Significant Changes In Expression Levels Research Articles

Identifying Immune Resistance Mechanisms to CD33/CD3 BiTE® Antibody Construct (AMG 330) Mediated Cytotoxicity

In our previous work, we showed elimination of primary acute myeloid leukemia (AML) cells by CD33/CD3 BiTE® antibody construct (AMG 330) mediated cytotoxicity (Krupka et al, Blood 2014). The goal of the present study was to identify innate and adaptive resistance mechanisms to AMG 330 mediated lysis of AML cells. Immune checkpoint molecules have been shown to be a highly relevant escape mechanism of malignant cells to evade innate and adaptive immunity. Previously, it was shown that AML cells upregulate the expression of inhibitory ligands in response to proinflammatory cytokines (Krönig et al, 2014). As AMG 330 mediated T-cell activation induces high levels of the proinflammatory cytokines IFNγ and TNFα, we assessed the constitutive and inducible expression profile of different immune checkpoint molecules on AML cell lines and primary AML cells, including PD-L1, HVEM, ILT3 and SLAMF7 by flow cytometry. No constitutive expression was observed for PD-L1 at time of primary diagnosis in 83.7% of the cases (103/123). In contrast, constitutive expression of HVEM and ILT3 was detected in 73.7% (42/57) and 91.9% (68/74) of patient samples, respectively. Adaptive resistance was evaluated by incubating AML cell lines and primary AML samples with IFNγ and TNFα. We observed an upregulation of PD-L1 and SLAMF7 on AML cell lines and on primary AML patient samples whereas HVEM and ILT3 did not show a significant change in expression level. To test the functional relevance of the immune checkpoint molecules upon AMG 330 mediated lysis, we used an ex vivo long term culture system that enabled us to analyse the dynamic process of receptor-ligand interaction over time. Blockade of the PD-1/PD-L1 interaction resulted in a significantly increase in AMG 330 mediated lysis of primary AML cells (n=9, p=0.03). Currently, blockade of the inducible molecule SLAMF7 in AMG 330 mediated cytotoxicity is being tested. Blocking of HVEM or ILT3 did not result in a significant increase in T cell activation and concomitant lysis of AML cells suggesting a less relevant role of HVEM and ILT3 in resistance to AMG 330 mediated cytotoxicity. The latter might also be influenced by the cytokine microenvironment which favours immune resistance of AML cells. Using a bead based multiplex assay we screened the bone marrow (BM) plasma from 16 AML patients and 3 healthy donors (HD) for the presence of 33 cytokines. The cytokine profile differed between AML patients and healthy donors (HDs). The plasma levels of IL-8, IP-10 and CXCL-16 were higher in the AML samples compared to those of HDs (p=0.0041, 0.0248 and 0.0289, respectively). In contrast, EGF, FLT3-ligand, RANTES and IL-4 were significantly lower in AML samples compared to HDs (p=0.0227, 0.0145, 0.0041 and 0.0041, respectively). However, we did observe a high inter-patient variability of cytokine composition in AML. To explore the functional relevance of the BM plasma on AMG 330 mediated cytotoxicity, cocultures of AML cell lines and HD T cells were set up using different sources of plasma including fetal calf serum (FCS) and patient derived BM plasma. Interestingly, AMG 330 mediated cytotoxicity was significantly reduced using patient derived BM plasma (n=5) compared to cultures containing FCS (n=4) (mean % lysis FCS 97.4 vs PT 70.6). This was accompanied by a considerable impairment in T-cell proliferation (mean % proliferation FKS 44.7% vs PT 26.6%). Currently, we are investigating which soluble factors are responsible for the immunosuppressive effects and if we can increase lysis efficacy and T-cell proliferation through specific blocking of them. In summary we have identified possible resistance mechanisms of AML cells to AMG 330 mediated cytotoxicity. Dynamic receptor-ligand interactions between target and effector cells as well as soluble factors contribute to AMG 330 mediated lysis of primary AML cells. We hypothesize that AMG 330 mediated cytotoxicity can be augmented through combinatorial approaches including PD-1 blockade. The significance of our findings will first be validated in an in vivo mouse model and prospectively translated into human studies. DisclosuresKrupka:AMGEN Research (Munich): Research Funding. Kufer:AMGEN Research (Munich): Employment, Equity Ownership. Kischel:AMGEN Research (Munich): Employment, Equity Ownership. Subklewe:AMGEN Research (Munich): Research Funding.

