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PubMed2004

Toxicogenomics in predictive toxicology in drug development.

The goal of toxicology is the assessment of possible risk to man. An emerging technology with the potential to have a major impact on risk assessment is toxicogenomics. In this review, we provide an overview of the many possibilities for toxicogenomics including technology platforms, data interpretation, and regulatory perspective and we give examples of toxicogenomics investigations. Toxicogenomics is a powerful tool for compound classification, for mechanistic studies, and for the detection of toxicity markers. Thus, toxicogenomics helps in the extrapolation of findings across species and increases predictability. Biomarkers are valuable in the evaluation of compounds at earlier development phases, improving clinical candidate selection. Caution regarding the interpretation of the results is still necessary. Nevertheless, toxicogenomics will accelerate preclinical safety assessments and improve the prediction of toxic liabilities, as well as of potential risk accumulation for drug-drug or drug-disease interactions.

Biomarkers↗
PubMed2006

Sex hormone-binding globulin expression in the endometria of women with polycystic ovary syndrome.

OBJECTIVE: To evaluate the protein and messenger RNA expression of sex hormone-binding globulin (SHBG) in endometria from women with polycystic ovary syndrome (PCOS). DESIGN: Case-control study. SETTING: Hospital research unit. PATIENT(S): Thirty-three women with PCOS, and 17 fertile, healthy women of similar age to those with PCOS. INTERVENTION(S): Endometrial and blood samples were obtained from women with PCOS (PCOSEs) and from control women (CEs) during the proliferative phase of the menstrual cycle. MAIN OUTCOME MEASURE(S): Expression studies for SHBG (immunohistochemistry and reverse transcription-polymerase chain reaction). Hormonal studies for determining sex steroids (T, P, and E(2)) and SHBG concentration. Insulin sensitivity was assessed by composite insulin sensitivity index (ISI(composite)). RESULT(S): In stroma, the protein expression of SHBG was lower in PCOSEs than in CEs. Epithelial cells had a similar expression of SHBG protein in both groups. Messenger RNA of variant 548 base pairs (wild-type) tended to be lower in PCOSEs compared to CEs. When PCOSEs were classified by insulin resistance, the PCOSEs with normal insulin sensitivity showed an expression of stromal SHBG similar to that observed in CEs. CONCLUSION(S): The low SHBG expression in the stromal compartment of endometria from women with PCOS with insulin resistance may contribute to generate an abnormal steroid milieu in the endometria of these women.

Adult↗
PubMed2026

Dealcoholized muscadine wine improved skin elasticity and oxidative stress biomarkers without affecting gut microbiome in women over 40 in a randomized controlled trial.

Muscadine wine has a unique polyphenol profile distinct from that of common wine, and limited research exists on its health benefits. This study aimed to investigate the effects of intake of dealcoholized muscadine wine (DMW) on skin health, oxidative stress, inflammatory biomarkers, and the gut microbiome. Seventeen healthy women were randomly assigned to consume 300 mL of DMW or a placebo daily for 6 weeks, separated by a 3-week washout period, in a randomized, single-blinded, crossover design. Skin health parameters were measured on the face and forearm. Oxidative stress and inflammatory biomarkers were assessed in plasma. Fecal bacterial DNA was sequenced using shotgun sequencing. DMW did not affect UVB-induced erythema compared to placebo. However, it significantly decreased transepidermal water loss and increased facial gross elasticity. Skin elasticity significantly improved on the forearm, whereas other skin parameters were not affected. DMW significantly decreased plasma levels of matrix metalloproteinase-9 and advanced glycation end products compared with placebo. However, the abundance, diversity, and functions of the gut microbiome were not affected. Polyphenol-rich DMW administered for six weeks improved certain skin health parameters and reduced oxidative and inflammatory stress, without affecting the gut microbiome in healthy women.

Humans↗
PubMed2005

Standardization strategy for quantitative PCR in human seminoma and normal testis.

