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Estrogen and progesterone receptor isoforms: clinical significance in breast cancer.

The identification and exploitation of biomarkers that may predict response to anti-cancer treatments has the capacity to revolutionize the way that patients with cancer are treated. In breast cancer, the estrogen receptor (ER) and the progesterone receptor (PgR) are known to have a significant predictive value in determining sensitivity to endocrine therapies. Tumor expression of ER or PgR is known to affect clinical outcome and this information is often used to determine a patient's optimal treatment regimen. However, the measurement of ER and PgR alone is more complex than originally thought and the impact of the recently identified isoforms of ER (ERalpha and ERbeta) and PgR (PgRA and PgRB), as well as several variant and mutant forms, upon the choice of treatment remains unclear. Therefore, ER and PgR expression alone are unlikely to determine a patient's optimal treatment regimen, particularly when the amount of 'cross-talk' between different pathways, such as the epidermal growth factor receptor pathway, is considered. In order to account for the complex cell-signaling environment that occurs in breast cancer, multifactorial techniques are needed to analyze tumor biomarker expression. The recent advances in genomic- or proteomic-based approaches has enabled molecular portraits of breast cancers to be painted, allowing biomarkers of response and prognosis to be identified and characterized more accurately than before. In the future, patients could be treated according to the molecular portrait of their tumor biomarker expression, maximizing the therapeutic benefit that each patient receives.

Biomarkers, Tumor↗

[The NOLA2 and RPS3A genes as highly informative markers for human squamous cell lung cancer].

cDNA libraries enriched with sequences that are differentially transcribed in normal and tumor tissues were prepared using the subtractive hybridization of mixtures of cDNAs from ten patients with squamous cell lung cancer and the corresponding mixtures of cDNAs from normal tissues of the same patients. An analysis of the libraries revealed two genes, NOLA2 and RPS3A, whose expression in patients with squamous cell lung cancer increased by 70%. A high frequency of enhanced expression of these genes in the cancer makes them highly informative markers of squamous cell lung cancer, which, together with other markers, can be used for reliable diagnosis of the disease.

Biomarkers, Tumor↗

Prediction of optimal versus suboptimal cytoreduction of advanced-stage serous ovarian cancer with the use of microarrays.

OBJECTIVE: The purpose of this study was to define gene expression patterns that are associated with the optimal versus suboptimal debulking of advanced-stage serous ovarian cancers. STUDY DESIGN: RNA from 44 advanced serous ovarian cancers (19 optimal, 25 suboptimal) was evaluated with microarrays that contain >22,000 genes. Genes were screened on the basis of their association with debulking status to obtain the top 120 differentially expressed genes. These genes were then used to develop a predictive model for debulking status, which was subjected to out-of-sample cross validation. RESULTS: We found that patterns of expression of 32 genes can distinguish between optimal and suboptimal debulking with 72.7% predictive accuracy. An analysis of the data that were based on clusters of co-ordinately expressed genes resulted in only a marginal improvement in predictive accuracy (75%). CONCLUSION: These data support the hypothesis that favorable survival that is associated with optimal debulking of advanced ovarian cancers is due to, at least in part, the underlying biologic characteristics of these cancers.

Biomarkers, Tumor↗

Identification of two novel markers for alveolar epithelial type I and II cells.

Alveolar epithelial type I and type II cells (AEC I and II) are closely aligned in alveolar surface. There is much interest in the precise identification of AEC I and II in order to separate and evaluate functional and other properties of these two cells. This study aims to identify specific AEC I and AEC II cell markers by DNA microarray using the in vitro trans-differentiation of AEC II into AEC I-like cells as a model. Quantitative real-time PCR confirmed five AEC I genes: fibroblast growth factor receptor-activating protein 1, aquaporin 5, purinergic receptor P2X 7 (P2X7), interferon-induced protein, and Bcl2-associated protein, and one AEC II gene: gamma-aminobutyric acid receptor pi subunit (GABRP). Immunostaining on cultured cells and rat lung tissue indicated that GABRP and P2X7 proteins were specifically expressed in AEC II and AEC I, respectively. In situ hybridization of rat lung tissue confirmed the localization of GABRP mRNA in type II cells. P2X7 and GABRP identified in this study could be used as potential AEC I and AEC II markers for studying lung epithelial cell biology and monitoring lung injury.

Animals↗

D-GPCR: a novel putative G protein-coupled receptor overexpressed in prostate cancer and prostate.

