Gene Expression Array Studies Research Articles

Abstract A161: A differentiation based therapeutic approach for KMT2A rearranged leukemia in infants and children

Abstract Introduction: Translocations in the KMT2A gene (KMT2A-r) in leukemia is an aggressive oncodriver. Currently, few therapeutic options are available for these patients and novel therapeutic strategies are urgently needed to improve outcomes. Characteristically, leukemic cells undergo a differentiation block at an early stage of development and agents that restore terminal differentiation represent an effective therapeutic strategy. Based on the initial reports that the inhibition of the Menin-KMT2A fusion is a potent inducer of leukemic cell differentiation, we sought to study a novel treatment approach to enhance the current treatment outcomes in KMT2A-r leukemia. Methods: Pediatric leukemia cells with and without KMT2A-r were studied. Differentiation was induced by the Menin inhibitor MI-463 for 12 days, followed by assessment of differentiation on day 6 and day 12 by Giemsa-Wright staining and visualization using the Infinity analyzer software. In the next set of experiments, the differentiated and undifferentiated cells were treated with common anti-leukemic chemotherapeutic agents and the induction of apoptosis and target modulation analyses were carried out by Annexin/PI staining and immunoblotting. The differentiated cells were also treated with a panel of 220 FDA approved agents, targeting diverse oncogenic pathways to generate a sensitivity signature specific to the differentiated cells. Gene expression array studies were used to identify differentially expressed genes in the two cell populations. Results: The KMT2A-r leukemia cells showed increased dose dependent sensitivity to MI-463. The highest drug sensitivity was exhibited by the infant leukemia cell line MV4-11. At 1µM, no significant loss of cell viability was noted but the rate of proliferation was significantly decreased compared to DMSO control, providing optimal conditions for differentiation. Leukemic cells cultured with MI-463 showed characteristic morphological changes of differentiation including vacuolated cytoplasm, kidney shaped nuclei and decreased nuclei to cytoplasmic ratio. Importantly, we found that the differentiated cells showed a similar chemosensitivity pattern but the sensitivity to AraC was greatly reduced. For example, in MV4-11 cells, IC50 was 170 nM compared to 8 nM in undifferentiated cells. Directed drug screen and differential gene expression studies identified specific growth and survival pathways that can be positively targeted in differentiated cells. Discussion: Data presented demonstrate the activity of MI-463 to induce cell death as well as to initiate differentiation in KMT2A-r cells. We further characterize the sensitivity profile of current chemotherapeutic agents for multi-agent treatment regimens and identify novel agents to optimize future treatment protocols. Differential gene expression analyses were used to understand the potential mechanisms of therapeutic vulnerabilities in these cells. Our results provide the first preclinical evidence to select agents and combinations to improve the outcomes in KMT2A-r leukemia in children. Citation Format: Ritul Sharma, Aru Narendran. A differentiation based therapeutic approach for KMT2A rearranged leukemia in infants and children [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A161.

HNF1β-associated cyst development and electrolyte disturbances are not explained by BAIAP2L2 expression.

Mutations or deletions in transcription factor hepatocyte nuclear factor 1 homeobox β (HNF1β) cause renal cysts and/or malformation, maturity-onset diabetes of the young and electrolyte disturbances. Here, we applied a comprehensive bioinformatic approach on ChIP-seq, RNA-seq, and gene expression array studies to identify novel transcriptional targets of HNF1β explaining the kidney phenotype of HNF1β patients. We identified BAR/IMD Domain Containing Adaptor Protein 2 Like 2 (BAIAP2L2), as a novel transcriptional target of HNF1β and validated direct transcriptional activation of the BAIAP2L2 promoter by a reporter luciferase assay. Using mass spectrometry analysis, we show that BAIAP2L2 binds to other members of the I-BAR domain-containing family: BAIAP2 and BAIAP2L1. Subsequently, the role of BAIAP2L2 in maintaining epithelial cell integrity in the kidney was assessed using Baiap2l2 knockout cell and mouse models. Kidney epithelial cells lacking functional BAIAP2L2 displayed normal F-actin distribution at cell-cell contacts and formed polarized three-dimensional spheroids with a lumen. In vivo, Baiap2l2 knockout mice displayed normal kidney and colon tissue morphology and serum and urine electrolyte concentrations were not affected. Altogether, our study is the first to characterize the function of BAIAP2L2 in the kidney in vivo and we report that mice lacking BAIAP2L2 exhibit normal electrolyte homeostasis and tissue morphology under physiological conditions.

