereas most ΔNβ-catenin–induced tumors are solid adenocarcinomas. Furthermore, quantification of the “reactive stroma index” indicates that abundant activated stroma correlates with accelerated tumor progression. Wnt1-expressing mammary epithelial cells induce Wnt-specific target gene expression in local stromal cells (Wnt1-induced secreted protein 1/CCN4) but also induce long-range effects. Thus, mice with rapid tumor progression have 2-fold more circulating endothelial progenitor cells in peripheral blood than control or ΔNβ-catenin transgenic mice. Using tagged bone marrow (BM) transplants, we show that BM-derived cells are massively recruited to infiltrate the stroma of Wnt1-induced tumors where they differentiate into multiple cell types. Thus, localized ectopic expression of the proto-oncogene Wnt1 in mammary glands induces systemic responses, and we propose that this response modifies the tumorigenic outcome. [Cancer Res 2008;68(24):10145–53]
Negative Regulation of AKT Activation by BRCA1
Authors: Xiang Tao , Ohashi Amiko , Huang Yuping , Pandita Tej K. , Ludwig Thomas , Powell Simon N. , Yang Qin
Published: December 2008

The breast cancer susceptibility gene 1 (BRCA1) plays a key role in mammary tumorigenesis. However, the reasons why silencing the Brca1 gene leads to tumorigenesis are not clearly understood. We report here that BRCA1 deficiency activates the AKT oncogenic pathway, one of the most common alterations associated with human malignancy. Mutation of Brca1 gene increases the phosphorylation and the kinase activity of AKT. The BRCA1-BRCT domains bind to phosphorylated AKT (pAKT) and lead to its ubiquitination toward protein degradation. BRCA1 mutant cells lacking the BRCT repeats accumulate nuclear pAKT and consequently inactivate the transcription functions of FOXO3a, a main nuclear target of pAKT. Our results show that BRCA1 is a negative regulator of the AKT pathway and imply the significance of the BRCA1/AKT pathway in tumorigenesis. [Cancer Res 2008;68(24):10040–4]
Racial Disparity in Breast Cancer and Functional Germ Line Mutation in Galectin-3 (rs4644): A Pilot Study
Authors: Balan Vitaly , Nangia-Makker Pratima , Schwartz Ann G. , Jung Young Suk , Tait Larry , Hogan Victor , Raz Tirza , Wang Yi , Yang Zeng Quan , Wu Gen Sheng , Guo Yongjun , Li Huixiang , Abrams Judith , Couch Fergus J. , Lingle Wilma L. , Lloyd Ricardo V. , Ethier Stephen P. , Tainsky Michael A. , Raz Avraham
Published: December 2008

For reasons largely unknown, Caucasian women are at a significantly higher risk of developing breast cancer than Asian women. Over a decade ago, mutations in BRCA1/2 were identified as genetic risk factors; however, the discovery of additional breast cancer genes and genes contributing to racial disparities are lacking. We report a functional germline mutation (polymorphism) in the galectin-3 gene at position 191 (rs4644) substituting proline with histidine (P64H), which results in susceptibility to matrix metalloproteinase cleavage and acquisition of resistance to drug-induced apoptosis. This substitution correlates with incidence of breast cancer and racial disparity. Genotype analysis of 338 Caucasian (194 disease free and 144 breast cancer patients) and 140 Asian (79 disease free and 61 breast cancer patients) women showed that the allele homozygous for H64 exists in disease free Caucasian and Asian women at a frequency of 12% and 5%, respectively, versus 37% and 82% in breast cancer patients. The data indicate that H/H allele is associated with increased breast cancer risk in both races. The data implicate galectin-3 H64 in breast cancer and explain, in part, the noted racial disparity, thus providing a novel target for diagnosis and treatment. [Cancer Res 2008;68(24):10045–50]
Second-Generation Anti–Carcinoembryonic Antigen Designer T Cells Resist Activation-Induced Cell Death, Proliferate on Tumor Contact, Secrete Cytokines, and Exhibit Superior Antitumor ActivityIn vivo: A Preclinical Evaluation
Authors: Emtage Peter C.R. , Lo Agnes S.Y. , Gomes Erica M. , Liu David L. , Gonzalo-Daganzo Rosa M. , Junghans Richard P.
Published: December 2008

Purpose: This report describes the development and preclinical qualification tests of second-generation anti-carcinoembryonic (CEA) designer T cells for use in human trials.

Experimental Design: The progenitor first-generation immunoglobulin-T-cell receptor (IgTCR) that transmits Signal 1-only effectively mediated chimeric immune receptor (CIR)–directed cytotoxicity, but expressor T cells succumbed to activation-induced cell death (AICD). The second-generation CIR (termed “Tandem” for two signals) was designed to transmit TCR Signal 1 and CD28 Signal 2 to render T cells resistant to AICD and provide prolonged antitumor effect in vivo.

