Candidate Molecular Markers Research Articles

Recent Candidate Molecular Markers: Vitamin D Signaling and Apoptosis Specific Regulator of p53 (ASPP) in Breast Cancer

Regardless of advances in treatment modalities with the invention of newer therapies, breast cancer remains a major health problem with respect to its diagnosis, treatment and management. This female malignancy with its tremendous heterogeneous nature is linked to high incidence and mortality rates, especially in developing region of the world. It is the malignancy composed of distinct biological subtypes with diverse clinical, pathological, molecular and genetic features as well as different therapeutic responsiveness and outcomes. This inconsistency can be partially overcome by finding novel molecular markers with biological significance. In recent years, newer technologies help us to indentify distinct biomarkers and increase our understanding of the molecular basis of breast cancer. However, certain issues need to be resolved that limit the application of gene expression profiling to current clinical practice. Despite the complex nature of gene expression patterns of cDNAs in microarrays, there are some innovative regulatory molecules and functional pathways that allow us to predict breast cancer behavior in the clinic and provide new targets for breast cancer treatment. This review describes the landscape of different molecular markers with particular spotlight on vitamin D signaling pathway and apoptotic specific protein of p53 (ASPP) family members in breast cancer.

Villin 1 is a predictive factor for the recurrence of high serum alpha‐fetoprotein‐associated hepatocellular carcinoma after hepatectomy

The prognostic assessment of patients with hepatocellular carcinoma (HCC) after resection is an important clinical issue. The present study investigated those genes associated with high serum alpha-fetoprotein (AFP), and their clinical significance, including prognosis and recurrence after hepatectomy. Based on gene expression analysis of 110 training HCC cases, 20 genes whose mRNA expression levels were significantly upregulated and 50 genes that were downregulated correlated with high serum AFP-associated HCC patients. Gene expression profiles of Villin1 (Vil1) were obtained in high serum AFP-associated HCC tumor tissues. In the present analysis, only VIL1 was significantly correlated with the recurrence of HCC. The results were validated independently using Taqman gene expression assays and immunostaining analysis. Results showed that the upregulation of VIL1 mRNA was also correlated with high serum PIVKAII, vascular invasion (P < 0.05), poor differentiation, an advanced cancer stage (P < 0.01) and recurrence-free survival (P = 0.017). The upregulation of VIL1 mRNA was observed more frequently in the early recurrence patients as compared to the late recurrence patients. Cox regression univariate and multivariate analyses indicated that high serum AFP levels (overall survival, HR 1.675, P = 0.002; FRS, HR 1.359, P = 0.039) and Vil1 protein expression (overall survival, HR 0.253, P = 0.009; FRS, HR 0.401, P = 0.041) were independent, unfavorable prognostic factors for overall and recurrence-free survival of patients. We demonstrated that the VIL1 gene is a potential candidate molecular marker for high serum AFP-associated HCC and a predictive candidate for the postoperative recurrence and poorer prognosis of HCC.

Molecular Pathology of Pancreatic Cancer: From Bench-to-Bedside Translation

Pancreatic ductal adenocarcinoma (referred here as pancreatic cancer) is a lethal disease with the worst prognosis among all solid tumors. Surgical resection represents the only hope for cure but it is possible only in patients that present with local disease (about 20% of cases). Whether dismal prognosis of pancreatic cancer is a result of late diagnosis or early dissemination to distant organ is still a debate. Moreover, this disease shows an intrinsic chemotherapeutic resistance that has been mainly ascribed to the presence of a dense stromal reaction that significantly impairs drugs delivery. Clinical management of pancreatic cancer patients relies on few molecular markers (e.g., the diagnostic marker CA19-9) that, however, present several limitations to their use. The clinical usefulness of somatic alterations in well-characterized genes (such as KRAS and TP53), whose detection is technically feasible in different biological samples, has been extensively investigated leading to inconsistent results. Furthermore, none of the candidate molecular markers identified in recent years has shown an appropriate clinical performance and therefore none is routinely used. This depicts a scenario where the identification of novel and effective clinical biomarkers is mandatory. Very recent genome-wide comprehensive studies have shed light on the high degree of genetic complexity and heterogeneity of the pancreatic cancers. Although far from being introduced into the clinical settings, results from those studies are expected to change definitively the perspective through which we look at the clinical management of pancreatic cancer patients towards a personalized cancer medicine.

