title: Gata2 is a master regulator of endometrial function and progesterone signaling [Affymetrix]

summary: The role of Gata2 in regulating uterine function including fertility, implantation, decidualization and P4 signaling in the mouse was investigated by the conditional ablation of Gata2 in the uterus using the (PR-cre) mouse and ChIP-seq for in vivo GATA2 binding sites in the murine uterus upon acute P4 administration.

overall_design: Gata2 gene ablation was confirmed by real-time PCR analysis in the PR-cre; Gata2fl/fl (termed Gata2d/d) uterus. While littermate controls are fertile, Gata2d/d females are completely infertile. Analysis of the infertility indicates that implantation does not occur, and the uterine stroma is incapable of undergoing the decidual reaction to support further embryonic development. Measure of P4 target genes including PR itself indicate a block in P4 target gene induction and that Gata2 regulates PR expression directly. Microarray analysis demonstrates that ablation of Gata2 leads to specific gene changes, including disruption of the Wnt signaling pathway, Progesterone receptor (PR) signaling, and Ihh signaling pathway. In addition we identified 46,183 GATA2 binding sites in P4 treatment conditions with 7,954 binding sites overlapping that of the PR.Taken together, these data demonstrate that Gata2 is a critical regulator of gene expression and function in the murine uterus.

first: Cory

last: Rubel

first: Rainer

last: Lanz

first: Heather

middle: L

last: Franco

first: Ertug

last: Kovanci

first: Sally

last: Camper

first: Qiang

last: Tong

first: Jae-Wook

last: Jeong

first: John

last: Lydon

first: Francesco

last: DeMayo


title: Expression Profiles of Breast Tumors from Singapore and Europe

status: Public on Mar 21 2013

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

country: USA

institute: Atrium Health Wake Forest Baptist

summary: To facilitate a better understanding of the molecular heterogeneity of breast cancer and to uncover gene-survival associations that segregate with distinct molecular subtypes, we recently compiled a meta-analytical database of over 2,000 human breast tumor expression profiles variously annotated for clinical and pathological variables and derived from various institutions worldwide. This database was utilized for the breast tumor study cited below: Nagalla, et. al., Genome Biology, 2013. While the majority of the tumor expression profiles included in this database derived from publicly accessible microarray repositories, a number of the samples had not been previously published. Here, we describe the origin of these samples and provide their associated clinical and pathological annotations with the hope that other investigators will be able to utilize these data in their own research.

overall_design: Breast tumor samples derived from the Institut Jules Bordet (IJB; Belgium), John Radcliffe Hospital (JRH; Oxford) and the National University Hospital (NUH, Singapore) were profiled on the Affymetrix U133A platform. The number of tumors profiled (n) and the corresponding dates of tumor diagnosis are as follows. IJB: n=41, 1994-2001; JRH: n=8, 1990-1993; and NUH: n=100, 2000-2002.

first: Lance

middle: D

last: Miller

first: Christos

last: Sotiriou

first: Benjamin

last: Mow

first: Thomas

middle: C

last: Putti

first: Michael

middle: A

last: Black

middle: W


title: De novo mutations in the genome organizer CTCF cause Intellectual Disability (RNA-Seq)

status: Public on Jun 01 2013

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

type: Expression profiling by high throughput sequencing

summary: An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift mutations and one de novo missense mutation in the CTCF gene in individuals with intellectual disability, microcephaly and growth retardation. Furthermore, a patient with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three patients with point mutations revealed deregulation of genes involved in signal transduction and emphasized the role of CTCF in enhancer-driven expression of genes. Our findings indicate that haploinsufficiency of CTCF affects genomic interaction of enhancers and their regulated gene promoters that drive developmental processes and cognition.

overall_design: Comparison of lymphocyte gene expression between 3 de novo CTCF mutation patients and 8 controls (4 technical replicates each, no biological replicates).

first: Christiane

last: Zweier

first: Jo

last: Huiqing Zhou


title: A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation

status: Public on Nov 04 2014

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: De novo mutations in the genome organizer CTCF cause Intellectual Disability


title: MLL4 prepares the enhancer landscape for FoxP3 induction via chromatin looping

status: Public on Jul 18 2017

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: MLL4 is an essential subunit of the H3K4 methylation complexes. We report that Mll4 deficiency compromised Treg development and resulted in substantial decreases in H3K4me1 and chromatin interaction at putative enhancers, a remarkable portion of which were not direct targets of MLL4 but were interacting with Mll4-bound sites. The decrease in H3K4me1 and chromatin interaction at the MLL4-unbound enhancers correlated with MLL4 binding at distant interacting regions. Deletion of an upstream MLL4 binding site reduced H3K4me1 at the FoxP3 regulatory elements looped to the MLL4 binding site and compromised both tTreg and iTreg differentiation. We show that MLL4 catalyses H3K4 methylation at distant unbound enhancers via chromatin looping, thus providing a new mechanism of regulating T cell enhancer landscape and impacting Treg differentiation.

