NOTCH Signaling Limits the Response of Low-Grade Serous Ovarian Cancers to MEK Inhibition

Low-grade serous ovarian cancer (LGSOC) is a rare subtype of epithelial ovarian cancer with high fatality rates in advanced stages due to its chemoresistant properties. LGSOC is characterized by activation of MAPK signaling, and recent clinical trials indicate that the MEK inhibitor (MEKi) trametinib may be a good treatment option for a subset of patients. Understanding MEKi-resistance mechanisms and subsequent identification of rational drug combinations to suppress resistance may greatly improve LGSOC treatment strategies. Both gain-of-function and loss-of-function CRISPR-Cas9 genome-wide libraries were used to screen LGSOC cell lines to identify genes that modulate the response to MEKi. Overexpression of MAML2 and loss of MAP3K1 were identified, both leading to overexpression of the NOTCH target HES1, which has a causal role in this process as its knockdown reversed MEKi resistance. Interestingly, increased HES1 expression was also observed in selected spontaneous trametinib-resistant clones, next to activating MAP2K1 (MEK1) mutations. Subsequent trametinib synthetic lethality screens identified SHOC2 downregulation as being synthetic lethal with MEKis. Targeting SHOC2 with pan-RAF inhibitors (pan-RAFis) in combination with MEKi was effective in parental LGSOC cell lines, in MEKi-resistant derivatives, in primary ascites cultures from patients with LGSOC, and in LGSOC (cell line-derived and patient-derived) xenograft mouse models. We found that the combination of pan-RAFi with MEKi downregulated HES1 levels in trametinib-resistant cells, providing an explanation for the synergy that was observed. Combining MEKis with pan-RAFis may provide a promising treatment strategy for patients with LGSOC, which warrants further clinical validation.

Visual cues added to a virtual environment paradigm do not improve motor arrests in Parkinson's disease

Objective. Elucidating how cueing alleviates freezing of gait (FOG) in Parkinson's disease (PD) would enable the development of more effective, personalized cueing strategies. Here, we aimed to validate a visual cueing virtual environment (VE) paradigm for future use in e.g. neuroimaging studies and behavioral studies on motor timing and scaling in PD patients with FOG.Approach. We included 20 PD patients with FOG and 16 age-matched healthy control subjects. Supine participants were confronted with a VE displaying either no cues, bars or staircases. They navigated forward using alternate suppression of foot pedals. Motor arrests (as proxy for FOG), and measures of motor timing and scaling were compared across the three VE conditions for both groups.Main results. VE cues (bars and staircases) did not reduce motor arrests in PD patients and healthy control subjects. The VE cues did reduce pedal amplitude in healthy control subjects, without effects on other motor parameters.Conclusion. We could not validate a visual cueing VE paradigm to study FOG. The VE cues possibly failed to convey the necessary spatial and temporal information to support motor timing and scaling. We discuss avenues for future research.

Hormone receptor expression and outcomes in low-grade serous ovarian carcinoma

OBJECTIVE

Low-grade serous ovarian carcinomas (LGSC) are frequently ER/PR positive, though the mechanisms by which ER/PR regulate prognosis or anti-estrogen treatment efficacy are poorly understood. We studied ER/PR expression in LGSC tumors and cell lines to evaluate patient outcomes and cellular treatment responses.

METHODS

LGSC tumors and patient-derived cell lines were studied from patients with advanced-stage (III/IV) disease. Tumor samples and clinical data were obtained from the Canadian Ovarian Experimental Unified Resource (COEUR-tissue microarray) and the Ovarian Cancer Research (OvCaRe) tissue bank. ER/PR expression was assessed by both Western blot and immunohistochemistry (IHC). Two different IHC scoring systems (simple and Allred) were used. Cox regression was used to identify factors (age, disease residuum, ER/PR status, etc.) associated with progression-free (PFS) and overall survival (OS). Estradiol and tamoxifen proliferation and viability experiments were performed in LGSC cell lines.

RESULTS

In 55 LGSC cases studied, median follow-up was 56 months (range 1-227). Fifty-three (96%) cases strongly expressed ER whereas 37 (67%) expressed PR. Cox-regression analysis showed that residuum (p < 0.001) was significantly associated with PFS, whereas both ER Allred score (p = 0.005) and residuum (p = 0.004) were significant for OS. None of the LGSC cell lines expressed PR. Loss of PR and ER expression over time was detected in LGSC tumors and cell lines respectively. Estrogen and tamoxifen treatment did not alter LGSC cell proliferation or viability in-vitro.

CONCLUSIONS

In patients with advanced LGSC, higher ER Allred scores were significantly associated with better overall survival. ER/PR expression changed over time in both LGSC tumors and cell lines. Better translational research models are needed to elucidate the molecular mechanisms of ER/PR signalling in LGSC.