Roles of ABCB1 gene polymorphisms and haplotype in susceptibility to breast carcinoma risk and clinical outcomes

Genetic variants of ABCB1 gene contributed to cancer susceptibility and interindividual differences in chemotherapy response. Therefore, we investigated the relevance between genetic variations in ABCB1 gene and both risk and clinical outcomes of breast carcinoma. A case-control study was performed on the SNPs C3435T, C1236T and G2677T/A in 1,173 Chinese breast carcinoma patients and 1,244 age- and sex-matched controls. These SNPs were typed by PCR-restriction fragment length polymorphism assays. We found the following: (1) ABCB1 C3435T, G2677T/A variants and haplotype 3435T-1236T-2677T significantly increased the risk of breast carcinoma [adjusted OR (95% CI): 1.281 (1.021-1.285), 1.326 (1.182-1.487) and 1.707 (1.498-1.945), respectively]. (2) A significantly enhanced therapeutic response was observed in both C3435T variants and haplotype 3435T-1236T-2677T after neoadjuvant anthracycline-based chemotherapy (n=148) [adjusted OR (95% CI): 2.695 (1.172-6.211) and 8.064 (1.085-58.823), respectively]. (3) Cox proportional hazards regression models showed that the hazards ratio (HR) for progression-free survival (PFS) associated with C3435T CC genotype was 1.664 (95% CI: 1.022-2.708, P=0.041). Kaplan-Meier curve showed that C3435T CC carriers had a poor prognosis than those with CT/TT carriers after anthracycline-based chemotherapy (P=0.043, n=762). Furthermore, ABCB1 C3435T variants showed a significantly prolonged both PFS and overall survival (OS) in patients with triple-negative (ER-/PR-/HER2-) status (P=0.001 and P=0.016, respectively; n=135). In addition, there was a significantly longer OS in patients with HER2-negative status who had G2677T/A variants (P=0.036, n=487). However, we did not find statistically significant association between C1236T genotypes and the risk or prognosis of breast carcinoma. These results suggest that ABCB1 gene C3435T, G2677T/A variations and haplotype 3435T-1236T-2677T relate to the risk and clinical outcomes of breast carcinoma and may function as candidate molecular markers of anthracycline chemosensitivity in breast carcinoma.

Mda-9/Syntenin Is Expressed in Uveal Melanoma and Correlates with Metastatic Progression

Uveal melanoma is an aggressive cancer that metastasizes to the liver in about half of the patients, with a high lethality rate. Identification of patients at high risk of metastases may provide indication for a frequent follow-up for early detection of metastases and treatment. The analysis of the gene expression profiles of primary human uveal melanomas showed high expression of SDCBP gene (encoding for syndecan-binding protein-1 or mda-9/syntenin), which appeared higher in patients with recurrence, whereas expression of syndecans was lower and unrelated to progression. Moreover, we found that high expression of SDCBP gene was related to metastatic progression in two additional independent datasets of uveal melanoma patients. More importantly, immunohistochemistry showed that high expression of mda-9/syntenin protein in primary tumors was significantly related to metastatic recurrence in our cohort of patients. Mda-9/syntenin expression was confirmed by RT-PCR, immunofluorescence and immunohistochemistry in cultured uveal melanoma cells or primary tumors. Interestingly, mda-9/syntenin showed both cytoplasmic and nuclear localization in cell lines and in a fraction of patients, suggesting its possible involvement in nuclear functions. A pseudo-metastatic model of uveal melanoma to the liver was developed in NOD/SCID/IL2Rγ null mice and the study of mda-9/syntenin expression in primary and metastatic lesions revealed higher mda-9/syntenin in metastases. The inhibition of SDCBP expression by siRNA impaired the ability of uveal melanoma cells to migrate in a wound–healing assay. Moreover, silencing of SDCBP in mda-9/syntenin-high uveal melanoma cells inhibited the hepatocyte growth factor (HGF)-triggered invasion of matrigel membranes and inhibited the activation of FAK, AKT and Src. Conversely syntenin overexpression in mda-9/syntenin-low uveal melanoma cells mediated opposite effects. These results suggest that mda-9/syntenin is involved in uveal melanoma progression and that it warrants further investigation as a candidate molecular marker of metastases and a potential therapeutic target.

Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp (&lt;I&gt;Cyprinus carpio&lt;/I&gt; L.)

Based on a full-sib family, the genetic linkage map was constructed with 246 microsatellite and 306 SNP markers, which was used to detect the QTLs for standard length (SL), body depth (H), body thickness (BT), and the ratio of standard length and body depth (SLH) in mirror carp by GridQTL software. The results indicated that a total of 14 related QTLs distributed on the 7 linkage groups were obtained. Seven QTLs were related to standard length, of which the linkage groups of LG6, LG17, LG21, LG23, and LG35 were at 5% significant level, and linkage group LG1 and LG28 were at 1% significant level, which explained 6.6%-12.6% of the phenotypic variance. Three QTLs were identified for body depth on the linkage groups of LG17, LG23 and LG28 (P amp; 0.01), accounting for 11.6%, 12.7%, and 15.6% of the phenotypic variance, respectively. Two QTLs were associated with body thickness on the linkage of LG23 and LG28 (P amp; 0.05), which explained 8.6% and 7.2% of the phenotypic variation, respectively. Two QTLs were responsible for the ratio of standard length and body depth on the linkage of LG21 and LG35 (P amp; 0.05), both of which explained 8.2% of the phenotypic variance. The results provide a useful reference for further candidate gene research and molecular marker assisted selection in mirror carp.

Are there any Pinus pinaster trees resistant to Bursaphelenchus xylophilus? Studies implemented in Portugal to address this question

The Pinewood nematode Bursaphelenchus xylophilus (PWN) was found to be responsible for maritime pine (Pinus pinaster) death for the first time in Europe in 1999, in a Portuguese forest south of Lisbon. It is the causal agent of the Pine Wilt Disease (PWD) and a quarantine organism in the European Union with approximately €80 million spent from 1999 – 2009 for attempting its eradication, which must also be added to direct losses from tree mortality. During this period, important progress has been made in understanding the relationships between PWN, its insect vector and the host tree/environmental factors that result in pine wilt in all countries affected but, especially, in Portugal. Although PWN can cause devastating tree mortality, there is also evidence that some tree species or individual trees within a species are either tolerant (i.e. support the nematode, but are not killed immediately) or resistant to the nematodes. In order to investigate the susceptibility of Pinus pinaster to Bursaphelenchus xylophilus as a first step for the establishment of methodologies for the improvement of its resistance, a research program was implemented recently in Portugal for this species, combining genomic and quantitative genetics approaches. Until now, more than 500 trees were phenotypically selected in a highly affected stand and monitored during two years, regarding their phytossanitary status. The percentage of mortality observed in the first year was about 10%, with this value decreasing to less than 5% in the second year. Around 200 trees (including 150 of the selected trees) were genotyped for 6 microsatellite loci and three combinations of AFLP markers. The genotyping results show a high diversity of genotypes, which may open good prospects for the selection of resistant plants to Bursaphelenchus xylophilus. At the same time, genomic and transcriptomic studies have been initiated with the final goal to discover candidate genes, loci and molecular markers related with disease resistance to PWN. With regards to the effects of the disease at a transcriptional level, the SSH technique was utilised to identify ESTs in P. pinaster and P. pinea when inoculated with PWN. ESTs were isolated, cloned, sequenced and identified using BlastN and BlastX, and clearly indicated that at an initial stage of the disease there is activation of a defence response at a molecular level, mainly related to oxidative stress, production of lignin and ethylene and post-transcriptional regulation of nucleic acids. 58% of the isolated sequences are not yet described, which shows the lack of genomic information currently available for pine. The results obtained are presented and discussed.

