scholarly journals 227 CONSTRUCTION OF STAGE-SPECIFIC cDNA MICROARRAY, AND ANALYSIS OF IN VITRO PRODUCED PRE-IMPLANATION STAGE BOVINE EMBRYOS FOR DEVELOPMENTAL COMPETENCE

2005 ◽  
Vol 17 (2) ◽  
pp. 264
Author(s):  
S. Mamo ◽  
C.A. Sargent ◽  
N.A. Affara ◽  
K. Wimmers ◽  
S. Ponsuksili ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Real Time Pcr ◽  
Large Scale ◽  
Expression Profiles ◽  
Developmental Competence ◽  
Cdna Clones ◽  
Bovine Embryo ◽  
Single Experiment

Microarray technology currently has wide acceptance as a research tool in the study of gene expression profiling, mainly as a result of its use for monitoring the expression profiles of thousands of genes in a single experiment. However, its use in analyzing gene expression in the pre-implantation stage of bovine embryo development has been limited for reasons such as the large amount of RNA required and the lack of bovine specific cDNA clone collections (Smith L and Greenfield A 2003 Hum. Mol. Genet. 12, 1–8). In this study, with the objectives of producing pre-implantation-stage-specific bovine cDNA clones and examining the developmental competence, eighty-two selected target clones of pre-implantation-stage-specific genes were prepared and spotted on the glass slide. Embryos were produced in vitro and mRNAs were isolated from contrasting probes of good quality matured oocytes and blastocyst-stage embryos using a Dynabead mRNA isolation kit by following the manufacturer's instructions. First-strand cDNA syntheses were primed with T7 Oligo d(T)21 primer, followed by random primed second-strand syntheses using a DOP master kit (Roche Diagnostics, Mannheim, Germany) and global amplification using the same primers used for the first- and second-strand syntheses. In vitro transcription was performed to amplify the RNA by using the AmpliScribe T7 transcription kit (EPICENTRE Technologies, Oldendorf, Germany), and the amplified RNA (aRNA) was purified using a RNeasy Mini kit (Qiagen, Hilden, Germany). Finally, the results of different RNA amplifications (aRNA) were tested by hybridization on microarrays and also using real-time PCR techniques. With these analyses, the sufficiency of the yield and linearity of amplification procedures were confirmed. Three micrograms each of aRNA were labelled with Cy3 and Cy5 dyes and hybridized to the array. After overnight incubation at 42°C, the slides were sequentially washed and scanned using an ArrayWorx biochip reader (Applied Precision, Marlborough, UK), and quantifications as well as all analyses were carried out using different TIGR software modules (Saeed AI et al. 2003 Biotechniques 34(2), 374–378). Analyses of the results of repeated hybridizations showed that 35 genes (43%), which belong to different functional groups, were differentially expressed between the two stages. Further independent analyses using real-time PCR confirmed the results of 25 genes. Hence, it is possible to conclude that the established methods can be used for large scale gene expression analysis, and the identified genes can be potential candidates for characterizing developmental competence.

209 9-cis RETINOIC ACID INHIBITS EXPRESSION OF AKR1B1 TRANSCRIPT IN THE BOVINE OOCYTES AND PRE-IMPLANTATION EMBRYOS

2013 ◽  
Vol 25 (1) ◽  
pp. 252
Author(s):  
G. K. Deb ◽  
S. R. Dey ◽  
K. S. Huque ◽  
M. Fokruzzaman ◽  
K. L. Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Retinoic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Embryo Implantation ◽  
Cumulus Cell ◽  
Prostaglandin F2α ◽  
Receptor Expression ◽  
Bovine Embryo