The use of molecular targets in novel strategies of tumor treatment largely depends on the identification of proteins with a tumor- or tissue-restricted expression. We identified the novel protein D-GPCR that is selectively overexpressed in human prostate cancer and prostate and belongs to the subfamily of odorant-like orphan G protein-coupled receptors. Quantification of D-GPCR transcripts in different human tissues by real-time PCR demonstrated 27-fold overexpression in prostate compared to skeletal muscle, the organ with second highest transcript numbers in males. Investigation of tumor/normal cDNA pairs obtained from 241 cancer patients including four prostate tumors confirmed the preferential expression in prostate. When comparing the mean transcript level of 15 prostate cancer tissues to their non-tumorous counterparts, D-GPCR was almost 6-fold upregulated. Coupled in vitro transcription and translation of D-GPCR cDNA produced a protein band of approximately 28 kDa. Recombinant, His-tagged protein was expressed in transfected HEK293 cells and gave rise to a 30 kDa band specifically detected by anti-His antibody. These data provide the basis for future studies evaluating the diagnostic potential of D-GPCR and its utility as a novel target in immunotherapy of prostate cancer.

Aged↗

Expression of myo-inositol oxygenase in tissues susceptible to diabetic complications.

Alterations of intracellular levels of myo-inositol (MI) have the potential to impact such cellular processes as signaling pathways and osmotic balance. Depletion of MI has been implicated in the etiology of diabetic complications; however, the mechanistic details remain sketchy. myo-Inositol oxygenase (MIOX-EC 1.13.99.1) catalyzes the first committed step of the only pathway of MI catabolism. In the present study, extra-renal tissues and cell types, including those affected by diabetic complications, were examined for MIOX expression. Western blotting results indicated that kidney is the only major organ where MIOX protein is expressed at detectable levels. Immunohistochemical examination of the kidney revealed that the proximal tubular epithelial cells are the only site of MIOX expression in the kidney. Reverse-transcription-polymerase chain reaction (RT-PCR) and Western immunoblot analyses, however, revealed that the cell lines ARPE-19 and HLE-B3, representing human retinal pigmented epithelium and lens epithelium, respectively, also express MIOX. In addition, quantitative real-time RT-PCR analysis of all major tissues in the mouse showed that the sciatic nerve contained MIOX transcript, which was found to be significantly higher than that observed in other non-renal organs. These results indicate that MIOX is found at lower levels in extra-renal tissues where diabetic complications, including nephropathy, neuropathy, retinopathy, and cataract, are frequently observed.

Animals↗

beta-Catenin, Nf-kappaB and FAS protein expression are independent events in head and neck cancer: study of their association with clinical parameters.

In spite of much effort, no good markers have yet been found for predicting prognosis or response to therapy in advanced head and neck squamous cell carcinoma (HNSCCs) patients. beta-catenin, a protein involved in the cytoskeleton, cell-cell adhesion and gene transcription, is a factor associated with tumour progression. Recently, an interaction has been reported between beta-catenin, and NF-kappaB coupled with an inverse association of beta-catenin, and FAS (CD95/APO-1) protein expression in breast and colorectal tumours. To confirm these observations and to test their clinical impact in HNSCCs we have evaluated the expression of beta-catenin, NF-kappaB and FAS proteins. We used tissue microarrays to simultaneously analyse the levels of these proteins immunohistochemically in 118 HNSCCs. Among the 113 tumours evaluable for beta-catenin, increased and decreased levels were detected in 41 (36%) and 62 (55%) of the tumours, respectively. beta-catenin, protein staining was mainly membranous but 10 tumours (9%) showed the clear presence of protein in the cytoplasm, and none in the nucleus. Moreover, 81% of the tumours had decreased FAS protein expression, indicating that loss of FAS protein is a common feature of HNSCCs. Abnormal or nuclear NF-kappaB staining was observed in 24% of the tumours. No association was detected between the expression levels of the proteins evaluated. Regarding clinical associations, tumours from the hypopharynx had significantly lower levels of beta-catenin expression than those from other locations (P<0.05). Moreover, our data revealed that patients whose tumours had low levels of beta-catenin protein expression had decreased survival probability (24.8 months vs. NR, P=0.03) and reduced response to therapy (15.4 vs. 43 months; P=0.01) compared with patients whose tumours had high levels of beta-catenin. Taken together, our observations indicate that beta-catenin, NF-kappaB and FAS expression are independent events during HNSCC development and that levels of beta-catenin protein may identify subsets of advanced HNSCCs patients with different prognosis and response to therapy capabilities.

