Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics

Previously, we showed that high-energy metabolites (lactate and ketones) "fuel" tumor growth and experimental metastasis in an in vivo xenograft model, most likely by driving oxidative mitochondrial metabolism in breast cancer cells. To mechanistically understand how these metabolites affect tumor cell behavior, here we used genome-wide transcriptional profiling. Briefly, human breast cancer cells (MCF7) were cultured with lactate or ketones, and then subjected to transcriptional analysis (exon-array). Interestingly, our results show that treatment with these high-energy metabolites increases the transcriptional expression of gene profiles normally associated with "stemness," including genes upregulated in embryonic stem (ES) cells. Similarly, we observe that lactate and ketones promote the growth of bonafide ES cells, providing functional validation. The lactate- and ketone-induced "gene signatures" were able to predict poor clinical outcome (including recurrence and metastasis) in a cohort of human breast cancer patients. Taken together, our results are consistent with the idea that lactate and ketone utilization in cancer cells promotes the "cancer stem cell" phenotype, resulting in significant decreases in patient survival. One possible mechanism by which these high-energy metabolites might induce stemness is by increasing the pool of Acetyl-CoA, leading to increased histone acetylation, and elevated gene expression. Thus, our results mechanistically imply that clinical outcome in breast cancer could simply be determined by epigenetics and energy metabolism, rather than by the accumulation of specific "classical" gene mutations. We also suggest that high-risk cancer patients (identified by the lactate/ketone gene signatures) could be treated with new therapeutics that target oxidative mitochondrial metabolism, such as the anti-oxidant and "mitochondrial poison" metformin. Finally, we propose that this new approach to personalized cancer medicine be termed "Metabolo-Genomics," which incorporates features of both 1) cell metabolism and 2) gene transcriptional profiling. Importantly, this powerful new approach directly links cancer cell metabolism with clinical outcome, and new therapeutic strategies for inhibiting the TCA cycle and mitochondrial oxidative phosphorylation in cancer cells.

Association of RB/p16-pathway perturbations with DCIS recurrence: dependence on tumor versus tissue microenvironment

The prevalence of ductal carcinoma in situ (DCIS) diagnoses has significantly increased as a result of active radiographic screening. Surgical resection and hormone and radiation therapies are effective treatments, but not all DCIS will progress to invasive breast cancer. Therefore, markers are needed to define tumors at low risk of recurrence and progression that can be treated by surgery alone rather than by adjuvant therapies. Initial analyses indicate that retinoblastoma (RB)-pathway perturbations occur at high frequency in DCIS and mirror the molecular alterations observed in invasive breast cancer. Particularly, the elevated expression of p16ink4a in DCIS was associated with loss of RB function and estrogen receptor-negative biology. Furthermore, high expression of p16ink4a in conjunction with Ki-67 was associated with increased risk of DCIS recurrence and progression to invasive disease in multivariate analyses. These data are consistent with a functional role for RB in modulating the invasive behavior of mammary epithelial cells. The tissue microenvironment is particularly relevant to the behavior of DCIS, and, surprisingly, elevated expression of p16ink4a in nonproliferative stroma was observed in a substantial fraction of cases. In this tissue compartment, p16ink4a expression was strongly associated with disease recurrence, independent of standard histopathologic features. Together, the data herein describe dual aspects of RB-pathway biology that are associated with disease recurrence through the epithelial or stromal compartment of DCIS.

Evidence for a stromal-epithelial "lactate shuttle" in human tumors: MCT4 is a marker of oxidative stress in cancer-associated fibroblasts