Quantitative real-time PCR has enabled quality evaluation of oocyte and pre-implantation embryo through monitoring expression of several molecular markers that are involved in metabolic activity, stress response, reprogramming, and other biological events. The aldo-keto reductase family 1 member B1 (AKR1B1) transcript is potentially involved in pregnancy failure through metabolism of progesterone and synthesis of prostaglandin F2α in the bovine uterine endometrium. High expression of the transcript in blastocysts correlates inhibition of embryo implantation and/or embryo resorption. Maturation of immature oocyte in presence of 9-cis retinoic acid (9-cis RA) increases in vitro bovine embryo development rates and embryo quality. These beneficial effects of 9-cis RA are mediated through multiple mechanisms, including FSH/LH receptor expression, polyadenylation, growth factor signalling, oxidative-stress protection, or decreasing oocyte TNFα gene expression and inhibiting cumulus cell apoptosis during maturation. The present study aimed to evaluate the effect of 9-cis RA on expression pattern of AKR1B1 transcript in the oocyte matured in vitro and embryos (8-cell and Day 8 blastocyst) produced from in vitro matured oocytes in presence or absence of 9-cis RA. Bovine cumulus–oocyte complexes, isolated from ovaries collected at the abattoir, were matured in vitro in the presence of zero (control) or 5 nM 9-cis RA in the maturation medium (TCM199 + 10% fetal bovine serum + 1 µg mL–1 β-oestradiol + 10 µg mL–1 follicle stimulating hormone + 0.6 mM cystein and 0.2 mM Na-pyruvate). After maturation, the oocytes were subjected to standardized in vitro embryo production protocol or oocyte samples were collected for gene expression analysis. The expression of AKR1B1 transcript was quantified in zona-free oocytes, 8-cell embryos, and Day 8 blastocysts by real-time PCR using SYBER green. Not less than 4 biological replicates (oocytes: 50 to 60 per replicate and 8-cell embryos/day-8 blastocyst: 3 to 5 per replicate) were done for each group. The expression was normalized against a minimum of 2 out of 4 reference transcripts (18S rRNA, β-actin, glyceraldehyde-3-phosphate dehydrogenase and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide) analysed each time with AKR1B1. The best combination of reference genes was automatically calculated by the CFX manager V1.1 program (Bio-Rad) based on M-value. The differences in gene expression levels were tested by Student’s t-test. Results indicated that 9-cis RA decreased expression of AKR1B1 transcript in the oocyte (1.0- v. 2.0-fold; P < 0.05), 8-cell-embryos (1.0- v. 10.1-fold; P < 0.03), and blastocyst (1.0- v. 2.1-fold; P < 0.03) compared with control. In conclusion, the present study indicates that 9-cis RA inhibits AKR1B1 transcript expression in oocytes and pre-implantation embryos.

scholarly journals Effects of different oocyte retrieval and in vitro maturation systems on bovine embryo development and quality

Zygote ◽  
2014 ◽  
Vol 23 (3) ◽  
pp. 367-377 ◽  
Author(s):  
Sandra Milena Bernal ◽  
Julia Heinzmann ◽  
Doris Herrmann ◽  
Bernd Timmermann ◽  
Ulrich Baulain ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Developmental Competence ◽  
Bovine Embryo ◽  
Global Methylation ◽  
Oocyte Developmental Competence

SummaryCyclic adenosine monophosphate (cAMP) modulators have been used to avoid spontaneous oocyte maturation and concomitantly improve oocyte developmental competence. The current work evaluated the effects of the addition of cAMP modulators forskolin, 3-isobutyl-1-methylxanthine (IBMX) and cilostamide during in vitro maturation on the quality and yields of blastocysts. The following experimental groups were evaluated: (i) slicing or (ii) aspiration and maturation in tissue culture medium (TCM)199 for 24 h (TCM24slicing and TCM24aspiration, respectively), (iii) aspiration and maturation in the presence of cAMP modulators for 30 h (cAMP30aspiration) and in vivo-produced blastocysts. In vitro-matured oocytes were fertilized and presumptive zygotes were cultured in vitro to assess embryo development. Cleavage, blastocyst formation, blastocyst cell number, mRNA abundance of selected genes and global methylation profiles were evaluated. Blastocyst rate/zygotes for the TCM24aspiration protocol was improved (32.2 ± 2.1%) compared with TCM24slicing and cAMP30aspiration (23.4 ± 1.2% and 23.3 ± 2.0%, respectively, P<0.05). No statistical differences were found for blastocyst cell numbers. The mRNA expression for the EGR1 gene was down-regulated eight-fold in blastocysts that had been produced in vitro compared with their in vivo counterparts. Gene expression profiles for IGF2R, SLC2A8, COX2, DNMT3B and PCK2 did not differ among experimental groups. Bovine testis satellite I and Bos taurus alpha satellite methylation profiles from cAMP30aspiration protocol-derived blastocysts were similar to patterns that were observed in their in vivo equivalents (P > 0.05), while those from the other groups were significantly elevated. It is concluded that retrieval, collection systems and addition of cAMP modulators can affect oocyte developmental competence, which is reflected not only in blastocyst rates but also in global DNA methylation and gene expression patterns.