Validation of the Auditory Stroop Task to increase cognitive load in walking tasks in healthy elderly and persons with Parkinson's disease

Background

The development of treatments for freezing of gait (FOG) in Parkinson’s disease (PD) requires experimental study set-ups in which FOG is likely to occur, and is amenable to therapeutic interventions. We explore whether the ‘Auditory Stroop Task’ (AST) can be used to increase cognitive load (and thereby elicit FOG), simultaneously with visual cues (as a therapeutic intervention for FOG). We additionally examined how these two contrasting effects might interact in affecting gait and FOG parameters.

Objectives

We investigated whether: (1) the ‘Auditory Stroop Task’ (AST) influences gait in healthy elderly and persons with PD who experience FOG, and increases the frequency of FOG events among PD patients; (2) the AST and visual cues interact; and (3) different versions of the AST exert different cognitive loads.

Methods

In ‘Experiment 1’, 19 healthy elderly subjects performed a walking task while performing a high and low load version of the AST. Walking with a random numbers task, and walking without cognitive load served as control conditions. In ‘Experiment 2’, 20 PD patients with FOG and 18 healthy controls performed a walking task with the AST, and no additional cognitive load as control condition. Both experiments were performed with and without visual cues. Velocity, cadence, stride length, and stride time were measured in all subjects. FOG severity was measured in patients.

Results

Compared to the control conditions, the AST negatively affected all gait parameters in both patients and controls. The AST did not increase the occurrence of FOG in patients. Visual cues reduced the decline in stride length induced by cognitive load in both groups. Both versions of the AST exerted similar effects on gait parameters in controls.

Conclusions

The AST is well-suited to simulate the effects of cognitive load on gait parameters, but not FOG severity, in gait experiments in persons with PD and FOG.

Blood flow velocity measured using the Retinal Function Imager predicts successful ranibizumab treatment in neovascular age-related macular degeneration: early prospective cohort study

PURPOSE

Anti-VEGF treatment has a potent vasoconstrictive effect. Early changes of retinal blood flow velocity (RBFV) measured using the Retinal Function Imager (RFI) combined with indicators of vascular status may help in predicting the visual outcome 1 month post injection in patients with neovascular age-related macular degeneration (nvAMD) under ranibizumab treatment. To develop a simple prediction model based on the change in RBFV 3 days post injection and indicators of a patient's vascular status to assess the probability of a successful visual outcome 1 month post injection.

METHODS

RBFV measured using RFI were prospectively collected pre-injection and 3 days post injection in 18 eyes of 15 patients. Indicators of vascular status (history of hypertension, diabetes mellitus without retinal affection, and smoking) were assessed by medical history. By univariate analyses, parameters associated with visual outcome were weighted (-1 to 6 points). A multivariate logistic regression model with the categorized visual outcome parameter (≥0 letters gained after 1 month) as the dependent variate and the sum score as the independent variate (continuous scale) was used to estimate the score value-specific probabilities of letters gained ≥0 1 month post injection.

RESULTS

The indicators of vascular status negatively influenced the likelihood of a letter gain ≥0 whereas an increase in the arterial RBFV strongly increased it. The area under the receiver operating characteristics curve for these parameters investigated was 0.71 (95% CI: 0.43-1.00).

CONCLUSION

Changes in the arterial RBFV following 3 days after ranibizumab injection combined with three indicators of the vascular status identified nvAMD patients with favorable visual outcome accurately.

Porphyromonas gingivalis, Treponema denticola and toll-like receptor 2 are associated with hypertensive disorders in placental tissue: a case-control study

AIM(S)

To explore the associations between the presence of periodontal pathogens and the expression of toll-like receptors (TLR-2 and TLR-4) in the placental tissue of patients with hypertensive disorders compared to the placentas of healthy normotensive patients.

MATERIAL AND METHODS

A case-control study was performed. From a cohort composed of 126 pregnant women, 33 normotensive healthy pregnant women were randomly selected, and 25 cases of patients with hypertensive disorders of pregnancy, including gestational hypertension and pre-eclampsia, were selected. Placental biopsy was obtained after aseptic placental collection at the time of delivery. All of the samples were processed and analysed for the detection of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Treponema denticola and Tannerella forsythia using the polymerase chain reaction (PCR) technique. Determination of the expressions of TLR-2 and TLR-4 was performed in samples of total purified protein isolated from placental tissues and analysed by ELISA. The data were assessed using descriptive statistics. The associations among variables were estimated through multiple logistic regression models and the Mann-Whitney test to evaluate the differences between the two groups.

RESULTS

A significant increase was observed in the expression of TLR-2 in the placentas of patients with hypertensive disorders (p = 0.04). Additionally, the multiple logistic regression models demonstrated an association between the presence of T. denticola and P. gingivalis in placental tissues and hypertensive disorders (OR: 9.39, p = 0.001, CI 95% 2.39-36.88 and OR: 7.59, p = 0.019, CI 95% 1.39-41.51, respectively).

CONCLUSIONS

In the present study, pregnant women with periodontal disease presented an association in the placental tissue between the presence of T. denticola and P. gingivalis and hypertensive disorders. Additionally, increased expression of TLR-2 was observed. However, further studies are required to determine the specific roles of periodontal pathogens and TLRs in the placental tissue of patients with pregnancy-related hypertensive disorders.