Recently, we proposed a new mechanism for understanding the Warburg effect in cancer metabolism. In this new paradigm, cancer-associated fibroblasts undergo aerobic glycolysis, and extrude lactate to "feed" adjacent cancer cells, which then drives mitochondrial biogenesis and oxidative mitochondrial metabolism in cancer cells. Thus, there is vectorial transport of energy-rich substrates from the fibroblastic tumor stroma to anabolic cancer cells. A prediction of this hypothesis is that cancer-associated fibroblasts should express MCT4, a mono-carboxylate transporter that has been implicated in lactate efflux from glycolytic muscle fibers and astrocytes in the brain. To address this issue, we co-cultured MCF7 breast cancer cells with normal fibroblasts. Interestingly, our results directly show that breast cancer cells specifically induce the expression of MCT4 in cancer-associated fibroblasts; MCF7 cells alone and fibroblasts alone, both failed to express MCT4. We also show that the expression of MCT4 in cancer-associated fibroblasts is due to oxidative stress, and can be prevented by pre-treatment with the anti-oxidant N-acetyl-cysteine. In contrast to our results with MCT4, we see that MCT1, a transporter involved in lactate uptake, is specifically upregulated in MCF7 breast cancer cells when co-cultured with fibroblasts. Virtually identical results were also obtained with primary human breast cancer samples. In human breast cancers, MCT4 selectively labels the tumor stroma, e.g., the cancer-associated fibroblast compartment. Conversely, MCT1 was selectively expressed in the epithelial cancer cells within the same tumors. Functionally, we show that overexpression of MCT4 in fibroblasts protects both MCF7 cancer cells and fibroblasts against cell death, under co-culture conditions. Thus, we provide the first evidence for the existence of a stromal-epithelial lactate shuttle in human tumors, analogous to the lactate shuttles that are essential for the normal physiological function of muscle tissue and brain. These data are consistent with the "reverse Warburg effect," which states that cancer-associated fibroblasts undergo aerobic glycolysis, thereby producing lactate, which is utilized as a metabolic substrate by adjacent cancer cells. In this model, "energy transfer" or "metabolic-coupling" between the tumor stroma and epithelial cancer cells "fuels" tumor growth and metastasis, via oxidative mitochondrial metabolism in anabolic cancer cells. Most importantly, our current findings provide a new rationale and novel strategy for anti-cancer therapies, by employing MCT inhibitors.

Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers

Breast cancer progression and metastasis are driven by complex and reciprocal interactions, between epithelial cancer cells and their surrounding stromal microenvironment. We have previously shown that a loss of stromal Cav-1 expression is associated with an increased risk of early tumor recurrence, metastasis and decreased overall survival. To identify and characterize the signaling pathways that are activated in Cav-1 negative tumor stroma, we performed gene expression profiling using laser microdissected breast cancer-associated stroma. Tumor stroma was laser capture microdissected from 4 cases showing high stromal Cav-1 expression and 7 cases with loss of stromal Cav-1. Briefly, we identified 238 gene transcripts that were upregulated and 232 gene transcripts that were downregulated in the stroma of tumors showing a loss of Cav-1 expression (p ≤ 0.01 and fold-change ≥ 1.5). Gene set enrichment analysis (GSEA) revealed "stemness," inflammation, DNA damage, aging, oxidative stress, hypoxia, autophagy and mitochondrial dysfunction in the tumor stroma of patients lacking stromal Cav-1. Our findings are consistent with the recently proposed "Reverse Warburg Effect" and the "Autophagic Tumor Stroma Model of Cancer Metabolism." In these two complementary models, cancer cells induce oxidative stress in adjacent stromal cells, which then forces these stromal fibroblasts to undergo autophagy/mitophagy and aerobic glycolysis. This, in turn, produces recycled nutrients (lactate, ketones and glutamine) to feed anabolic cancer cells, which are undergoing oxidative mitochondrial metabolism. Our results are also consistent with previous biomarker studies showing that the increased expression of known autophagy markers (such as ATG16L and the cathepsins) in the tumor stroma is specifically associated with metastatic tumor progression and/or poor clinical outcome.

Therapeutically activating RB: reestablishing cell cycle control in endocrine therapy-resistant breast cancer

The majority of estrogen receptor (ER)-positive breast cancers are treated with endocrine therapy. While this is effective, acquired resistance to therapies targeted against ER is a major clinical challenge. Here, model systems of ER-positive breast cancers with differential susceptibility to endocrine therapy were employed to define common nodes for new therapeutic interventions. These analyses revealed that cell cycle progression is effectively uncoupled from the activity and functional state of ER in these models. In this context, cyclin D1 expression and retinoblastoma tumor suppressor protein (RB) phosphorylation are maintained even with efficient ablation of ER with pure antagonists. These therapy-resistant models recapitulate a key feature of deregulated RB/E2F transcriptional control. Correspondingly, a gene expression signature of RB-dysfunction is associated with luminal B breast cancer, which exhibits a relatively poor response to endocrine therapy. These collective findings suggest that suppression of cyclin D-supported kinase activity and restoration of RB-mediated transcriptional repression could represent a viable therapeutic option in tumors that fail to respond to hormone-based therapies. Consistent with this hypothesis, a highly selective CDK4/6 inhibitor, PD-0332991, was effective at suppressing the proliferation of all hormone refractory models analyzed. Importantly, PD-0332991 led to a stable cell cycle arrest that was fundamentally distinct from those elicited by ER antagonists, and was capable of inducing aspects of cellular senescence in hormone therapy refractory cell populations. These findings underscore the clinical utility of downstream cytostatic therapies in treating tumors that have experienced failure of endocrine therapy.