Housekeeping genes are commonly used as endogenous references in quantitative RT-PCR. Ideally these genes are constitutionally expressed by all cell types and do not vary under experimental conditions. Tissues of 9 normal testes and 22 classical pure seminoma were obtained for RNA-extraction. Real-time RT-PCR was used to examine the mRNA-expression of ubiquitin C, beta-actin, GAPDH, 18S ribosomal RNA (18S rRNA) and porphobilinogen-deaminase (PBGD). Additionally, 3 normal testicular tissues and 39 seminoma, including 1 normal testis and 17 seminoma of the RT-PCR group, were utilized for microarray analyses. Ubiquitin C (protein degradation) was down-regulated, GAPDH (carbohydrate metabolism), beta-actin (cytoskeleton), 18S rRNA (ribosome) and PBGD (porphyrin metabolism) were up-regulated in seminoma. A normalization of the target gene data with up-regulated housekeeping genes would equalize or underestimate up-regulated data and overestimate down-regulated data. We demonstrate that none of the investigated housekeeping genes is suitable for normalization of the target gene RT-PCR data, but may be essential for tumor metabolism in human seminoma. Further, we developed a standardization strategy, which is applicable to many experimental investigations.

Biomarkers, Tumor↗
PubMed2005

Evolution of microarray analysis.

Reddy's very thorough review of the history of gene expression analysis of neurodegenerative disease made me think about the early days of microarrays, so I want to reminisce a little before commenting on the evolution of the technology and some issues that I think still continue to plague us.

Alzheimer Disease↗
PubMed2002

Detection of increased icb-1 transcript levels in maturing HL-60 cells: a novel marker for granulocytic and monocytic in vitro differentiation.

Human gene icb-1 was initially described as a gene with increased expression in endometrial tumor cells differentiated in vitro by culture on a reconstituted basement membrane. We provide evidence for a more general involvement of icb-1 gene function in cellular differentiation processes. We report the up-regulation of icb-1 transcript levels in HL-60 promyelocytic leukemia cells during their in vitro differentiation induced by all-trans retinoic acid, vitamin D(3) or DMSO. Increased icb-1 mRNA levels could be observed both in monocytic and granulocytic differentiation. We also report the identification of the novel icb-1 splice variants icb-1beta and gamma, and the spleen-specific isoform icb-1delta. Expression of icb-1 can be used as a novel marker for in vitro differentiation processes of HL-60 cells.

Alternative Splicing↗
PubMed2002

Disruption of germ cell-Sertoli cell interactions leads to spermatogenic defects.

In the aging human testis, partially regressed tubules contain Sertoli cells with an altered appearance and reduced numbers of germ cells. Investigating the effects of aging on Sertoli cell-germ cell interactions from Brown Norway rats, we have found that a selective breakdown in germ cell-Sertoli interactions could lead to severe reductions in male fertility. Previous studies have identified two specific inducible germ cell markers (a von Ebner's-like protein and the Huntington disease protein) and two specific inducible Sertoli cell markers (a sertonin receptor and a novel gene) that are expressed in Sertoli cell-germ cell cocultures and in vivo [Endocrinology 140 (1999a) 5754; J. Biol. Chem. 27 (1999b) 10737]. We find that germ cells from aged regressed testes are unable to respond to selective signals from Sertoli cells, although germ cells from aged normal sized testes respond well. Similarly, Sertoli cells from aged regressed testes fail to respond to certain signals from young germ cells. We propose that selective disruptions in communication between Sertoli cells and germ cells contribute to germ cell loss during aging.

Aging↗
PubMed2006

Secretory protein enrichment and analysis: an optimized approach applied on cancer cell lines using 2D LC-MS/MS.

Reliable methods for profiling secretory proteins are highly desirable for the identification of biomarkers of disease progression. Secreted proteins are often masked by high amounts of protein supplements in the culture medium. We have developed an efficient method for the enrichment and analysis of the secretome of different cancer cell lines, free of essential contaminants. The method is based on the optimization of cell incubation conditions in protein-free medium. Secreted proteins are concentrated and fractionated using a reversed-phase tC2 Sorbent, followed by peptide mass fingerprinting for protein identification. An average of 88 proteins were identified in each cancer cell line, of which more than 76% are known to be secreted, possess a signal peptide or a transmembrane domain. Given the importance of secreted proteins as a source for early detection and diagnosis of disease, this approach may help to discover novel candidate biomarkers with potential clinical significance.

Cell Culture Techniques↗
PubMed2000

Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms.