Abstract P4-02-12: Genomic Evolution of Endocrine-Resistant Breast Cancer Cell Lines Reveals Molecular Aberrations Consistent with Biological Phenotype

Suppression of estrogen synthesis using aromatase inhibitors (AIs) is highly effective in the treatment of postmenopausal women with estrogen receptor alpha-positive (ER+) breast cancer. Third generation AIs are superior to adjuvant tamoxifen resulting in improved disease-free survival and a lower incidence of side effects. Unfortunately, one of the consequences of long-term estrogen deprivation or exhaustive endocrine therapy is the development of drug resistance. We and others have shown that acquisition of resistance to long term estrogen deprivation or to selective estrogen receptor modulators (SERMs) in breast cancer cells is accompanied by an increase in malignant cell behavior. The Jordan Laboratory has developed in vitro and in vivo models of endocrine-resistant breast cancer that mimic pathobiology observed in anti-hormone refractory breast tumors. MCF-7:5C and MCF-7:2A are two ER+ human breast cancer cell lines derived from long term estrogen deprivation of hormone-dependent MCF-7 cells. MCF-7:TAM2 and MCF-7:RAL2 are also ER+ derivatives of MCF-7 that are resistant to tamoxifen and raloxifene, respectively. These models of resistance share several phenotypic and molecular characteristics, which differ dramatically from the isogenic parental line. Differences include robust growth in estrogen-deprived medium, mesenchymal morphology, and increased invasiveness and motility in vitro. They also exhibit elevated AKT activity, loss of E-cadherin, and additional molecular markers consistent with malignant progression. We have conducted an array-based genomic study to elucidate molecular mechanisms associated with development of endocrine resistance in each model. We observed a high degree of genomic evolution in all endocrine-resistant models. Several regions of common genomic aberration were observed in the MCF-7:5C and MCF-7:2A cells that indicate significant deregulation of glycolysis and glucose metabolism, a metabolic process known to be driven by activated AKT. Gene ontology analysis of genes differentially expressed by both MCF-7:5C and MCF-7:2A also highlighted deregulated AKT signaling and cell cycle control in these cells. Interestingly, amplification of the estrogen receptor 1 (ESR1) gene, which encodes estrogen receptor alpha, was observed in MCF-7:5C and MCF-7:2A models but not in the SERM-resistant models supporting diversity underlying mechanisms of endocrine resistance depending on therapies used. This study indicates that biological drivers of endocrine resistance can be identified using integrated genomic and bioinformatic approaches. We are currently prioritizing the likely molecular drivers of endocrine-resistant disease using high throughput RNAi technology.

Grant support: Department of Defense Breast Program under award number BC050277 Center of Excellence (V.C. Jordan). Views and opinions of and endorsements by the author(s) do not reflect those of the U.S. Army or the Department of Defense.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-12.

In vitro assessment of AhR-mediated activities of TCDD in mixture with humic substances

Humic substances (HS) are ubiquitous natural products of decomposition of dead organic matter. HS is present in most freshwaters at concentrations ranging from 0.5 to 50mg L(-1). Organic carbon can represent 20% dry weight of sediments. Recently, the interaction of dissolved HS with the aryl hydrocarbon receptor (AhR) has been demonstrated. The AhR is a cytosolic receptor to which persistent organic pollutants (POPs) can bind and many of their toxic effects are mediated through interactions with this receptor. We describe in vitro effects (using H4IIE-luc cells) of binary mixtures of various HS with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), since in contaminated environments these compounds occur simultaneously. Six out of 12 HS samples activated AhR even at environmentally relevant concentrations (17 mg L(-1)), but did not reach the full AhR-activation even at excessive concentration. In simultaneous exposure of H4IIE-luc to HS (17 mg L(-1)) and TCDD (1.2 pM) without any preincubation prior to exposure, either significant additive or facilitative effects were observed. No negative interactions, due to possible sorption of TCDD to HS was observed. Nevertheless, if the HS-TCDD binary mixture was preincubated for 6 days prior to the exposure on H4IIE-luc cells, the additive and facilitative effects were less due to possible sorption of TCDD onto HS. Similar results were obtained from analogous experiments with greater concentrations of both TCDD and HS.

Use of independent genome-wide assays to discover HOXA signature in colon and rectal cancers and validate a role in tumorigenesis