Solute carrier protein family may involve in radiation-induced radioresistance of non-small cell lung cancer

To find new signaling pathways that may be involved in the cellular response to ionizing radiation. Two radioresistant subclones (A549/R and SPCA1/R) derived from lung adenocarcinoma cell lines A549 and SPCA1 were established after eight rounds of sublethal irradiation. The new subclones were tested for radioresistant features using clonogenic assay and apoptosis analysis. The genes expressed differentially were screened with cDNA microarray analysis consisting of 48,000 transcript probes and confirmed by quantitative real-time PCR. Stable and significant radioresistance was observed in the screened subclones. The microarray analysis showed 65 genes were up-regulated and 141 genes down-regulated in SPCA1/R cells. The up-regulated and down-regulated genes were 708 and 230 in A549/R cells, respectively. Twenty-seven altered genes were consistent in both subclones. Interestingly, members the of human solute carrier (SLC) gene superfamily were among in 27 genes. The differentially expressed genes in both cell lines may contribute to their radioresistant phenotype. This extensive list of genes identified in the experiment provides a large body of potentially valuable information for studying the molecular mechanism(s) of radiosensitivity and identification of candidate molecular markers of radiation sensitivity. Thus, to our knowledge, the SLC gene superfamily is the first being reported to involve in acquired radioresistance.

P53 and Cyclooxygenase-2 Expression are Directly Associated with Cyclin D1 Expression in Radical Prostatectomy Specimens of Patients with Hormone-Naïve Prostate Cancer

Prostate cancer (PCa) is a potentially curable disease when diagnosed in early stages and subsequently treated with radical prostatectomy (RP). However, a significant proportion of patients tend to relapse early, with the emergence of biochemical failure (BF) as an established precursor of progression to metastatic disease. Several candidate molecular markers have been studied in an effort to enhance the accuracy of existing predictive tools regarding the risk of BF after RP. We studied the immunohistochemical expression of p53, cyclooxygenase-2 (COX-2) and cyclin D1 in a cohort of 70 patients that underwent RP for early stage, hormone naïve PCa, with the aim of prospectively identifying any possible interrelations as well as correlations with known prognostic parameters such as Gleason score, pathological stage and time to prostate-specific antigen (PSA) relapse. We observed a significant (p = 0.003) prognostic role of p53, with high protein expression correlating with shorter time to BF (TTBF) in univariate analysis. Both p53 and COX-2 expression were directly associated with cyclin D1 expression (p = 0.055 and p = 0.050 respectively). High p53 expression was also found to be an independent prognostic factor (p = 0.023). Based on previous data and results provided by this study, p53 expression exerts an independent negative prognostic role in localized prostate cancer and could therefore be evaluated as a useful new molecular marker to be added in the set of known prognostic indicators of the disease. With respect to COX-2 and cyclin D1, further studies are required to elucidate their role in early prediction of PCa relapse after RP.

A potential role for the homeoprotein Hhex in hepatocellular carcinoma progression

Hepatocellular carcinoma (HCC), the most common primary malignant tumor of the liver, often associated with the dysregulation of transcriptional pathways involved in cell growth and differentiation. The hematopoietically expressed homeobox protein (Hhex) is an important transcription factor throughout liver development and is essential to liver bud formation and hepatoblast differentiation. Here, we report a relationship between Hhex expression and HCC. First, adenovirus-mediated Hhex delivery into the hepatoma cell line, Hepa1-6, resulted in decreased expression of several proto-oncogenes (c-Jun and Bcl2), increased expression of some tumor suppressor genes (P53 and Rb), and enhanced expression of a cluster of hepatocytic and bile ductular markers. Second, Hhex expression significantly attenuated Hepa1-6 tumorigenicity in nude mice. Third, we report a correlation between Hhex expression and the differentiation state of human HCC. In 24 cases of clinical specimens, there was a significant difference in Hhex expression between poorly differentiated HCC and well-differentiated HCC (P < 0.001). Taken together, these results indicate that Hhex is a potential candidate molecular marker for HCC pathological evaluation, suggesting a need to evaluate Hhex as a potential target for therapeutic intervention.