A de novo supernumerary genomic discontinuous ring chromosome 21 in a child with mild intellectual disability

Small supernumerary marker chromosomes (sSMCs) are structurally abnormal extra chromosomes that cannot be unambiguously identified or characterized by conventional banding techniques alone, and they are generally equal in size or smaller than chromosome 20 of the same metaphase spread. Small supernumerary ring chromosomes (sSRCs), a smaller class of marker chromosomes, comprise about 10% of the cases. For various reasons these marker chromosomes have been the most difficult to characterize; although specific syndromes have not yet been defined, 60% of cases are associated with an abnormal phenotype. The chromosomal material involved, the degree and tissutal distribution of mosaicism, and the possible presence of uniparental disomy, are the important factors determining whether or not the ring chromosome will give rise to symptoms. Using conventional and molecular cytogenetics approaches we identified a de novo chromosome 21 sSRC in a child with speech delay and mild intellectual disability. By using aCGH analysis and SNP arrays, we report the presence of two discontinuous regions of chromosome 21 and the paternal origin of the sSRC. A thorough neuropsychiatric evaluation is also provided. Only few other cases of complex discontinuous ring chromosomes have been described in detail.

Abstract 2982: Impact of the RB-pathway in breast cancer heterogeneity and therapeutic response

Molecular heterogeneity in breast cancer is associated with differential prognosis and response to therapy. However, in spite of extensive molecular classification, pathways that can be specifically targeted to understand the basis of disease and improve treatment remain poorly understood within specific subtypes of breast cancer. The retinoblastoma tumor suppressor (RB) pathway is deregulated in most cancers; however varied mechanisms of inactivation have significant impacts on tumor biology. Here novel mechanistic and preclinical models were combined with analyses of tumor specimens to decipher the differential impact of the RB-pathway within breast cancer subtypes and as a specific target for patient stratification and therapeutic targeting.

Initial gene expression datasets encompassing over 2000 breast cancer patient samples were used to demonstrate a striking dichotomy in the mechanisms of RB functional inactivation within subtypes of disease. In ER-positive breast cancer, disruption of RB-pathway function was associated with poor prognosis and failure of endocrine therapy. Functional studies demonstrate that such therapeutic failure largely occurs in the presence of an intact Rb gene, as a result of deregulated mitogenic signaling. In such models of hormone refractory disease we demonstrate that pharmacological activation of RB is a potent second-line therapy. In contrast, in ER-negative tumor populations RB inactivation occurs in 40-50% of cases. This event yields complete loss of RB protein, as occurs through genetic and epigenetic mechanisms. Strikingly, in ER-negative disease RB loss is associated with improved response to chemotherapy and longer relapse-free survival. The basis for improved response involves both deregulation of cell cycle checkpoints and apoptotic processes. Ongoing analyses are using synthetic-lethal and combination-therapy approaches to rationally target RB-status in the management of breast cancer.

In total, these studies define a clear role for RB-pathway as a determinant of tumor heterogeneity in breast cancer that can be leveraged to more effectively treat breast cancer.

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 2982. doi:10.1158/1538-7445.AM2011-2982

Abstract 5375: Reestablishing cell cycle control in breast cancers through therapeutic CDK4/6 inhibition