overall_design: ChIP-Seq profile of MLL4 binding in mouse Naive CD4+ T cells. ChIP-Seq of histone modification H3K4me1, H3K27me3, H3K27ac, RNA-Seq of gene expression, Hi-C of chromatin conformation capturing in control Naive CD4 T cells and Mll4 KO cells. Chip-Seq of H3K4me1 in control cells and Naive CD4+ T cells in which a MLL4-bound regulatory region upstream to the foxp3 gene were KO by the Crispr technique.

first: Katarzyna

last: Placek

first: Kairong

last: Cui

first: Dunfang

last: Zhang

first: Yi

last: Ding

first: Ji-Eun

last: Lee

first: Younghoon

last: Jang

first: Chaochen

last: Wang

first: Joanne

middle: E

last: Konkel

first: Jiuzhou

last: Song

first: Chengyu

last: Liu

first: Kai

last: Ge

first: Wanjun

last: Chen

first: Keji

last: Zhao


title: De novo mutations in the genome organizer CTCF cause Intellectual Disability (ChIP-Seq)

first: Jo Huiqing

last: Zhou

overall_design: ChIP-seq analysis of CTCF genomic binding sites in lymphocytes of a control individual (no replicates).

first: Christiane

last: Zweier


title: Molecular diagnosis of T cell-mediated rejection in human kidney transplant biopsies; Molecular diagnosis of antibody-mediated rejection in human kidney transplants

status: Public on Feb 13 2013

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary:
Histologic diagnosis of T cell-mediated rejection in kidney transplant biopsies has limited reproducibility because it is based on non-specific lesions using arbitrary rules that are subject to differing interpretations. We used microarray results from 403 indication biopsies previously given histologic diagnoses to develop a molecular classifier that assigned a molecular T cell-mediated rejection score to each biopsy. Independent assessment of the biopsies by multiple pathologists confirmed considerable disagreement on the presence of TCMR features: 79-88% accuracy and 35-69% sensitivity. The agreement of the molecular T cell-mediated rejection score with the histology diagnosis was similar to agreement among individual pathologists: accuracy 89%, sensitivity 51%. However, the score also predicted the consensus among pathologists, being highest when all agreed. Many discrepancies between the scores and the histologic diagnoses were in situations where histology is unreliable e.g. scarred biopsies. The score correlated with histologic lesions and gene sets associated with T cell-mediated rejection. The transcripts most often selected by the classifier were expressed in effector T cells, dendritic cells, or macrophages or inducible by interferon-gamma. Thus the T cell-mediated rejection score offers an objective assessment of kidney transplant biopsies, predicting the consensus opinion among multiple pathologists, and offering insights into underlying disease mechanisms.

Antibody-mediated rejection is a major cause of kidney transplant failure, but the current diagnostic system misses most cases due to dependency on subjective non-standardized tests. We hypothesized that molecular features could provide a test to address this problem. We classified 403 biopsies by a reference standard based on microcirculation lesions and donor-specific HLA antibody, and used microarray analysis to develop a classifier that assigned each biopsy a score reflecting the probability of antibody-mediated rejection. The scores correlated with donor-specific antibody and histologic lesions: 42/45 biopsies with antibody-mediated rejection scores >0.5 had both donor-specific antibody and microcirculation lesions. Intermediate scores (0.2-0.5) were more ambiguous, but became more specific combined with donor-specific antibody. Compared to diagnoses based on histology-plus-donor-specific antibody, the scores had sensitivity 0.67; specificity 0.90. Donor-specific antibody improved the specificity to 0.97. The score correlated not only with diagnoses of individual pathologists but with the consensus among multiple pathologists. The classifier used transcripts expressed in endothelial cells (e.g. CDH13, DARC, ROBO4) and NK cells (e.g. CX3CR1, FGFBP2), as well as IFNG-inducible transcripts e.g. CXCL11. Thus the molecular phenotype of antibody-mediated rejection provides not only an objective test that predicts microcirculation lesions and donor-specific HLA antibody, but also offers mechanistic insights.

overall_design:
All consenting renal transplant patients undergoing biopsies for cause as standard of care. 403 samples and 8 controls (nephrectomies).