Abstract 3589: Dovitinib (TKI258), a multikinase inhibitor of FGFR, PDGFR, and VEGFR tyrosine kinases, induces growth inhibition in endometrial carcinoma cells

Abstract Background: Endometrial carcinoma is the most common gynecological malignancy in the western world. Activating mutations of the fibroblast growth factor receptor 2 (FGFR2) have been described in 12-16% of endometrial cancers. Moreover, vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), and platelet-derived growth factor (PDGF) and their receptors are involved in the neovascularization, invasiveness, and metastatic potential of endometrial cancer. Therefore, suppression of FGFR/VEGFR/PDGFR signaling by TKI258 may represent a novel approach for treatment of endometrial cancer. Experimental Design: The aims of this study were 1.) to assess the effect of TKI258 on tumor cell growth in two-dimensional (2D) and three-dimensional (3D) culture assays using a panel of 20 human endometrial cancer cell lines, 2.) to identify candidate molecular markers predicting sensitivity using baseline gene expression profiling and mutational analyses, and 3.) to determine the in vivo antineoplastic activity of TKI258 in endometrial cancer xenograft models. In addition, we screened 200 fresh frozen endometrial cancer specimens to comprehensively assess the distribution pattern of PI3K, PTEN, and FGFR mutations in endometrial cancer. Results: Concentration-dependent anti-proliferative effects of TKI285 using 2D assays were seen in all endometrial cancer cell lines tested, but varied significantly between individual cell lines (IC50 range: 0.42µM – 3.06 µM). The three most sensitive endometrial cancer cell lines demonstrated activating FGFR2 mutations (MFE296: N549K, IC50 0.42µM; AN3CA: N549K and K310R, IC50 0.50µM; MFE280: S252W, IC50 0.66µM). Assessment of TKI258 responses in 3D assays demonstrated similar results to those observed in 2D culture assays in that the 3 cell lines harboring FGFR2 mutations were the most sensitive to TKI258 achieving 100% growth inhibition at a concentration of 1µM. AN3CA and MFE296 endometrial cancer cells formed xenografts in nude mice and antitumor activity was studied in both models. Inhibition of p-FGFR, p-PDGFR, p-VEGFR-2, pAKT and p-ERK1/2 were observed. Comprehensive data on the pattern of PI3K, PTEN and FGFR mutations in endometrial cancer will be provided. Conclusion: TKI258 demonstrates significant antitumor activity in endometrial cancer cells with FGFR2 mutations. This study provides a strong rationale for the clinical evaluation of TKI258 in patients with endometrial cancer, specifically in those harboring FGFR2 mutations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3589. doi:10.1158/1538-7445.AM2011-3589

Drosophilagenomes and the development of affordable molecular markers for species genotyping

The recent completion of genome sequencing of 12 species of Drosophila has provided a powerful resource for hypothesis testing, as well as the development of technical tools. Here we take advantage of genome sequence data from two closely related species of Drosophila, Drosophila simulans and Drosophila sechellia, to quickly identify candidate molecular markers for genotyping based on expected insertion or deletion (indel) differences between species. Out of 64 candidate molecular markers selected along the second and third chromosome of Drosophila, 51 molecular markers were validated using PCR and gel electrophoresis. We found that the 20% error rate was due to sequencing errors in the genome data, although we cannot rule out possible indel polymorphisms. The approach has the advantage of being affordable and quick, as it only requires the use of bioinformatics tools for predictions and a PCR and agarose gel based assay for validation. Moreover, the approach could be easily extended to a wide variety of taxa with the only limitation being the availability of complete or partial genome sequence data.