BNIP3L/Nix-induced mitochondrial fission, mitophagy, and impaired myocyte glucose uptake are abrogated by PRKA/PKA phosphorylation

ABSTRACT Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor BNIP3L/Nix is responsive to lipotoxicity and accumulates in response to a high-fat (HF) feeding. To provide a better understanding of this observation, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the reported roles of these phospholipids and BNIP3L in mitochondrial dynamics, we investigated aberrant mitochondrial turnover as a mechanism of impaired myocyte insulin signaling. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that BNIP3L accumulation triggers mitochondrial depolarization, calcium-dependent activation of DNM1L/DRP1, and mitophagy. In addition, BNIP3L can inhibit insulin signaling through activation of MTOR-RPS6KB/p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and RHEB. Finally, we demonstrate that BNIP3L-induced mitophagy and impaired glucose uptake can be reversed by direct phosphorylation of BNIP3L by PRKA/PKA, leading to the translocation of BNIP3L from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of BNIP3L, mitochondrial turnover, and impaired myocyte insulin signaling during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggest a mechanism by which exercise or pharmacological activation of PRKA may overcome myocyte insulin resistance. Abbreviations: BCL2: B cell leukemia/lymphoma 2; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; DNM1L/DRP1: dynamin 1-like; FUNDC1: FUN14 domain containing 1; IRS1: insulin receptor substrate 1; MAP1LC3A/LC3: microtubule-associated protein 1 light chain 3 alpha; MFN1: mitofusin 1; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; OPA1: OPA1 mitochondrial dynamin like GTPase; PDE4i: phosphodiesterase 4 inhibitor; PLD1: phospholipase D1; PLD6: phospholipase D family member 6; PRKA/PKA: protein kinase, AMP-activated; PRKCD/PKCδ: protein kinase C, delta; PRKCQ/PKCθ: protein kinase C, theta; RHEB: Ras homolog enriched in brain; RPS6KB/p70S6K: ribosomal protein S6 kinase; SQSTM1/p62: sequestosome 1; YWHAB/14-3-3β: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta

Array data extractor (ADE): a LabVIEW program to extract and merge gene array data

BackgroundLarge data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists.FindingsHere, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets.ConclusionsAlthough existing software allows for complex data analyses, the LabVIEW based program presented here, “Array Data Extractor (ADE)”, provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge.

Differentially Expressed Genes in the Pre-Eclamptic Placenta: A Systematic Review and Meta-Analysis

ObjectiveTo systematically review the literature on human gene expression data of placental tissue in pre-eclampsia and to characterize a meta-signature of differentially expressed genes in order to identify novel putative diagnostic markers.Data SourcesMedline through 11 February 2011 using MeSH terms and keywords related to placenta, gene expression and gene expression arrays; GEO database using the term “placent*”; and reference lists of eligible primary studies, without constraints.MethodsFrom 1068 studies retrieved from the search, we included original publications that had performed gene expression array analyses of placental tissue in the third trimester and that reported on differentially expressed genes in pre-eclampsia versus normotensive controls. Two reviewers independently identified eligible studies, extracted descriptive and gene expression data and assessed study quality. Using a vote-counting method based on a comparative meta-profiling algorithm, we determined a meta-signature that characterizes the significant intersection of differentially expressed genes from the collection of independent gene signatures.ResultsWe identified 33 eligible gene expression array studies of placental tissue in the 3rd trimester comprising 30 datasets on mRNA expression and 4 datasets on microRNA expression. The pre-eclamptic placental meta-signature consisted of 40 annotated gene transcripts and 17 microRNAs. At least half of the mRNA transcripts encode a protein that is secreted from the cell and could potentially serve as a biomarker.ConclusionsIn addition to well-known and validated genes, we identified 14 transcripts not reported previously in relation to pre-eclampsia of which the majority is also expressed in the 1st trimester placenta, and three encode a secreted protein.