Results: A CIR was created that combines portions of CD28, TCRζ, and a single chain antibody domain (sFv) specific for CEA into a single molecule (IgCD28TCR). As designed, the gene-modified Tandem T cells exhibit the new property of being resistant to AICD, showing instead an accelerated proliferation on tumor contact. Tandem T cells are more potent than first generation in targeting and lysing CEA+ tumor. Tandem T cells secrete high levels of interleukin-2 and IFNγ on tumor contact that first-generation T cells lacked, but secretion was exhaustible, suggesting a need for interleukin-2 supplementation in therapy even for these second-generation agents. Finally, second-generation T cells were more effective in suppressing tumor in animal models.

Conclusion: An advanced generation of anti-CEA designer T cells is described with features that promise a more potent and enduring antitumor immune response in vivo. These preclinical data qualify the human use of this agent that is currently undergoing trial in patients with CEA+ cancers.
High Shed Antigen Levels within Tumors: An Additional Barrier to Immunoconjugate Therapy
Authors: Zhang Yujian , Pastan Ira
Published: December 2008

Shedding of cell surface antigens is an important biological process that is used by cells to modulate responses to signals in the extracellular environment. Because antibody-based therapies of cancer target cell surface antigens, it is important to understand more about the shedding process and how it affects tumor responses to this type of therapy. Up to now most attention has been focused on measuring the concentration of shed antigens in the blood and using these to determine the presence of a tumor and as a measure of response. The recent finding that the concentration of the tumor antigen mesothelin is extremely high within the interstitial space of tumors, where it can block antibody action, and that the concentration of shed mesothelin within the tumor is lowered by chemotherapy has important implications for the successful treatment of solid tumors by immunoconjugates and whole antibodies.
Protein Expression Profiling in Esophageal Adenocarcinoma Patients Indicates Association of Heat-Shock Protein 27 Expression and Chemotherapy Response
Authors: Langer Rupert , Ott Katja , Specht Katja , Becker Karen , Lordick Florian , Burian Maria , Herrmann Ken , Schrattenholz Andre , Cahill Michael A. , Schwaiger Markus , Hofler Heinz , Wester Hans-Jurgen
Published: December 2008

Purpose: To identify pretherapeutic predictive biomarkers in tumor biopsies of patients with locally advanced esophageal adenocarcinomas treated with neoadjuvant chemotherapy, we used an explorative proteomic approach to correlate pretherapeutic protein expression profiles with tumor response to neoadjuvant chemotherapy.

Experimental Design: Thirty-four patients with locally advanced esophageal adenocarcinomas who received neoadjuvant platin/5-fluorouracil–based chemotherapy before surgical resection were enrolled in this study. Response to chemotherapy was determined (a) by the amount of decline of [18F]fluorodeoxyglucose tumor uptake 2 weeks after the start of chemotherapy measured by positron emission tomography and (b) by histopathologic evaluation of tumor regression after surgical resection. Explorative quantitative and qualitative protein expression analysis was done through a quantitative differential protein expression analysis that used dual-isotope radioactive labeling of protein extracts. Selected identified biomarkers were validated by immunohistochemistry and quantitative real time reverse transcription-PCR.

Results: Proteomic analysis revealed four cellular stress response–associated proteins [heat-shock protein (HSP) 27, HSP60, glucose-regulated protein (GRP) 94, GRP78] and a number of cytoskeletal proteins whose pretherapeutic abundance was significantly different (P < 0.001) between responders and nonresponders. Immunohistochemistry and gene expression analysis confirmed these data, showing a significant association between low HSP27 expression and nonresponse to neoadjuvant chemotherapy (P = 0.049 and P = 0.032, respectively).

Conclusions: Albeit preliminary, our encouraging data suggest that protein expression profiling may distinguish cancers with a different response to chemotherapy. Our results suggest that response to chemotherapy may be related to a different activation of stress response and inflammatory biology in general. Moreover, the potential of HSPs and GRPs as biomarkers of chemotherapy response warrants further validation.
Triple-Negative Breast Cancer: Risk Factors to Potential Targets
Authors: Schneider Bryan P. , Winer Eric P. , Foulkes William D. , Garber Judy , Perou Charles M. , Richardson Andrea , Sledge George W. , Carey Lisa A.
Published: December 2008