The bacterium Pseudomonas aeruginosa permanently colonizes cystic fibrosis lungs despite aggressive antibiotic treatment. This suggests that P. aeruginosa might exist as biofilms--structured communities of bacteria encased in a self-produced polymeric matrix--in the cystic fibrosis lung. Consistent with this hypothesis, microscopy of cystic fibrosis sputum shows that P. aeruginosa are in biofilm-like structures. P. aeruginosa uses extracellular quorum-sensing signals (extracellular chemical signals that cue cell-density-dependent gene expression) to coordinate biofilm formation. Here we found that cystic fibrosis sputum produces the two principal P. aeruginosa quorum-sensing signals; however, the relative abundance of these signals was opposite to that of the standard P. aeruginosa strain PAO1 in laboratory broth culture. When P. aeruginosa sputum isolates were grown in broth, some showed quorum-sensing signal ratios like those of the laboratory strain. When we grew these isolates and PAO1 in a laboratory biofilm model, the signal ratios were like those in cystic fibrosis sputum. Our data support the hypothesis that P. aeruginosa are in a biofilm in cystic fibrosis sputum. Moreover, quorum-sensing signal profiling of specific P. aeruginosa strains may serve as a biomarker in screens to identify agents that interfere with biofilm development.

4-Butyrolactone↗
PubMed2025

PD-1 transcriptomic landscape across cancers and implications for immune checkpoint blockade outcome.

Programmed cell death protein 1 (PD-1) is a critical immune checkpoint receptor and a target for cancer immune checkpoint inhibitors (ICI). We investigated PD-1 transcript expression across cancer types and its correlations to clinical outcomes. Using a reference population, PD-1 expression was calculated as percentiles in 489 of 514 patients (31 cancer types) with advanced/metastatic disease. PD-1 RNA expression varied across and within cancer types; pancreatic and liver/bile duct malignancies displayed the highest rates of high PD-1 (21.82% and 21.05%, respectively). Elevated CTLA-4, LAG-3, and TIGIT RNA expression were independently correlated with high PD-1. Although high PD-1 was not associated with outcome in immunotherapy-naïve patients (n = 272), in patients who received ICIs (n = 217), high PD-1 transcript expression was independently correlated with prolonged survival (hazard ratio 0.40; 95%CI, 0.18-0.92). This study identifies PD-1 as an important biomarker in predicting ICI outcomes, and advocates for comprehensive immunogenomic profiling in cancer management.

Journal Article↗
PubMed2006

Orbital lymphatics: do they exist?

INTRODUCTION: Although the lymphatic system was first described almost 400 years ago, it is only in very recent years that researchers have been able to identify lymphatic channels with reasonable accuracy. Through advances in molecular biology and the development of endothelial cell markers the long held view that the human orbit is devoid of lymphatics has now been challenged. DISCUSSION: This review discusses the current evidence on this topic, which confirms the presence of orbital lymphatics in lachrymal gland and optic nerve sheath.

Biomarkers↗
PubMed2005

Elevated expression of survivin-splice variants predicts a poor outcome for soft-tissue sarcomas patients.

The aim of this study was to investigate the level and the prognostic value of the expression of different survivin transcript variants--survivin, survivin-DeltaEx3 and survivin-2B--in tumours of 76 soft tissue sarcoma (STS) patients. The expression of survivin transcript variants in STS tissue samples and in 12 nonmalignant control tissues was analysed by quantitative RT-PCRs. Expression levels of all survivin transcript variants were strongly elevated in STS compared to normal tissues. A positive correlation between expression of splice variants and tumour stage was found (P=0.02; chi2 test). The multivariate Cox's proportional hazards regression model revealed a 7.3-fold increased risk of tumour-related death for patients with survivin-DeltaEx3 overexpressing tumours (P=0.007). The effect of surivivin (wildtype variant) and survivin-2B was less pronounced but still significant (2.2- and 1.9-fold, resp., P<0.05 each). Our results show for the first time that mRNA expression of survivin-variants is significantly correlated to a poor prognosis for STS patients, and we suggest expression of survivin splice variants together with tumour stage as independent predictor of survival.

Biomarkers, Tumor↗
PubMed2005

Novel strategies for the early detection and prevention of lung cancer.

Lung cancer is the leading cause of cancer death in the United States. Despite evidence of molecular abnormalities in biological specimens, progress in this disease is hampered by the lack of diagnostic markers useful for clinical practice. The majority of patients with lung cancer are still diagnosed at an advanced stage, when prognosis is poor. This article reviews new strategies being studied for the early detection of lung cancer. These strategies involve new methods of imaging (including low-dose computed tomography [CT] scanning), DNA analysis, and proteomic-based techniques. These strategies have not only improved our understanding of lung cancer but show promise in offering better survival to patients with this deadly disease. Of paramount importance in the search for methods of early detection is the need for the identification of the ideal population to screen, a multidisciplinary approach, and validation of promising techniques.