Note: The Sample 'characteristics' were updated on June 11, 2022.

first: Joana

last: Selleres

first: Jeff

last: Reeve

first: Philip

middle: F

last: Halloran


title: Differentially expressed genes after treatment with chemotherapy in breast cancer and their correlation with pathologic response

status: Public on Dec 12 2012

city: Jaen

first: Laura

last: Vera

state: Jaen

address: Avenida del Ejercito Español 10

department: Department of Oncology

institute: Hospital Medico-Quirurgico de Jaen


title: Expression data from breast cancer FNA biopsies from patients ( (USO samples)

status: Public on Dec 11 2012

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Tumor samples were obtained from patients with stage II-III breast cancer before starting neoadjuvant chemotherapy with four cycles of 5-fluorouracil/epirubicin/cyclophosphamide (FEC) followed by four cycles of docetaxel/capecitabine (TX) on US Oncology clinical trial 02-103. Most patients with HER-2-positive cancer also received trastuzumab (H).

overall_design: Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to affymetrix microarrays according to manufacturer protocol.

first: Lajos

last: Pusztai

first: Frankie

last: Holmes

first: Joyce

last: O'Shaughnessy


title: Differentially expressed genes after treatment with chemotherapy in breast cancer and their correlation with pathologic good response (Miller & Payne grades 4 and 5)

summary: The aim of this study was to compare the gene expression profile changes breast tumors after the treatment with Anthracyclines and Taxanes. To this end, an oligonucleotide microarray was performed (Affymetrix’s HG-U133 Plus 2.0 array). This gene expression study was carried out on the biopsied tumor samples previous being treated with chemotherapy, and subsequently compared with themselves once treatment schedule ended. The post-chemotherapy biopsy was obtained from the surgical piece. The goal of this study was the finding of several genes related to apoptosis, proliferation, differentiation, survival and transformation-related genes and correlating their differences in expression with the degree of response to chemotherapy, determined by the Miller and Payne histological grading system.

overall_design: After informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy treatment based on Anthracyclines and Taxanes (Treatment A: Epirubicin 90 mg/m2-Cyclophosphamide 600 mg/m2, 3 cycles bi-weekly and Taxol 150 mg/m2-Gemcitabine 2500 mg/m2, 6 cycles bi-weekly ± weekly Herceptin 4 mg/Kg during the first week, 2 mg/Kg for the remaining 11 cycles; Treatment B: Doxorubicin 60 mg/m2-Pemetrexed 500 mg/m2, 4 cycles tri-weekly and Taxotere 100 mg/m2, 4 cycles tri-weekly; Treatment C: Doxorubicin 60 mg/m2-Cyclophosphamide 600 mg/m2, 4 cycles tri-weekly and Taxotere 100 mg/m2, 4 cycles tri-weekly) were recruited for this study. Pre-chemotherapy and post-chemotherapy biopsies were examined by a pathologist who determined the Miller & Payne grade for each patient. Matching pairs of pre-chemotherapy and post-chemotherapy samples were divided into 3 groups according to Miller & Payne grade: group of bad response (Miller & Payne grades 1 and 2), group of mid response (Miller & Payne grade 3) and group of good response (Miller & Payne grades 4 and 5). Gene expression analysis was performed in paired samples as follows: bad response group post-chemotherapy biopsy vs pre-chemotherapy biopsy (Bad Final vs Initial). For this assay were necessary 13 samples being chosen according to histopathologic criteria (Miller & Payne grades 4 and 5). Of them, 10 samples were paired and 3 pre-chemotherapy samples from patients that experienced a good response to chemotherapy were also included in this experimental series. Other comparisons in which this group of samples was involved include: Initial Bad vs Good, Initial Good vs Mid, Final Mid vs Good and Final Bad vs Good. This gene expression profiling was carried out making use of Affymetrix’s GeneChip technology, with the Affymetrix’s HG-U133 Plus 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was directly extracted by a RNeasy Mini kit and homogenized by QIAshredder columns under manufacturer’s instructions. The quality and quantity of the obtained RNA, was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. Once again, the quality and quantity of the obtained cRNA, was checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered for remove the control sequences and those with a hybridization signal near to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the less presented in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised PCA analysis and clustering, gene expression statistical significances were identified by two regression models taking into account the pathologic response to chemotherapy and if the sample was obtained before or after chemotherapy treatment. Supervised PCA analysis and clustering were performed with processed data. Partek Genomics Suite v7.3.1 (Partek) software was employed for the statistic analysis and clustering.