scholarly journals Bovine blastocysts with developmental competence to term share similar expression of developmentally important genes although derived from different culture environments

Reproduction ◽  
2011 ◽  
Vol 142 (4) ◽  
pp. 551-564 ◽  
Author(s):  
N Ghanem ◽  
D Salilew-Wondim ◽  
A Gad ◽  
D Tesfaye ◽  
C Phatsara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Developmental Competence ◽  
Bovine Embryo ◽  
Placental Development ◽  
Similar Expression ◽  
Maternal Interaction

This study was conducted to investigate the gene expression profile of in vivo-derived bovine embryo biopsies based on pregnancy outcomes after transferring to recipients. For this, biopsies of 30–40% embryos were taken from grade I blastocysts (International Embryo Transfer Society Manual) and the remaining 60–70% of the intact embryos were transferred to recipients. Frozen biopsies were pooled into three distinct groups based on the pregnancy outcome after transferring the corresponding parts, namely those resulting in no pregnancy (NP), pregnancy loss (PL), and calf delivery (CD). Array analysis revealed a total of 41 and 43 genes to be differentially expressed between biopsies derived from blastocysts resulting in NP versus CD and PL versus CD respectively. Genes regulating placental development and embryo maternal interaction (PLAC8) were found to be upregulated in embryo biopsies that ended up with CD. Embryo biopsies that failed to induce pregnancy were enriched with mitochondrial transcripts (Fl405) and stress-related genes (HSPD1). Overall, gene expression profiles of blastocysts resulting in NP and CD shared similar expression profiles with respect to genes playing significant roles in preimplantation development of embryo. Finally, comparing the transcript signatures of in vivo- and in vitro-derived embryos with developmental competence to term revealed a similarity in the relative abundance of 18 genes. Therefore, we were able to present a genetic signature associated with term developmental competence independent of the environmental origin of the transferred blastocysts.

189 TRANSCRIPTIONAL PROFILING OF HISTONE-MODIFYING GENES DURING BOVINE PRE-IMPLANTATION EMBRYO DEVELOPMENT IN VITRO

2009 ◽  
Vol 21 (1) ◽  
pp. 193
Author(s):  
G. D. Linger ◽  
C. L. Bormann ◽  
M. D. Peoples ◽  
M. C. Golding ◽  
C. R. Long
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Profiles ◽  
Geometric Mean ◽  
Cell Stage ◽  
Embryonic Genome ◽  
Morula Stage

The proper removal of gametic epigenetic marks and coordinated re-establishment of the epigenome is critical to mammalian embryonic development. This global reprogramming of the embryonic genome includes fluctuations in both DNA methylation and histone modifications that are necessary to control chromatin structure and thus gene expression. In the bovine model, epigenetic changes occur from fertilization through blastocyst stages; in particular, and concurrent with the maternal-embryonic transition, de novo DNA methylation begins at the 8-cell stage. In order to understand which factors might be playing key roles in this epigenetic process, we used quantitative real-time PCR to characterize the temporal expression profiles of several genes involved in DNA and/or histone methylation: G9a, SetB1, Suv39h1, Suv420h1, SmyD3, Suz12, and LSH. Bovine ova and embryos were produced via in vitro maturation, fertilization, and culture from multiple pools of ova. Groups of 12–25 bovine ova or embryos, pooled at the 2-, 4 to 7-, mid 8-, late 8-, 12 to 16-cell, morula, and blastocyst stages, were washed twice through 1X PBS and stored in RNA lysis buffer at –80°C until further use. RNA was isolated from each sample using the RNeasy® Mini kit (Qiagen, Valencia, CA, USA), optimized for isolating RNA from single embryos, and treated to remove any contaminating genomic DNA. cDNA was generated with iScript™ reverse transcriptase (Bio-Rad Laboratories, Hercules, CA, USA) and diluted 1:10 with RNase/DNase-free water for further use in real-time PCR. Relative gene expression from each RNA sample was calculated in triplicate using the SYBR Green comparative Ct method (Applied Biosystems, Foster City, CA, USA) adjusted for individual PCR efficiencies (Bustin 2003) and normalized to the geometric mean Ct of 3 endogenous controls (GAPDH, YWHAZ, and SDHA) in order to account for differences in both cell number and amount of total mRNA present in each sample (Goossens et al. 2005). G9a and SetB1, both lysine-specific methyltransferases, were expressed at their highest levels in the metaphase II (MII) oocyte and 2-cell stage, before expression decreased gradually to basal levels by the morula and blastocyst stages. Suv39h1, Suv420h1, and SmyD3, also lysine-specific methyltransferases, all shared a similar pattern of expression: transcript levels were fairly high in the MII oocyte, increased at the 2-cell stage, then gradually dropped off around the 8–16-cell stage to basal levels by the morula stage. Interestingly, Suz12 and LSH both showed low expression from the MII oocyte until the 4 to 7-cell stage, increased dramatically at the 8-cell stage, then decreased again by the morula stage. Suz12 is a member of several Polycomb group complexes (PRCs); LSH associates with PRC-mediated gene silencing as well as DNMT3a and 3b. These data suggest that Suz12 and LSH may be implicated in bovine embryonic genome activation, while the latter genes are active during earlier cleavage events. Ongoing studies will evaluate the role of each of these epigenetic modifiers in bovine pre-implantation embryos by selective silencing via RNA interference.