Anticarcinogenic Agents↗
PubMed2007

Molecular markers of early Parkinson's disease based on gene expression in blood.

Parkinson's disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular multigene marker here identified is associated with risk of PD in 66 samples of the training set comprising healthy and disease controls [third tertile cross-validated odds ratio of 5.7 (P for trend 0.005)]. It is further validated in 39 independent test samples [third tertile odds ratio of 5.1 (P for trend 0.04)]. Insights into disease-linked processes detectable in peripheral blood are offered by 22 unique genes differentially expressed in patients with PD versus healthy individuals. These include the co-chaperone ST13, which stabilizes heat-shock protein 70, a modifier of alpha-synuclein misfolding and toxicity. ST13 messenger RNA copies are lower in patients with PD (mean +/- SE 0.59 +/- 0.05) than in controls (0.96 +/- 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD.

Biomarkers↗
PubMed2005

Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis.

MOTIVATION: Robust computer algorithms are required to interpret the vast amounts of proteomic data currently being produced and to generate generalized models which are applicable to 'real world' scenarios. One such scenario is the classification of bacterial species. These vary immensely, some remaining remarkably stable whereas others are extremely labile showing rapid mutation and change. Such variation makes clinical diagnosis difficult and pathogens may be easily misidentified. RESULTS: We applied artificial neural networks (Neuroshell 2) in parallel with cluster analysis and principal components analysis to surface enhanced laser desorption/ionization (SELDI)-TOF mass spectrometry data with the aim of accurately identifying the bacterium Neisseria meningitidis from species within this genus and other closely related taxa. A subset of ions were identified that allowed for the consistent identification of species, classifying >97% of a separate validation subset of samples into their respective groups. AVAILABILITY: Neuroshell 2 is commercially available from Ward Systems.

Algorithms↗
PubMed2005

Analysis of recursive gene selection approaches from microarray data.

MOTIVATION: Finding a small subset of most predictive genes from microarray for disease prediction is a challenging problem. Support vector machines (SVMs) have been found to be successful with a recursive procedure in selecting important genes for cancer prediction. However, it is not well understood how much of the success depends on the choice of the specific classifier and how much on the recursive procedure. We answer this question by examining multiple classifers [SVM, ridge regression (RR) and Rocchio] with feature selection in recursive and non-recursive settings on three DNA microarray datasets (ALL-AML Leukemia data, Breast Cancer data and GCM data). RESULTS: We found recursive RR most effective. On the AML-ALL dataset, it achieved zero error rate on the test set using only three genes (selected from over 7000), which is more encouraging than the best published result (zero error rate using 8 genes by recursive SVM). On the Breast Cancer dataset and the two largest categories of the GCM dataset, the results achieved by recursive RR are also very encouraging. A further analysis of the experimental results shows that different classifiers penalize redundant features to different extent and this property plays an important role in the recursive feature selection process. RR classifier tends to penalize redundant features to a much larger extent than the SVM does. This may be the reason why recursive RR has a better performance in selecting genes.

Algorithms↗
PubMed2006

Early diagnosis and predictors of malignancy of adnexal masses.

PURPOSE OF REVIEW: Ovarian cancer is an important cause of death among women with a malignant gynecological tumor. Cure rates for the disease at an early stage are around 80-90%, but survival is only 50% as the majority of women already show advanced disease upon diagnosis. The combination of gynecological examination, ultrasonography, and systemic tumor marker assay is considered to be a good strategy for the early diagnosis of ovarian neoplasia. RECENT FINDINGS: Today, new technologies such as ultrasonography and tumor marker assay have increased the diagnosis rate for adnexal masses. These non-invasive methods, however, frequently do not distinguish benign conditions from malignant ones, which results in unnecessary surgery. Transvaginal ultrasonography is useful for diagnosing adnexal masses, but benign and malignant adnexal masses can present similar morphological characteristics. Combination with color Doppler ultrasonography and/or tumor markers may improve the accuracy of the method. Gene-expression array, proteomics and mathematical models form new approaches, but proper prospective studies are needed to validate them. SUMMARY: The techniques of pelvic examination, ultrasonography, color Doppler ultrasonography, and tumor markers can be indicated for the diagnosis of ovarian cancer. The differentiation between benign and malignant ovarian tumor is, however, a clinical challenge. Until better diagnostic methods become available, patients and their physicians can use these techniques to decide on management.

Adnexal Diseases↗