first: Vera-Ramirez

last: Laura

first: Sanchez-Rovira

last: Pedro

first: Ramirez-Torotosa

last: Cesar

first: Quiles

last: Jose

last: MCarmen

first: Lorente


title: Genomic predictors of response to doxorubicin versus docetaxel in breast cancer

status: Public on May 27 2011

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Low topo2a expression and ER-negative status were predictors of response to doxorubicin, while small tumor size and ER-negative status predicted response to docetaxel.  Docetaxel was superior to doxorubicin in triple-negative/basal-like tumors, while no significant differences between these drugs were seen in the remaining intrinsic subtypes

Keywords: reference x sample

overall_design: reference x sample

first: M

middle: M

last: Martin


title: Differentially expressed genes after treatment with chemotherapy in breast cancer and their correlation with pathologic bad response (Miller & Payne grades 1 and 2)

overall_design: After informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy treatment based on Anthracyclines and Taxanes (Treatment A: Epirubicin 90 mg/m2-Cyclophosphamide 600 mg/m2, 3 cycles bi-weekly and Taxol 150 mg/m2-Gemcitabine 2500 mg/m2, 6 cycles bi-weekly ± weekly Herceptin 4 mg/Kg during the first week, 2 mg/Kg for the remaining 11 cycles; Treatment B: Doxorubicin 60 mg/m2-Pemetrexed 500 mg/m2, 4 cycles tri-weekly and Taxotere 100 mg/m2, 4 cycles tri-weekly; Treatment C: Doxorubicin 60 mg/m2-Cyclophosphamide 600 mg/m2, 4 cycles tri-weekly and Taxotere 100 mg/m2, 4 cycles tri-weekly ) were recruited for this study. Pre-chemotherapy and post-chemotherapy biopsies were examined by a pathologist who determined the Miller & Payne grade for each patient. Matching pairs of pre-chemotherapy and post-chemotherapy samples were divided into 3 groups according to Miller & Payne grade: group of bad response (Miller & Payne grades 1 and 2), group of mid response(Miller & Payne grade 3) and group of good response (Miller & Payne grades 4 and 5). Gene expression analysis was performed in paired samples as follows: bad response group post-chemotherapy biopsy vs pre-chemotherapy biopsy (Bad Final vs Initial). For this assay were necessary 28 samples being chosen according to histopathologic criteria (Miller & Payne grades 1 and 2). Of them, 26 samples were paired, 1 pre-chemotherapy sample and 1 post-chemotherapy sample from patients that experienced a bad response to chemotherapy were also included in this experimental series. Other comparisons in which this group of samples was involved include: Initial Bad vs Good, Initial Bad vs Mid, Final Bad vs Good and Final Bad vs Mid. This gene expression profiling was carried out making use of Affymetrix’s GeneChip technology, with the Affymetrix’s HG-U133 Plus 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was directly extracted by a RNeasy Mini kit and homogenized by QIAshredder columns under manufacturer’s instructions. The quality and quantity of the obtained RNA, was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. Once again, the quality and quantity of the obtained cRNA, was checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered for remove the control sequences and those with a hybridization signal near to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the less presented in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised PCA analysis and clustering, gene expression statistical significances were identified by two regression models taking into account the pathologic response to chemotherapy and if the sample was obtained before or after chemotherapy treatment. Supervised PCA analysis and clustering were performed with processed data. Partek Genomics Suite v7.3.1 (Partek) software was employed for the statistic analysis and clustering.

last: Vera-Ramirez

first: Pedro

last: Sanchez-Rovira

first: Cesar

last: Ramirez-Tortosa

first: Jose

last: Quiles

first: MCarmen

last: Lorente


title: Differential allelic expression in normal breast tissue

status: Public on May 03 2012

city: Cambridge

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: Most loci contributing to breast cancer susceptibility identified by the recent genome-wide association studies (GWAS) are predicted to have a regulatory function. Additionally, the early phases of the GWAS studies have generated long lists of possible candidates that need to be prioritised for follow-up studies. Integration of allelic expression mapping and disease association data should enable the identification of those GWAS hits with higher cis-regulatory potential. Our aims are (1) to assess how well functional data and disease risk are correlated and (2) to help prioritise and select the strongest candidates from the GWAS scan for further follow-up and functional analysis. We are performing genome-wide differential allelic expression (DAE) analysis to identify loci with cis-regulatory potential in sixty-four normal breast tissue samples. Using the Illumina Exon510S-Duo BeadChips, we have identified 34K informative SNPs of which approximately 8K (23.5%) displayed DAE. Two SNPs showed monoallelic expression suggesting possible new imprinted loci. We are mapping the cis-regulatory loci by fitting a linear regression model with permutations to DAE ratios vs genotype at SNPs within ±250kb of the RefSeq gene corresponding to the DAE SNP. We will combine our data with the UK GWAS1 and GWAS2 studies for breast cancer susceptibility, to generate a list of genes that show regulatory variation for further evaluation as candidates. This is the first genome-wide differential allelic expression study in normal breast tissue, and one of the first in a primary tissue. We predict that this will be a powerful approach to validate/identify susceptibility loci and to unravel some of the biology underlying breast cancer susceptibility.

