Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro

Background

Cancer prevention trials using different types of antioxidant supplements have been carried out at several occasions and one of the investigated compounds has been the antioxidant N-acetyl-L-cysteine (NAC). Studies at the cellular level have previously demonstrated that a single supplementation of NAC induces a ten-fold more rapid differentiation in normal primary human keratinocytes as well as a reversion of a colon carcinoma cell line from neoplastic proliferation to apical-basolateral differentiation [1]. The investigated cells showed an early change in the organization of the cytoskeleton, several newly established adherens junctions with E-cadherin/β-catenin complexes and increased focal adhesions, all features characterizing the differentiation process.

Methods

In order to investigate the molecular mechanisms underlying the proliferation arrest and accelerated differentiation induced by NAC treatment of NHEK and Caco-2 cells in vitro, we performed global gene expression analysis of NAC treated cells in a time series (1, 12 and 24 hours post NAC treatment) using the Affymetrix GeneChip™ Human Genome U95Av2 chip, which contains approximately 12,000 previously characterized sequences. The treated samples were compared to the corresponding untreated culture at the same time point.

Results

Microarray data analysis revealed an increasing number of differentially expressed transcripts over time upon NAC treatment. The early response (1 hour) was transient, while a constitutive trend was commonly found among genes differentially regulated at later time points (12 and 24 hours). Connections to the induction of differentiation and inhibition of growth were identified for a majority of up- and down-regulated genes. All of the observed transcriptional changes, except for seven genes, were unique to either cell line. Only one gene, ID-1, was mutually regulated at 1 hour post treatment and might represent a common mediator of early NAC action.

The detection of several genes that previously have been identified as stimulated or repressed during the differentiation of NHEK and Caco-2 provided validation of results. In addition, real-time kinetic PCR analysis of selected genes also verified the differential regulation as identified by the microarray platform.

Conclusion

NAC induces a limited and transient early response followed by a more consistent and extensively different expression at later time points in both the normal and cancer cell lines investigated. The responses are largely related to inhibition of proliferation and stimulation of differentiation in both cell types but are almost completely lineage specific. ID-1 is indicated as an early mediator of NAC action.

Slow genetic divergence of Helicobacter pylori strains during long-term colonization

The genetic variability of Helicobacter pylori is known to be high compared to that of many other bacterial species. H. pylori is adapted to the human stomach, where it persists for decades, and adaptation to each host results in every individual harboring a distinctive bacterial population. Although clonal variants may exist within such a population, all isolates are generally genetically related and thus derived from a common ancestor. We sought to determine the rate of genetic change of H. pylori over 9 years in two asymptomatic adult patients. Arbitrary primed PCR confirmed the relatedness of individual subclones within a patient. Furthermore, sequencing of 10 loci ( approximately 6,000 bp) in three subclones per time and patient revealed only two base pair changes among the subclones from patient I. All sequences were identical among the patient II subclones. However, PCR amplification of the highly divergent gene amiA revealed great variation in the size of the gene between the subclones within each patient. Thus, both patients harbored a single strain with clonal variants at both times. We also studied genetic changes in culture- and mouse-passaged strains, and under both conditions no genetic divergence was found. These results suggest that previous estimates of the rate of genetic change in H. pylori within an individual might be overestimates.

Expression profile of genes associated with antimetastatic gene:nm23-Mediated metastasis inhibition in breast carcinoma cells

Metastases of various malignancies have been shown to be inversely related to the abundance of nm23 protein expression. However, the downstream pathways involved in nm23-mediated suppression of metastasis have not been elucidated. In the present investigation, we used cDNA microarrays to identify novel genes and functional pathways in nm23-mediated spontaneous breast metastasis. Microarray experiments were performed in a pair of cell lines, namely, C-100 (only vector transfected; highly metastatic) and H1-177 (nm23 transfected; low metastatic), derived from human mammary carcinoma cell line MDA-MB-435. The cDNA microarray analysis using GeneSpring software revealed significant as well as consistent alterations in the expression (up- and downregulation) of 2158 genes in a total of 18889 genes between high and low metastatic cells. Some of these genes were grouped into 6 functional categories, namely, invasion and metastasis, apoptosis and senescence, signal transduction molecules and transcription factors, cell cycle and repair, adhesion, and angiogenesis to extrapolate an association between these genes and different functional pathways involved in nm23-regulated metastasis. The results suggest that nm23 gene plays a major role in metastasis and its mechanism of action of metastasis suppression may involve downregulation of genes associated with cell adhesion, motility (integrins alpha2, -8, -9, -L and -V, collagen type VIII alpha1, fibronectin 1, catenin, TGF-beta2, FGF7, MMP14 and 16, ErbB2) and possibly certain tumor/metastasis suppressors (2 members of SWI/SNF-related matrix-associated proteins 2 and 5 and PTEN).

