Gene expression in inherited breast cancer

The Autophagy-Inducing Mechanisms of Vitexin, Cinobufacini, and Physalis alkekengi Hydroalcoholic Extract against Breast Cancer in vitro and in vivo

OBJECTIVES

Owing to inefficiency of chemotherapy towards cancer treatment, formulation and application of herbal drug compounds will open new avenues with this regard. In this study, the anticancer effects of itexin, cinobufacini, and Physalis alkekengi (P. alkekengi) were assessed.

METHODS

Herein, synergistic effects of vitexin, cinobufacini, and P. alkekengi hydroalcoholic extract were assessed against estrogen-receptor (EGFR2)-positive breast cancer mouse model. Sixty ER + breast cancer BALB/c mice (six groups each including ten members) were included. The anticancer effects of P. alkekengi hydroalcoholic extract, vitexin, and cinobufacini were administered against EGFR2 cancerous cells for 14 days. The tumor size, cytotoxic effects, and expression of Beclin-1, LC3-II, and ATG5 autophagy-related genes were investigated using RT-qPCR technique. The data was analyzed using chi-square, ANOVA, and multinomial logistic regression tests.

KEY FINDINGS

The 50% lethal dose (LD50) of P. alkekengi and vitexin against the breast cancer cells included 12 mg/kg, respectively, while cinobufacini LD50 was 24 mg/kg but had no toxicity against CRL7242 breast normal cells. Furthermore, 24 mg/kg of the P. alkekengi, vitexin, and cinobufacini significantly increased the ATG5, Beclin-1, and LC3-II gene expression.

CONCLUSION

Considering anticancer effects of P. alkekengi, vitexin, and cinobufacini against breast cancer through induction of the autophagy pathway, the compound formulations can be applied as anticancer therapies.

Genetic Predisposition to Breast and Ovarian Cancers: How Many and Which Genes to Test?

Breast and ovarian cancers are some of the most common tumors in females, and the genetic predisposition is emerging as one of the key risk factors in the development of these two malignancies. BRCA1 and BRCA2 are the best-known genes associated with hereditary breast and ovarian cancer. However, recent advances in molecular techniques, Next-Generation Sequencing in particular, have led to the identification of many new genes involved in the predisposition to breast and/or ovarian cancer, with different penetrance estimates. TP53, PTEN, STK11, and CDH1 have been identified as high penetrance genes for the risk of breast/ovarian cancers. Besides them, PALB2, BRIP1, ATM, CHEK2, BARD1, NBN, NF1, RAD51C, RAD51D and mismatch repair genes have been recognized as moderate and low penetrance genes, along with other genes encoding proteins involved in the same pathways, possibly associated with breast/ovarian cancer risk. In this review, we summarize the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and the associated genetic disorders. Furthermore, we discuss the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.

Bioinformatics Resources for Cancer Research with an Emphasis on Gene Function and Structure Prediction Tools

The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases), pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.

Evaluation of the protective effect of Nigella sativa extract and its primary active component thymoquinone against DMBA-induced breast cancer in female rats

INTRODUCTION

The historical use of black cumin seed (Nigella sativa) dates back centuries, being embedded in Arabian culture and having a long history of unsurpassed medicinal value with versatility to treat a wide range of ailments. Thymoquinone (TQ) is now known to be the primary active constituent of black cumin seed oil (BCS oil) responsible for its medicinal effects and also showing promise for treatment of cancer.

MATERIAL AND METHODS

In the current study, we have studied the effects of TQ and BCS oil on tumor markers (MDA, LDH, ALP and AST), histopathological alterations and the regulation of several genes (Brca1, Brca2, Id-1 and P53 mutation) related to breast cancer in female rats induced by 7,12-dimethylbenz[a]anthracene (DMBA) treatment. Rats received a single dose (65 mg/kg b.w.) of DMBA via an intragastric tube to induce breast cancer. Animals that received DMBA were treated orally with 1, 5, 10 mg/kg of TQ or BCS oil via an intragastric tube three times per week for 4 months.