overall_design: Allelic gene expression of normal breast sample from healthy controls.

first: Ana

middle: T

first: Roslin

last: Russell


title: Microarray-based molecular subtyping of breast cancer

status: Public on Apr 24 2011

city: Taipei

last: Kao

state: Taiwan

address: 125 Lih-Der Road, Peitou District

department: Research

country: Taiwan

institute: Koo Foundation SYS Cancer Center

summary:
The primary goal of this study is to identify molecular subtypes of breast cancer through gene expression profiles of 327 breast cancer samples and determine molecular and clinical characteristics of different breast cancer subtypes.
We studied expression signatures of different cellular functions (e.g., cell proliferation/cell cycle, wound response, tumor stromal response, vascular endothelial normalization, drug esponse genes, etc.) in different breast cancer molecular subtypes and investigated how microarray-based breast cancer molecular subtypes may be used to guide treatment.

overall_design: Gene expression profiles of 327 breast cancer samples were determined using total RNA and Affymetrix U133 plus 2.0 arrays.

first: K

middle: J


title: GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer

status: Public on Mar 20 2012

city: Suita

first: Shinzaburo

last: Noguchi

state: Osaka

address: 2-2-E10 Yamada-oka

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University, Graduate School of Medicine

summary: The purpose of the present study was to investigate the association of glutathione S-transferase P1 (GSTP1) expression with resistance to neoadjuvant paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide (P-FEC) in human breast cancers. The relationship of GSTP1 expression and GSTP1 promoter hypermethylation with intrinsic subtypes was also investigated. In this study, primary breast cancer patients (n = 123, stage II-III) treated with neoadjuvant P-FEC were analyzed. Tumor samples were obtained by vacuum-assisted core biopsy before P-FEC. GSTP1 expression was determined using immunohistochemistry, GSTP1 promoter methylation index (MI) using bisulfite methylation assay and intrinsic subtypes using DNA microarray. The pathological complete response (pCR) rate was significantly higher in GSTP1-negative tumors (80.0%) than GSTP1-positive tumors (30.6%) (P = 0.009) among estrogen receptor (ER)-negative tumors but not among ER-positive tumors (P = 0.267). Multivariate analysis showed that GSTP1 was the only predictive factor for pCR (P = 0.013) among ER-negative tumors. Luminal A, luminal B and HER2-enriched tumors showed a significantly lower GSTP1 positivity than basal-like tumors (P = 0.002, P < 0.001 and P = 0.009, respectively), while luminal A, luminal B and HER2-enriched tumors showed a higher GSTP1 MI than basal-like tumors (P = 0.076, P < 0.001 and P < 0.001, respectively). In conclusion, these results suggest the possibility that GSTP1 expression can predict pathological response to P-FEC in ER-negative tumors but not in ER-positive tumors. Additionally, GSTP1 promoter hypermethylation might be implicated more importantly in the pathogenesis of luminal A, luminal B and HER2-enriched tumors than basal-like tumors.

overall_design: Fresh frozen tumor samples obtained by vacuum-assisted core biopsy from one hundred and fifteen patients were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Tomohiro

last: Miyake

first: Takahiro

last: Nakayama

first: Yasuto

last: Naoi

first: Noriaki

last: Yamamoto

first: Yoko

last: Otani

first: Seung-Jin

last: Kim

first: Kenzo

last: Shimazu

first: Atsushi

last: Shimomura

first: Naomi

last: Maruyama

first: Yasuhiro

last: Tamaki


title: Differentially expressed genes after treatment with chemotherapy in breast cancer and their correlation with pathologic mid-response (Miller & Payne grade 3)