One hallmark of cancer is the deregulation of cell cycle machinery, which ultimately serves to promote aberrant proliferation that fuels tumorigenesis and progression. Particularly, the cyclin D1/Rb/E2F axis plays a crucial role in the development of disease by serving to connect aberrant mitogenic signaling with cell cycle transcriptional programs. In this context, the role of estrogen receptor (ER) in breast cancers has been previously described to exert influence upstream of this axis. While first-line strategies targeting ER activity are prevalent and initially effective in the majority of ER-positive breast cancers, acquired resistance and therapeutic failure remain a major clinical challenge. Current analyses have revealed that cell cycle progression is effectively uncoupled from the activity and functional state of ER in these models. As a gene expression signature of cyclin D/Rb/E2F-dysfunction was found to be associated with luminal B breast cancers (which are known to exhibit a relatively poor response to endocrine therapy), the prevalence of ER dysfunction occurring upstream of cyclin D1 suggests that targeting CDK 4/6 activity may be effective. To this end, we examined the therapeutic response to a CDK 4/6 inhibitor (PD-0332991) in human breast cancer cell lines and demonstrated a highly-specific role for Rb in mediating this response, which was dependent on transcriptional repression manifest through E2F activity. These analyses additionally demonstrated that the chronic loss of Rb can promote evolution to a CDK4/6-independent state and near complete resistance to PD-0332991. In addition to these studies, model systems of ER-positive breast cancers with differential susceptibility to endocrine therapy were employed to define common nodes for new therapeutic interventions. These collective findings suggest that suppression of cyclin D-supported kinase activity and restoration of Rb-mediated transcriptional repression could represent a viable therapeutic option in tumors that fail to respond to hormone-based therapies. Consistent with this hypothesis, CDK4/6 inhibiton was effective at suppressing the proliferation of all hormone refractory models analyzed. Combined, these findings underscore the clinical utility of mediating aberrant cell cycle progression through down-stream cytostatic therapies in treating tumors that have experienced failure of first line and endocrine-based therapy, and provide rationale for incorporation of CDK 4/6 inhibition into current existing therapeutic regimens.

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 5375. doi:10.1158/1538-7445.AM2011-5375

Abstract 3906: Gene expression profiling of ductal carcinoma in situ reveals novel alterations in the tumor and stromal compartments related to progession and outcome of invasive breast cancer

An increasing number of women are diagnosed with ductal carcinoma in situ (DCIS). DCIS is non-obligate precursor to invasive breast cancer. Mechanisms leading to development and progression of DCIS to invasive breast cancer (IBC) are still largely unknown. When DCIS and IBC coexist in the same lesion, their transcriptional profiles are nearly identical; however, there are very few studies investigating gene expression in pure DCIS. The goal of this study was to compare gene expression profiles of microdissected epithelial and stromal components of pure DCIS and IBC. Epithelium and stroma were laser microdissected from 10 cases of pure DCIS and 10 invasive breast carcinomas. DCIS and IBC were matched with regard to estrogen, progesterone receptor and HER2 expression. Gene expression was analyzed using Affymetrix Human Exon 1.0 ST microarrays. Analyses of gene expression in IBC and DCIS revealed a number of differentially expressed genes in the epithelial (n=211) and stromal (n=143) LCM obtained cells. In the epithelial compartment many of the genes specifically associated with IBC are part of previously described epithelial to mesenchymal transition, metastasis and myoepithelial cell gene expression signatures. Consistent with these findings, gene ontology analyses found overrepresentation of GO Biological Process terms such as ‘cell adhesion’ (44 genes, p = 1.47E-14), ‘extracellular matrix organization’ (16 genes, p = 3.46E-09), ‘skeletal system development’ (22 genes, p = 5.87E-07) and ‘vasculature development’ (14 genes, P = 4.56E-03). Applying differentially expressed epithelial genes to a larger invasive breast cancer dataset showed association with decreased metastasis free and progression free survival.

Our study reveals that pure dcis and invasive breast cancer are distinct at the transcriptome level. Future work will show if genes differentially expressed between IBC and pure DCIS may be useful for identifying at the time of diagnosis DCIS patients likely to progress to IBC.

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 3906. doi:10.1158/1538-7445.AM2011-3906

Variants in genes involved in functional pathways associated with hypertension in African Americans

Essential hypertension (HBP) is a complex trait with a substantial heritable component. The purpose of this study was to determine if variants in the G-protein coupled receptor Kinase-4 (GRK4), nitric oxide synthase-3 (NOS3), or angiotensin converting enzyme (ACE) genes are associated singly or through complex interactions, with HBP in African Americans aged 18-49 years. TaqMan Assays were used for genotyping the GRK4 and NOS3 variants. The ACE I/D variant was obtained by polymerase chain reaction and electrophoresis. Allelic association tests were performed for the five markers using PLINK. Logistic regression models were fitted to investigate associations between HBP status and the genetic markers. Multilocus analyses were also conducted. The study included 173 hypertensives and 239 normotensives, with stratification into obese and nonobese groups. The GRK4 A486V variant was negatively associated with HBP in the nonobese group (p = 0.048). The TT/CT genotype of GRK4 A486V was associated with decreased risk for HBP relative to the CC genotype after adjusting for age, sex, and body mass index (p = 0.028). Individuals having at least one NOS3 A allele and GRK4 R65L genotype GG had odds of HBP of 2.97 relative to GG homozygotes for NOS3 and GRK4 R65L. These results show very modest effects and do not fully replicate previous studies.