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Background: Rectal cancer differs from colon cancer in terms of prognosis. Here we present genome-wide expression analysis of 79 colon and rectal tumors and gene dosage analysis of 34 archival colorectal tumors in paraffin (FFPE). Methods: Expression data were acquired ( http://expo.intgen.org/geo/home.do ) from Affymetrix experiments analyzed with GeneSpring software version 7.3 (Silicon Genetics, CA). Expression data were normalized ’per chip’ normalized to the 50th percentile of all values; and ’per gene’ normalized to the median expression level across all samples. Expression Project for Oncology (expO) samples included colon (n=50) and rectum (n=29). Differentially expressed genes were identified by parametric test for which variances were not assumed equal (Welch ANOVA). Array comparative genomic hybridization (aCGH) were performed separately on an independent set of FFPE colorectal tumors (n=34) by 244 K microarrays for CGH, Agilent Technologies, CA and with platform embedded analyses tools of CGH Analytics software and ADM-1 bioinformatics. Functional assay by knockout of HOXA9 promoter by lentiviral sh-RNAi construct was performed on colon cancer cell lines shown to have increased HOXA9 dosage and expression. Results: The analysis of expO colon and rectal cancers generated 42 genes with significant differential expression, 26 showed an increased expression of > 2 fold in colon versus rectal samples. Transcription factor family HOXA9 was the most highly expressed (3.8 fold) in colon versus rectal cancer. The aCGH data showed a low level gain of the HOXA gene to be the most frequent dosage alteration (38%). Validation by IHC and qRT-PCR showed 80% and 76% concordance, respectively. Functional assay by sh-RNAi in cell lines (compared to vehicle only) showed marked decrease in cellular viability (40 to 60%), marked morphologic change and a significantly increased apoptotic rate. Conclusion: Multiple genome-wide assays have identified HOXA9 as differentially dosed and expressed in colon and rectal tumors. Compelling functional data from sh-RNAi experiments suggests a tumorigenic role for HOXA9 in altered apoptosis.

No significant financial relationships to disclose.

Profiling human gene expression with cDNA microarrays

As a result of genomics initiatives worldwide, it has become increasingly easy to obtain cDNA clones representing the 3 ends of many human genes. This unit describes methods that allow these clones to be used as hybridization detectors in a highly parallel assay of gene expression. Protocols are provided for preparing cDNA microarrays, extracting RNA from cells of interest and preparing fluorescently labeled cDNA representations of the message pools, and hybridizing the labeled cDNAs to the microarrays.

Profiling human gene expression with cDNA microarrays

As a result of genomics initiatives worldwide, it has become increasingly easy to obtain cDNA clones representing the 3' ends of many human genes. This unit describes methods that allow these clones to be used as hybridization detectors in a highly parallel assay of gene expression. Protocols are provided for preparing cDNA microarrays, extracting RNA from cells of interest and preparing fluorescently labeled cDNA representations of the message pools, and hybridizing the labeled cDNAs to the microarrays.

Changes of AhR-mediated activity of humic substances after irradiation

Humic substances (HS) and natural organic matter (NOM) are natural organic compounds ubiquitous in the environment. However, some studies indicate that both HS and NOM can act as xenobiotics, e.g. induce hormone-like effects in fish, amphibians and invertebrates. Molecules of these substances contain a number of aromatic rings and conjugated double bonds--the so called chromophores. Irradiation of dissolved HS and NOM can lead to a series of photochemical reactions which can act on these substances itself, or on other substances present in aquatic environment along with HS and NOM such as e.g. xenobiotics. In our previous study, we have found significant interactions of five humic acids (HA) with cytosolic aryl hydrocarbon receptor (AhR) in an in vitro bioassay based on H4IIE-luc cells. In the present study, we have studied the changes in AhR-mediated activities both of HS and NOM after irradiation that simulated natural solar light. Nine different HS and two NOM samples were irradiated in Pyrex tubes with a medium-pressure mercury lamp for a duration of 0 to 52 h (which corresponds to 0-52 d natural solar radiation). Original concentrations of the samples were 50 mg L(-1), and the greatest concentration of HS and NOM photoproducts subsequently tested in the bioassay was 17 mg L(-1), which is an environmentally relevant concentration. After irradiation the absorbances of all the samples were less than the original materials. The AhR-mediated activity of the HA-Fluka and HA Sodium Salt were partially decreased by irradiation. The activities of other HS and NOM, that were either AhR-active or -inactive were not changed by irradiation. The results of the study demonstrate that AhR-mediated activities of two active HA is caused by both photo-stable and photo-labile AhR activators, while the other three active HA contain only photo-stable AhR activators. Potential mechanisms of the observed irradiation-induced changes in AhR-mediated activities are discussed.

Identification of therapeutic targets in angiosarcoma

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Background: Human angiosarcoma is an aggressive malignancy with ability to invade locally and metastasize widely. Even with a multimodality approach, the local recurrence rate is 81% and 5 year disease-free survival is 17% for all comers. Durability of the responses to treatment options such as paclitaxel is 4 to 5 months. Our previous work shows that enhanced cell migration and invasion are integral to the chemoresistant angiosarcoma phenotype. However the molecular mechanism of this is unknown. Methods: In order to address this and to identify new therapeutic strategies, we analyzed formalin fixed paraffin embedded (FFPE) archival angiosarcoma specimens from 17 consecutive patients at our institution to identify aberrations at the DNA level that were highly prevalent. DNA was extracted from FFPE angiosarcoma specimens using the proteinase K method. Good quality DNA with an yield more than 5 micrograms was obtained from 10 out of 17 patients and these samples were assayed for DNA dosage differences compared to genomic reference DNA using array comparative genomic hybridization. High density 244K Agilent arrays were used to evaluate these specimens to enhance the precision of the estimates in this rare disease. Results: Statistically significant (p<0.001) aberrations with prevalence greater than 50% were noted in several genes including NOTCH2, MAML1 (notch signaling intermediate), oncomodulin, calnexin, sequestosome1, zinc finger proteins and ADAMTS2. This is particularly important since Notch and its ligand Jagged are developmental genes critical to tumorigenesis and there is emerging evidence of their role in endothelial activation. Conclusions: Aberrations involving the notch signaling pathway occur with a high prevalence in angiosarcomas and may serve as a target for therapeutic intervention.

