PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer

Inhibition of WEE1 kinase by AZD1775 has shown promising results in clinical cancer trials, but markers predicting AZD1775 response are lacking. Here we analysed AZD1775 response in a panel of human breast cancer (BC) cell lines by global proteome/transcriptome profiling and identified two groups of basal-like BC (BLBCs): ‘PTEN low’ BLBCs were highly sensitive to AZD1775 and failed to recover following removal of AZD1775, while ‘PTEN high’ BLBCs recovered. AZD1775 induced phosphorylation of DNA-PK, protecting cells from replication-associated DNA damage and promoting cellular recovery. Deletion of DNA-PK or PTEN, or inhibition of DNA-PK sensitized recovering BLBCs to AZD1775 by abrogating replication arrest, allowing replication despite DNA damage. This was linked to reduced CHK1 activation, increased cyclin E levels and apoptosis. In conclusion, we identified PTEN and DNA-PK as essential regulators of replication checkpoint arrest in response to AZD1775 and defined PTEN as a promising biomarker for efficient WEE1 cancer therapy.

Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice

Ionising radiation (IR) is a recognised carcinogen responsible for cancer development in patients previously treated using radiotherapy, and in individuals exposed as a result of accidents at nuclear energy plants. However, the mutational signatures induced by distinct types and doses of radiation are unknown. Here, we analyse the genetic architecture of mammary tumours, lymphomas and sarcomas induced by high (56Fe-ions) or low (gamma) energy radiation in mice carrying Trp53 loss of function alleles. In mammary tumours, high-energy radiation is associated with induction of focal structural variants, leading to genomic instability and Met amplification. Gamma-radiation is linked to large-scale structural variants and a point mutation signature associated with oxidative stress. The genomic architecture of carcinomas, sarcomas and lymphomas arising in the same animals are significantly different. Our study illustrates the complex interactions between radiation quality, germline Trp53 deficiency and tissue/cell of origin in shaping the genomic landscape of IR-induced tumours.

Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation

Human immune systems are variable, and immune responses are often unpredictable. Systems-level analyses offer increased power to sort patients on the basis of coordinated changes across immune cells and proteins. Allogeneic stem cell transplantation is a well-established form of immunotherapy whereby a donor immune system induces a graft-versus-leukemia response. This fails when the donor immune system regenerates improperly, leaving the patient susceptible to infections and leukemia relapse. We present a systems-level analysis by mass cytometry and serum profiling in 26 patients sampled 1, 2, 3, 6, and 12 months after transplantation. Using a combination of machine learning and topological data analyses, we show that global immune signatures associated with clinical outcome can be revealed, even when patients are few and heterogeneous. This high-resolution systems immune monitoring approach holds the potential for improving the development and evaluation of immunotherapies in the future.

Are porous tantalum cups superior to conventional reinforcement rings?

Background and purpose - Porous tantalum cups have been introduced as an alternative to various reinforcement rings in revision hip surgery. We hypothesized that porous tantalum cups would be superior to Müller acetabular roof reinforcement rings (MARRs) in revision hip surgery with re-revision for aseptic loosening as the primary outcome measure. Patients and methods - 207 hips operated with either a porous tantalum cup (TM cup, n = 111) or a MARR (n = 96) at index procedure were identified in our local arthroplasty register. Acetabular defects were classified according to Paprosky. There were 96 men and 111 women with a median age of 71 (35-95) years, presenting acetabular defect size type I in 39 cases, IIA in 22, IIB in 27, IIC in 43, IIIA in 32, and IIIB in 37 cases. Analysis of medical records identified all patients with subsequent re-revision and reasons for re-revisions. Kaplan-Meier survival functions were used to estimate implant survival. Results - With re-revision for aseptic loosening as the endpoint, the 6-year unadjusted cumulative survival was 97% (95% CI: 94-100) for TM cups and 96% (CI: 92-100) for MARR (p = 0.6). Using re-revision for any reason as the endpoint, 6-year survival was 87% (CI: 81-94) for TM cups and 95% (CI: 90-99) for MARR (p = 0.06). The main reason for re-revision in the TM group was dislocation (n = 10), followed by loosening (n = 3), whereas the main reason for re-revision in the MARR group was aseptic loosening (n = 8). Duration of the index procedure and perioperative blood loss were lower in the TM group. Interpretation - Both TM and MARR lead to good 6-year results in acetabular revision surgery. The methods differ in their respective failure mechanisms. We conclude that TM cups are a valuable treatment option in acetabular revision surgery, but the reasons underlying dislocations after the use of TM cups must be analyzed further.

Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth

A role for Hedgehog (Hh) signalling in the development of colorectal cancer (CRC) has been proposed. In CRC and other solid tumours, Hh ligands are upregulated; however, a specific Hh antagonist provided no benefit in a clinical trial. Here we use Hh reporter mice to show that downstream Hh activity is unexpectedly diminished in a mouse model of colitis-associated colon cancer, and that downstream Hh signalling is restricted to the stroma. Functionally, stroma-specific Hh activation in mice markedly reduces the tumour load and blocks progression of advanced neoplasms, partly via the modulation of BMP signalling and restriction of the colonic stem cell signature. By contrast, attenuated Hh signalling accelerates colonic tumourigenesis. In human CRC, downstream Hh activity is similarly reduced and canonical Hh signalling remains predominantly paracrine. Our results suggest that diminished downstream Hh signalling enhances CRC development, and that stromal Hh activation can act as a colonic tumour suppressor.

The Hedgehog signalling pathway can drive tumorigenesis. Here, the authors show that in a colitis-associated colon cancer model downstream Hedgehog signalling is restricted to the stroma and its over-activation can inhibit tumorigenesis, associated with activation of BMP signaling.

Abstract 3881: Breast cancer proteogenomics landscape defines subtype specific protein level regulations and reveals proteins coded by pseudogenic loci

The advancement of mass spectrometry (MS) based proteomics has been tremendous in recent years and is expected to continue due to the rapid developments in instrument technology and bioinformatic analysis. These methods have enabled us to discover predictive protein markers for anti-estrogen treatment of estrogen receptor positive breast cancer 1, 2. Recently proteogenomics has emerged as an exciting area, combining proteomics with genomics and transcriptomics. We have published a proteogenomics workflow which can be used to discover new protein coding loci via an unbiased 6 reading frame translation (6-FT) search even in well-annotated higher eukaryotes such as human and mouse3. Herein we present a quantitative proteomics and proteogenomics analysis, using our high resolution isoelectric focusing (HiRIEF) aided proteogenomics method3,4, on breast tumors obtained from five breast cancer subtypes. Protein products from 12645 genes are identified and roughly 10000 proteins are quantified across the entire cohort of 45 breast cancer tissues. The resulting quantitative proteome landscape recapitulates the PAM50 subtypes. The breast cancer proteome defines clusters indicative of stroma, immune response, basal, adipocyte, proliferation, and steroid response related components. Additionally, a proteogenomics search of the 6-FT of the entire human genome reveals novel pseudogenic protein coding regions (n = 150) as well as peptides derived from lncRNA (n = 79). Finally, customized databases including variant peptides derived from SNPs, mutations, and splice junction peptides are used to analyze protein level events related to variants. This proteogenomics analysis for both new open reading frames and sequence variants reveals novel proteins expressed in a tumor specific manner in several studied individuals, with some being related to known sub-types. Taken together, this study reveals the proteome profiles are related to transcriptomics, copy number, and metabolic activity in specific tumors, proving our proteogenomics workflow provides novel information on the breast cancer molecular landscape.

1. Johansson, H.J. et al. Proteomics profiling identify CAPS as a potential predictive marker of tamoxifen resistance in estrogen receptor positive breast cancer. Clinical proteomics 12, 8 (2015).

2. Johansson, H.J. et al. Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer. Nat Commun 4, 2175 (2013).

3. Branca, R.M. et al. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nature methods 11, 59-62 (2014).

4. Boekel J, et.al. Multi-omic data analysis using Galaxy. Nature Biotechnol. 2015 Feb 6;33(2):137-9.

Citation Format: Henrik Johansson, Yafeng Zhu, Mads Haugland, Kristine Sahlberg, Erik Fredlund, Mikael Huss, Nathaniel Vacanti, Miriam Range Aure, Bengt Sennblad, Sanela Kjellqvist, Lukas Orre, Ola Christian Lingjaerde, Anne-Lise Borresen-Dale, Janne Lehtio. Breast cancer proteogenomics landscape defines subtype specific protein level regulations and reveals proteins coded by pseudogenic loci. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3881.