Cyclin D1 is a selective modifier of androgen-dependent signaling and androgen receptor function

D-type cyclins regulate cellular outcomes in part through cyclin-dependent, kinase-independent mechanisms that modify transcription factor action, and recent in vivo studies showed that cyclin D1 associates with a large number of transcriptional regulators in cells of the retina and breast. Given the frequency of cyclin D1 alterations in cancer, it is imperative to delineate the molecular mechanisms by which cyclin D1 controls key transcription factor networks in human disease. Prostate cancer was used as a paradigm because this tumor type is reliant at all stages of the disease on androgen receptor (AR) signaling, and cyclin D1 has been shown to negatively modulate AR-dependent expression of prostate-specific antigen (KLK3/PSA). Strategies were employed to control cyclin D1 expression under conditions of hormone depletion, and the effect of cyclin D1 on subsequent androgen-dependent gene expression was determined using unbiased gene expression profiling. Modulating cyclin D1 conferred widespread effects on androgen signaling and revealed cyclin D1 to be a selective effector of hormone action. A subset of androgen-induced target genes, known to be directly regulated by AR, was strongly suppressed by cyclin D1. Analyses of AR occupancy at target gene regulatory loci of clinical relevance demonstrated that cyclin D1 limits AR residence after hormone stimulation. Together, these findings reveal a new function for cyclin D1 in controlling hormone-dependent transcriptional outcomes and demonstrate a pervasive role for cyclin D1 in regulating transcription factor dynamics.

Abstract P4-01-04: The Impact of the Retinoblastoma Tumor Suppressor Pathway in Her2 Positive Breast Cancer Pathogenesis and Therapeutic Response

Extensive studies have shown that breast cancer is associated with molecular aberrations that underlie the distinct subtypes of disease that exhibit differential prognosis and susceptibility to targeted therapeutic. A critical oncogenic event used to classify breast cancers is the amplification or overexpression of the human epidermal growth factor receptor 2 (Her2). Tumors harboring Her2 overexpression present aggressive characteristics related to metastatic spread and poor overall disease outcome. However, such tumors are also susceptible to targeted therapeutic agents which effectively impinge on this oncogene. Strikingly, those events that cooperate with Her2 and modulate susceptibility to targeted therapeutics remain poorly understood. Here the significance of the retinoblastoma tumor suppressor (RB) pathway in the context of Her2 positive breast cancer pathogenesis and therapeutic response was evaluated. In silico and histological analyses suggested that a subset of Her2 positive tumors exhibit compromised RB function. To model interactions between Her2 and the RB-pathway genetic deletion and knockdown strategies were employed in the context of Her2 driven tumors. These studies revealed that RB loss accelerated disease progression of such models and further enhanced the aggressive tumor phenotype.

To delineate the functionality of the RB-pathway downstream from therapeutic interventions targeting Her2, two complimentary approaches were used. First, the ability to effectively intercede in Her2-positive tumors using drugs that specifically activate the RB-pathway was interrogated. The data revealed that specific CDK4/6 targeted therapies were highly effective at limiting the growth of Her2-positive tumor cells. Second, the impact of RB status on the response the Her2/EGFR antagonist lapatinib was evaluated. These studies demonstrated that loss of RB compromises the effectiveness of lapatinib in the treatment of Her2 positive breast cancer cell lines. Ongoing studies are evaluating the spontaneous mechanisms of resistance to Her2 targeted therapeutics and the significance of reestablishing RB function as a therapeutic alternative in such cancers. Together, these studies underscore the importance of the interplay between Her2 signaling and cell cycle control in breast cancer, and how this crosstalk influences the response to targeted therapeutics in the treatment of breast cancer.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-01-04.