No significant financial relationships to disclose.

Chromosomal aberrations and gene expression profiles in non-small cell lung cancer

Alterations in genomic content and changes in gene expression levels are central characteristics of tumors and pivotal to the tumorigenic process. We analyzed 23 non-small cell lung cancer (NSCLC) tumors by array comparative genomic hybridization (array CGH). Aberrant regions identified included well-characterized chromosomal aberrations such as amplifications of 3q and 8q and deletions of 3p21.31. Less frequently identified aberrations such as amplifications of 7q22.3-31.31 and 12p11.23-13.2, and previously unidentified aberrations such as deletion of 11q12.3-13.3 were also detected. To enhance our ability to identify key acting genes residing in these regions, we combined array CGH results with gene expression profiling performed on the same tumor samples. We identified a set of genes with concordant changes in DNA copy number and expression levels, i.e. overexpressed genes located in amplified regions and underexpressed genes located in deleted regions. This set included members of the Wnt/beta-catenin pathway, genes involved in DNA replication, and matrix metalloproteases (MMPs). Functional enrichment analysis of the genes both overexpressed and amplified revealed a significant enrichment for DNA replication and repair, and extracellular matrix component gene ontology annotations. We verified the changes in expressions of MCM2, MCM6, RUVBL1, MMP1, MMP12 by real-time quantitative PCR. Our results provide a high resolution map of copy number changes in non-small cell lung cancer. The joint analysis of array CGH and gene expression analysis highlights genes with concordant changes in expression and copy number that may be critical to lung cancer development and progression.

AhR-mediated and antiestrogenic activity of humic substances

Humic substances (HS) were for decades regarded as inert in the ecosystems with respect to their possible toxicity. However, HS have been recently shown to elicit various adverse effects generally attributed to xenobiotics. In our study, we used MVLN and H4IIE-luc cell lines stably transfected with luciferase gene under control of estrogen receptor (ER) and Ah receptor (AhR; receptor connected with so-called dioxin-like toxicity) for assessment of anti/estrogenic and AhR-mediated effects of 12 commercially available humic substances. Out of those, five humic acids were shown to induce AhR-mediated activity with relative potencies related to TCDD 2.6 x 10(-8)-7.4 x 10(-8). Organic extracts of HS solutions also elicited high activities what means that lipophilic molecules are responsible for a great part of effect. However, relatively high activity remaining in extracted solution suggests also presence of polar AhR-agonists. Contribution of persistent organic compounds to the observed effects was ruled out by H(2)SO(4) treatment. Eight out of twelve HS elicited significant antiestrogenic effects with IC(50) ranging from 40 to 164 mg l(-1). The possible explanations of the antiestrogenic effect include sorption of 17-beta-estradiol (E2) on HS, changes in membrane permeability for E2 or another specific mechanism.

Frequency of potential therapeutic targets identified by immunohistochemistry (IHC) and DNA microarray (DMA) in tumors from patients who have progressed on multiple therapeutic agents

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An important question that arises when caring for patients referred for phase I clinical trials is, if one studied the patients’ tumors carefully enough, would there be targets in those patients’ tumors for which a therapeutic agent might already be available. Perhaps treating the patient with that therapeutic agent would be better than trying the phase I agent. To address that issue we have performed IHC assays for up to 13 targets (e.g. Her2/neu, ER, c-kit, etc.) as well as a two color Agilent oligonucleotide microarray with 17, 085 unique probes, on tumors from patients with advanced cancer who have exhausted conventional therapy and who were undergoing a procedure for a cancer related matter (e.g. obstruction, ascites, etc.). Ninety-one patients had excess tissue submitted from the procedure, immediately frozen and subjected to microarray analysis and had IHC performed on sections obtained from the paraffin blocks prepared as part of their standard surgical workup. IHC was considered positive if ≥ 30% of tumor cells were scored as +1 or greater staining. For microarray studies the gene expressions were called significantly increased or decreased if the fold change in expression relative to the nominal tissue of origin reference was significant at p≤0.001. For the 91 patients where frozen tumor was submitted 89 (98%) of them had RNA that was of excellent quality. The findings were a surprise in that IHC identified an average of 1.2 targets (for which a conventional therapeutic agent is available) per patient (range 0 - 4 targets). The DMA identified an average of 3.3 targets per patient (range 0 - 8 targets). Overall, a target was found for 89 (98%) of the patients. This data indicates that using IHC and DMA one can consistently find a potential target for which we have a therapeutic agent in patients’ tumors even thought they have progressed on prior therapies. This has implications for patients’ planning on participating in phase I clinical trials. It is important to conduct a prospective clinical trial to determine whether the targets discovered using IHC and DMA can be used to select therapy which will further benefit the patient who would otherwise be participating in a phase I clinical trial.