Molecular and clinicopathological markers of prognosis in breast cancer

A vast body of research in breast cancer prognostication has accumulated. Yet despite this, patients within current prognostic categories may have significantly different outcomes. There is a need to more accurately divide those cancer types associated with an excellent prognosis from those requiring more aggressive therapy. Gene expression array studies have revealed the numerous molecular breast cancer subtypes that are associated with differing outcomes. Furthermore, as next generation technologies evolve and further reveal the complexities of breast cancer, it is likely that existing prognostic approaches will become progressively refined. Future prognostication in breast cancer requires a morphomolecular, multifaceted approach involving the assessment of anatomical disease extent and levels of protein, DNA and RNA expression. One of the major challenges in prognostication will be the integration of potential assays into existing clinical systems and identification of appropriate patient subgroups for analysis.

Treatment of Triple-Negative Breast Cancer Using Anti-EGFR–Directed Radioimmunotherapy Combined with Radiosensitizing Chemotherapy and PARP Inhibitor

Triple-negative breast cancer (TNBC) is associated with poor survival. Chemotherapy is the only standard treatment for TNBC. The prevalence of BRCA1 inactivation in TNBC has rationalized clinical trials of poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors. Similarly, the overexpression of epidermal growth factor receptor (EGFR) rationalized anti-EGFR therapies in this disease. However, clinical trials using these 2 strategies have not reached their promise. In this study, we used EGFR as a target for radioimmunotherapy and hypothesized that EGFR-directed radioimmunotherapy can deliver a continuous lethal radiation dose to residual tumors that are radiosensitized by PARP inhibitors and chemotherapy. We analyzed EGFR messenger RNA in published gene expression array studies and investigated EGFR protein expression by immunohistochemistry in a cohort of breast cancer patients to confirm EGFR as a target in TNBC. Preclinically, using orthotopic and metastatic xenograft models of EGFR-positive TNBC, we investigated the effect of the novel combination of (177)Lu-labeled anti-EGFR monoclonal antibody, chemotherapy, and PARP inhibitors on cell death and the survival of breast cancer stem cells. In this first preclinical study of anti-EGFR radioimmunotherapy in breast cancer, we found that anti-EGFR radioimmunotherapy is safe and that TNBC orthotopic tumors and established metastases were eradicated in mice treated with anti-EGFR radioimmunotherapy combined with chemotherapy and PARP inhibitors. We showed that the superior response to this triple-agent combination therapy was associated with apoptosis and eradication of putative breast cancer stem cells. Our data support further preclinical investigations toward the development of combination therapies using systemic anti-EGFR radioimmunotherapy for the treatment of recurrent and metastatic TNBC.

The epigenetics of Alzheimer's disease — additional considerations

The critical commentaries following our review of the epigenetics of Alzheimer's disease (AD) amplify a number of key points with respect to the role of 1-carbon metabolism, the phenomenon of allele-specific methylation, the potentially critical explanatory link provided by epigenetic mechanisms for genome-wide association and large-scale gene expression array studies, and new therapeutic approaches afforded by epigenetic manipulation in Alzheimer's disease.