A haplotype framework for cystic fibrosis mutations in Iran

This is the first comprehensive profile of cystic fibrosis transmembrane conductance regulator (CFTR) mutations and their corresponding haplotypes in the Iranian population. All of the 27 CFTR exons of 60 unrelated Iranian CF patients were sequenced to identify disease-causing mutations. Eleven core haplotypes of CFTR were identified by genotyping six high-frequency simple nucleotide polymorphisms. The carrier frequency of 2.5 in 100 (1 in 40) was estimated from the frequency of heterozygous patients and suggests that contrary to popular belief, cystic fibrosis may be a common, under-diagnosed disease in Iran. A heterogeneous mutation spectrum was observed at the CFTR locus in 60 cystic fibrosis (CF) patients from Iran. Twenty putative disease-causing mutations were identified on 64 (53%) of the 120 chromosomes. The five most common Iranian mutations together represented 37% of the expected mutated alleles. The most frequent mutation, DeltaF508 (p.F508del), represented only 16% of the expected mutated alleles. The next most frequent mutations were c.1677del2 (p.515fs) at 7.5%, c.4041C>G (p.N1303K) at 5.6%, c.2183AA>G (p.684fs) at 5%, and c.3661A>T (p.K1177X) at 2.5%. Three of the five most frequent Iranian mutations are not included in a commonly used panel of CF mutations, underscoring the importance of identifying geographic-specific mutations in this population.

Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities

PURPOSE

Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression.

EXPERIMENTAL DESIGN

We exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy-Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis.

RESULTS

A total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8-18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17-0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia.

CONCLUSIONS

We have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy.

Gene Expression Analysis of Human Epidermal Keratinocytes after N-Acetyl L-Cysteine Treatment Demonstrates Cell Cycle Arrest and Increased Differentiation

OBJECTIVES

Several cancer prevention programmes have previously been executed using treatment of antioxidant compounds. The antioxidant N-acetyl L-cysteine (NAC), a membrane-permeable aminothiol, is a sulfhydryl reductant reducing oxidised glutathione, as well as being a precursor of intracellular cysteine and glutathione. A previous report based on the cellular response to NAC treatment showed that NAC induced a 10-fold more rapid differentiation in normal primary keratinocytes as well as a reversion of a colon carcinoma cell line from neoplastic proliferation to apical-basolateral differentiation. In order to investigate molecular events underlying the changes in proliferation and differentiation induced by NAC treatment, we performed global gene expression analysis of normal human epidermal keratinocytes in a time series.

METHODS

Treated samples were compared to untreated samples through a reference design using a spotted cDNA array comprising approximately 30,000 features. B statistics was used to identify differentially expressed genes, and RT-PCR of a selected set of genes was performed to verify differential expression.

RESULTS

The number of differentially expressed genes increased over time, starting with 0 at 30 min, 73 at 3 h and increasing to 952 genes at 48 h. Results of the expression analysis showed arrest of the cell cycle and an upregulation of cytoskeletal reorganisation, implicating increased differentiation. A comparison to gene ontology groups indicated downregulation of a large number of genes involved in cell proliferation and regulation of the cell cycle.

CONCLUSIONS

A significant fraction of the differentially expressed genes could be classified according to their role in the differentiation process, demonstrating that NAC regulates the conversion from proliferation to differentiation at a transcriptional level.

Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues

The growing collection of publicly available high-throughput data provides an invaluable resource for generating preliminary in silico data in support of novel hypotheses. In this study we used a cross-dataset meta-analysis strategy to identify novel candidate genes and genetic variations relevant to paclitaxel/carboplatin-induced myelosuppression and neuropathy. We identified genes affected by drug exposure and present in tissues associated with toxicity. From ten top-ranked genes 42 non-synonymous single nucleotide polymorphisms (SNPs) were identified in silico and genotyped in 94 cancer patients treated with carboplatin/paclitaxel. We observed variations in 11 SNPs, of which seven were present in a sufficient frequency for statistical evaluation. Of these seven SNPs, three were present in ABCA1 and ATM, and showed significant or borderline significant association with either myelosuppression or neuropathy. The strikingly high number of associations between genotype and clinically observed toxicity provides support for our data-driven computations strategy to identify biomarkers for drug toxicity.