RESULTS

We found that TQ and then BCS reduced the rate of tumor markers (levels of MDA and LDH as well as ALP and AST activities), inhibited the histopathological alterations and decreased the expression of the Brca1, Brca2, Id-1 and P53 mutations in mammary tissues of female rats induced by DMBA treatment.

CONCLUSIONS

The results suggest that TQ and BCS oil exert a protective effect against breast carcinogens. The antioxidant property of TQ and BCS oil is mediated by their actions and investigating other underlying mechanisms merits further studies.

Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer

Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals.

Induction of apoptosis in human breast cancer cells via caspase pathway by vernodalin isolated from Centratherum anthelminticum (L.) seeds

BACKGROUND

Centratherum anthelminticum (L.) seeds (CA) is a well known medicinal herb in Indian sub-continent. We recently reported anti-oxidant property of chloroform fraction of Centratherum anthelminticum (L.) seeds (CACF) by inhibiting tumor necrosis factor-α (TNF-α)-induced growth of human breast cancer cells. However, the active compounds in CACF have not been investigated previously.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, we showed that CACF inhibited growth of MCF-7 human breast cancer cells. CACF induced apoptosis in MCF-7 cells as marked by cell size shrinkage, deformed cytoskeletal structure and DNA fragmentation. To identify the cytotoxic compound, CACF was subjected to bioassay-guided fractionation which yielded 6 fractions. CACF fraction A and B (CACF-A, -B) demonstrated highest activity among all the fractions. Further HPLC isolation, NMR and LC-MS analysis of CACF-A led to identification of vernodalin as the cytotoxic agent in CACF-A, and -B. 12,13-dihydroxyoleic acid, another major compound in CACF-C fraction was isolated for the first time from Centratherum anthelminticum (L.) seeds but showed no cytotoxic effect against MCF-7 cells. Vernodalin inhibited cell growth of human breast cancer cells MCF-7 and MDA-MB-231 by induction of cell cycle arrest and apoptosis. Increased of reactive oxygen species (ROS) production, coupled with downregulation of anti-apoptotic molecules (Bcl-2, Bcl-xL) led to reduction of mitochondrial membrane potential (MMP) and release of cytochrome c in both human breast cancer cells treated with vernodalin. Release of cytochrome c from mitochondria to cytosol triggered activation of caspase cascade, PARP cleavage, DNA damage and eventually cell death.

CONCLUSIONS/SIGNIFICANCE

To the best of our knowledge, this is the first comprehensive study on cytotoxic and apoptotic mechanism of vernodalin isolated from the Centratherum anthelminticum (L.) seeds in human breast cancer cells. Overall, our data suggest a potential therapeutic value of vernodalin to be further developed as new anti-cancer drug.

Cancer predisposing BARD1 mutations in breast-ovarian cancer families

The breast cancer susceptibility gene BARD1 (BRCA1-associated RING domain protein, MIM# 601593) acts with BRCA1 in DNA double-strand break (DSB) repair and also in apoptosis initiation. We screened 109 BRCA1/2 negative high-risk breast and/or ovarian cancer patients from North-Eastern Poland for BARD1 germline mutations using a combination of denaturing high-performance liquid chromatography and direct sequencing. We identified 16 different BARD1 sequence variants, five of which are novel. Three of them were suspected to be pathogenic, including a protein truncating nonsense mutation (c.1690C>T, p.Gln564X), a splice mutation (c.1315-2A>G) resulting in exon 5 skipping, and a silent change (c.1977A>G) which alters several exonic splicing enhancer motifs in exon 10 and results in a transcript lacking exons 2-9. Our findings suggest that BARD1 mutations may be regarded as cancer risk alleles and warrant further investigation to determine their actual contribution to non-BRCA1/2 breast and ovarian cancer families.