Abstract 1109: AAGUGC-microRNAs are an integral part of an oncogenic signaling network driving non-small cell lung cancer proliferation

microRNA dysregulation is a common feature of cancer cells, but the complex roles of microRNAs in cancer are not fully elucidated. Here we used functional genomics to identify oncogenic microRNAs in non-small cell lung cancer (NSCLC) and to evaluate their impact on response to EGFR targeting therapy. Our data demonstrates that microRNAs with an AAGUGC-motif in their seed-sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors.

Using miR-372 as a prototypic AAGUGC-miRNA we set out to identify target mRNAs and an explanation to the discovered phenotype. Global transcriptomics, proteomics and target prediction, resulted in the identification of more than 500 candidate target mRNAs, including several tumor suppressors involved in the G1/S transition. The clinical relevance of our findings were evaluated by analysis of public domain data of NSCLC patients, revealing that almost 200 of the candidate target mRNAs showed a negative correlation to AAGUGC-miRNAs. In addition, the analysis of NSCLC clinical data supported the link between this microRNA seed-family and cancer cell proliferation and indicated that high expression of this type of microRNAs is associated with shorter relapse free survival.

Expanding the analysis to include additional types of cancer revealed large differences in expression of AAGUGC-miRNA both within and between cancer types. In general the results from the analysis of NSCLC was replicated in other cancer types, where expression of AAGUGC-miRNAs was associated with decreased mRNA levels of tumor suppressor targets and increased expression of genes involved in proliferation.

In conclusion we propose that AAGUGC-microRNAs are an integral part of an oncogenic signaling network, and that these findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.

Citation Format: Yan Zhou, Oliver Frings, Erik Fredlund, Jorrit Boekel, Rui M. Branca, Lukas M. Orre. AAGUGC-microRNAs are an integral part of an oncogenic signaling network driving non-small cell lung cancer proliferation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1109.

Molecular stratification of metastatic melanoma using gene expression profiling: Prediction of survival outcome and benefit from molecular targeted therapy

Melanoma is currently divided on a genetic level according to mutational status. However, this classification does not optimally predict prognosis. In prior studies, we have defined gene expression phenotypes (high-immune, pigmentation, proliferative and normal-like), which are predictive of survival outcome as well as informative of biology. Herein, we employed a population-based metastatic melanoma cohort and external cohorts to determine the prognostic and predictive significance of the gene expression phenotypes. We performed expression profiling on 214 cutaneous melanoma tumors and found an increased risk of developing distant metastases in the pigmentation (HR, 1.9; 95% CI, 1.05-3.28; P=0.03) and proliferative (HR, 2.8; 95% CI, 1.43-5.57; P=0.003) groups as compared to the high-immune response group. Further genetic characterization of melanomas using targeted deep-sequencing revealed similar mutational patterns across these phenotypes. We also used publicly available expression profiling data from melanoma patients treated with targeted or vaccine therapy in order to determine if our signatures predicted therapeutic response. In patients receiving targeted therapy, melanomas resistant to targeted therapy were enriched in the MITF-low proliferative subtype as compared to pre-treatment biopsies (P=0.02). In summary, the melanoma gene expression phenotypes are highly predictive of survival outcome and can further help to discriminate patients responding to targeted therapy.

Frequency and distribution of Notch mutations in tumor cell lines

BACKGROUND

Deregulated Notch signaling is linked to a variety of tumors and it is therefore important to learn more about the frequency and distribution of Notch mutations in a tumor context.

METHODS

In this report, we use data from the recently developed Cancer Cell Line Encyclopedia to assess the frequency and distribution of Notch mutations in a large panel of cancer cell lines in silico.