Biomarkers, Tumor↗

The strong induction of metallothionein gene following cadmium exposure transiently affects the expression of many genes in Eisenia fetida: a trade-off mechanism?

Metal pollution causes disturbances at various levels of biological organization in most species. Important physiological functions could be affected in the exposed individuals and among the main physiological functions, immunity may provide one (or more) effector(s) whose expression can be directly affected by a metal exposure in various macroinvertebrates. Protein expressions were studied in order to test them as molecular biomarkers of metal exposure in Eisenia fetida. Selected effectors were calmodulin, heat shock proteins, superoxide dismutase, catalase, metallothionein, beta-adrenergic receptor kinase, pyruvate carboxylase, transcriptionally controlled tumor protein, protein kinase C, ubiquitin and cyclophilin-A. The level of expression of each gene was analysed in whole organism following exposures to cadmium in soil using real-time PCR. Metallothionein, transcriptionally controlled tumor protein and cyclophilin-A expression were also measured following copper exposures in soil because these genes seemed to be sensitive to copper. This work enabled to distinguish metallothionein and cyclophilin-A among the 15 selected effectors. A strong decrease of the number of transcripts was also detected for most effectors soon after the exposure to cadmium suggesting that a trade-off mechanism occurs.

Animals↗

Gene expression analysis and clinical diagnosis.

BACKGROUND: A new basis for diagnostic tests is being provided by the vast amount of data on gene expression that are now becoming available through large-scale measurement of mRNA abundance. The insights gained from these resources are most likely going to provide both a better basic understanding of disease mechanisms, and to identify molecular markers for more precise diagnoses and for prediction of prognosis and treatment response. METHODS: Some quantitative RT-PCR assays are utilized today for diagnosis of both malignant and non-malignant disease, but the use of gene expression measurements in clinical medicine can be expected to increase dramatically. CONCLUSIONS: There are important technical issues that must be adequately solved in order to obtain robust assays, such as standardized protocols with appropriate quality controls that ensure reliable data for the specific samples being analysed and good inter-laboratory reproducibility.

Biomarkers, Tumor↗

State of the science: molecular classifications of breast cancer for clinical diagnostics.

Over the past few years, the study of genomics has embarked on developing gene expression-based classifications for tumors-an initiative that promises to revolutionize cancer medicine. High-throughput genomic platforms, such as microarray and SAGE, have found gene expression signatures that correlate to important clinical parameters used in current staging and are providing additional information that will improve standard of care. Although implementing a molecular taxonomy for prognosis and treatment would likely benefit cancer patients, there remain significant obstacles to using these assays within the current diagnostic framework. Since most genomic assays are being performed from fresh tissue, there is a need to either change the practice of formalin-fixing and paraffin-embedding tissue or adapting the assays for use on degraded RNA specimens. To date, even the most mature data sets, such as molecular classifications for breast cancer, still fall short of the number of patients needed to generalize the results to treating large populations. To implement these assays in large scale, there will need to be standardization of sample procurement, preparation, and analysis. Certainly, the greatest improvements in patient care will come through tailored therapies as genomics is coupled with clinical trials that randomize cohorts to different treatments. This manuscript reviews the current standards of care, presents progress that is being made in the development of genomic assays for breast cancer and discusses options for implementing these new tests into the clinical setting.

Biomarkers, Tumor↗

Genome-based identification of diagnostic molecular markers for human lung carcinomas by PLS-DA.

Partial least squares discriminant analysis (PLS-DA) provides a sound statistical basis for the selection of a limited number of gene transcripts most effective in discriminating different lung tumoral histotypes. The potentialities of the PLS-DA approach are pointed out by its ability to identify genes which, according to current knowledge, are considered molecular markers for colon cancer diagnostics and classification. Indeed application of PLS-DA to in vivo data allowed identification of a set of genes able to discriminate primary lung tumours from colon metastases.

Biomarkers, Tumor↗

Mitochondrial DNA deletions inhibit proteasomal activity and stimulate an autophagic transcript.