Sieving Treatment Biomarkers from Blood Gene-Expression Profiles: A Pharmacogenomic Update on two types of Multiple Sclerosis Therapy

Interferon-β (IFN-β) and glatiramer acetate are routinely used to inhibit disease activity in multiple sclerosis, but their mechanisms of action are incompletely understood. Individual treatment responses vary and candidate molecular markers that predict them have yet to be established. Why some patients respond poorly to a certain treatment while others respond well is addressed by the pharmacogenomic approach, which postulates that the molecular response to treatment correlates with the clinical effects, and thus seeks biological markers to estimate prognosis, guide therapy, comprehend the drugs' mechanisms of action and offer insights into disease pathogenesis. A poor clinical response can be owing to genetic variants in drug receptors or signaling components, or the appearance of neutralizing antibodies that interfere with the drug's binding efficacy. Independently, such mechanisms could lead to inadequate, that is to say unchanged, molecular responses, or exceedingly increased or decreased changes. By means of DNA microarray studies, various research groups endeavour to establish a clinically relevant relationship between the biological response to these drugs and treatment effects. Molecular profiles obtained in this way differ in the pattern and number of modulated genes, suggesting the existence of an individual 'drug-response fingerprint'. To further unravel the underlying regulatory interaction structure of the genes responsive to these immunotherapies represents a daunting but inevitable task. In this article, we focus on longitudinal ex vivo transcriptomic studies in multiple sclerosis and its therapy. We will discuss recurrently reported biomarker candidates, emphasizing those of immunologically meaning, and review studies with network module outputs.

Biomarkers of immunosuppressant organ toxicity after transplantation: status, concepts and misconceptions

Introduction: A major challenge in transplantation is improving long-term organ transplant and patient survival. Immunosuppressants protect the transplant organ from alloimmune reactions, but sometimes also exhibit limiting side effects. The key to improving long-term outcome following transplantation is the selection of the correct immunosuppressive regimen for an individual patient for minimizing toxicity while maintaining immunosuppressive efficacy.Areas covered: Proteomics and metabolomics have the potential to develop sensitive and specific diagnostic tools for monitoring early changes in cell signal transduction, regulation and biochemical pathways. Here, we review the steps required for the development of molecular markers from discovery, mechanistic and clinical qualification to regulatory approval, and present a critical discussion of the current status of molecular marker development as relevant for the management and individualization of immunosuppressive drug regimens.Expert opinion: Although metabolomics and proteomics-based studies have yielded several candidate molecular markers, most published studies are poorly designed, statistically underpowered and/or often have not gone beyond the discovery stage. Most molecular marker candidates are still at an early stage. Due to the high complexity of and the resources required for diagnostic marker development, initiatives and consortia organized and supported by funding agencies and regulatory agencies will be critical.

Specific Alterations of MicroRNA Transcriptome and Global Network Structure in Colorectal Carcinoma after Cetuximab Treatment

The relationship between therapeutic response and modifications of microRNA (miRNA) transcriptome in colorectal cancer (CRC) remains unknown. We investigated this issue by profiling the expression of 667 miRNAs in 2 human CRC cell lines, one sensitive and the other resistant to cetuximab (Caco-2 and HCT-116, respectively), through TaqMan real-time PCR. Caco-2 and HCT-116 expressed different sets of miRNAs after treatment. Specifically, 21 and 22 miRNAs were differentially expressed in Caco-2 or HCT-116, respectively (t test, P < 0.01). By testing the expression of differentially expressed miRNAs in CRC patients, we found that miR-146b-3p and miR-486-5p are more abundant in K-ras-mutated samples with respect to wild-type ones (Wilcoxon test, P < 0.05). Sixty-seven percent of differentially expressed miRNAs were involved in cancer, including CRC, whereas 19 miRNA targets had been previously reported to be involved in the cetuximab pathway and CRC. We identified 25 transcription factors putatively controlling these miRNAs, 11 of which have been already reported to be involved in CRC. On the basis of these data, we suggest that the downregulation of let-7b and let-7e (targeting K-ras) and the upregulation of miR-17* (a CRC marker) could be considered as candidate molecular markers of cetuximab resistance. Global network functional analysis (based on miRNA targets) showed a significant overrepresentation of cancer-related biological processes and networks centered on critical nodes involved in epidermal growth factor receptor internalization and ubiquitin-mediated degradation. The identification of miRNAs, whose expression is linked to the efficacy of therapy, should allow the ability to predict the response of patients to treatment and possibly lead to a better understanding of the molecular mechanisms of drug response.