RESULTS

Our results show that the mutation frequency of Notch receptor and ligand genes is at par with that for established oncogenes and higher than for a set of house-keeping genes. Mutations were found across all four Notch receptor genes, but with notable differences between protein domains, mutations were for example more prevalent in the regions encoding the LNR and PEST domains in the Notch intracellular domain. Furthermore, an in silico estimation of functional impact showed that deleterious mutations cluster to the ligand-binding and the intracellular domains of NOTCH1. For most cell line groups, the mutation frequency of Notch genes is higher than in associated primary tumors.

CONCLUSIONS

Our results shed new light on the spectrum of Notch mutations after in vitro culturing of tumor cells. The higher mutation frequency in tumor cell lines indicates that Notch mutations are associated with a growth advantage in vitro, and thus may be considered to be driver mutations in a tumor cell line context.

The mutational landscapes of genetic and chemical models of Kras-driven lung cancer

Next-generation sequencing of human tumours has refined our understanding of the mutational processes operative in cancer initiation and progression, yet major questions remain regarding factors that induce driver mutations, and the processes that shape their selection during tumourigenesis. We performed whole-exome sequencing (WES) on adenomas from three mouse models of non-small cell lung cancer (NSCLC), induced by exposure to carcinogens (Methylnitrosourea (MNU) and Urethane), or by genetic activation of Kras (Kras^LA2). Although the MNU-induced tumours carried exactly the same initiating mutation in Kras as seen in the Kras^LA2 model (G12D), MNU tumours had an average of 192 non-synonymous, somatic single nucleotide variants (SNVs), compared to only 6 in tumours from the Kras^LA2 model. In contrast, the Kras^LA2 tumours exhibited a significantly higher level of aneuploidy and copy number alterations (CNAs) compared to the carcinogen-induced tumours, suggesting that carcinogen and genetically-engineered models adopt different routes to tumour development. The wild type (WT) allele of Kras has been shown to act as a tumour suppressor in mouse models of NSCLC. We demonstrate that urethane-induced tumours from WT mice carry mostly (94%) Q61R Kras mutations, while those from Kras heterozygous animals carry mostly (92%) Q61L mutations, indicating a major role of germline Kras status in mutation selection during initiation. The exome-wide mutation spectra in carcinogen-induced tumours overwhelmingly display signatures of the initiating carcinogen, while adenocarcinomas acquire additional C>T mutations at CpG sites. These data provide a basis for understanding the conclusions from human tumour genome sequencing that identified two broad categories based on relative frequency of SNVs and CNAs¹, and underline the importance of carcinogen models for understanding the complex mutation spectra seen in human cancers.

CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer

SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCF^FBXO28 activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCF^FBXO28 plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer.

Murine microenvironment metaprofiles associate with human cancer etiology and intrinsic subtypes

PURPOSE

Ionizing radiation is a well-established carcinogen in rodent models and a risk factor associated with human cancer. We developed a mouse model that captures radiation effects on host biology by transplanting unirradiated Trp53-null mammary tissue to sham or irradiated hosts. Gene expression profiles of tumors that arose in irradiated mice are distinct from those that arose in naïve hosts. We asked whether expression metaprofiles could discern radiation-preceded human cancer or be informative in sporadic breast cancers.

EXPERIMENTAL DESIGN

Affymetrix microarray gene expression data from 56 Trp53-null mammary tumors were used to define gene profiles and a centroid that discriminates tumors arising in irradiated hosts. These were applied to publicly available human cancer datasets.

RESULTS

Host irradiation induces a metaprofile consisting of gene modules representing stem cells, cell motility, macrophages, and autophagy. Human orthologs of the host irradiation metaprofile discriminated between radiation-preceded and sporadic human thyroid cancers. An irradiated host centroid was strongly associated with estrogen receptor-negative breast cancer. When applied to sporadic human breast cancers, the irradiated host metaprofile strongly associated with basal-like and claudin-low breast cancer intrinsic subtypes. Comparing host irradiation in the context of TGF-β levels showed that inflammation was robustly associated with claudin-low tumors.