Analyzing Gene Expression through Real Time PCR while Neo-tissue Regeneration using Developed Tissue Constructs

2020 ◽  
pp. 15-34
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Tissue Regeneration ◽  
Real Time Pcr ◽  
Molecular Level ◽  
Northern Blotting ◽  
Tissue Constructs ◽  
Low Sensitivity

Real-time PCR offers a wide area of application to analyze the role of gene activity in various biological aspects at the molecular level with higher specificity, sensitivity and the potential to troubleshoot with post-PCR processing and difficulties. With the recent advancement in the development of functional tissue graft for the regeneration of damaged/diseased tissue, it is effective to analyze the cell behaviour and differentiation over tissue construct toward specific lineage through analyzing the expression of an array of specific genes. With the ability to collect data in the exponential phase, the application of Real-Time PCR has been expanded into various fields such as tissue engineering ranging from absolute quantification of gene expression to determine neo-tissue regeneration and its maturation. In addition to its usage as a research tool, numerous advancements in molecular diagnostics have been achieved, including microbial quantification, determination of gene dose and cancer research. Also, in order to consistently quantify mRNA levels, Northern blotting and in situ hybridization (ISH) methods are less preferred due to low sensitivity, poor precision in detecting gene expression at a low level. An amplification step is thus frequently required to quantify mRNA amounts from engineered tissues of limited size. When analyzing tissue-engineered constructs or studying biomaterials–cells interactions, it is pertinent to quantify the performance of such constructs in terms of extracellular matrix formation while in vitro and in vivo examination, provide clues regarding the performance of various tissue constructs at the molecular level. In this chapter, our focus is on Basics of qPCR, an overview of technical aspects of Real-time PCR; recent Protocol used in the lab, primer designing, detection methods and troubleshooting of the experimental problems.

195 ALTERED mRNA TRANSCRIPT EXPRESSION OF IN VITRO- VERSUS IN VIVO-MATURED PORCINE OOCYTES

2012 ◽  
Vol 24 (1) ◽  
pp. 210
Author(s):  
L. D. Spate ◽  
B. K. Redel ◽  
K. M. Whitworth ◽  
W. G. Spollen ◽  
S. M. Blake ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Real Time ◽  
Real Time Pcr ◽  
Genetic Background ◽  
Cumulus Cells ◽  
Developmental Competence ◽  
Illumina Genome Analyzer ◽  
Similar Genetic Background