Identification of AGR3 as a potential biomarker though public genomic data analysis of triple-negative (TN) versus triple-positive (TP) breast cancer (BC)

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Background: TNBCs have an aggressive clinical phenotype with worse prognosis than TPBC. Here we sought to identify other genomic changes in patients with TN vs. TPBC, by mining TCGA breast cancer genomic data using the NextBio Clinical platform. Methods: Breast cancer patients with decreased (n=51) and increased (n=46) ER/PR/HER2 mRNA levels were selected with the molecular filter in NB Clinical. Top-ranked differentially expressed genes were identified then analyzed via NB Research, which comprises a library of individually curated publically available research and clinical grade genomic data. Results: Whole transcriptome analysis of TNBC and TPBC patients identified anterior gradient-3 (AGR3), a protein disulfide isomerase, as most downregulated (TNBC vs. TPBC, fold change = -178.2, p=2.7E-32). AGR3 mRNA was reduced in 94% of TNBC and increased in 96% of TPBC patients. AGR3 was hypomethylated in 50% of TPBC vs. 4% of TNBC patients, suggesting regulation by methylation. When the entire breast cancer cohort was stratified by AGR3 expression, underexpression was prevalent in younger patients (<50 yr, 39%) compared to those with overexpression (<50 yr, 23%). Further, 63% of AGR3 underexpressing patients had severe TP53 mutations vs. 19% with AGR3 overexpression. Breast cancer was most correlated to AGR3 in the NextBio Disease Atlas, with supporting data from 110 studies. AGR3 expression was decreased in ER- vs. ER+, PR- vs. PR+, HER2- vs. HER2+, and G3 vs. G1 tumors, and AGR3 promoter was hypermethylated in ER- vs. ER+, consistent with the TCGA results. Body Atlas showed strongest AGR3 expression in mucosa, fallopian tube, breast, and epithelial cells, in line with its proposed role in epithelial barrier function. Knockdown Atlas results showed TP53 mutation associated with reduced AGR3 mRNA, and the PharmacoAtlas showed positive regulation of AGR3 by estrogen analogues. Conclusions: Using the NextBio Clinical and Research platforms, we identified AGR3 as a marker of TNBC vs. TPBC that correlates with TP53 mutation status. AGR3 may provide an alternate route of TNBC treatment. Its potential in regulating epithelial barrier function may provide insights into the mechanism of disease progression.

Disruption of protocadherin function and correlation with metastasis and cancer progression in TCGA patients

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Background: Protocadherins (PCDH) are a large family of calcium-dependent cell–cell adhesion molecules involved in tissue morphogenesis. Inactivation of PCDH locus genes are implicated in a number of oncogenic processes—hypermethylation of the PCDH gamma locus is present in Wilms’ tumors and arises after tumor development and the epigenetic silencing of PCDHGA11 occurs in the course of parenchymal invasion by astrocytomas. Assessment of PCDH function may help guide treatment decisions and provide a marker for metastasis in specific cancers. Methods: Identification of altered PCDH locus genes in TCGA patient samples was performed using the NextBio Clinical platform which provides access to the genomic and clinical data available in the TCGA dataset. The NextBio Research platform was used to correlate curated public experimental data and identify deleterious genomic changes associated with the PCDH locus and disease. Results: A nearly 3-fold increase in the frequency of potentially detrimental somatic mutations in PCDHGB4 was observed in breast cancer patients with extensive lymph node metastases (N3) compared to those with a lower degree of lymph node metastasis (N0-N2) (p value = 0.015). No other cancers appeared to have genomic changes deleterious to PCDHGB4 function, including ovarian and uterine cancer. Using the NextBio Research platform, breast cancer was found to be the 3rd most correlated disease with PCDHGB4, strongly correlating with RNA downregulation, DNA hypermethylation, and copy number loss. Other deleterious genomic changes in the PCDH locus were identified in ovarian (PCDHG), renal (PCDHA), and lung (PCDHA) cancers. Conclusions: Using the NextBio Clinical and Research platforms to analyze available TCGA data, disruption of PCDH function was found to correlate with increased metastasis only in certain cancers and with specific locus-disease pairings. Examination of PCDH locus perturbations may provide insight into a patient’s risk of developing metastatic disease. Further examination of the tissue specific alteration in PCDH genes may also aid in identifying unique cell adhesion pathways leading to metastasis in distinct tissues.