Plastic and Evolutionary Gene Expression Responses Are Correlated in European Grayling (Thymallus thymallus) Subpopulations Adapted to Different Thermal Environments.

Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary gene expression. We have previously shown that the gene expression profiles of European grayling (Thymallus thymallus) populations inhabiting different thermal environments include both plastic and evolutionary components. However, whether the plastic and evolutionary responses were in the same direction was not investigated in detail, nor was the identity of the specific genes involved. In this study, we show that the plastic changes in protein expression in response to different temperatures are highly correlated with the evolutionary response in grayling subpopulations adapted to different thermal environments. This finding provides preliminary evidence that the plastic response most likely facilitates adaptation during the early phases of colonization of thermal environments. The proteins that showed significant changes in expression level between warm and cold temperature treatments were mostly related to muscle development, which is consistent with earlier findings demonstrating muscle mass differentiation between cold and warm grayling populations.

Proteomic investigation of the severe preeclampsia treatment by low molecular weight heparin

Purpose: The primary goal of this study is to investigate the mechanism of severe preeclampsia (PE) treatment by low molecular weight heparin (LMWH). Materials and Methods: Using two-dimensional difference in-gel electrophoresis (2D-DIGE) combined with matrix assisted laser desorption ionization-time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF) approach to identify the proteins that expressed differently in the serum samples of five patients before and after subcutaneous injection of LMWH (0.4 ml/person). Results: Seven protein spots were identified in 2D-DIGE that show significant change in expression level after LMWH treatment. Further analysis of seven protein spots with MALDI-TOF/TOF identified six different proteins. To confirm the proteomic data, two meaningful proteins of the six proteins, alpha-1-acid glycoprotein (AGP) and serotransferrin are subjected to immunoblotting. All of the proteins are obviously down-regulated after LMWH treatment. Conclusions: PE is a pregnancy-specific disease that clinically manifests as new-onset hypertension and proteinuria after 20 weeks of gestation. LMWH is an effective treatment of severe PE. The present proteomics based investigation may provide a new angle to understand the mechanism of severe PE treatment with LMWH.

Aberrantly expressed mRNAs and long non-coding RNAs in patients with invasive ductal breast carcinoma: a pilot study.

Invasive ductal breast carcinoma (IDBC) is the most prevalent type of invasive breast cancer in females; however, the pathogenesis of IDBC remains to be elucidated. Therefore, the identification of novel markers may enhance current understanding of the initiation and development of IDBC as well as elucidate potential therapeutic targets for effective treatment of IDBC. In the present study, a pilot study was conducted to screen for potential mRNAs and long non-coding (lnc)RNAs that exhibit aberrantly altered expression in patients with IDBC. Fresh breast cancer specimens and normal breast tissues were obtained from three female patients with IDBC aged ≥60 years following a modified radical mastectomy without chemotherapy. Expression levels of 44,244 probes were detected and included in the analysis, of which 22,078 (49.9%) were mRNAs and 22,166 (50.1%) were lncRNAs. Potential marker screening was performed using paired t-tests (criterion 1), false discovery rates (FDR; criterion 2) and sure independence screening procedures based on distance correlations (DC-SIS; criterion 3). The results showed that in IDBC tissues 3,510 probes had a ≥2-fold statistically significant change in expression levels compared to those in the corresponding normal breast tissue (P<0.05); in addition, following FDR analysis, 353 probes were found to have significantly altered expression levels. Furthermore, DC-SIS analysis identified 18 probes (12 mRNA and 6 lncRNAs) with significantly altered expression levels in IDBC tissue; these 18 probes therefore demonstrated significant results in all three criteria. Several of the mRNAs identified have been previously reported to be involved in signal transduction, protein binding, and cancer pathways, and the present study revealed that the majority of their gene products were located in the cytoplasm. Two of the six identified lncRNAs demonstrated a >10-fold decrease in expression levels in IDBC tissues compared to that in the normal breast tissue. However, further studies are required in order to elucidate the biological functions of the identified probes.

BB0238, a presumed tetratricopeptide repeat-containing protein, is required during Borrelia burgdorferi mammalian infection.