In contrast to oocytes matured in vitro, porcine embryos that result from in vivo maturation and fertilization have a high developmental competence and readily make the transition from oocyte to blastocyst. This observation led us to investigate the transcript profile differences between in vivo- and in vitro-matured porcine oocytes. For the in vivo-matured group, oviducts of 3 gilts of similar genetic background were flushed 2 days after detection of standing oestrus. MII oocytes were collected in pools of 10 and snap frozen in liquid nitrogen for RNA isolation. The in vitro-matured oocytes were obtained by euthanizing 3 gilts, again with a similar genetic background and recovering the ovaries. Follicles (2 to 8 mm in size) were aspirated and oocytes with multiple layers of cumulus cells and uniform cytoplasm were placed in M-199 supplemented with LH, FSH and epidermal growth factor for 42 h. Upon maturation, cumulus cells were stripped and the healthy MII oocytes were collected in pools of 10 and snap frozen. Total RNA was extracted from 3 pools of 10 oocytes for both treatments using an All prep DNA/RNA micro isolation kit (Qiagen, Valencia, CA, USA). Complementary DNA was synthesized using oligo (dT′) primed reverse transcriptase with superscript III (Invitrogen, Carlsbad, CA, USA). Second-strand cDNA was synthesized using DNA polymerase I and sequenced using Illumina Genome Analyzer II. All reads were aligned to a custom-built porcine transcriptome. There were over 18 million reads in the 2 maturation groups that tiled to the 34 433-member transcriptome: 1317 transcripts were detected with a P ≤ 0.1 (Students t-test), a minimum of 7 reads in at least 1 of the treatments and ≥2-fold difference. Real-time PCR was used on selected transcripts. Comparative CT Method was used on an IQ real-time PCR system with the Bio–Rad SYBR green mix. Statistical differences were determined using the Proc general linear model procedure of SAS (SAS Institute Inc., Cary, NC) and means separated with a l.s.d. (P ≤ 0.05). The misrepresented transcripts from the sequencing data were also characterized using the functional annotation tool DAVID. Twelve pathways were overrepresented in the in vitro-matured oocytes (the top 4 are pathways to cancer, spliceosome, cell cycle and ubiquitin-mediated proteolysis). Eight pathways were underrepresented in the in vitro-matured oocytes (the top 4 are cytoskeleton regulation, T-cell receptor signaling pathway, ubiquitin-mediated proteolysis and cell cycle). Eight transcripts were selected for real-time PCR. ZP2 was higher in the in vitro-matured oocytes as determined by both sequencing and real time. ATG4, HSP90, UBAP2 and SOX4 were not different, regardless of assay. SLC7A3, MRPS36 and PDHX2 were not different based on sequencing, but based on real-time MRPS36 and PDHX2, were higher in the in vivo group and SLC7A3 was higher in the in vitro group. In conclusion, there is an abundance of misregulated transcripts and altered pathways in in vitro-matured oocytes. This dataset is a tool that may provide clues to improve the in vitro maturation process so that in vitro-matured oocytes will be more like their in vivo-matured counterparts, thus improving developmental competence. Funded by Food for the 21st Century.

Early T-Cell Precursor-ALL in Adult T-ALL.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 911-911 ◽  
Author(s):  
Martin Neumann ◽  
Sandra Heesch ◽  
Stefan Schwartz ◽  
Nicola Gökbuget ◽  
Dieter Hoelzer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Real Time ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Real Time Pcr ◽  
Expression Profiles ◽  
Lymphoblastic Leukemia ◽  
Gene Expression Profiles ◽  
Study Group