The retinoblastoma tumor suppressor controls androgen signaling and human prostate cancer progression

Retinoblastoma (RB; encoded by RB1) is a tumor suppressor that is frequently disrupted in tumorigenesis and acts in multiple cell types to suppress cell cycle progression. The role of RB in tumor progression, however, is poorly defined. Here, we have identified a critical role for RB in protecting against tumor progression through regulation of targets distinct from cell cycle control. In analyses of human prostate cancer samples, RB loss was infrequently observed in primary disease and was predominantly associated with transition to the incurable, castration-resistant state. Further analyses revealed that loss of the RB1 locus may be a major mechanism of RB disruption and that loss of RB function was associated with poor clinical outcome. Modeling of RB dysfunction in vitro and in vivo revealed that RB controlled nuclear receptor networks critical for tumor progression and that it did so via E2F transcription factor 1-mediated regulation of androgen receptor (AR) expression and output. Through this pathway, RB depletion induced unchecked AR activity that underpinned therapeutic bypass and tumor progression. In agreement with these findings, disruption of the RB/E2F/nuclear receptor axis was frequently observed in the transition to therapy resistance in human disease. Together, these data reveal what we believe to be a new paradigm for RB function in controlling prostate tumor progression and lethal tumor phenotypes.

RB-pathway disruption in breast cancer: differential association with disease subtypes, disease-specific prognosis and therapeutic response

In breast cancer, inactivation of the RB tumor suppressor gene is believed to occur via multiple mechanisms to facilitate tumorigenesis. However, the prognostic and predictive value of RB status in disease-specific clinical outcomes has remained uncertain. We investigated RB pathway deregulation in the context of both ER-positive and ER-negative disease using combined microarray datasets encompassing over 900 breast cancer patient samples. Disease-specific characteristics of RB pathway deregulation were investigated in this dataset by evaluating correlation among pathway genes as well as differential expression across patient tumor populations defined by ER status. Survival analysis among these breast cancer samples demonstrates that the RB-loss signature is associated with poor disease outcome within several independent cohorts. Within the ER-negative subpopulation, the RB-loss signature is associated with improved response to chemotherapy and longer relapse-free survival. Additionally, while individual genes in the RB target signature closely reproduce its prognostic value, they also serve to predict and monitor response to therapeutic compounds, such as the cytostatic agent PD-0332991. These results indicate that the RB-loss signature expression is associated with poor outcome in breast cancer, but predicts improved response to chemotherapy based on data in ER-negative populations. While the RB-loss signature, as a whole, demonstrates prognostic and predictive utility, a small subset of markers could be sufficient to stratify patients based on RB function and inform the selection of appropriate therapeutic regimens.

Abstract 3870: Distinct and cooperative functions of the RB and p53 tumor suppressors in genotoxic response and tumorigenesis

The compound inactivation of RB and p53 is a frequent occurrence in human cancers. At a molecular level, the RB and p53 pathways intersect at multiple points that have critical implications for cell cycle control and tumorigenesis. To examine the cooperation of these proteins in the response to genotoxic damage, we used a combination of genetic deletion and dominant negative strategies in vitro, and liver-specific genetic deletion in vivo. In vitro, RB proficiency was sufficient to maintain cell cycle checkpoint in response to genotoxic stress, independent of p53 status. In contrast, RB-deficient cells displayed deregulated cell growth, resulting in aggressive recovery from DNA damage. Strikingly, while disruption of the RB and p53 pathways alone does not result in transformation, the RB-deficient, recurred cell populations were tumorigenic. These in vitro findings indicate that RB is a critical suppressor of tumorigenesis, beyond that of p53, and a significant factor in the evolution of cells during genotoxic challenge. To further examine the cooperation of RB and p53 in vivo, a model of liver tumorigenesis was employed. Interestingly, these in vivo studies confirmed that while compound inactivation of the RB and p53 pathways in liver tissue promoted deregulated cell cycle control, this was not sufficient for transformation. However, loss of RB and p53 cooperated in promoting aberrant cell proliferation and mitosis in the presence of genotoxic challenge by DEN (diethyl-nitrosamine), ultimately resulting in enhanced tumorigenesis. Strikingly, loss of RB alone promoted S-phase entry as a result of genotoxic challenge, but there was an uncoupling of this event from productive mitosis. In contrast, the combined loss of RB/p53 resulted in further deregulation of DNA replication that was accompanied by a productive mitotic entry. These data indicate that, while both RB and p53 can contribute to appropriate replicative control, p53 plays a dominant role in mediating G2/M regulation. Furthermore, RB/p53-deficient livers displayed rapid progression to highly aggressive HCC within the span of six months, which was not observed in either RB-deficient or p53-deficient livers. Combined, these studies indicate that RB and p53 play distinct and cooperating roles in modulating response to genotoxic stress and tumorigenesis. Discovering the mechanism behind this cooperation could uncover a critical facet of tumor etiology and provide a means by which to treat this complex disease.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3870.