Identification of target genes and pathways associated with chicken microRNA miR-143

MicroRNA (miRNA) is a family of small regulatory RNAs that post-transcriptionally regulate many biological functions including growth and development. Recently, the expression of chicken miRNA miR-143 was identified by using a deep sequencing approach. In other vertebrate species, miR-143 functions as a regulator of adipocyte differentiation and as a tumour suppressor. However, little is known about the biological function(s) of miR-143 in chickens. To study the functions of chicken miR-143, DNA microarray analysis and a dual luciferase reporter assay were employed to identify genes directly targeted by miR-143 as well as other biologically relevant genes. Microarray analysis indicated that 124 genes were differentially expressed upon in vitro anti-miR-143 treatment in embryonic chick splenocytes (P-value cutoff <0.01). Many of these genes are associated with cell proliferation, apoptosis and tumourigenesis. Six of the up-regulated genes possess at least one potential miR-143 binding site in their 3'UTRs, of these the binding sites of PYCR2, PSTPIP1 and PDCD5 were validated by an in vitro luciferase reporter assay. In addition, several potential targets with important biological functions were identified by the miRanda algorithm and experimentally confirmed. These targets include KLF5, MAP3K7, TARDBP and UBE2E3, which have conserved miR-143 binding sites across multiple vertebrate species. Potential chicken specific miR-143 target sites were also validated for LPIN1, PCK2, PYCR2, METTL14, SLC2A2 and TNFSF10. Overall, the current study suggests that miR-143 is ubiquitously expressed among tissues and is likely to be involved in the regulation of cell proliferation and apoptosis.

The influence of common polymorphisms on breast cancer

Breast cancer is one of the most frequently diagnosed cancers in the Western world and a significant cause of mortality worldwide. A small proportion of cases are accounted for by high-penetrance monogenic predisposition genes; however, this explains only a small fraction (less than 5%) of all breast cancers. Increasingly with advances in molecular technology and the development of large research consortia, the locations and identities of many low-penetrance genetic variants are being discovered. However, each variant has a very small effect similar to or smaller than many of the known environmental risk factors. It is therefore unlikely that these variants will be appropriate for predictive genetic testing, although they may identify novel pathways and genes which provide new insights and targets for therapeutic intervention. The future challenges will be identifying causal variants and determining how these low-penetrance alleles interact with each other and with environmental factors in order to usefully implement them in the practice of clinical medicine. Furthermore, it is clear that breast cancer comes in many forms with the tumour pathology and immunohistochemical profile already being used routinely as prognostic indicators and to inform treatment decisions. However, these indicators of prognosis are imperfect; two apparently identical tumours may have very different outcomes in different individuals. Inherited genetic variants may well be one of the other factors that need to be taken into account in assessing prognosis and planning treatment.

Use of gene expression profiles of peripheral blood lymphocytes to distinguish BRCA1 mutation carriers in high risk breast cancer families

Mutations in two major genes, BRCA1 and BRCA2, account for up to 30% of families with hereditary breast cancer. Unfortunately, in most families there is little to indicate which gene should be targeted first for mutation screening, which is labor intensive, time consuming and often prohibitively expensive. As BRCA1 is a tumor suppressor gene involved in various cellular processes, heterozygous mutations could deregulate dependent pathways, such as DNA damage response, and disturb transcriptional activity of genes involved in the downstream signaling cascade. We investigated gene expression profiling in peripheral blood lymphocytes to evaluate this strategy for distinguishing BRCA1 mutation carriers from non-carriers. RNA from whole blood samples of 15 BRCA1 mutation carriers and 15 non-carriers from BRCA1 or BRCA2 families were hybridized to Agilent Technologies Whole Human Genome OligoMicroarrays (4 × 44 K multiplex format) containing 41,000 unique human genes and transcripts. Gene expression data were analyzed with Welch’s t-tests and submitted to hierarchical clustering (GeneSpring GX software, Agilent Technologies). Statistical analysis revealed a slight tendency for 133 genes to be differentially expressed between BRCA1 mutation carriers and non-carriers. However, hierarchical clustering of these genes did not accurately discriminate BRCA1 mutation carriers from non-carriers. Expression variation for these genes according to BRCA1 mutation status was weak. In summary, microarray profiling of untreated whole blood does not appear to be informative in identifying breast cancer risk due to BRCA1 mutation.