The Lyme disease spirochete, Borrelia burgdorferi, occupies both a tick vector and mammalian host in nature. Considering the unique enzootic life cycle of B. burgdorferi, it is not surprising that a large proportion of its genome is composed of hypothetical proteins not found in other bacterial pathogens. bb0238 encodes a conserved hypothetical protein of unknown function that is predicted to contain a tetratricopeptide repeat (TPR) domain, a structural motif responsible for mediating protein-protein interactions. To evaluate the role of bb0238 during mammalian infection, a bb0238-deficient mutant was constructed. The bb0238 mutant was attenuated in mice infected via needle inoculation, and complementation of bb0238 expression restored infectivity to wild-type levels. bb0238 expression does not change in response to varying culture conditions, and thus, it appears to be constitutively expressed under in vitro conditions. bb0238 is expressed in murine tissues during infection, though there was no significant change in expression levels among different tissue types. Localization studies indicate that BB0238 is associated with the inner membrane of the spirochete and is therefore unlikely to promote interaction with host ligands during infection. B. burgdorferi clones containing point mutations in conserved residues of the putative TPR motif of BB0238 demonstrated attenuation in mice that was comparable to that in the bb0238 deletion mutant, suggesting that BB0238 may contain a functional TPR domain.

Comparative analysis of cigarette smoke induced cellular proteome distributions on bovine aortic endothelial cells

Cigarette smoke is a contributory factor for the cardiovascular disease, lung diseases and cancers as the dominant illnesses. The proteomic analysis of bovine aortic endothelial cells (BAECs) exposed to cigarette smoke has been performed in the broad (Non-linear pH 3–11) and narrow (Linear pH 4–7) range by using two-dimensional gel electrophoresis (2-DE). Out of an average 950 spots observed in 2-DE gels under pH 3–11, the expression level of 25 proteins significantly increased with an increase of cigarette smoke extract (CSE) level, whereas 21 proteins were strongly down-regulated. In narrow (4–7) pH range analysis, 80 proteins showed a significant change in expression level as compared with control. Some of the proteins were found to show similar spot intensity patterns in both the linear (4–7) and nonlinear (3–11) pH ranges. Most of the proteins identified in both pH conditions were found to be involved in apoptosis, inflammation, transcription modulator, signal transduction pathway, ROS production, cell proliferation and extracellular structure formation. In addition, extracellular structural proteins also responded to apoptotic signaling as an indicator. The findings of the present study can be used as an early biomarker to indicate the risks of cigarette smoke related diseases and also in the design of new therapeutic and diagnostic approaches to control these diseases.

Comparative transcriptomic analysis of the heat stress response in the filamentous fungus Metarhizium anisopliae using RNA-Seq.

The entomopathogenic fungus Metarhizium anisopliae is widely used for biological control of a variety of insect pests. The effectiveness of the microbial pest control agent, however, is limited by poor thermotolerance. The molecular mechanism underlying the response to heat stress in the conidia of entomopathogenic fungi remains unclear. Here, we conducted high-throughput RNA-Seq to analyze the differential gene expression between control and heat treated conidia of M. anisopliae at the transcriptome level. RNA-Seq analysis generated 6,284,262 and 5,826,934 clean reads in the control and heat treated groups, respectively. A total of 2,722 up-regulated and 788 down-regulated genes, with a cutoff of twofold change, were identified by expression analysis. Among these differentially expressed genes, many were related to metabolic processes, biological regulation, cellular processes and response to stimuli. The majority of genes involved in endocytic pathways, proteosome pathways and regulation of autophagy were up-regulated, while most genes involved in the ribosome pathway were down-regulated. These results suggest that these differentially expressed genes may be involved in the heat stress response in conidia. As expected, significant changes in expression levels of genes encoding heat shock proteins and proteins involved in trehalose accumulation were observed in conditions of heat stress. These results expand our understanding of the molecular mechanisms of the heat stress response of conidia and provide a foundation for future investigations.

Differential soybean gene expression during early phase of infection with Mungbean yellow mosaic India virus.