Bimodal gene expression and biomarker discovery

With insights gained through molecular profiling, cancer is recognized as a heterogeneous disease with distinct subtypes and outcomes that can be predicted by a limited number of biomarkers. Statistical methods such as supervised classification and machine learning identify distinguishing features associated with disease subtype but are not necessarily clear or interpretable on a biological level. Genes with bimodal transcript expression, however, may serve as excellent candidates for disease biomarkers with each mode of expression readily interpretable as a biological state. The recent article by Wang et al, entitled "The Bimodality Index: A Criterion for Discovering and Ranking Bimodal Signatures from Cancer Gene Expression Profiling Data," provides a bimodality index for identifying and scoring transcript expression profiles as biomarker candidates with the benefit of having a direct relation to power and sample size. This represents an important step in candidate biomarker discovery that may help streamline the pipeline through validation and clinical application.

Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality

Background

Gene expression is controlled over a wide range at the transcript level through complex interplay between DNA and regulatory proteins, resulting in profiles of gene expression that can be represented as normal, graded, and bimodal (switch-like) distributions. We have previously performed genome-scale identification and annotation of genes with switch-like expression at the transcript level in mouse, using large microarray datasets for healthy tissue, in order to study the cellular pathways and regulatory mechanisms involving this class of genes. We showed that a large population of bimodal mouse genes encoding for cell membrane and extracellular matrix proteins is involved in communication pathways. This study expands on previous results by annotating human bimodal genes, investigating their correspondence to bimodality in mouse orthologs and exploring possible regulatory mechanisms that contribute to bimodality in gene expression in human and mouse.

Results

Fourteen percent of the human genes on the HGU133A array (1847 out of 13076) were identified as bimodal or switch-like. More than 40% were found to have bimodal mouse orthologs. KEGG pathways enriched for bimodal genes included ECM-receptor interaction, focal adhesion, and tight junction, showing strong similarity to the results obtained in mouse. Tissue-specific modes of expression of bimodal genes among brain, heart, and skeletal muscle were common between human and mouse. Promoter analysis revealed a higher than average number of transcription start sites per gene within the set of bimodal genes. Moreover, the bimodal gene set had differentially methylated histones compared to the set of the remaining genes in the genome.

Conclusion

The fact that bimodal genes were enriched within the cell membrane and extracellular environment make these genes as candidates for biomarkers for tissue specificity. The commonality of the important roles bimodal genes play in tissue differentiation in both the human and mouse indicates the potential value of mouse data in providing context for human tissue studies. The regulation motifs enriched in the bimodal gene set (TATA boxes, alternative promoters, methlyation) have known associations with complex diseases, such as cancer, providing further potential for the use of bimodal genes in studying the molecular basis of disease.

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins

BACKGROUND

Recent studies have placed gene expression in the context of distribution profiles including housekeeping, graded, and bimodal (switch-like). Single-gene studies have shown bimodal expression results from healthy cell signaling and complex diseases such as cancer, however developing a comprehensive list of human bimodal genes has remained a major challenge due to inherent noise in human microarray data. This study presents a two-component mixture analysis of mouse gene expression data for genes on the Affymetrix MG-U74Av2 array for the detection and annotation of switch-like genes. Two-component normal mixtures were fit to the data to identify bimodal genes and their potential roles in cell signaling and disease progression.

RESULTS

Seventeen percent of the genes on the MG-U74Av2 array (1519 out of 9091) were identified as bimodal or switch-like. KEGG pathways significantly enriched for bimodal genes included ECM-receptor interaction, cell communication, and focal adhesion. Similarly, the GO biological process "cell adhesion" and cellular component "extracellular matrix" were significantly enriched. Switch-like genes were found to be associated with such diseases as congestive heart failure, Alzheimer's disease, arteriosclerosis, breast neoplasms, hypertension, myocardial infarction, obesity, rheumatoid arthritis, and type I and type II diabetes. In diabetes alone, over two hundred bimodal genes were in a different mode of expression compared to normal tissue.