first: Laura

last: Vera

overall_design: After informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy treatment based on Anthracyclines and Taxanes (Treatment A: Epirubicin 90 mg/m2-Cyclophosphamide 600 mg/m2, 3 cycles bi-weekly and Paclitaxel 150 mg/m2-Gemcitabine 2500 mg/m2, 6 cycles bi-weekly ± weekly Herceptin 4 mg/Kg during the first week, 2 mg/Kg for the remaining 11 cycles; Treatment B: Doxorubicin 60 mg/m2-Pemetrexed 500 mg/m2, 4 cycles tri-weekly and Docetaxel 100 mg/m2, 4 cycles tri-weekly; Treatment C: Doxorubicin 60 mg/m2-Cyclophosphamide 600 mg/m2, 4 cycles tri-weekly and Docetaxel 100 mg/m2, 4 cycles tri-weekly ) were recruited for this study. Pre-chemotherapy and post-chemotherapy biopsies were examined by a pathologist who determined the Miller & Payne grade for each patient. Matching pairs of pre-chemotherapy and post-chemotherpy samples were divided into 3 groups according to Miller & Payne grade: group of bad response (Miller & Payne grades 1 and 2), group of mid response (Miller & Payne grade 3) and group of good response (Miller & Payne grades 4 and 5). Gene expression analysis was performed in paired samples as follows: mid response group post-chemotherapy biopsy vs pre-chemotherapy biopsy (Mid final vs initial). For this assay were necessary 20 samples being chosen according to histopathologic criteria (Miller & Payne grade 3). Other comparisons in which this group of samples was involved include: Initial Good vs Mid, Initial Bad vs Mid, Final Bad vs Mid and Final Good vs Mid. This gene expression profiling was carried out making use of Affymetrix’s GeneChip technology, with the Affymetrix’s HG-U133 Plus 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was directly extracted by a RNeasy Mini kit and homogenized by QIAshredder columns under manufacturer’s instructions. The quality and quantity of the obtained RNA, was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. Once again, the quality and quantity of the obtained cRNA, was checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered for remove the control sequences and those with a hybridization signal near to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the less presented in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised PCA analysis and clustering, gene expression statistical significances were identified by two regression models taking into account the pathologic response to chemotherapy and if the sample was obtained before or after chemotherapy treatment. Supervised PCA analysis and clustering were performed with processed data. Partek Genomics Suite v7.3.1 (Partek) software was employed for the statistic analysis and clustering.

last: Vera-Ramirez

first: Pedro

last: Sanchez-Rovira

first: Cesar

last: Ramirez-Tortosa

first: Jose


title: Vascular lineage-specific transcriptome

status: Public on Apr 01 2011

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich


title: Identification of genes whose expression is affected by hedgehog RNAi in spider embryos

status: Public on Mar 31 2011

city: Takatsuki

first: Hiroki

last: Oda

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

summary: In the spider Achaearanea tepidariorum, Hedgehog (Hh) signaling plays a key role in the formation of the two major embryonic axes. Analyses of expression patterns of the spider hh homolog, At-hh, suggested that Hh signaling might be involved in the subsequent segmentation process also. In this microarray experiment, we attempted to identify candidate genes whose expressions are regulated by Hh signaling during early phases of spider segmentation.

overall_design: The objective of this experiment was a screen for genes whose expressions might be affected by parental RNA interference (pRNAi) against At-hh in spider embryos. Oligonucleotide probes were designed based on accumulated A. tepidariorum EST sequences and embedded in custom microarrays (12K x2). Total RNA was extracted from late stage 5 embryos derived from a mated female before and after injection of dsRNA targeted for At-hh. Gene expression levels were compared between the untreated (normal) and the At-hh pRNAi-treated samples. Probes for At-hh and a homolog of Drosophila orthodenticle, At-otd, served as positive controls to validate this experiment.

first: Yasuko

last: Akiyama-Oda


title: Biomarker analysis of neoadjuvant Doxorubicin/Cyclophosphamide followed by Ixabepilone or Paclitaxel in early-stage breast cancer

status: Public on Jan 01 2013

city: Princeton

first: Christine

last: Horak

state: NJ

address: Route 206 and Province Line Road

institute: Bristol-Myers Squibb

summary:
A randomized, open-label, multicenter, phase II trial (NCT00455533) enrolled previously untreated women with histologically-confirmed primary invasive breast adenocarcinoma (T2–3, N0–3, M0, tumor size ≥2.0 cm), regardless of hormone receptor or HER2 expression status. Patients received sequential neoadjuvant therapy starting with 4 cycles of AC (doxorubicin 60 mg/m2 intravenously and cyclophosphamide 600 mg/m2 intravenously) given every 3 weeks, followed by 1:1 randomization to either ixabepilone (40 mg/m2 3-hour infusion) every 3 weeks for 4 cycles, or paclitaxel (80 mg/m2 1-hour infusion) weekly for 12 weeks.
Fresh tumor biopsies at screening were a mandatory prerequisite for study entry for biomarker analyses. Gene expression profiling was performed by Affymetrix GeneChip to determine if pre-specified gene models could distinguish between the clinical activity of two microtubule stabilizing agents, ixabepilone and paclitaxel.