Abstract 1561: The white adipose tissue is a rich reservoir of two distinct CD34+ mesenchymal and endothelial progenitor populations with a catalytic role in cancer progression

Abstract A catalytic role has been proposed in neoplastic angiogenesis and cancer progression for bone marrow-derived circulating endothelial progenitors (CEPs). However, in preclinical and clinical studies the quantitative role of marrow-derived CEPs in cancer vascularization was found to be extremely variable. We have found that the human and murine white adipose tissue (WAT) is a very rich reservoir (containing a mean of 320 times more CD45-CD34+ progenitors/mL than the marrow) of two distinct CD45-CD34+ perivascular cell populations with mesenchymal and endothelial differentiation potential. When compared to marrow-derived CD34+ cells in gene expression array studies, purified WAT-CD34+ cells expressed similar levels of stemness-related genes such as Nanog, Sox2, Lin28 and others, and significantly increased levels of angiogenesis-related genes such as CD144, VEGFR2, ALK1 and others. In vitro the two WAT-CD34+ human populations generated fibroblasts, mature mesenchymal cells and mature endothelial cells and endothelial tubes. In aging mice, the number of WATCD34+ cells significantly declined in some WAT compartments but not in the mammary fat pad. When compared to marrow-derived progenitor cells, WAT-CD34+ cells expressed significantly increased (8 fold) levels of FAP-alpha, a crucial suppressor of anti-tumor immunity (Kraman et al, Science 2010). The co-injection of human WATCD34+ cells from lipofilling procedures significantly increased tumor growth and metastases in orthotopic models of human breast cancer in NSG mice, where human WATCD34+ cells contributed to tumor stroma and vascularization. A novel brain/adipocyte-BDNF/leptin axis has been recently proposed to play a potentially relevant role in cancer progression (Cao et al, Cell 2010). WATCD34+ progenitors express high levels of the receptors involved in this axis and our studies suggest a catalytic role in cancer progression and metastases. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1561. doi:10.1158/1538-7445.AM2011-1561

Altered expression of middle and inner ear cytokines in mouse otitis media

The inner ear is at risk for sensorineural hearing loss in both acute and chronic otitis media (OM), but the mechanisms underlying sensorineural hearing loss are unknown. Previous gene expression array studies have shown that cytokine genes might be upregulated in the cochleas of mice with acute and chronic OM. This finding implies that the inner ear could manifest a direct inflammatory response to OM that may cause sensorineural damage. Therefore, to better understand inner ear cytokine gene expression during OM, quantitative real-time polymerase chain reaction and immunohistochemistry were used in mouse models to evaluate middle and inner ear inflammatory and remodeling cytokines. Basic science experiment. An acute OM model was created in Balb/c mice by a transtympanic injection of Streptococcus pneumoniae in one ear; the other ear was used as a control. C3H/HeJ mice were screened for unilateral chronic OM, with the noninfected ear serving as a control. Both acute and chronic OM caused both the middle ear and inner tissues in these two mouse models to overexpress numerous cytokine genes related to tissue remodeling (tumor necrosis factor-α, bone morphogenetic proteins, fibroblast growth factors) and angiogenesis (vascular endothelial growth factor), as well as inflammatory cell proliferation (interleukin [IL]-1α,β, IL-2, IL-6). Immunohistochemistry confirmed that both the middle ear and inner ear tissues expressed these cytokines. Cochlear tissues are capable of expressing cytokine mRNA that contributes to the inflammation and remodeling that occur in association with middle ear disease. This provides a potential molecular basis for the transient and permanent sensorineural hearing loss often reported with acute and chronic OM.

SAFB1 Mediates Repression of Immune Regulators and Apoptotic Genes in Breast Cancer Cells