Deletions within the mitochondrial DNA (mtDNA) cause Kearns Sayre syndrome (KSS) and chronic progressive external opthalmoplegia (CPEO). The clinical signs of KSS include muscle weakness, heart block, pigmentary retinopathy, ataxia, deafness, short stature, and dementia. The identical deletions occur and rise exponentially as humans age, particularly in substantia nigra. Deletions at >30% concentration cause deficits in basic bioenergetic parameters, including membrane potential and ATP synthesis, but it is poorly understood how these alterations cause the pathologies observed in patients. To better understand the consequences of mtDNA deletions, we microarrayed six cell types containing mtDNA deletions from KSS and CPEO patients. There was a prominent inhibition of transcripts encoding ubiquitin-mediated proteasome activity, and a prominent induction of transcripts involved in the AMP kinase pathway, macroautophagy, and amino acid degradation. In mutant cells, we confirmed a decrease in proteasome biochemical activity, significantly lower concentration of several amino acids, and induction of an autophagic transcript. An interpretation consistent with the data is that mtDNA deletions increase protein damage, inhibit the ubiquitin-proteasome system, decrease amino acid salvage, and activate autophagy. This provides a novel pathophysiological mechanism for these diseases, and suggests potential therapeutic strategies.

Autophagy↗

Role of LAG-3 in regulatory T cells.

Regulatory T cells (Tregs) limit autoimmunity but also attenuate the magnitude of antipathogen and antitumor immunity. Understanding the mechanism of Treg function and therapeutic manipulation of Tregs in vivo requires identification of Treg-selective receptors. A comparative analysis of gene expression arrays from antigen-specific CD4(+) T cells differentiating to either an effector/memory or a regulatory phenotype revealed Treg-selective expression of LAG-3, a CD4-related molecule that binds MHC class II. Antibodies to LAG-3 inhibit suppression by induced Tregs both in vitro and in vivo. Natural CD4(+)CD25(+) Tregs express LAG-3 upon activation, which is significantly enhanced in the presence of effector cells, whereas CD4(+)CD25(+) Tregs from LAG-3(-/-) mice exhibit reduced regulatory activity. Lastly, ectopic expression of LAG-3 on CD4(+) T cells significantly reduces their proliferative capacity and confers on them suppressor activity toward effector T cells. We propose that LAG-3 marks regulatory T cell populations and contributes to their suppressor activity.

Adoptive Transfer↗

Distribution and origins of polycyclic aromatic hydrocarbons (PAHs) in riverine, estuarine, and marine sediments in Thailand.

To assess the status of polycyclic aromatic hydrocarbon (PAH) contamination in coastal and riverine environments in Thailand, we collected 42 surface sediment samples from canals, a river, an estuary, and coastal areas in Thailand in 2003 and analyzed them for PAHs with 3-7 benzene rings by gas chromatography-mass spectrometry (GC-MS). The total concentration of PAHs ranged from 6 to 8399 ng/g dry weight. The average total PAH concentrations were 2290+/-2556 ng/g dry weight (n=8) in canals, 263+/-174 (n=11) in the river, 179+/-222 (n=9) in the estuary, and 50+/-56 (n=14) in coastal areas. Comparison of the concentration range with a worldwide survey of sedimentary PAH concentrations ranked PAH contamination in Thai sediments as low to moderate. The ratio of the sum of methylphenanthrenes to phenanthrene (MP/P ratio) allows discrimination of PAH sources between petrogenic (>2) and pyrogenic (<0.5) origins. Sediments from urban canals in Bangkok showed the highest PAH concentrations and petrogenic signatures (MP/P=1.84+/-0.98 [n=6] in canal sediments) with abundant alkylated PAHs, indicating major sources of petrogenic PAHs in the city. To identify the sources of the petrogenic inputs in Thailand, we analyzed triterpanes, biomarkers of petroleum pollution, in the sediment samples and in potential source materials. Hopane profiles were remarkably uniform throughout the nation, suggesting a diffuse single source (e.g. automobiles). Molecular profiles of hopanes and PAHs in sediments from the urban canals were similar to those in street dust, indicating that street dust is one of the major sources of petrogenic PAHs in the urban area. On the other hand, low levels of PAHs (approximately 50 ng/g) with a pyrogenic signature (MP/P ratio approximately 0.5) were widely recorded in remote areas of the coast and the Chao Phraya River. These pyrogenic PAHs may be atmospherically transported throughout the nation. Middle and lower reaches of the Chao Phraya River, the river mouth, and the upper Gulf of Thailand showed intermediate concentrations and profiles of PAHs, indicating mixtures of petrogenic and pyrogenic origins. Perylene was abundant in sediments, representing up to approximately 60% of total identified PAHs. High inputs of soil due to frequent heavy rains could contribute to the high perylene abundance in the sediments. Sedimentary PAH concentrations decreased offshore with a half distance of approximately 10 km in the upper Gulf off the mouth of the Chao Phraya River. This is probably due to active deposition of laterally transported riverborne particles.