Mungbean yellow mosaic India virus (MYMIV), a bipartite begomovirus, causes yellow mosaic disease to soybean. Studies related to host gene expression in response to begomovirus infection have mostly been performed with systemically infected tissues at a later period of infection. In this study, soybean gene expression analysis has been performed to understand local responses against MYMIV at an early stage of infection before appearance of detectable limit of late viral transcripts. 444 soybean transcripts belonging to eleven functional categories showed significant changes in expression level at two days after infection. MYMIV infection resulted in enhanced expression of genes associated with hypersensitive response, programmed cell death and resistance response pathways and reduced expression of genes for photosynthesis and sugar transport. Comparative expression analysis of selected transcripts in the susceptible and a resistant variety displayed differential expression of host genes involved in intercellular virus movement and long distance signaling of systemic acquired resistance.

Proteomic analysis of human substantia nigra identifies novel candidates involved in Parkinson's disease pathogenesis

Parkinson's disease (PD) pathology spreads throughout the brain following a region-specific process predominantly affecting the substantia nigra (SN) pars compacta. SN exhibits a progressive loss of dopaminergic neurons responsible for the major cardinal motor symptoms, along with the occurrence of Lewy bodies in the surviving neurons. To gain new insights into the underlying pathogenic mechanisms in PD, we studied postmortem nigral tissues dissected from pathologically confirmed PD cases (n = 5) and neurologically intact controls (n = 8). Using a high-throughput shotgun proteomic strategy, we simultaneously identified 1795 proteins with concomitant quantitative data. To date, this represents the most extensive catalog of nigral proteins. Of them, 204 proteins displayed significant expression level changes in PD patients versus controls. These were involved in novel or known pathogenic processes including mitochondrial dysfunction, oxidative stress, or cytoskeleton impairment. We further characterized four candidates that might be relevant to PD pathogenesis. We confirmed the differential expression of ferritin-L and seipin by Western blot and demonstrated the neuronal localization of gamma glutamyl hydrolase and nebulette by immunohistochemistry. Our preliminary findings suggest a role for nebulette overexpression in PD neurodegeneration, through mechanisms that may involve cytoskeleton dynamics disruption. All MS data have been deposited in the ProteomeXchange with identifier PXD000427 (http://proteomecentral.proteomexchange.org/dataset/PXD000427).

Altered Retinal MicroRNA Expression Profiles in Early Diabetic Retinopathy: An In Silico Analysis

Purpose: MicroRNAs (miRNAs) – as negative regulators of target genes – are associated with various human diseases, but their precise role(s) in diabetic retinopathy (DR) remains to be elucidated. The aim of this study was to elucidate the involvement of miRNAs in early DR using in silico analysis to explore their gene expression patterns.Methods: We used the streptozotocin (STZ)-induced diabetic rat to investigate the roles of miRNAs in early DR. Retinal miRNA expression profiles from diabetic versus healthy control rats were examined by miRNA array analysis. Based on several bioinformatic systems, specifically, gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we identified signatures of the potential pathological processes, gene functions, and signaling pathways that are influenced by dysregulated miRNAs. We used quantitative real-time polymerase chain reaction (qRT-PCR) to validate six (i.e. those with significant changes in expression levels) of the 17 miRNAs that were detected in the miRNA array. We also describe the significant role of the miRNA-gene network, which is based on the interactions between miRNAs and target genes.Results: GO analysis of the 17 miRNAs detected in the miRNA array analysis revealed the most prevalent miRNAs to be those related to biological processes, olfactory bulb development and axonogenesis. These miRNAs also exert significant influence on additional pathways, including the mitogen-activated protein and calcium signaling pathways. Six of the seventeen miRNAs were chosen for qRT-PCR validation. With the exception of a slight difference in miRNA-350, our results are in close agreement with the differential expressions detected by array analysis.Conclusions: This study, which describes miRNA expression during the early developmental phases of DR, revealed extensive miRNA interactions. Based on both their target genes and signaling pathways, we suggest that miRNAs perform critical regulatory functions during the early stages of DR evolution.

Transcriptomic microarray analysis of BoMac cells after infection with bovine foamy virus

Bovine foamy virus (BFV) infections are highly prevalent among cattle worldwide. However, relatively little is known about the impact of this virus on the host immune system. In our study, we focused on a bovine macrophage cell line (BoMac) and examined changes in the BoMac transcriptome after in vitro infection with BFV using bovine BLOPlus oligo microarrays. One hundred twenty-four genes showed significant changes in expression level. The biological process categories found to be enriched include metabolic processes, cell communication, transport, immune system processes, and response to extracellular stimuli. RT-qPCR was applied to confirm the results obtained for representative genes.