Common genetic variation in candidate genes and susceptibility to subtypes of breast cancer

Association studies have been widely used to search for common low-penetrance susceptibility alleles to breast cancer in general. However, breast cancer is a heterogeneous disease and it has been suggested that it may be possible to identify additional susceptibility alleles by restricting analyses to particular subtypes. We used data on 710 single nucleotide polymorphisms (SNP) in 120 candidate genes from a large candidate gene association study of up to 4,470 cases and 4,560 controls to compare the results of analyses of "overall" breast cancer with subgroup analyses based on the major clinicopathologic characteristics of breast cancer (stage, grade, morphology, and hormone receptor status). No SNP was highly significant in overall effects analysis. Subgroup analysis resulted in substantial reordering of ranks of SNPs, as assessed by the magnitude of the test statistics, and some associations that were not significant for an overall effect were detected in subgroups at a nominal 5% level adjusted for multiple testing. The most significant association of CCND1 SNP rs3212879 with estrogen receptor-negative tumor types (P = 0.001) did not reach genome-wide significance levels. These results show that it may be possible to detect associations using subgroup analysis that are missed in overall effects analysis. If the associations we found can be replicated in independent studies, they may provide important insights into disease mechanisms in breast cancer.

Y179C, F486L and N550H are BRCA1 variants that may be associated with breast cancer in a Sicilian family: results of a 5-year GOIM (Gruppo Oncologico dell'Italia Meridionale) prospective study

BACKGROUND

Over 600 different pathogenic mutations have been identified in the BRCA1 gene. Nevertheless, numerous missense mutations of unknown biological function still exist. Understanding of biological significance of these mutations should help in genetic counselling to carriers and their families.

PATIENTS AND METHODS

A total of 104 patients with breast and/or ovarian cancer whose genetic counselling answered the criteria of the American Society of Clinical Oncology (ASCO 2003), were prospectively screened for mutations in all coding exons of the BRCA1 gene by automatic direct sequencing.

RESULTS

During these mutational screening procedures one case presented three mutations classified in the Breast Cancer Information Core Database as unknown variants. These were 655A/G found in exon 8 of BRCA1, 1575T/C and 1767A/C found in exon 11 of the same gene. The identification of the three unknown variants in the proband (16SIRIO) and in her mother and sister indicates that such alterations exist in cis.

CONCLUSIONS

Our results suggest that the charge and stechiometry variations determined by the changes in the amino acids Y179C, F486L and N550H might produce an effect on the conformation of the protein and, consequently, on its function.

The autoimmune contrivance: genetics in the mouse model

Autoimmunity and inheritance of complex characters behold an explosive interest in biology over the last 15 years. Research in the genetics of autoimmunity has been impelled by the isolation of genetic markers allowing tracing of heredity. The annotation and sequencing of the human and mouse genomes provide with the potential for further advancements, through the development of new technologies. This review aims to summarize advances made in the autoimmunity field, centered in type 1 diabetes in the NOD mouse model. It also aims to demonstrate that animal models, albeit some phenotypic and genetic dissimilarities with the human diseases, still remain the best way to move towards an understanding of the molecular mechanisms involved in autoimmunity. Assessing the current state of research in this field together with the increasing potential of novel biotechnology advancements, new insights to disease pathogenesis and discovery of molecular targets for intervention strategies are anticipated in the coming years.