CONCLUSIONS

Detection of radiation-preceded human cancer by the irradiated host metaprofile raises possibilities of assessing human cancer etiology. Moreover, the association of the irradiated host metaprofiles with estrogen receptor-negative status and claudin-low subtype suggests that host processes similar to those induced by radiation underlie sporadic cancers.

The microRNA body map: dissecting microRNA function through integrative genomics

While a growing body of evidence implicates regulatory miRNA modules in various aspects of human disease and development, insights into specific miRNA function remain limited. Here, we present an innovative approach to elucidate tissue-specific miRNA functions that goes beyond miRNA target prediction and expression correlation. This approach is based on a multi-level integration of corresponding miRNA and mRNA gene expression levels, miRNA target prediction, transcription factor target prediction and mechanistic models of gene network regulation. Predicted miRNA functions were either validated experimentally or compared to published data. The predicted miRNA functions are accessible in the miRNA bodymap, an interactive online compendium and mining tool of high-dimensional newly generated and published miRNA expression profiles. The miRNA bodymap enables prioritization of candidate miRNAs based on their expression pattern or functional annotation across tissue or disease subgroup. The miRNA bodymap project provides users with a single one-stop data-mining solution and has great potential to become a community resource.

GOBO: gene expression-based outcome for breast cancer online

Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the heterogeneity of breast cancer emphasizes the need for validation of prognostic gene signatures in larger sample sets stratified into relevant subgroups. Here, we describe a multifunctional user-friendly online tool, GOBO (http://co.bmc.lu.se/gobo), allowing a range of different analyses to be performed in an 1881-sample breast tumor data set, and a 51-sample breast cancer cell line set, both generated on Affymetrix U133A microarrays. GOBO supports a wide range of applications including: 1) rapid assessment of gene expression levels in subgroups of breast tumors and cell lines, 2) identification of co-expressed genes for creation of potential metagenes, 3) association with outcome for gene expression levels of single genes, sets of genes, or gene signatures in multiple subgroups of the 1881-sample breast cancer data set. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform.

The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma

The miR-17-92 microRNA cluster is often activated in cancer cells, but the identity of its targets remains elusive. Using SILAC and quantitative mass spectrometry, we examined the effects of activation of the miR-17-92 cluster on global protein expression in neuroblastoma (NB) cells. Our results reveal cooperation between individual miR-17-92 miRNAs and implicate miR-17-92 in multiple hallmarks of cancer, including proliferation and cell adhesion. Most importantly, we show that miR-17-92 is a potent inhibitor of TGF-β signaling. By functioning both upstream and downstream of pSMAD2, miR-17-92 activation triggers downregulation of multiple key effectors along the TGF-β signaling cascade as well as direct inhibition of TGF-β-responsive genes.

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

Different classes of non-coding RNAs, including microRNAs, have recently been implicated in the process of tumourigenesis. In this study, we examined the expression and putative functions of a novel class of non-coding RNAs known as transcribed ultraconserved regions (T-UCRs) in neuroblastoma. Genome-wide expression profiling revealed correlations between specific T-UCR expression levels and important clinicogenetic parameters such as MYCN amplification status. A functional genomics approach based on the integration of multi-level transcriptome data was adapted to gain insights into T-UCR functions. Assignments of T-UCRs to cellular processes such as TP53 response, differentiation and proliferation were verified using various cellular model systems. For the first time, our results define a T-UCR expression landscape in neuroblastoma and suggest widespread T-UCR involvement in diverse cellular processes that are deregulated in the process of tumourigenesis.

Real-time PCR detection of Fusarium species in Swedish oats and correlation to T-2 and HT-2 toxin content