Identification of candidate molecular markers of nasopharyngeal Carcinoma by tissue microarray and in situ hybridization

To scan differentially expressed genes and to identify candidate molecular markers in nasopharyngeal carcinoma (NPC), we analyzed cDNA microarray data by GenMAPP to find specifically expressed genes in NPC and used tissue microarray and in situ hybridization techniques to confirm our microarray results. Our cDNA microarray results showed that TSPAN-1 and DPP10 genes were down-expressed in NPC, and COX7B and RFC2 genes were over-expressed in NPC. Real-time quantitative reverse transcription-PCR and in situ hybridization (ISH) techniques confirmed that TSPAN-1 and DPP10 genes had only 40.72 and 40.70% positive expression in NPC, but had high positive expression in chronic inflammation of nasopharyngeal mucosa (P < 0.01). However, COX7B and RFC2 genes were high positive rate in NPC (84.24 and 64.53%, respectively) than in normal control tissues. The data suggested that TSPAN-1, DPP10, COX7B and RFC2 genes might be the putative molecular markers of NPC.

Differential Response to Trichloroethylene-Induced Hepatosteatosis in Wild-Type and PPARα-Humanized Mice

BackgroundTrichloroacetic acid, an oxidative metabolite of trichloroethylene (TRI), is a ligand of the peroxisome proliferator-activated receptor α (PPAR) α, which is involved in lipid homeostasis and anti-inflammation.ObjectiveWe examined the role of mouse and human PPARα in TRI-induced hepatic steatosis and toxicity.MethodsMale wild-type (mPPARα), Pparα-null, and humanized PPARα (hPPARα) mice on an Sv/129 background were exposed via inhalation to 0, 1,000, and 2,000 ppm TRI for 8 hr/day for 7 days. We assessed TRI-induced steatosis or hepatic damage through biochemical and histopathological measurements.ResultsPlasma alanine aminotransferase and aspartate aminotransferase activities increased in all mouse lines after exposure to 1,000 and 2,000 ppm TRI. Exposure induced hepatocyte necrosis and inflammatory cells in all mouse lines, but hepatic lipid accumulation was observed only in Pparα-null and hPPARα mice. No differences were observed in TRI-mediated induction of hepatic PPARα target genes except for a few genes that differed between mPPARα and hPPARα mice. However, TRI significantly increased expression of triglyceride (TG)-synthesizing enzymes, diacylglicerol acyltransferases, and PPARγ in Pparα-null and hPPARα mice, which may account for the increased TG in their livers. TRI exposure elevated nuclear factor-kappa B (NFκB) p52 mRNA and protein in all mice regardless of PPARα genotype.ConclusionsNFκB-p52 is a candidate molecular marker for inflammation caused by TRI, and PPARα may be involved in TRI-induced hepatosteatosis. However, human PPARα may afford only weak protection against TRI-mediated effects compared with mouse PPARα.

Variability of carotenoid biosynthesis in orange colored Capsicum spp.

Pepper, Capsicum spp., is a worldwide crop valued for heat, nutrition, and rich pigment content. Carotenoids, the largest group of plant pigments, function as antioxidants and as vitamin A precursors. The most abundant carotenoids in ripe pepper fruits are β-carotene, capsanthin, and capsorubin. In this study, the carotenoid composition of orange fruited Capsicum lines was defined along with the allelic variability of the biosynthetic enzymes. The carotenoid chemical profiles present in seven orange pepper varieties were determined using a novel UPLC method. The orange appearance of the fruit was due either to the accumulation of β-carotene, or in two cases, due to only the accumulation of red and yellow carotenoids. Four carotenoid biosynthetic genes, Psy, Lcyb, CrtZ-2, and Ccs were cloned and sequenced from these cultivars. This data tested the hypothesis that different alleles for specific carotenoid biosynthetic enzymes are associated with specific carotenoid profiles in orange peppers. While the coding regions within Psy and CrtZ-2 did not change in any of the lines, the genomic sequence contained introns not previously reported. Lcyb and Ccs contained no introns but did exhibit polymorphisms resulting in amino acid changes; a new Ccs variant was found. When selectively breeding for high provitamin A levels, phenotypic recurrent selection based on fruit color is not sufficient, carotenoid chemical composition should also be conducted. Based on these results, specific alleles are candidate molecular markers for selection of orange pepper lines with high β-carotene and therefore high provitamin A levels.