Embryonic reversions and lineage infidelities in tumour cells: genome-based models and role of genetic instability

Reversions to "embryonic precursor"-type cells and infidelities of tumour cell lineage (including metaplasias) have been recognized as aspects of various tumour types since the 19th century. Since then, evidence of these phenomena has been obtained from numerous clinical, biochemical, immunological and molecular biological studies. In particular, microarray studies have suggested that "aberrant" expressions of relevant genes are common. An unexplained aspect of the results of these studies is that, in many tumour types, the embryonic reversion or lineage infidelity only occurs in a proportion of cases. As a parallel development during the molecular biological investigation of tumours over the last several decades, genetic instability has been found much more marked, at least in some preparations of tumour cells, than that identified by means of previous karyotypic investigations of tumours. This study reviews examples of embryonic reversion and lineage infidelity phenomena, which have derived from the various lines of investigation of cancer over the last 150 or so years. Four categories of circumstances of the occurrence of embryonic reversions or lineage infidelities have been identified - (i) as part of the defining phenotype of the tumour, and hence being presumably integral to the tumour type, (ii) present ab initio in only some cases of the tumour type, and presumably being regularly associated with, but incidental to, the essential features of the tumour type, (iii) occurring later in the course of the disease and thus being possibly a manifestation of in vivo genetic instability and "tumour progression" and (iv) arising probably by genetic instability, during the processes, especially cell culture, associated with ex vivo investigations. Genomic models are described which might account for the origin of these phenomena in each of these circumstances.

[What place for DNA microarray in inflammatory diseases?]

PURPOSE

DNA chip is a recently developed technique allowing analysis of thousands of genes at the same time in multiple biological samples. In few years it has become an obligatory step in massive gene expression study. The enormous quantity of results generated and the new way of thinking allowed make this kind of study a true revolution.

KEY MESSAGE AND RECENT FACTS

The enormous discovery potential permitted by the accomplishment of multiple genomes sequencing and the advent of technologies allowing massive gene expression analyses have totally modified the diseases approach. Considering the obtainment of a real full picture of the transcriptional activity in an organ, tissue or cell is now legitimate. DNA microarray is obviously not the only technique allowing such type of analysis but it is without contest the technology which is the most popular and the one which has been recently the subject of the most important developments. It is certainly the technology which brought the main advances in tumour classification and discovery of new biomarkers. The first results based on this technology in inflammatory diseases have recently been reported.

PERSPECTIVE AND PROJECTS

The optimal use of DNA microarrays will necessitate a powerful statistical analysis and an high quality biological experimentation. Strict standard and quality criteria are developing. Obviously, the DNA chips have a role to play in multifactorial inflammatory diseases mainly through their potential to bring new answers to diagnostic and pathophysiological problems. One potential development of the technique in such diseases will be the definition of disease specific gene profiles and the generation of chips allowing the detection of few targeted genes with all the known mutations of these genes. The correlation of global or targeted gene expression with clinical and pathological data will allow a new step forward in the understanding and taking care of inflammatory diseases.

Evaluation of gene expression profile of keratinocytes in response to JP-8 jet fuel

The skin is the principal barrier against any environmental insult. Therefore, there is a high risk for a large number of military and civilian personnel exposed to jet fuel JP-8 to suffer percutaneous absorption of this fuel. This paper reports the use of cDNA microarray to identify the gene expression profile in normal human epidermal keratinocytes exposed to JP-8 for 24-h and 7-day periods. The effects of JP-8 exposure on keratinocytes at these two different periods induced a set of genes with altered expression in response to this type of insult. Microarray data were visualized using a novel algorithm based on simple statistical analyses to reduce data dimensionality and identify subsets of discriminant genes. Predictive neural networks were built using a multiplayer perceptron to carry out a proper classification task in microarray data in the untreated versus JP-8-treated samples. The pattern of expressions in response to JP-8 provides evidences that detoxificant-related and cell growth regulator genes with the most variability in the level of expression may be useful genetic markers in adverse health effects of personnel exposed to JP-8. The approaches in our analysis provide a simple, safe, novel, and effective method that is reliable in identifying and analyzing gene expression in samples treated with JP-8 or over potential toxic agents. Gene expression data from these studies can be used to build accurate predictive models that separate different molecular profiles. The data establish the use and effectiveness of these approaches for future prospective studies.