Contamination of Fusarium moulds and subsequent production of mycotoxins is a common problem in cereals grown in Northern Europe. Oats is the third most important cereal crop in Sweden and is commonly contaminated by Fusarium. To date there are no published reports on the distribution of trichothecene-producing Fusaria in Swedish oats and correlation to T-2 and HT-2, the two most dominant toxins. Identification of Fusarium species by traditional methods requires specific skill and experience and quantification of specific species is not possible. Using modern molecular methods such as real-time PCR both identification and quantification of specific Fusarium species are possible directly from the food or feed samples. In this study, specific methods for Fusarium langsethiae, Fusarium sporotrichioides, Fusarium graminearum, Fusarium culmorum and Fusarium poae as well as for the total amount of DNA from trichothecene-producing species were evaluated with respect to precision, robustness and efficiency and then used in the analysis of oat samples. Sixty-two oat samples were taken from field trial harvests from 2006-2008 in the central and southern parts of Sweden and analysed for the presence of Fusarium species by using species-specific real-time PCR-based methods with TaqMan or SYBR Green biochemistry. The T-2 and HT-2 toxin content was analysed by gas chromatography with electron capture detection of the toxins' pentafluoropropyl derivatives. The results showed that F. langsethiae and F. poae were the most dominant Fusarium species among those tested in Swedish oats during this period. The DNA level of F. langsethiae correlated well with the level of T-2 and HT-2 toxin (r=0.7), indicating that this species was the most important producer of T-2 and HT-2 toxins in Swedish oats during the sampling period (2006 to 2008). It can also be concluded that real-time PCR is a powerful tool when studying Fusarium species distribution in oats.

Hypoxia-inducible factor-2alpha correlates to distant recurrence and poor outcome in invasive breast cancer

Differential regulation as well as target gene specificity of the two hypoxia-inducible factor (HIF)-alpha subunits HIF-1alpha and HIF-2alpha in various tumors and cell lines have been suggested. In breast cancer, the prognostic significance of HIF-1alpha is not clear-cut and that of HIF-2alpha is largely unknown. Using IHC analyses of HIF-1alpha, HIF-2alpha, and vascular endothelial growth factor (VEGF) expression in a tissue microarray of invasive breast cancer specimens from 512 patients, we investigated the expression patterns of the 2 HIF-alpha subunits in relation to established clinicopathologic variables, VEGF expression, and survival. HIF-1alpha and HIF-2alpha protein levels and their effect on survival were additionally analyzed in a second cohort of 179 patients. To evaluate the individual role of each subunit in the hypoxic response and induction of VEGF, HIF-alpha protein and HIF-alpha and VEGF mRNA levels were further studied in cultured breast cancer cells after hypoxic induction and/or knockdown of HIF-alpha subunits by siRNA by Western blot and Quantitative Real-Time PCR techniques. We showed that although HIF-1alpha and HIF-2alpha protein levels in breast cancer specimens were not interrelated, high levels of both HIF-1alpha and HIF-2alpha associated to high VEGF expression. HIF-2alpha expression was an independent prognostic factor associated to reduced recurrence-free and breast cancer-specific survival, whereas HIF-1alpha did not exhibit these correlations. In cultured cells, acute hypoxia induced both HIF-proteins. At prolonged hypoxia, HIF-2alpha remained accumulated, whereas HIF-1alpha protein levels decreased, in agreement with the oxygen level and time-dependent induction of HIFs recently reported in neuroblastoma.

Transcriptional adaptation of neuroblastoma cells to hypoxia

Low oxygen pressure (hypoxia) is a physiological condition that has been linked to tumor progression and increased malignancy in several cancer forms. Cells of the childhood neoplasm neuroblastoma respond to hypoxia by attaining a lower grade of differentiation, which clinically is associated with poor prognosis. Furthermore, expression of the hypoxia inducible factor-2alpha correlates to poor outcome in neuroblastoma patients. In this report we have by microarray analysis studied transcriptional changes in seven neuroblastoma cell lines subjected to long term hypoxia. We find the gene regulatory response to be highly dependent on cell line background, however, a set of genes was coherently regulated by hypoxia and these genes are correlated to known hypoxia-induced transcriptional profiles.

Hypoxia inducible factor-2alpha in cancer

Poorly oxygenated (hypoxic) tumors are frequently more aggressive compared to corresponding tumors that are better oxygenated. Adaptation to hypoxia is primarily mediated by two closely related hypoxia inducible transcription factor complexes, HIF-1 and HIF-2, which become stabilized and activated at low oxygen levels. Whether HIF-1 and HIF-2 have different roles in tumorigenesis is an open question and an issue we discuss. With focus on HIF-2, we summarize reported phenotypical changes of HIF genetic models and HIF expression patterns during normal development, in adult non-malignant tissues and in tumors. We further address the much-discussed subject of target gene preferences between HIF-1 and HIF-2, given that both transcription factors bind to the same DNA motif. Finally, we also discuss the observations that the oxygen-sensitive HIF-2alpha subunit is accumulated and active under non-hypoxic conditions as exemplified by HIF-2alpha expressing tumor macrophages and neuroblastoma cells located in seemingly well-vascularized tumor regions and how this phenomenon is related to tumor aggressiveness.