Triple-negative breast cancer has recently been recognized as an important subgroup of breast cancer with a distinct outcome and therapeutic approach when compared with other subgroups of breast cancer. Triple-negative breast cancer comprises primarily, but not exclusively, a molecularly distinct subtype of breast cancer, the basal-like subtype. We do not yet have an assay to identify basal-like breast cancer in clinical samples, so triple-negative breast cancer has become a commonly used proxy for this subtype. The molecular biology and pathophysiology of triple-negative breast cancer are not completely understood, but understanding is improving rapidly with the advent of sophisticated molecular biology platforms. Moreover, the established risk factors of breast cancer as a whole may not apply to this unique subgroup of patients. Finally, because triple-negative breast cancer is defined by the absence of a target, there are currently limitations to using a tailored therapeutic approach, leaving conventional cytotoxic therapies as the mainstay. Active preclinical and clinical research programs focus on defining the clinical behavior, delineating the risk factors, and more completely understanding the molecular biology of triple-negative breast cancer to improve prevention, optimize conventional agents, and unveil novel therapeutic targets. This CCR focus article will review the current state of the art on triple-negative breast cancer.
Evidence for Polyclonal Origin of Multifocal Clear Cell Renal Cell Carcinoma
Authors: Cheng Liang , MacLennan Gregory T. , Zhang Shaobo , Wang Mingsheng , Zhou Ming , Tan Puay-Hoon , Foster Stephanie , Lopez-Beltran Antonio , Montironi Rodolfo
Published: December 2008

Purpose: Renal cell carcinomas are often multifocal. We investigated the genomic signatures of multifocal clear cell renal cell carcinoma to determine whether multiple tumors in the same kidney bear a clonal relationship to one another.

Experimental Design: A total of 62 tumors from 26 patients who underwent radical nephrectomy were examined. All patients had multiple separate clear cell renal carcinomas. Loss of heterozygosity analyses were done using five microsatellite polymorphic markers that represent putative tumor suppressor genes on chromosome 3p14 (D3S1300), 7q31 (D7S522), 8p22 (D8S261), 9p21 (D9S171), and 17p13 (TP53). X chromosome inactivation analyses were also done on the renal tumors from the 10 female patients. Chromosome 3p deletion status was determined by dual color interphase fluorescence in situ hybridization analysis in all tumors.

Results: Nineteen of the 26 (73%) patients with multifocal clear cell renal cell carcinoma showed allelic loss in at least 1 of 5 microsatellite loci in separate tumors analyzed. A disconcordant pattern of allelic loss between coexisting kidney tumors was observed in 7 cases. Six cases showed discordant 3p deletion patterns by dual color interphase fluorescence in situ hybridization analysis. Of the eight informative female cases studied by X chromosome inactivation, one showed a discordant nonrandom pattern of X chromosome inactivation. Overall, evidence of independent origin of the multifocal renal tumors was observed in 12 of 26 cases (46%).

Conclusions: Our data suggest that in a significant number of cases of multifocal clear cell renal cell carcinoma, the spatially separate tumors are of different clonal origin and arise independently.
Neuropilin-2–Mediated Tumor Growth and Angiogenesis in Pancreatic Adenocarcinoma
Authors: Dallas Nikolaos A. , Gray Michael J. , Xia Ling , Fan Fan , van Buren George , Gaur Puja , Samuel Shaija , Lim Sherry J. , Arumugam Thiruvengadam , Ramachandran Vijaya , Wang Huamin , Ellis Lee M.
Published: December 2008

Purpose. Neuropilin-2 (NRP-2) is a coreceptor for vascular endothelial growth factor (VEGF) on endothelial cells. NRP-2 is overexpressed in pancreatic ductal adenocarcinoma (PDAC) cells relative to nonmalignant ductal epithelium. This study determined the role of NRP-2 in PDAC cells.

Experimental Design. NRP-2 expression was reduced in PDAC cells with stable short-hairpin RNA (shRNA) transfection. Western blotting was done to evaluate signaling intermediates. Migration and invasion studies were carried out in Boyden chambers. Anchorage-independent growth was assessed by soft-agar colony formation. In vivo growth was evaluated using murine subcutaneous and orthotopic xenograft models. Immunohistochemical analysis evaluated in vivo proliferation and angiogenesis.

Results. shRNA-NRP-2 decreased NRP-2 levels without affecting neuropilin-1 levels. Akt activation was decreased in clones with reduced NRP-2 (shRNA-NRP-2). shRNA-NRP-2 cells showed decreased migration, invasion, and anchorage-independent growth compared with control cells. In vitro proliferation rates were similar in control- and shRNA-transfected cells. Subcutaneous and orthotopic xenografts from shRNA-transfected cells were significantly smaller than those resulting from control-transfected cells (P < 0.05). Furthermore, shRNA-NRP-2 tumors exhibited less cellular proliferation and decreased microvascular area relative to control tumors (P < 0.05). Constitutive expression of the angiogenic mediator Jagged-1 was reduced in shRNA-NRP-2 cells, whereas vascular endothelial growth factor levels were unchanged.

Conclusion. Reduction of NRP-2 expression in PDAC cells decreased survival signaling, migration, invasion, and ability to grow under anchorage-independent conditions. In vivo, reduction of NRP-2 led to decreased growth of xenograft tumors and decreased vascular area, which was associated with decreased Jagged-1 levels. NRP-2 is a potential therapeutic target on PDAC cells.