Conservation of Breast Cancer Molecular Subtypes and Transcriptional Patterns of Tumor Progression Across Distinct Ethnic Populations

PURPOSE

Breast cancers can display distinct clinical characteristics in different ethnic populations. Previous studies involving European and United States patients have shown that breast tumors can be divided by their gene expression profiles into distinct "molecular subtypes." In this report, we surveyed a series of invasive and preinvasive breast tumors from Asian-Chinese patients to investigate whether similar subtypes could also be observed in this ethnic group.

EXPERIMENTAL DESIGN AND RESULTS

An analysis of expression profiles generated from 11 nonmalignant breast tissues, 17 ductal carcinomas in situ (DCIS) and 98 invasive carcinomas identified three broad molecular subtypes of breast [estrogen receptor (ER)+, ERBB2+ and ER-] in the Asian-Chinese population. These subtypes were highly similar to the "Luminal," "ERBB2+," and "Basal" molecular subtypes defined in previous studies, and the subtype-specific expression signatures were also observed in preinvasive DCIS tumors. By comparing the expression profiles of nonmalignant DCIS and invasive breast cancers for two subtypes (ER+ and ERBB2+), we identified several genes that were regulated in both a common and subtype-specific manner during the normal/DCIS and DCIS/invasive carcinoma transitions. Several of these genes were validated by comparison with another recently published similar, but not identical, study.

CONCLUSIONS

Our results suggest that molecularly similar subtypes of breast cancer are indeed broadly conserved between Asian and Caucasian patients, and that these subtypes are already present at the preinvasive stage of carcinogenesis. To our knowledge, this study is among the first to directly compare the expression profiles of breast tumors across two different ethnic populations.

Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells

Selective estrogen receptor modulators (SERMs) such as tamoxifen are effective in the treatment of many estrogen receptor-positive breast cancers and have also proven to be effective in the prevention of breast cancer in women at high risk for the disease. The comparative abilities of tamoxifen versus raloxifene in breast cancer prevention are currently being compared in the Study of Tamoxifen and Raloxifene trial. To better understand the actions of these compounds in breast cancer, we have examined their effects on the expression of approximately 12,000 genes, using Affymetrix GeneChip microarrays, with quantitative PCR verification in many cases, categorizing their actions as agonist, antagonist, or partial agonist/antagonist. Analysis of gene stimulation and inhibition by the SERMs trans-hydroxytamoxifen (TOT) and raloxifene (Ral) or ICI 182,780 (ICI) and by estradiol (E2) in estrogen receptor-containing MCF-7 human breast cancer cells revealed that (a) TOT was the most E2-like of the three compounds, (b) all three compounds either partially or fully antagonized the action of E2 on most genes, with the order of antagonist activity being ICI > Ral > TOT, (c) TOT and Ral, but not ICI, displayed partial agonist/partial antagonist activity on a number of E2-regulated genes, (d) several stimulatory cell cycle-related genes were down-regulated exclusively by ICI, (e) the estrogen-like activity of Ral nearly always overlapped with that of TOT, indicating that Ral has little unique agonist activity different from that of TOT, and (f) some genes were specifically up-regulated by TOT but not Ral, ICI, or E2. Hence, gene expression profiling can discern fundamental differences among SERMs and provides insight into the distinct biologies of TOT, Ral, and ICI in breast cancer.

Genetic alteration and gene expression modulation during cancer progression

Cancer progresses through a series of histopathological stages. Progression is thought to be driven by the accumulation of genetic alterations and consequently gene expression pattern changes. The identification of genes and pathways involved will not only enhance our understanding of the biology of this process, it will also provide new targets for early diagnosis and facilitate treatment design. Genomic approaches have proven to be effective in detecting chromosomal alterations and identifying genes disrupted in cancer. Gene expression profiling has led to the subclassification of tumors. In this article, we will describe the current technologies used in cancer gene discovery, the model systems used to validate the significance of the genes and pathways, and some of the genes and pathways implicated in the progression of preneoplastic and early stage cancer.