Abstract Abstract 911 Introduction: Recently, a small subgroup of pediatric acute T-lymphoblastic leukemia (T-ALL) was described, which is closely associated with the gene expression profile of early T-cell precursors (ETPs). This subtype, termed ETP-ALL, showed a highly unfavorable outcome compared to non-ETP(='typical')-ALL. Based on the results of Coustan-Smith et al. (Lancet Oncology, 2009), the Italian national study Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP) and St-Jude Children's hospital modified their treatment in children with ETP-ALL to a more intensive regime including stem cell transplantation. ETP-ALL is characterized by a specific immunophenotype (CD1a-, CD8-, CD5weak with expression of stem cell or myeloid markers). Here we explored the existence of ETP-ALL in adults and further studied the molecular characteristics of this specific T-ALL subtype. Patients and methods: We examined the gene expression profiles of 86 adult T-ALL patients obtained from the Microarray Innovations in LEukemia (MILE) multicenter study (HG-U133 Plus 2.0, Affymetrix, Haferlach et al., JCO in press). In addition, bone marrow of 296 patients from the German Acute Lymphoblastic Leukemia Multicenter Study Group (GMALL) were analyzed by flow cytometry and expression levels of BAALC, IGFBP7, MN1, and WT1 were determined by real-time-PCR. Results: Using the published list of differentially expressed genes in ETPs (Coustan-Smith et al. 2009) we performed unsupervised clustering analyses of the 86 T-ALL samples. A cluster of 17 samples (19.8%) displayed an ETP-associated gene expression profile and were defined as ETP-ALL. Comparing the gene expression profiles of ETP-ALL and typical T-ALL, 2065 probe sets were differentially expressed in ETP-ALL (FDR 0.05). In addition to genes used for classification, we also identified genes known to be involved in the pathogenesis of T-ALL (e.g. PROM1, BCL2, LMO2, LYL1). In particular, stem cell associated genes such as, BAALC (2.52-fold, p=0.003), IGFBP7 (2.76-fold, p=0.002) or MN1 (3.41-fold, p<0.001) were upregulated in ETP-ALL, whereas HOX11 (45-fold, p=0.004), a marker for thymic T-ALL, was downregulated. An independent cohort of 297 patient samples from the GMALL study group was examined by flow cytometry and real-time PCR. 19 (6.4%) samples revealed the ETP-ALL immunophenotype. As expected, all patient samples were found in the group of early T-ALL, representing 23.5% of all early T-ALLs. There was a significant correlation between a lower leukocyte count at first diagnosis and the classification of ETP-ALL (p=0.001). Gene expression measured by real-time-PCR was performed for genes associated with poor outcome in T-ALL: BAALC (2.11-fold, p<0.001) and IGFBP7 (3.59-fold, p=0.003) were significantly upregulated in the group of ETP-ALL. Similarly, the genes MN1 (4.52-fold, p<0.001) and WT1 (2.76-fold, p=0.036), described as poor prognostic markers in cytogenetically normal AML, were also upregulated in ETP-ALL. Conclusion: In adult T-ALL, a subset of patients shares the gene expression profil and immunophenotype of ETP-ALL, which is in line with recent findings in pediatric patients. The gene expression profile of this subset is significantly correlated to stem cell associated markers predictive for inferior outcome in T-ALL. Interestingly, adverse factors in CN-AML are also aberrantly expressed in ETP-ALL suggesting a myeloid origin of ETPs and indicating a closer relationship between ETP-ALL and AML. The prognostic impact and the determination of the most appropiate set of markers needs to be further investigated. These results support the GMALL strategy to regard early T-ALL patients as high risk with assignment to stem cell transplantation. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Equity Ownership.

Gene expression signature predicts chemoresponse of microdissected papillary serous ovarian tumors

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 5064-5064
Author(s):  
L. Ozbun ◽  
T. Bonome ◽  
M. E. Johnson ◽  
M. Radonovich ◽  
C. Pise-Masison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Gene List ◽  
Response To Therapy ◽  
Advanced Stage ◽  
Protein Ubiquitination ◽  
Ovarian Cancers

5064 Background: The purpose of this study was to identify a predictive gene signature for chemoresponse in patients with advanced stage papillary serous ovarian cancer. Methods: Expression profiling was performed on 50 chemonaive, microdissected advanced stage papillary serous ovarian cancers using Affymetrix Human Genome U133 Plus 2.0 microarrays. Chemoresistance was defined as disease progression while the patients remained on primary chemotherapy. Nine normal human ovarian surface epithelial (HOSE) brushings were also assessed to quantify normal gene expression levels. Validation was performed by quantitative real time PCR using the HOSE isolates and microdissected ovarian tumor samples. Results: A supervised learning algorithm applied to genes differentially expressed between chemosensitive/resistance tumors (p < 0.001) using leave-one-out cross-validation (LOOCV), identified over 2000 genes associated with tumor chemosensitivity. The chemoresponsive gene list was further refined to 576 genes by including only genes used for all LOOCV iterations. An independent gene list was generated comparing expression profiles of chemoresistant tumors to HOSE. The two lists were compared to identify common genes, generating final classifier list of 75 genes that included genes involved in apoptosis, RNA processing, protein ubiquitination, transcription regulation, and other novel genes. We hypothesized genes identified in both data sets would be predictive and biologically relevant. Of these 75 genes, 20 were validated by real-time PCR. Validated genes were ranked by a univariate t-stat value to further resolve the predictor. 4 multivariate predictor algorithms demonstrated the 10 top ranked validated genes maximixed prediction accuracy (compound covariate, 91%; diagonal linear discriminant analysis, 91%; 3-nearest neighbor, 86%; nearest centroid, 95%). The predictive value of these genes will be evaluated on an independent sample set. Conclusions: Gene expression profiling can distinguish between chemosensitive and chemoresistant ovarian cancers. This signature can predict response to therapy and has identified novel biologically and clinically relevant targets. No significant financial relationships to disclose.

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