The scaffold attachment factors SAFB1 and SAFB2 are paralogs, which are involved in cell cycle regulation, apoptosis, differentiation, and stress response. They have been shown to function as estrogen receptor corepressors, and there is evidence for a role in breast tumorigenesis. To identify their endogenous target genes in MCF-7 breast cancer cells, we utilized a combined approach of chromatin immunoprecipitation (ChIP)-on-chip and gene expression array studies. By performing ChIP-on-chip on microarrays containing 24,000 promoters, we identified 541 SAFB1/SAFB2-binding sites in promoters of known genes, with significant enrichment on chromosomes 1 and 6. Gene expression analysis revealed that the majority of target genes were induced in the absence of SAFB1 or SAFB2 and less were repressed. Interestingly, there was no significant overlap between the genes identified by ChIP-on-chip and gene expression array analysis, suggesting regulation through regions outside the proximal promoters. In contrast to SAFB2, which shared most of its target genes with SAFB1, SAFB1 had many unique target genes, most of them involved in the regulation of the immune system. A subsequent analysis of the estrogen treatment group revealed that 12% of estrogen-regulated genes were dependent on SAFB1, with the majority being estrogen-repressed genes. These were primarily genes involved in apoptosis, such as BBC3, NEDD9, and OPG. Thus, this study confirms the primary role of SAFB1/SAFB2 as corepressors and also uncovers a previously unknown role for SAFB1 in the regulation of immune genes and in estrogen-mediated repression of genes.

Altered retinoic acid (RA)‐induced lineage specification of mouse embryonic stem cells (mESCs) following a transient pulse of a histone deacetylase inhibitor.

RA treatment during mESC differentiation results in predominantly neural specification. A transient pulse of the histone deacetylase inhibitor, Trichostatin A (TSA), during early mESC differentiation via embryoid body (EB) formation results in maintenance of undifferentiated characteristics. Our objective was to determine whether a pulse of TSA followed by RA alters neural lineage specification. Undifferentiated mESCs are exposed to 100 nM of TSA during the first 24h of 3 days of EB formation. EBs are plated and RA added for an additional 4 days. Selected RT‐PCR shows repressed neural marker expression and only a small increase in a few endoderm markers. Gene expression array studies analyzed using a lineage annotated gene database demonstrates a marked increase in expression of numerous placental genes and confirms diminished neural gene expression. Immunofluorescence for the trophoblast marker Plac1, shows increased levels in TSA‐pulsed, RA‐treated cells with minimal expression in RA‐only differentiated cells. Conversely, the neural specific product, Doublecortin, is highly expressed in the RA‐only treated cells and shows diminished protein levels in TSA‐pulsed, RA‐treated cells. We conclude that transient TSA treatment prior to RA induces a dramatic lineage switch characterized by repressed neural differentiation and marked trophoblast induction. Supported by NIH grant RO1DK064243 to MKF.

Bayesian Unsupervised Learning with Multiple Data Types

We propose Bayesian generative models for unsupervised learning with two types of data and an assumed dependency of one type of data on the other. We consider two algorithmic approaches, based on a correspondence model, where latent variables are shared across datasets. These models indicate the appropriate number of clusters in addition to indicating relevant features in both types of data. We evaluate the model on artificially created data. We then apply the method to a breast cancer dataset consisting of gene expression and microRNA array data derived from the same patients. We assume partial dependence of gene expression on microRNA expression in this study. The method ranks genes within subtypes which have statistically significant abnormal expression and ranks associated abnormally expressing microRNA. We report a genetic signature for the basal-like subtype of breast cancer found across a number of previous gene expression array studies. Using the two algorithmic approaches we find that this signature also arises from clustering on the microRNA expression data and appears derivative from this data.

HDAC Inhibitor Plus Doxorubicin Combinations Reverse Apoptosis Resistance in Myeloma Cells by Triggering Cathepsin-Mediated Bax Activation