CONCLUSION

This research identified and annotated bimodal or switch-like genes in the mouse genome using a large collection of microarray data. Genes with bimodal expression were enriched within the cell membrane and extracellular environment. Hundreds of bimodal genes demonstrated alternate modes of expression in diabetic muscle, pancreas, liver, heart, and adipose tissue. Bimodal genes comprise a candidate set of biomarkers for a large number of disease states because their expressions are tightly regulated at the transcription level.

Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets

BACKGROUND

Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves were used to assess the prediction error of each profile for classification. We compared the prediction error of profiles correlated with molecular phenotype against profiles correlated with relapse-free status. Prediction error of profiles identified with supervised univariate feature selection algorithms were compared to profiles selected randomly from a) all genes on the microarray platform and b) a list of known disease-related genes (a priori selection). We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms.

RESULTS

Highly discriminative expression profiles were produced on both simulated gene expression data and expression data from breast cancer and lymphoma datasets on the basis of ER and BCL-6 expression, respectively. Use of relapse-free status to identify profiles for prognosis prediction resulted in poorly discriminative decision rules. Supervised feature selection resulted in more accurate classifications than random or a priori selection, however, the difference in prediction error decreased as the number of features increased. These results held when decision rules were applied across-datasets to samples profiled on the same microarray platform.

CONCLUSION

Our results show that many gene sets predict molecular phenotypes accurately. Given this, expression profiles identified using different training datasets should be expected to show little agreement. In addition, we demonstrate the difficulty in predicting relapse directly from microarray data using supervised machine learning approaches. These findings are relevant to the use of molecular profiling for the identification of candidate biomarker panels.

Pathway-specific differences between tumor cell lines and normal and tumor tissue cells

Background

Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue.

Methods

This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM).

Results

Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways.

Conclusion

Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines.

Mechanical properties of vesicles. I. Coordinated analysis of osmotic swelling and lysis

To determine how transmembrane osmotic gradients perturb the structure and dynamics of biological membranes, we examined the effects of medium dilution on the structures of osmolyte-loaded lipid vesicles. Our preparations were characterized by dynamic light scattering (DLS) and nuclear magnetic resonance (NMR) spectroscopies. Populations of Escherichia coli phosphatidylethanolamine (PE) or dioleoylphosphatidylglycerol (DOPG) vesicles prepared by the pH jump technique were variable and polymodal in size distribution. Complex and variable structural changes occurred when PE vesicles were diluted with hypotonic buffer. Such vesicles could not be used as model systems for the analysis of membrane mechanical properties. NaCl-loaded, DOPG vesicles prepared by extrusion through 100 nm (diameter) pores were reproducible and monomodal in size distribution and unilamellar, whereas those prepared by extrusion through 200-, 400-, or 600-nm pores were variable and polymodal in size distribution and/or multilamellar. Time and pressure regimes associated with osmotic lysis of extruded vesicles were defined by monitoring release of carboxyfluorescein, a self-quenching fluorescent dye. Corresponding effects of medium dilution on vesicle structure were assessed by DLS spectroscopy. These experiments and the accompanying analysis (Hallett, F.R., J. Marsh, B.G. Nickel, and J.M. Wood. 1993. Biophys. J. 64:000-000) revealed conditions under which vesicles are expected to reside in a consistently strained state.

The differential effect of cigarette smoke on the growth of bacteria found in humans

The effect of cigarette smoke on growth of those species of bacteria that are considered common potential human pathogens was examined in vitro. Smoke from both mentholated and nonmentholated cigarettes inhibited the growth of Gram-positive cocci to a greater degree than that of Gram-negative rods. Staphylococcus aureus, Streptococcus pneumoniae, and a variety of other streptococci were inhibited at a smoke solution dilution of 1:8. Enteric bacteria such as Klebsiella, Enterobacter, and Pseudomonas were not affected by a 1:1 dilution of the solution. As with the Gram-positive cocci, the Neisseria species and Branhamella were also inhibited at a dilution of 1:8. Culture results of the mouth of 15 smokers and 15 nonsmokers showed that the smokers have a propensity to develop heavy Gram-negative bacterial colonization.