Growth-dependent toxicity of Photorhabdus temperata in katydid Paratlanticus ussuriensis

The oral toxicity of the symbiotic bacteria Photorhabdus temperata was investigated in various developmental stages of Paratlanticus ussuriensis. Supernatants of Photorhabdus culture medium were mixed into an artificial diet, which was fed to various stages of immature nymphs and adults of P. ussuriensis. Mortality was highest in the first instar nymph but decreased in older stages of immature nymphs. Adult females were not killed upon oral ingestion of P. ussuriensis, but their fecundity was significantly inhibited to 29.3% of that of control. In addition, the effects of oral ingestion of the symbiont culture media on the expression rates of three heat shock protein 70 genes (hsp70a, hsp70b, and hsp70c) in third instar nymphs of P. ussuriensis were determined by quantitative real-time RT-PCR analysis. There were no significant changes in expression levels in comparison with control, which suggests that hsp genes may not be associated with the mechanism of Photorhabdus toxicity. Our results imply that Photorhabdus culture media is highly effective in killing younger immature nymphs and also suppressing adult reproduction of P. ussuriensis.

Dysregulated microRNAs in non-cirrhotic hepatocellular carcinoma

MicroRNAs (miRNAs) are endogenous non-coding 21–23 nucleotide RNAs that are involved in post-transcriptional regulation. They control various cellular processes, one of which is tumorigenesis. miRNAs have been implicated in the pathogenesis of hepatocellular carcinoma (HCC), the most common primary liver cancer. To find yet-to-be-identified miRNAs associated with HCC tumorigenesis, we resected HCC and adjacent non-tumor liver tissues from patients and excluded liver tissues harboring fibrosis from further analysis. We then carried out miRNA microarray analysis with miRNAs extracted from the tissues. Sixteen miRNAs displayed a significant change in expression levels between non-tumor and HCC liver tissues. To validate the microarray findings, we transfected HEK293 cells with miR-128 alone or miR-128 and plasmid encoding luciferase fused to the 3′ untranslated region (UTR) of E2F3, a predicted target of miR-128. As expected, miR-128 downregulated luciferase activities of E2F3 3′UTR fused to luciferase, confirming that E2F3 is a target gene of miR-128. Identification of miRNAs dysregulated in non-cirrhotic HCC will further the understanding of the pathogenesis of non-cirrhotic HCC.

Recombinant adenovirus-p53 combined with chemotherapy in treatment of locally advanced cervical cancer (a phase II study).

5525 Background: To evaluate the efficacy and safety of recombinant adenovirus-p53 (rAd-p53) combined with chemotherapy in treatment of locally advanced cervical cancer. Methods: Forty patients with stage IIb2 IV locally advanced cervical cancer were randomly divided into 2 groups: 20 patients receiving gene plus chemotherapy (PCG) and 20 receiving sole chemotherapy (CG). The patients in PCG were given one course of PVB (cisplatin + vincristine + pingyangmycin) and 5 times intratumoral injections of rAd-p53 at a dose of 2 x 1012 viral particles once per 3 days. The CG patients received a sole course of PVB. The study patients were followed up for at least one year. The VEGF, p53, Bax, and p21 protein expression in pre- and post-treatment tumor tissues were examined by immunohistochemistry. Results: The response was evaluated at 3 months after treatments. The response rates (CR + PR) were 95% and 75% for the PCG and CG patients, respectively. P53 proteins were strongly expressed in the tumor tissues from both groups. There were no significant changes in expression level of the p53 protein in the tumor tissue from pre- and post-treatment. However, the VEGF, Bax, and p21 protein expressions significantly increased in PCG after treatment. The overall one-year survive rates were 90% and 65%, respectively. A mild to medium grade of fever was found in 90% of the PCG patients. No serious of adverse events relative to rAd-p53 were observed. Conclusions: Combined the rAd-p53 gene with chemotherapy is an effective treatment for the patients with advanced cervical cancer. The rAd-p53 gene therapy is a safe treatment.