overall_design:
Three core needle tumor tissue biopsies were obtained from all subjects before neoadjuvant therapy with AC and immediately combined in RNAlater® solution for subsequent RNA extraction, cRNA labeling and gene expression profiling.  Pre-specified gene models were tested for their capacity to distinguish pathologic complete response rates between the AC followed by ixabepilone versus the AC followed by paclitaxel treatment regimens.
All samples were collected prior to treatment.  All subject received cyclophosphamide/doxorubicin (AC) prior to randomization to either Ixabepilone or Paclitaxel.

first: David

last: Liu


title: Identification of the vascular lineage-specific transcriptome

summary:
Angiogenesis and lymphangiogenesis have important roles in cancer progression and chronic inflammatory diseases, but efficient therapies against these diseases have been hampered by the lack of identified vascular lineage-specific markers and growth factors. Using transcriptional profiling of matched pairs of human dermal blood vascular and lymphatic endothelial cells, we first identified 236 lymphatic and 342 blood vascular signature genes. In silico analyses of the biologic pathways associated with these genes revealed lineage-specific functions for each cell type. Using a selection of 85 identified vascular lineage-specific genes, we developed a TaqMan RT-PCR-based, microfluidic card-formatted low-density microvascular differentiation array (LD-MDA) that was used to reliably identify and quantify the degree of lineage-specific differentiation in different types of endothelial cells, and to detect admixture of lymphatic endothelial cells in commercial preparations of microvascular endothelial cells. Application of Prediction Relevance Ranking and analysis of variance of LD-MDA expression profiles of 43 lesional skin samples obtained from patients with the chronic inflammatory disease psoriasis led to identification of cytokines which are significantly associated with angiogenesis or lymphangiogenesis in vivo. In particular, interleukin-7 and fibroblast growth factor-12 were identified as novel (lymph)angiogenic factors. This technology provides a novel tool to quantify lineage-specific vascular differentiation and to characterize (lymph)angiogenesis in clinical samples obtained from angiogenic diseases.
Keywords: cell type comparison

overall_design: For the identification of the LEC specific transcriptome, probes with present calls (S/N greater than 3, Quality Flag less than 5,000) in the LEC samples were selected for further analysis. For the identification of the BVEC specific transcriptome, the same filtering was performed on BVEC samples. LEC specific signature genes were identified based on a log2 ratio (LEC/BVEC) greater-than and equal-to 1, whereas BVEC specific signature genes were selected based on a log2 ratio less-than or equal-to -1 in each of the three matched pairs of LEC and BVEC.

first: Thomas

last: Fuchs

first: Weiniu

last: Gan

first: Rainer

last: Kunstfeld

first: Joachim

last: Buhmann

first: Ulrich

last: Mrowietz

first: Sascha

last: Gerdes

first: Michael

last: Detmar


title: Termination of diapause in response to long days in Wyeomyia smithii

status: Public on Feb 13 2010

city: Eugene

first: Kevin

middle: James

last: Emerson

state: OR

address: 5289 University of Oregon

department: Center for Ecology and Evolutionary Biology

institute: University of Oregon

summary:
Gene expression of two populations was compared at a daylength intermediate to the two population critical photoperiods after 0 and 6 days.  Genes with interaction terms are candidates for involvement in long-day response.