Disruption of protocadherin function as an indicator of cancer progression

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Background: Protocadherins (PCDH) are a large family of calcium-dependent cell–cell adhesion molecules that are involved in tissue morphogenesis, in particular the development of the central nervous system. Recently, alteration of PCDH alpha/beta/gamma locus genes have been implicated in a number of oncogenic processes: hypermethylation of the PCDH locus in Wilms’ tumor progression and metastasis, differential expression of some PCDH genes between bone and brain metastases in breast cancer patients, and epigenetic silencing of PCDH gamma A11 in astrocytoma invasion of the adjacent parenchyma. Assessment of PCDH function could help guide treatment decisions by aiding in the identification of cancer patients who are more likely to develop metastases. Methods: Identification of altered PCDH locus genes in cancer patient samples was performed using the NextBio platform which incorporates curated public genomic data from numerous sources, including TCGA, GEO, COSMIC, and others. Correlation of numerous data types was used to identify deleterious mutations, altered RNA expression, and copy number changes that were indicative of metastasis or a more advanced disease state. Results: A nearly 3-fold increase in the frequency of potentially detrimental somatic mutations in the PCDH gamma locus was observed in breast and ovarian cancer patients with extensive lymph node metastases (N3) compared to patients with a lower degree of lymph node metastasis (N0-N2). Similarly, expression of PCDH locus genes was down-regulated in cases of lymphoma, in metastatic samples across a number of diseases, and in diseases that commonly result in lymph node metastases including breast and lung cancer. Conclusions: Stratification of patient subgroups based on molecular signatures has become increasingly important for both assigning patients to appropriate clinical trials as well as providing insight into effective treatment options. Examination of PCDH perturbations may provide insight into a patient’s risk of developing a metastatic disease, in particular metastases to lymph nodes, and help identify patients who may benefit from a more aggressive treatment regimen.

Abstract 2989: Identification of a potential tumor suppressor function for SNX9 by mining public genomic data

Members of the sorting nexin (SNX) family of proteins are involved in intracellular trafficking and endocytosis processes, with functions essential to regulation of cell surface receptor levels and subsequent signaling by receptor-mediated endocytosis. Detrimental mutations and altered expression of SNX genes have been found in several cancers and tumor cell lines. A recent publication (Mao et al. AJCR 2011) identified a chromosomal translocation that created a SNX9:UNC5C fusion gene in prostate cancer cells. UNC5C is a known tumor suppressor gene. Although SNX9 is known to regulate degradation of EGFR, a well-established prognostic marker for lung cancer, no tumorigenic role has been identified for SNX9. We investigated associations of SNX9 to cancer phenotypes by mining curated public genomic data available in NextBio. Integration of diverse datatypes such as gene/miRNA expression, methylation, and copy-number variation in NextBio allowed us to uncover several lines of evidence which indicated that SNX9 activity is altered in many types of cancer. i) Loss of the SNX9 gene was observed in many different cancers including multiple myeloma, leukemia, lymphoma, melanoma, glioblastoma, renal clear cell carcinoma, and breast cancer. ii) Hypermethylation of SNX9, indicative of overall gene silencing, occurred in colorectal cancer, breast cancer and glioblastoma. iii) The miRNA predicted to target SNX9, miR-493-5p, was up-regulated in prostate, testicular, liver, and lung cancers. iv) SNX9 gene expression was down regulated relative to normal tissues in multiple myeloma, leukemia, lymphoma, cancers of the skin, breast, prostate and more. Correlations within the data suggest an association between the loss of SNX9 and more aggressive or recurrent disease; SNX9 is reduced in higher grade, metastatic clear cell carcinoma relative to lower grade, non-metastatic clear cell carcinoma. In myeloma and leukemia patients, lower SNX9 expression in primary tumors correlated with earlier relapsing disease. SNX9 expression was also lower when comparing recurring with primary acute myeloid leukemia. Querying our PharmacoAtlas application revealed that SNX9 gene expression was altered by a number of anti-neoplastic therapies. For example, paclitaxel, bortezomib, and letrozole treatments were each found to increase SNX9 gene expression in breast cancer cells whereas doxorubicin treatment resulted in decreased SNX9 expression. The integrative analysis of curated public genomic data drawn from thousands of studies strongly supports a hypothesis that SNX9 is a putative tumor suppressor and biomarker for more aggressive forms of cancer. As genomic technologies are applied to patient evaluation and therapeutic guidance, integrating multiple lines of evidence from research and clinical data to identify biomarkers such as SNX9 will increasingly inform clinical decision making.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2989. doi:1538-7445.AM2012-2989