[Table: see text]

Epithelial cell contact-induced alterations in Salmonella enterica serovar Typhi lipopolysaccharide are critical for bacterial internalization

The invasion of Pseudomonas aeruginosa and Salmonella enterica serovar Typhi into epithelial cells depends on the cystic fibrosis transmembrane conductance regulator (CFTR) protein as an epithelial receptor. In the case of P. aeruginosa, the bacterial ligand for CFTR is the outer core oligosaccharide portion of the lipopolysaccharide (LPS). To determine whether serovar Typhi LPS is also a bacterial ligand mediating internalization, we used both P. aeruginosa and serovar Typhi LPS as a competitive inhibitor of serovar Typhi invasion into the epithelial cell line T84. P. aeruginosa LPS containing a complete core efficiently inhibited serovar Typhi invasion. However, neither killed wild-type Typhi cells nor purified LPS were effective inhibitors. LPS from mutant Typhi strains defective in O side-chain synthesis, but with an apparently normal core, was capable of inhibiting invasion, but LPS obtained from a deeper rough mutant strain with alterations in fast-migrating core oligosaccharide failed to inhibit invasion. Lastly, exposure of wild-type serovar Typhi to T84 cultures before heat killing resulted in a structural alteration in its LPS that allowed the heat-killed cells to inhibit invasion of wild-type serovar Typhi. These data indicate that the serovar Typhi LPS core, like the P. aeruginosa LPS core, is a ligand mediating internalization of bacteria by epithelial cells, and that exposure of this ligand on wild-type Typhi is induced by the bacteria's interaction with host cells.

Induction of gene expression as a monitor of exposure to ionizing radiation

The complex molecular responses to genotoxic stress are mediated by a variety of regulatory pathways. The transcription factor TP53 plays a central role in the cellular response to DNA-damaging agents such as ionizing radiation, but other pathways also play important roles. In addition, differences in radiation quality, such as the exposure to high-LET radiation that occurs during space travel, may influence the pattern of responses. The premise is developed that stress gene responses can be employed as molecular markers for radiation exposure using a combination of informatics and functional genomics approaches. Published studies from our laboratory have already demonstrated such transcriptional responses with doses of gamma rays as low as 2 cGy, and in peripheral blood lymphocytes (PBLs) irradiated ex vivo with doses as low as 20 cGy. We have also found several genes elevated in vivo 24 h after whole-body irradiation of mice with 20 cGy. Such studies should provide insight into the molecular responses to physiologically relevant doses, which cannot necessarily be extrapolated from high-dose studies. In addition, ongoing experiments are identifying large numbers of potential biomarkers using microarray hybridization and various irradiation protocols including expression at different times after exposure to low- and high-LET radiation. Computation-intensive informatics analysis methods are also being developed for management of the complex gene expression profiles resulting from these experiments. With further development of these approaches, it may be feasible to monitor changes in gene expression after low-dose radiation exposure and other physiological stresses that may be encountered during manned space flight, such as the planned mission to Mars.

The rfaH gene, which affects lipopolysaccharide synthesis in Salmonella enterica serovar Typhi, is differentially expressed during the bacterial growth phase

We have cloned and sequenced the rfaH gene from Salmonella enterica serovar Typhi strain Ty2. The gene showed a high degree of similarity to the rfaH genes from Escherichia coli K-12 and S. enterica serovar Typhimurium. A rfaH mutant was constructed by site-directed mutagenesis. This mutant produced a rough lipopolysaccharide (LPS), with an incomplete core region. The defect in LPS expression that results from the rfaH mutation was corrected by a plasmid carrying the intact gene. The plasmid-borne rfaH gene also restored normal LPS synthesis in a rfaH mutant of E. coli. Reverse transcription-polymerase chain reaction analyses were performed to determine the effects of various environmental conditions on the expression of rfaH. The transcription of rfaH showed a growth-phase-dependent regulation, with maximal expression at the late exponential phase. Other environmental conditions, such as temperature or medium osmolarity, did not affect transcription of rfaH.

Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling

Androgen deprivation therapy for advanced prostate cancer is often effective, but not curative. Molecular pathways mediating the therapeutic response and those contributing to the subsequent hormone-refractory cell growth remain poorly understood. Here, cDNA microarray analysis of human CWR22 prostate cancer xenografts during the course of androgen deprivation therapy revealed distinct global gene expression profiles in primary, regressing and recurrent tumors. Elucidation of the genes involved in the transition between these states implicated specific molecular mechanisms in therapy failure and tumor progression. First, we identified a set of androgen-responsive genes whose expression decreased during the therapy response, but was then systematically restored in the recurrent tumors. In addition, altered expression of genes that encode known targets of rapamycin or that converge on the PI3K/AKT/FRAP pathway was observed in the recurrent tumors. Further suggestion for the involvement of these genes in hormone-refractory prostate cancer came from the observation that cells established from the recurrent xenografts were strongly inhibited in vitro by rapamycin. The results of this functional genomic analysis suggest that the combined effect of re-expression of androgen-responsive genes as well as the activation of rapamycin-sensitive signaling may drive prostate cancer progression, and contribute to the failure of androgen-deprivation therapy.