Gene Expression Profiling of Allogeneic Islet Grafts in an Experimental Mouse Model Before Rejection or Tolerance Phenotypes Arise

BackgroundIt has been reported that an HY antigen-mismatched islet transplantation can induce peripheral tolerance. However, the factors that initiate the peripheral tolerance are not clear. This study was designed to examine which genes were most important for the induction of peripheral tolerance. MethodsIslets from female Balb/c and male C57BL/6 mice were transplanted underneath the left perirenal capsule of female C57BL/6 recipient mice rendered diabetic by intraperitoneal injection of streptozotocin. Before rejection or tolerance phenotypes arose, we harvested islet grafts for cDNA microarray analysis. ResultsMinor antigen-mismatched islets transplanted into recipient mice showed no rejection or tolerance phenotypes until 12 days posttransplantation. When we confirmed, decreased functional islet grafts and increased inflammatory cell infiltration. Gene expression profiles revealed differences in expression among groups. Major histocompatibility complex-mismatched islets induced upregulation of 209 genes and downregulation of 10 genes compared with the HY antigen-mismatched islet (2-fold; P < .05). Of these, 3 genes exhibited significant changes in expression levels in Balb/c donor islet grafts compared with C57BL/6 donor islet grafts: Gad1, Gdf10, and Scg2 (P < .01). ConclusionsThe present study suggested that 3 genes showed a significant relationship to protection against graft rejection. The identification of these genes may help to understand signaling pathways, involved in the communication between transplanted islet grafts and recipients in vivo.

Differential analysis of gene regulation at transcript resolution with RNA-seq

Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses numerous statistical challenges. We present Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. Cuffdiff 2 robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1, which we show is required for lung fibroblast and HeLa cell cycle progression. Loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle. Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies.

Age- and behaviour-related changes in the expression of biogenic amine receptor genes in the antennae of honey bees (Apis mellifera)

We recently identified changes in amine-receptor gene expression in the antennae of the honey bee that correlate with shifts in the behavioural responsiveness of worker bees towards queen mandibular pheromone. Here we examine whether variations in expression of amine-receptor genes are related to age and/or to behavioural state. Colonies with a normal age structure were used to collect bees of different ages, as well as pollen foragers of unknown age. Single- and double-cohort colonies were established also to generate nurses and pollen foragers of the same age. Amdop1 was the only gene examined that showed no significant change in expression levels across the age groups tested. However, expression of this gene was significantly higher in 6-day-old nurses than in pollen foragers of the same age. Levels of expression of Amdop2 were very variable, particularly during the first week of adult life, and showed no correlation with nursing or foraging behaviour. Amdop3 and Amtyr1 expression levels changed dramatically with age. Interestingly, Amtyr1 expression was significantly higher in 15-day-old pollen foragers than in same-age nurses, whereas the opposite was true for Amoa1. While Amoa1 expression in the antennae was lower in 6- and 15-day-old pollen foragers than in nurses of the same age, differences in gene expression levels between nurses and pollen foragers could not be detected in 22-day-old bees. Our data show dynamic modulation of gene expression in the antennae of worker bees and suggest a peripheral role for biogenic amines in regulating behavioural plasticity in the honey bee.

Cullin 7 and Fbxw 8 expression in trophoblastic cells is regulated via oxygen tension: implications for intrauterine growth restriction?

Objective: The F-box protein Fbxw8 is a cofactor of Cullin 7 (Cul7), which regulates protein transfer to the proteasome and cell growth. Cul7 or Fbxw8 deficiency is associated with intrauterine growth restriction (IUGR) due to abnormal placental development leading to poor oxygen supply to the fetus. We studied the role of hypoxia for Fbxw8 and Cul7 expression in trophoblastic cells. Methods: Immunomagnetic bead-separated extravillous trophoblast (EVT) and villous trophoblast (VT) and trophoblast cell lines were incubated with 1 or 8% O2. Fbxw8 and Cul7 expression was determined in IUGR versus matched control placentas. Results: Fbxw8 was expressed uniformly in trophoblasts, whereas Cul7 expression was most prominent in trophoblast cell lines. Hypoxia reduced expression of Cul7 and Fbxw8 in all trophoblastic cells, except for villous trophoblasts. In vivo, Cul7 and Fbxw8 were detected in syncytiotrophoblast cells, VT, and EVT cells. Although no significant changes in expression levels of Fbxw8 or Cul7 were noted in IUGR compared with control placentas, Fbxw8 expression correlated negatively with gestational age in the control, but not in the IUGR group. Conclusion: Fbxw8 and Cul7 expression reveals a complex regulation in trophoblastic cells. Our findings suggest that dysregulation of Cul7 and Fbxw8 expression might affect trophoblast turnover in IUGR.