Combining drugs that inhibit different antiapoptotic pathways will be useful in overcoming drug resistance in multiple myeloma (MM). Since histone deacetylase inhibitors (HDACi) affect multiple pathways of cancer progression by relaxing chromatin; their ability to reverse apoptosis resistance in MM in combination with a DNA damaging agent (doxorubicin) was investigated. Sodium butyrate (SB) (0.15 mM, 0.3 mM and 0.6 mM) and vorinostat (0.3 uM and 0.6 μM) were used as HDACi and doxorubicin (10 nM, 20 nM and 40 nM) was used as a DNA damaging agent. Percent survival of fresh MM cells was assessed with flow cytometry and viability of MM cell lines (NCI H929, RPMI 8226 and U266) was measured with alamar blue. Molecular mechanisms of synergy between HDACi and doxorubicin were characterized in MM cell lines using TUNEL assay for apoptosis, immunofluorescence microscopy for apoptosis-inducing factor (AIF) release and Bax conformational change. Cathepsin B (Cat B) and calpain activity were measured using kits from Biovision Inc. Gene expression array studies were carried out using Human V6 Illumina chip. Treatment of mononuclear cells containing stromal and plasma cells (CD138+) from bone marrow aspirates of 22 patients with SB (0.6 mM), doxorubicin (40 nM) or with their combinations for 72 hr markedly decreased the percentage survival of CD138+ cells. One way repeated measures of ANOVA showed a significant (P<0.0001) reduction in percentage of CD138+ survival by combination treatment with mean survival 47.9+6.6% vs. 73.6+5.3% (SB) or 83.8+4.3% (doxorubicin) as single agents. Similarly, vorinostat, a clinically relevant HDACi in combination with doxorubicin also markedly reduced the percentage survival of fresh MM cells further suggesting the clinical relevance of the drug combinations evaluated. Although combinations of SB and doxorubicin synergistically (with a combination index of <1 in Chou and Talalay analysis) reduced the viability of all MM cell lines, combination treatment induced marked apoptosis only in 3 out of 5 MM cell lines tested (Figure 1). Studies undertaken to understand the molecular basis of differential apoptosis sensitivity revealed that SB plus doxorubicin induced apoptosis in a caspase independent manner and differential release of AIF and Endonuclease G from mitochondria correlated with differential sensitivity. Among various proapoptotic factors analyzed, activation and mitochondrial translocation of Bax was found to be associated with AIF release in co-localization studies (Figure 2). SB plus doxorubicin induced Bax activation in a caspase independent manner by synergistically increasing the activity of Cat B. Thioredoxin an inhibitor of Cathepsin is overexpressed in tumor cells including MM. Studies have shown that Thioredoxin and its inhibitory protein thioredoxin interacting protein (TXIN) were induced by doxorubicin and HDACi respectively. Consistent with this, in gene expression array studies, relative to NCI H929 and U266 cells, mRNA levels of TXIN were 2X higher in apoptosis sensitive RPMI 8226 cells and were further increased another 3X by vorinostat. In apoptosis resistant NCI H929 and U266 cells vorinostat failed to upregulate TXIN. These results support a model for HDACi plus doxorubicin induced caspase independent apoptosis in MM by an increase in expression of Cathepsin and TXIN with a concurrent decrease in thioredoxin. Under this condition the activity calpain, a lysosomal enzyme that is also capable of activating Bax remained unchanged. More importantly, in apoptosis resistant cell lines (NCI H929 and U266) HDACi plus doxorubicin combination failed to increase Cat B activity, conformational change of Bax and mitochondrial release of AIF. A block in the pathway defined here may lead to development of resistance in MM to HDAC inhibitors or doxorubicin. [Display omitted] [Display omitted]

Akt Inhibitor A-443654 Interferes with Mitotic Progression by Regulating Aurora A Kinase Expression

Both Akt and Aurora A kinase have been shown to be important targets for intervention for cancer therapy. We report here that Compound A (A-443654), a specific Akt inhibitor, interferes with mitotic progression and bipolar spindle formation. Compound A induces G2/M accumulation, defects in centrosome separation, and formation of either monopolar arrays or disorganized spindles. On the basis of gene expression array studies, we identified Aurora A as one of the genes regulated transcriptionally by Akt inhibitors including Compound A. Inhibition of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, either by PI3K inhibitor LY294002 or by Compound A, dramatically inhibits the promoter activity of Aurora A, whereas the mammalian target of rapamycin inhibitor has little effect, suggesting that Akt might be responsible for up-regulating Aurora A for mitotic progression. Further analysis of the Aurora A promoter region indicates that the Ets element but not the Sp1 element is required for Compound A-sensitive transcriptional control of Aurora A. Overexpression of Aurora A in cells treated with Compound A attenuates the mitotic arrest and the defects in bipolar spindle formation induced by Akt inhibition. Our studies suggest that that Akt may promote mitotic progression through the transcriptional regulation of Aurora A.