The Ca2+-binding proteins S100A8 and S100A9 are encoded by novel injury-regulated genes

To gain insight into the molecular mechanisms underlying cutaneous wound repair, we performed a large scale screen to identify novel injury-regulated genes. Here we show a strong up-regulation of the RNA and protein levels of the two Ca(2+)-binding proteins S100A8 and S100A9 in the hyperthickened epidermis of acute murine and human wounds and of human ulcers. Furthermore, both genes were expressed by inflammatory cells in the wound. The increased expression of S100A8 and S100A9 in wound keratinocytes is most likely related to the activated state of the keratinocytes and not secondary to the inflammation of the skin, since we also found up-regulation of S100A8 and S100A9 in the epidermis of activin-overexpressing mice, which develop a hyperproliferative and abnormally differentiated epidermis in the absence of inflammation. Furthermore, S100A8 and S100A9 expression was found to be associated with partially differentiated keratinocytes in vitro. Using confocal microscopy, both proteins were shown to be at least partially associated with the keratin cytoskeleton. In addition, cultured keratinocytes efficiently secreted the S100A8/A9 dimer. These results together with previously published data suggest that S100A8 and S100A9 are novel players in wound repair, where they might be involved in the reorganization of the keratin cytoskeleton in the wounded epidermis, in the chemoattraction of inflammatory cells, and/or in the defense against microorganisms.

Comparative study of ovatifolin antioxidant and growth inhibition activities

A comparative study on the effect of arturin (1), ovatifolin (3), deacetylovatifolin (5), and their 1-acetoxyarturin (2), 8-acetoxyovatifolin (4), 1,10-epoxyovatifolin (6), and 11,13-dihydroovatifolin (7) derivatives, isolated from Podanthus ovatifolius and Podanthus mitiqui, on the seedling growth, germination, and respiration of several monocot and dicot weedy target species was carried out. In addition to the inhibitory activity on the bleaching of crocin induced by alkoxyl radicals, these compounds also displayed scavenging properties toward DPPH in TLC autographic and spectrophotometric assays. The results indicate that ovatifolin (3), deacetylovatifolin (5), epoxyovatifolin (6), dihydroovatifolin (7), and the CH(2)Cl(2) extract interfere with pre-emergence of seedlings at the level of respiration. These compounds appear to have selective effects on the radicle and shoot growth of Physalis ixocarpa and Trifolium pratense. Their allelopathic effects are comparable to those of parthenolide, a know natural growth inhibitor.

Genome-wide expression changes induced by HTLV-1 Tax: evidence for MLK-3 mixed lineage kinase involvement in Tax-mediated NF-kappaB activation

The Tax protein of human T-lymphotropic virus type 1 (HTLV-1), an oncoprotein that transactivates viral and cellular genes, plays a key role in HTLV-1 replication and pathogenesis. We used cDNA microarrays to examine Tax-mediated transcriptional changes in the human Jurkat T-cell lines JPX-9 and JPX-M which express Tax and Tax-mutant protein, respectively, under the control of an inducible promoter. Approximately 300 of the over 2000 genes examined were differentially expressed in the presence of Tax. These genes were grouped according to their function and are discussed in the context of existing findings in the literature. There was strong agreement between our results and genes previously reported as being Tax-responsive. Genes that were differentially expressed in the presence of Tax included those related to apoptosis, the cell cycle and DNA repair, signaling factors, immune modulators, cytokines and growth factors, and adhesion molecules. Functionally, we provide evidence that one of these genes, the mixed-lineage kinase MLK-3, is involved in Tax-mediated NF-kappa-B signaling. Our current results provide additional insights into Tax-mediated signaling.

Physiological function as regulation of large transcriptional programs: the cellular response to genotoxic stress

The responses to ionizing radiation and other genotoxic environmental stresses are complex and are regulated by a number of overlapping molecular pathways. One such stress signaling pathway involves p53, which regulates the expression of over 100 genes already identified. It is also becoming increasingly apparent that the pattern of stress gene expression has some cell type specificity. It may be possible to exploit these differences in stress gene responsiveness as molecular markers through the use of a combined informatics and functional genomics approach. The techniques of microarray analysis potentially offer the opportunity to monitor changes in gene expression across the entire set of expressed genes in a cell or organism. As an initial step in the development of a functional genomics approach to stress gene analysis, we have recently demonstrated the utility of cDNA microarray hybridization to measure radiation-stress gene responses and identified a number of previously unknown radiation-regulated genes. The responses of some of these genes to DNA-damaging agents vary widely in cell lines from different tissues of origin and different genetic backgrounds. While this again highlights the importance of a cellular context to genotoxic stress responses, it also raises the prospect of expression-profiling of cell lines, tissues, and tumors. Such profiles may have a predictive value if they can define regions of 'expression space' that correlate with important endpoints, such as response to cancer therapy regimens, or identification of exposures to environmental toxins.