Recruitment of HIF-1alpha and HIF-2alpha to common target genes is differentially regulated in neuroblastoma: HIF-2alpha promotes an aggressive phenotype

In neuroblastoma specimens, HIF-2alpha but not HIF-1alpha is strongly expressed in well-vascularized areas. In vitro, HIF-2alpha protein was stabilized at 5% O2 (resembling end capillary oxygen conditions) and, in contrast to the low HIF-1alpha activity at this oxygen level, actively transcribed genes like VEGF. Under hypoxia (1% O2), HIF-1alpha was transiently stabilized and primarily mediated acute responses, whereas HIF-2alpha protein gradually accumulated and governed prolonged hypoxic gene activation. Knockdown of HIF-2alpha reduced growth of neuroblastoma tumors in athymic mice. Furthermore, high HIF-2alpha protein levels were correlated with advanced clinical stage and high VEGF expression and predicted poor prognosis in a clinical neuroblastoma material. Our results demonstrate the relevance of HIF-2alpha in neuroblastoma progression and have general tumor biological implications.

Hypoxia-induced dedifferentiation of tumor cells--a mechanism behind heterogeneity and aggressiveness of solid tumors

Histopathological examination of solid tumors frequently reveals pronounced tumor cell heterogeneity with regards to cell organization, cell morphology, cell size, nuclei morphology, etc. Analyses of gene expression patterns by immunohistochemistry or in situ hybridization techniques further strengthen the actual presence of phenotypic heterogeneity, often demonstrating substantial diversity within a given tumor. The molecular mechanisms underlying the phenotypic heterogeneity are very complex with genetic, epigenetic and environmental components. Hypoxia, shortage in oxygen, greatly influences cellular phenotypes by altering the expression of specific genes, and is an important contributor to intra- and inter-tumor cell diversity as revealed by the pronounced but non-uniform expression of hypoxia-driven genes in solid tumors (reviewed in [Semenza GL. Targeting HIF-1 for cancer therapy. Nat Rev Cancer 2003;3:721-32; Harris AL. Hypoxia--a key regulatory factor in tumour growth. Nat Rev Cancer 2002;2:38-47.]). The oxygen pressure in solid tumors is generally lower than in the surrounding non-malignant tissues, and tumors exhibiting extensive hypoxia have been shown to be more aggressive than corresponding tumors that are better oxygenized [Vaupel P. Oxygen transport in tumors: characteristics and clinical implications. Adv Exp Med Biol 1996;388:341-51; Vaupel P, Thews O, Hoeckel M. Treatment resistance of solid tumors: role of hypoxia and anemia. Med Oncol 2001;18:243-59.]. We recently observed that hypoxic neuroblastoma cells and breast cancer cells lose their differentiated gene expression patterns and develop stem cell-like phenotypes [Jögi A, Øra I, Nilsson H, Lindeheim A, Makino Y, Poellinger L, et al. Hypoxia alters gene expression in human neuroblastoma cells toward an immature and neural crest-like phenotype. Proc Natl Acad Sci USA 2002;99:7021-6; Helczynska K, Kronblad A, Jögi A, Nilsson E, Beckman S, Landberg G, et al. Hypoxia promotes a dedifferentiated phenotype in ductal breast carcinoma in situ. Cancer Res 2003;63:1441-4.]. As low stage of differentiation in neuroblastoma and in breast cancer is linked to poor prognosis, hypoxia-induced dedifferentiation will not only contribute to tumor heterogeneity but could also be one mechanism behind increased aggressiveness of hypoxic tumors. The effect(s) of hypoxia on tumor cell differentiation status is the focus of this review.