Identification of candidate molecular markers predicting chemotherapy resistance in non-small cell lung cancer

Empirical chemotherapy for patients with non-small cell lung cancer (NSCLC) is recommended, even without knowledge of the tumor's specific biological characteristics, and many patients may not benefit. The goal of this study was to identify potential serum biomarkers that influence resistance to chemotherapy, and to build a model that could be used to predict resistance to chemotherapy of patients with advanced NSCLC. A total of 97 NSCLC patients were classified as stage IIIB and stage IV. The chemotherapy regimen was cisplatin plus docetaxel. All patients received two cycles of chemotherapy. Serum protein profiles were detected using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) and the spectra were analyzed with a support vector machine (SVM). For the 93 eligible patients, 22 patients had a partial response (23.7%); 27 patients had stable disease (29.0%) and 44 (47.3%) had progressive disease. One hundred and twenty-eight mass peaks were detected from the chemotherapy sensitive group and the chemotherapy resistant group by receiver operator characteristic curve. The top 10 peaks with the highest area under the curve values were selected, randomly combined, and fed into the SVM. The SVM model with the highest accuracy was used as the diagnostic model. The model constructed using five protein peaks with mass/charge ratios of 3955 Da, 6207 Da, 7992 Da, 9214 Da, and 15,086 Da separated the chemotherapy resistant group from the chemotherapy sensitive group with a sensitivity of 83.3% and specificity of 85.7%. SELDI-TOF MS may provide a useful means in the search for serum biomarkers for predicting chemotherapy resistance in patients with advanced NSCLC.

Influence of ovarian stage on transcript profiles in fathead minnow ( Pimephales promelas) ovary tissue

Interpretation of toxicogenomic experiments conducted with ovary tissue from asynchronous-spawning small fish species is complicated by background variation in the relative abundance and proportion of follicles at different stages within the ovary tissue sample. This study employed both real-time quantitative polymerase chain reaction and a 15,000 gene oligonucleotide microarray to examine variation in the fathead minnow ( Pimephales promelas) ovarian transcriptional profile as a function of quantitative and qualitative differences in ovarian histology. The objectives were to provide data that could potentially aid interpretation of future toxicogenomics experiments, identify putative stage-related transcriptional markers, and generate insights into basic biological regulation of asynchronous oocyte development. Multiple lines of evidence from the present study indicate that variation in the transcriptional profile is primarily dependent on the relative abundance of previtellogenic versus vitellogenic follicles in the ovary. Due to the relatively small proportions of mature ovulated follicles or atretic follicles in the overall follicle population, few potential transcriptional markers of maturation, ovulation, or atresia could be identified. However, among the 460 differentially expressed genes identified in the present study, several targets, including HtrA serine peptidase 3 ( htra3), tissue inhibitor of metalloproteinase 3 ( timp3), aquaporin 8 ( aqp8), transgelin 2 like ( tagln2), Nedd4 family interacting protein 2 ( ndfip2), chemokine ligand 12a ( cxcl12a), midkine-related growth factor ( mdka), and jagged 1b ( jag 1b) exhibited responses and functional properties that support them as candidate molecular markers of significant shift in gross ovarian stage. Genes associated with a diversity of functions including cellular development, morphogenesis, coated vesicle transport, sexual reproduction, and neuron development, among others, were statistically enriched within the list of 460 genes differentially expressed among different ovarian classes. Overall, results of this study provide insights into background variation in ovary transcript profiles that should aid and enhance the interpretation of toxicogenomic data generated in experiments conducted with small, asynchronous-spawning fish species.