Biological indicators for the identification of ionizing radiation exposure in humans

While the effects of acute high-dose irradiation are well-documented, less is known about the effects of low level chronic radiation exposure. Physical dosimetry cannot always be relied upon, so dose estimates and determination of past radiation exposure must often be based upon biological indicators. Some of the established methods used in the assessment of nuclear accidents are reviewed here, including cytogenetic analyses, mutation-based assays and electron spin resonance. As interest in research on low-level radiation exposures expands, there is an increasing need for new biomarkers that can identify exposed individuals in human populations. Developments in high-throughput gene expression profiling may enable future development of a rapid and noninvasive testing method for application to potentially exposed populations.

Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus)

Human herpesvirus 8 (HHV-8), a gammaherpesvirus implicated in Kaposi's sarcoma, primary effusion lymphoma, and Castleman's disease, encodes several pathogenically important cellular homologs. To define the HHV-8 transcription program, RNA obtained from latently infected body cavity-based lymphoma 1 cells induced to undergo lytic replication was used to query a custom HHV-8 DNA microarray containing nearly every known viral open reading frame. The patterns of viral gene expression offer insights into the replication and pathogenic strategies of HHV-8.

Gene-expression profiles in hereditary breast cancer

BACKGROUND

Many cases of hereditary breast cancer are due to mutations in either the BRCA1 or the BRCA2 gene. The histopathological changes in these cancers are often characteristic of the mutant gene. We hypothesized that the genes expressed by these two types of tumors are also distinctive, perhaps allowing us to identify cases of hereditary breast cancer on the basis of gene-expression profiles.

METHODS

RNA from samples of primary tumor from seven carriers of the BRCA1 mutation, seven carriers of the BRCA2 mutation, and seven patients with sporadic cases of breast cancer was compared with a microarray of 6512 complementary DNA clones of 5361 genes. Statistical analyses were used to identify a set of genes that could distinguish the BRCA1 genotype from the BRCA2 genotype.

RESULTS

Permutation analysis of multivariate classification functions established that the gene-expression profiles of tumors with BRCA1 mutations, tumors with BRCA2 mutations, and sporadic tumors differed significantly from each other. An analysis of variance between the levels of gene expression and the genotype of the samples identified 176 genes that were differentially expressed in tumors with BRCA1 mutations and tumors with BRCA2 mutations. Given the known properties of some of the genes in this panel, our findings indicate that there are functional differences between breast tumors with BRCA1 mutations and those with BRCA2 mutations.

CONCLUSIONS

Significantly different groups of genes are expressed by breast cancers with BRCA1 mutations and breast cancers with BRCA2 mutations. Our results suggest that a heritable mutation influences the gene-expression profile of the cancer.

Chromosome arm-specific multicolor FISH

Several systems for 24-color fluorescence in situ hybridization (FISH) have been developed and applied to karyotyping and detection of chromosomal abnormalities. We have developed a 42-color multicolor FISH (mFISH) technique (armFISH), which permits the detection of chromosomal aberrations at the resolution of chromosome arms. The armFISH uses a commercially available mFISH reagent kit (24XCyte, MetaSystems GmbH) supplemented with a set of differentially labeled chromosome arm-specific painting probes (arm-kit, comprising either p- or q-arms of all human chromosomes, except the p-arm of the acrocentric- and Y chromosomes). The mFISH-probe cocktail and the arm-kit are combined and hybridized together to metaphase chromosomes. The armFISH is analyzed in two steps; first, the conventional mFISH image analysis is performed, followed by the arm-kit analysis to reveal the chromosome arms involved. The examples demonstrate the utility of armFISH in defining chromosomal rearrangements of human cancers.

Identification of potential mRNA biomarkers in peripheral blood lymphocytes for human exposure to ionizing radiation

Since early in the Atomic Age, biological indicators of radiation exposure have been sought, but currently available methods are not entirely satisfactory. Using cDNA microarray hybridization to discover new potential biomarkers, we have identified genes expressed at increased levels in human peripheral blood lymphocytes after ex vivo irradiation. We recently used this technique to identify a large set of ionizing radiation-responsive genes in a human cell line (Oncogene 18, 3666-3672, 1999). The present set of radiation markers in peripheral blood lymphocytes was identified 24 h after treatment, and while the magnitude of mRNA induction generally decreased over time, many markers were still significantly elevated up to 72 h after irradiation. In all donors, the most highly responsive gene identified was DDB2, which codes for the p48 subunit of XPE, a protein known to play a crucial role in repair of ultraviolet (UV) radiation damage in DNA. Induction of DDB2, CDKN1A (also known at C1P1/WAF1) and XPC showed a linear dose-response relationship between 0.2 and 2 Gy at 24 and 48 h after irradiation, with less linearity at earlier or later times. These results suggest that relative levels of gene expressions in peripheral blood cells may provide estimated of environmental radiation exposures.

Molecular classification of cutaneous malignant melanoma by gene expression profiling

The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.