Zebrafish as a Cancer Model

The zebrafish has developed into an important model organism for biomedical research over the last decades. Although the main focus of zebrafish research has traditionally been on developmental biology, keeping and observing zebrafish in the lab led to the identification of diseases similar to humans, such as cancer, which subsequently became a subject for study. As a result, about 50 articles have been published since 2000 in which zebrafish were used as a cancer model. Strategies used include carcinogenic treatments, transplantation of mammalian cancer cells, forward genetic screens for proliferation or genomic instability, reverse genetic target-selected mutagenesis to inactivate known tumor suppressor genes, and the generation of transgenics to express human oncogenes. Zebrafish have been found to develop almost any tumor type known from human, with similar morphology and, according to gene expression array studies, comparable signaling pathways. However, tumor incidences are relatively low, albeit highly comparable between different mutants, and tumors develop late in life. In addition, tumor spectra are sometimes different when compared with mice and humans. Nevertheless, the zebrafish model has created its own niche in cancer research, complementing existing models with its specific experimental advantages and characteristics. Examples of these are imaging of tumor progression in living fish by fluorescence, treatment with chemical compounds, and screening possibilities not only for chemical modifiers but also for genetic enhancers and suppressors. This review aims to provide a comprehensive overview of the state of the art of zebrafish as a model in cancer research. (Mol Cancer Res 2008;6(5):685-94).

Heterogeneity of breast cancer and implications of adjuvant chemotherapy

Historically, in selecting adjuvant chemotherapy for patients with breast cancer, anatomy, including tumor size and nodal status, has played the primary role. As a result of analyses of genomic and clinical data, breast cancers are now thought to be a family of diseases. Major subtypes of breast cancer include HER-2 positive disease, basal-like or triple negative tumors, and at least two types of hormonally sensitive cancers. Using the nomenclature developed in the gene expression array studies, these two types are often referred to as luminal A and luminal B. Estrogen receptor negative tumors relapse earlier than estrogen receptor positive tumors. In general, estrogen receptor negative cancers are also more responsive to chemotherapy. In contrast, estrogen positive tumors appear to be somewhat less responsive to chemotherapy, but endocrine therapy can be of substantial benefit in decreasing the risk of disease recurrence. Women with HER-2 positive disease derive significant benefit with the use of trastuzumab. The role of chemotherapy in preventing disease recurrence in patients with estrogen receptor positive tumors is being reevaluated. Recent data suggests that chemotherapy has the greatest benefit in those patients with estrogen receptor positive cancers whose tumors are HER-2 positive disease, weakly ER positive, and/or have high nuclear grade. In the future, breast cancer treatment will be more targeted to the tumor and tailored to the individual with the use of genomic and clinical data.

Bayesian sparse hidden components analysis for transcription regulation networks

In systems like Escherichia Coli, the abundance of sequence information, gene expression array studies and small scale experiments allows one to reconstruct the regulatory network and to quantify the effects of transcription factors on gene expression. However, this goal can only be achieved if all information sources are used in concert. Our method integrates literature information, DNA sequences and expression arrays. A set of relevant transcription factors is defined on the basis of literature. Sequence data are used to identify potential target genes and the results are used to define a prior distribution on the topology of the regulatory network. A Bayesian hidden component model for the expression array data allows us to identify which of the potential binding sites are actually used by the regulatory proteins in the studied cell conditions, the strength of their control, and their activation profile in a series of experiments. We apply our methodology to 35 expression studies in E.Coli with convincing results. www.genetics.ucla.edu/labs/sabatti/software.html The supplementary material are available at Bioinformatics online.