Notch signaling in neuroblastoma

Neuroblastoma is a pediatric tumor that originates from precursor cells of the sympathetic nervous system that have discontinued their normal differentiation program. This review is focused on involvement of the Notch signaling cascade in the process of differentiation in neuroblastoma cells and normal cells of the sympathetic nervous system. Hypoxia induces dedifferentiation of neuroblastoma cells in vivo and in vitro, and under oxygen-compromised conditions the Notch cascade is activated. This activation might promote development of the dedifferentiated phenotype. The implications of these observations for tumor biology are also discussed.

Metabolite profiles of the biocontrol yeast Pichia anomala J121 grown under oxygen limitation

The biocontrol yeast Pichia anomala J121 prevents mould growth during the storage of moist grain under low oxygen/high carbon dioxide conditions. Growth and metabolite formation of P. anomala was analyzed under two conditions of oxygen limitation: (a) initial aerobic conditions with restricted oxygen access during the growth period and (b) initial microaerobic conditions followed by anaerobiosis. Major intra- and extracellular metabolites were analyzed by high-resolution magic-angle spinning (HR-MAS) NMR and HPLC, respectively. HR-MAS NMR allows the analysis of major soluble compounds inside intact cells, without the need for an extraction step. Biomass production was higher in treatment (A), whereas the specific ethanol production rate during growth on glucose was similar in both treatments. This implies that oxygen availability affected the respiration and not the fermentation of the yeast. Following glucose depletion, ethanol was oxidized to acetate in treatment (A), but continued to be produced in (B). Arabitol accumulated in the culture substrate of both treatments, whereas glycerol only accumulated in treatment (B). Trehalose, arabitol, and glycerol accumulated inside the cells in both treatments. The levels of these metabolites were generally significantly higher in treatment (B) than in (A), indicating their importance for P. anomala during severe oxygen limitation/anaerobic conditions.

A PP2C phosphatase containing a PAS domain is required to convey signals of energy stress to the sigmaB transcription factor of Bacillus subtilis

The sigmaB transcription factor of the bacterium Bacillus subtilis is activated by growth-limiting energy or environmental challenge to direct the synthesis of more than 100 general stress proteins. Although the signal transduction pathway that conveys these stress signals to sigmaB is becoming increasingly well understood, how environmental or energy stress signals enter this pathway remains unknown. We show here that two PP2C serine phosphatases - RsbP, which is required for response to energy stress, and RsbU, which is required for response to environmental stress - each converge on the RsbV regulator of sigmaB. According to the current understanding of sigmaB regulation, in unstressed cells the phosphorylated RsbV anti-anti-sigma is unable to complex the RsbW anti-sigma, which is then free to bind and inactivate sigmaB. We can now advance the model that either PP2C phosphatase, when triggered by its particular class of stress, can remove the phosphate from RsbV and thereby activate sigmaB. The action of the previously described RsbU is known to be controlled by dedicated upstream signalling components that are activated by environmental stress. The action of the RsbP phosphatase described here requires an energy stress, which we suggest is sensed, at least in part, by the PAS domain in the amino-terminal region of the RsbP phosphatase. In other bacterial signalling proteins, similar PAS domains and their associated chromophores directly sense changes in intracellular redox potential to control the activity of a linked output domain.

Self-reported drug use among recently admitted jail inmates: estimating prevalence and treatment needs

This primarily methodological paper compares self-reported recent cocaine use among recently admitted jail inmates (N = 375) with hair assay results screened for 90 days. Contrasts between self-reported use and hair assay results are examined with special attention to individual differences, interviewers' ratings of truthfulness for each respondent, and whether or not the respondent actually qualified as being substance dependent. Results showed that the likelihood of admitting cocaine use was positively related to having received drug misuse treatment before, and negatively related to being Hispanic. Evidence is also presented which indicates that the lower levels of disclosure among Hispanics may have been due to poorer communication. Interviewers proved to be relatively adept at discerning between truthful and nontruthful respondents. Finally, results are presented which suggest that, despite considerable underreporting among the overall sample, subjects who actually qualified as being substance dependent were much more likely to honestly report recent cocaine use.