Abstract 1660: Lack of correlation between in silico projection of function for CYP19A1 and NFκB1 SNPs and qRT-PCR-determined gene expression levels in colon tissue

Abstract The ability to link functional genetic variants with disease risk leads to advances in diagnostics and therapeutics. There are an estimated 10 million single nucleotide polymorphisms (SNPs), thus computerized projection programs that predict SNP-based alterations in functionality are used for genotyping experiments. We explored if projection programs could accurately predict functionality in colon samples. TagSNPs were identified for the CYP19A1 and NFκB1 genes, and normal colon tissue samples were genotyped for the tagSNPs and phenotyped using Taqman gene expression assays. Associations between SNPs and gene expression were noted and compared with projected outcomes from FastSNP (Academia Sinica). Of 25 CYP19A1 SNPs chosen for analysis, 10 were predicted to have no effect, 14 to alter transcription factor (TF) binding sites, and 1 to have a sense/synonymous coding change. Of those that were predicted to have no effect, one (rs17523880) showed significant changes in CYP19A1 expression levels (p=0.05 when adjusted for age, sex, and race). Two of the SNPs predicted to alter TF binding (rs1902584, rs6493497) showed a change in expression levels (p&amp;lt;=0.01), and there was no expression change in the SNP with synonymous coding change. In a case-control study exploring genetic associations in colon cancer and utilizing the same SNPs, three of the SNPs that were predicted to have no change (rs1961177, rs17523880, rs3751591) were found to be significantly associated with colon cancer (p&amp;lt;0.01, p=0.015, p&amp;lt;0.01). Of those, one (rs17523880) was associated with change in expression in our samples (p=0.05). In the case-control study, significant interactions between CYP19A1 and NFκB1 SNPs and colon cancer were reported. Thus, we also examined 11 NFκB1 SNPs, five of which were predicted to have no functional effect, and six of which were predicted to alter TF binding sites. Of the SNPs with no predicted functional consequences, three (rs3821958, rs1801, rs3774964) were associated with significant changes in gene expression (p&amp;lt;0.01 to p=0.04), and of those with projected TF binding site alterations, two were associated with a significant change in expression levels (rs4648090, p&amp;lt;0.01; rs3755867, p=0.04). Further, of two NFκB1 SNPs that interacted with CYP19A1 SNPs in the case control study, both were projected to have no effect on function, but were significantly associated with expression in our samples ((rs3821958, rs3774964; p&amp;lt;0.01). Future studies will include protein expression and enzymatic activity in these samples, and exploration in other tissues. In summary, while prediction programs are useful for choosing candidate SNPs for large scale assays, they cannot be relied on for accuracy, and functional effects of significant SNPs in disease association studies should be confirmed empirically in order to design treatment and prevention strategies. 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 1660. doi:1538-7445.AM2012-1660

MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress

Switchgrass has increasingly been recognized as a dedicated biofuel crop for its broad adaptation to marginal lands and high biomass. However, little is known about the basic biology and the regulatory mechanisms of gene expression in switchgrass, particularly under stress conditions. In this study, we investigated the effect of salt and drought stress on switchgrass germination, growth and the expression of small regulatory RNAs. The results indicate that salt stress had a gradual but significant negative effect on switchgrass growth and development. The germination rate was significantly decreased from 82% for control to 36% under 1% NaCl treatment. However, drought stress had little effect on the germination rate but had a significant effect on the growth of switchgrass under the severest salinity stress. Both salt and drought stresses altered the expression pattern of miRNAs in a dose-dependent manner. However, each miRNA responded to drought stress in a different pattern. Salt and drought stress changed the expression level of miRNAs mainly from 0.9-fold up-regulation to 0.7-fold down-regulation. miRNAs were less sensitive to drought treatment than salinity treatment, as evidenced by the narrow fold change in expression levels. Although the range of change in expression level of miRNAs was similar under salt and drought stress, no miRNAs displayed significant change in expression level under all tested salt conditions. Two miRNAs, miR156 and miR162, showed significantly change in expression level under high drought stress. This suggests that miR156 and miR162 may attribute to the adaption of switchgrass to drought stress and are good candidates for improving switchgrass as a biofuel crop by transgenic technology.