Chromosome 13q12 encoded Rho GTPase activating protein suppresses growth of breast carcinoma cells, and yeast two-hybrid screen shows its interaction with several proteins

We have characterized the cDNA for a Rho GTPase activating protein (GAP) mapping to chromosome 13q12. The cDNA was characterized by determining the complete sequence of a 4.8 kb cDNA clone that represents the 5' untranslated region (UTR), the translated region, and the 3' UTR. The protein has a sterile alpha-motif (SAM), a distinct GAP domain, and a conserved START (StAR related lipid transfer) domain. The cDNA has 5 instability motifs (ATTTA) in the 3' UTR and one motif in the translated region between GAP and START domains. The RhoGAP transcript is truncated in some breast carcinoma cell lines and it has low expression in other breast cancer cell lines as compared to a normal breast cell line. We have previously observed the absence of RhoGAP transcript in a breast tumor specimen. A GST-fusion of the RhoGAP was tested for its specificity on RhoA, Cdc42, and Rac1. The protein was most active for RhoA. Transfection of RhoGAP into MCF7 cells significantly inhibited cell growth. The introduction of the RhoGAP construct into MDAMB231 cells that had previously been transfected with a p21 construct did not affect cell proliferation, indicating the involvement of p21 in Rho-mediated proliferation of cancer cells. NIH3T3 cells overexpressing RhoGAP showed considerable inhibition of stress fiber formation. Several cDNAs were identified as RhoGAP interactors by using the yeast two-hybrid assay system. These cDNAs correspond to SWI/SNF, alpha-tubulin, HMG CoA reductase, and TAX1 binding protein (TAX1BP1). The interaction with HMG CoA reductase may partially explain the growth inhibition of breast carcinoma cells by statin class of cholesterol lowering drugs. The biological significance of the interacting proteins is discussed in the context of their involvement in tumorigenesis. Our results indicate that loss of RhoGAP or its altered activity suppresses the growth of breast tumor cells. The presence of various motifs in RhoGAP and its interaction with several other proteins suggest that the protein may regulate Rho signaling in multiple ways and possibly function in a Rho-independent manner.

Advantages and limitations of microarray technology in human cancer

Cancer is a highly variable disease with multiple heterogeneous genetic and epigenetic changes. Functional studies are essential to understanding the complexity and polymorphisms of cancer. The final deciphering of the complete human genome, together with the improvement of high throughput technologies, is causing a fundamental transformation in cancer research. Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously. This technology promises to lead to improvements in developing rational approaches to therapy as well as to improvements in cancer diagnosis and prognosis, assuring its entry into clinical practice in specialist centers and hospitals within the next few years. Predicting who will develop cancer and how this disease will behave and respond to therapy after diagnosis will be one of the potential benefits of this technology within the next decade. In this review, we highlight some of the recent developments and results in microarray technology in cancer research, discuss potentially problematic areas associated with it, describe the eventual use of microarray technology for clinical applications and comment on future trends and issues.

Profiling of estrogen up- and down-regulated gene expression in human breast cancer cells: insights into gene networks and pathways underlying estrogenic control of proliferation and cell phenotype