Environmental Monitoring↗

Searching for biomarkers of developmental toxicity with microarrays: normal eye morphogenesis in rodent embryos.

Gene expression arrays reveal the potential linkage of altered gene expression with specific adverse effects leading to disease phenotypes. But how closely do microarray data reflect early physiological or pharmacological measures that predict toxic event(s)? To explore this issue, we have undertaken experiments in early mouse embryos exposed to various teratogens during neurulation stages with the aim of correlating large-scale changes in gene expression across the critical period during exposure. This study reports some of the large-scale changes in gene expression that can be detected in the optic rudiment of the developing mouse and rat embryo across the window of development during which the eye is exceedingly sensitive to teratogen-induced micro-/anophthalmia. Microarray analysis was performed on RNA from the headfold or ocular region at the optic vesicle and optic cup stages when the ocular primordium is enriched for Pax-6, a master control gene for eye morphogenesis. Statistical selection of differentially regulated genes and various clustering techniques identified groups of genes in upward or downward trajectories in the normal optic primordium during early eye development in mouse and rat species. We identified 165 genes with significant differential expression during eye development, and a smaller subset of 58 genes that showed a tight correlation between mouse-rat development. Significantly over-represented functional categories included fatty acid metabolism (up-regulated) and glycolysis (down-regulated). From studies such as these that benchmark large-scale gene expression during normal embryonic development, we may be able to identify the panel of biomarkers that best correlate with species differences and the risks for developmental toxicity.

Animals↗

Persistent prostate-specific antigen expression after neoadjuvant androgen depletion: an early predictor of relapse or incomplete androgen suppression.

OBJECTIVES: To analyze post-androgen depletion (AD) primary tumors to identify markers of treatment failure because AD does not reduce the probability of prostate-specific antigen (PSA) failure after prostatectomy. METHODS: Tumors removed by radical prostatectomy after 3 months of AD from 21 patients were analyzed for gene expression using oligonucleotide arrays. Differences between patients with and without relapse were identified using a conservative significance criteria of a threefold change and delta 0.68, ensuring a false discovery rate of less than 11%. RESULTS: At 50 months of follow-up, 7 of the 18 evaluable patients developed a biochemical recurrence. Gleason grade, pretherapy PSA level, T stage, and margin status were similar between the two groups. Patients with recurrence had greater post-AD PSA levels than those without recurrence (0.87 versus 0.19 ng/mL; P = 0.042). Gene expression analysis revealed 35 probe sets overexpressed in tumors from patients who relapsed. Among the highest ranked probe sets were PSA and other androgen-responsive genes. Serum PSA values during AD revealed similar findings. After 40 days of AD, the PSA level in those without recurrence was 1.21 ng/mL versus 4.5 ng/mL in those with recurrence (P = 0.0034). Immunohistochemistry of post-AD tumors also demonstrated a high PSA staining intensity in many tumors that recurred relative to those that didn't. CONCLUSIONS: The results of our study show that early recurrence is associated with expression of androgen-responsive genes. Surprisingly, these could be identified as early as 3 months after the initiation of AD therapy. Whether this represents a failure to abrogate androgen receptor mediated signaling with androgen depletion or early reactivation of signaling is under study.

Androgen Antagonists↗

Discovery of genes implicated in placode formation.

The peripheral nervous system of the head is derived from cranial ectodermal placodes and neural crest cells. Placodes arise from thickenings in the cranial ectoderm that invaginate or ingress to form sensory ganglia and the paired sense organs. We have combined embryological techniques with array technology to identify genes that are expressed as a consequence of placode induction. As a secondary screen, we used whole mount in situ hybridization to determine the expression of candidate genes in various placodal domains. The results reveal 52 genes that are found in one or more placodes, including the olfactory, trigeminal, and otic placodes. Expression of some of these genes is retained in placodal derivatives. Furthermore, several genes are common to both neural crest and ectodermal placodes. This study presents the first array of candidate genes implicated in placode development, providing numerous new molecular markers for various stages of placode formation. Importantly, the results uncover previously unknown commonalities in genes expressed by multiple placodes and shared properties between placodes and other migratory cells, like neural crest cells.

Animals↗