Estrogens are known to regulate the proliferation of breast cancer cells and to alter their cytoarchitectural and phenotypic properties, but the gene networks and pathways by which estrogenic hormones regulate these events are only partially understood. We used global gene expression profiling by Affymetrix GeneChip microarray analysis, with quantitative PCR verification in many cases, to identify patterns and time courses of genes that are either stimulated or inhibited by estradiol (E2) in estrogen receptor (ER)-positive MCF-7 human breast cancer cells. Of the >12,000 genes queried, over 400 showed a robust pattern of regulation, and, notably, the majority (70%) were down-regulated. We observed a general up-regulation of positive proliferation regulators, including survivin, multiple growth factors, genes involved in cell cycle progression, and regulatory factor-receptor loops, and the down-regulation of transcriptional repressors, such as Mad4 and JunB, and of antiproliferative and proapoptotic genes, including B cell translocation gene-1 and -2, cyclin G2, BCL-2 antagonist/killer 1, BCL 2-interacting killer, caspase 9, and TGFbeta family growth inhibitory factors. These together likely contribute to the stimulation of proliferation and the suppression of apoptosis by E2 in these cells. Of interest, E2 appeared to modulate its own activity through the enhanced expression of genes involved in prostaglandin E production and signaling, which could lead to an increase in aromatase expression and E2 production, as well as the decreased expression of several nuclear receptor coactivators that could impact ER activity. Our studies highlight the diverse gene networks and metabolic and cell regulatory pathways through which this hormone operates to achieve its widespread effects on breast cancer cells.

Current and potential uses for DNA microarrays in transplantation medicine: lessons from other disciplines

DNA microarrays are used to study simultaneous gene expression in thousands of genes. This tool has moved beyond proof-of-principle and its integration into medical practice is slowly becoming a reality. This technology has enabled unparalleled progress into the study of complex polygenic diseases. Although cancer research introduced DNA microarrays into the medical arena other disciplines are beginning to exploit the power of this technology to advance medical research. In this review we outline aspects of the design of a microarray experiment from the choice of platform, through the experimental procedure to the analysis of the results. We review the current applications and speculate on potential applications of this technology with particular reference to transplantation medicine.

Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach

Partial least squares discriminant analysis (PLS-DA) is a partial least squares regression of a set Y of binary variables describing the categories of a categorical variable on a set X of predictor variables. It is a compromise between the usual discriminant analysis and a discriminant analysis on the significant principal components of the predictor variables. This technique is specially suited to deal with a much larger number of predictors than observations and with multicollineality, two of the main problems encountered when analysing microarray expression data. We explore the performance of PLS-DA with published data from breast cancer (Perou et al. 2000). Several such analyses were carried out: (1) before vs after chemotherapy treatment, (2) estrogen receptor positive vs negative tumours, and (3) tumour classification. We found that the performance of PLS-DA was extremely satisfactory in all cases and that the discriminant cDNA clones often had a sound biological interpretation. We conclude that PLS-DA is a powerful yet simple tool for analysing microarray data.

DNA microarray and cancer

Since the discovery of the first oncogene 26 years ago, a large body of research has convincingly demonstrated that the initiation and progression of cancers involve the accumulation of genetic aberrations in the cell. Many techniques have been developed to identify these genetic abnormalities. The recent completion of human genome sequencing and advances in DNA microarray technology allow rapid genetic analysis to take place on a genome-wide scale and have revolutionized the way cancers are studied. This ground-breaking approach of studying cancer promises to provide a better understanding of the underlying mechanism for tumorigenesis, more accurate diagnosis, more comprehensive prognosis, and more effective therapeutic interventions.

The Systemic Progression of Human Cancer: A Focus on the Individual Disseminated Cancer Cell—The Unit of Selection

The metastatic progression of solid tumors is discussed controversially. Because metastasis is usually lethal, it appears as an end point of successive cellular changes. This has led to the prevailing interpretation that genetic changes, in addition to those present in the most advanced clone of the primary tumor, are required to initiate invasion, dissemination, and growth at anatomically distant sites. It has become possible to detect and analyze single disseminated cancer cells at ectopic sites long before metastasis can be diagnosed by standard clinical techniques. Because the finding of single disseminated cancer cells correlates with the subsequent development of distant metastasis, these cells have been identified as the precursors of metastasis. Their direct molecular-genetic characterization, however, shows that dissemination occurs very early in the process of accumulation of genetic changes and suggests that metastases may seldom be derived from the dominant clone of the primary tumor. In contrast, it appears that cancer cell evolution explores a multitude of variant cells from which systemic cancer can develop independently. This review integrates data derived by different approaches into a model of systemic cancer progression.