The mosquito Wyeomyia smithii overwinters in a larval diapause that is initiated, maintained and terminated by day length (photoperiod).  We use a forward genetic approach to investigate covert transcriptional events involved in the termination of diapause following exposure to long-days.
We incorporate a novel approach that compares two populations (DB - southern, DR - northern) that differentially respond to a single day length.
After six long days, 50% of individuals of population DB have terminated diapause and are irrevocably committed to development, though no phenotyping differences are observed.  We can compare gene expression between these two populations after six long days and zero long days.  The zero long day treatment will control for evolved differences between the populations and the 6 long day treatment allows for the identification of genes that are differentially expressed due to different responses to a single daylength.
We identify 30 transcripts associated with differential response to day length.  All of the corresponding genes with a previously annotated function are consistent with a role in the termination of diapause, with downstream developmental events, or with the transition from potentially oxygen-poor to oxygen-rich environments; none appears to be specifically part of the photoperiodic switch mechanism itself.  However, among 10 unannotated genes, a gene homologous to Drosophila melanogaster CG13043 emerges from three separate forward genetic screens as a leading candidate for a gene contributing to the photoperiodic timing mechanism itself (photoperiodic switch).  We name this gene photoperiodic response gene 1 (prg1). Prg1 is up-regulated under long-day response conditions, is located under a QTL for critical photoperiod and is associated with critical photoperiod after 25 generations of recombination from a cross between extreme phenotypes.  Three independent forward genetic approaches identify prg1 as a gene either involved in the photoperiodic switch mechanism or very tightly linked to a gene that is.  We conclude that continued forward genetic approaches will be central to understanding not only the molecular basis of photoperiodism and diapause, but also the evolutionary potential of temperate and polar animal populations when confronted with rapid climate change.

overall_design: 4 treatments, (Population DR, Day 0; Population DB, Day 0; Population DR, Day 6, Population DB, Day6), one dye swap (treatment Cy3 or Cy5,  each replicated three times for a total of 24 arrays

first: William

last: Bradshaw

first: Christina

last: Holzapfel


title: Expression data from breast cancer FNA biopsies from patients

status: Public on Sep 15 2010

first: Yuan

last: Qi

summary:
The behavior of breast cancers and their response to different chemotherapy treatments depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell.
We used gene expression values from 30 probes on affymetrix U133A chips to calculate a score that would predict if a breast cancer is likely to achieve pathological complete response to chemotherapy consisting of T/FAC.

overall_design: Pre-treatment FNA from primary tumors or axillary lymph node metastases were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

first: Lajos

last: Pusztai

first: Adel

last: Tabchy


title: Expression data from breast cancer FNA biopsies from patients (US samples)

status: Public on Feb 07 2011

first: TAKAYUKI

last: IWAMOTO

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

summary:
This is Phase II Trial of 4courses of 5-fluorouracil, doxorubicin and cyclophosphamide follwed by 4 additional courses of weekly docetaxel and capecitabine administered as Preoperative Therapy for Patients with Locally Advanced Breast Cancer, Stages II and III by US oncology (PROTOCOL 02-103)
We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively.

overall_design: Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

first: Frankie

last: Holmes

first: Joyce

last: O'Shaughnessy

first: Takayuki

last: Iwamoto


title: small RNAs sequences from grafted Arabidopsis thaliana and Nicotiana benthamiana tissues

status: Public on Mar 24 2010

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary:
A silencing signal in plants with an RNA specificity determinant moves through plasmodesmata and the phloem. To identify the mobile RNA we grafted Arabidopsis thaliana shoots to roots that would be a recipient for the silencing signal. Using high throughput sequencing as a sensitive detection method and mutants to block small RNA (sRNA) biogenesis in either source or recipient tissue, we detected endogenous and transgene specific sRNA that moved across the graft union.  Surprisingly we found that the mobile endogenous sRNAs account for a substantial proportion of the sRNA in roots and we provide evidence that 24nt mobile sRNAs direct epigenetic modifications in the genome of the recipient cells. Mobile sRNA thus represents a mechanism for transmitting the specification of epigenetic modification and could affect genome defence and responses to external stimuli that have persistent effects in plants.

Keywords: Small RNA Analysis, Epigenetics

sample_organism:
Arabidopsis thaliana
Nicotiana benthamiana

overall_design: 34 unique samples, 15 Biological Replicates

first: Attila

last: Molnar

first: Charles

last: Melnyk

first: Andrew

last: Bassett

first: Thomas

last: Hardcastle

first: Ruth

last: Dunn

first: David

last: Baulcombe


status: Public on Dec 31 2010

summary:
We assess if distinct biological processes might be associated with chemotherapy sensitivity in the different clinical subsets of breast cancers.
We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively.


title: MAQC-II Project: human breast cancer (BR) data set

status: Public on Feb 04 2010

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

summary: The human breast cancer (BR) data set (endpoints D and E) was contributed by the University of Texas M. D. Anderson Cancer Center (MDACC, Houston, TX, USA). Gene expression data from 230 stage I-III breast cancers were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. Patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer. Response to preoperative chemotherapy was categorized as a pathological complete response (pCR = no residual invasive cancer in the breast or lymph nodes) or residual invasive cancer (RD), and used as endpoint D for prediction. Endpoint E is the clinical estrogen-receptor status as established by immunohistochemistry. RNA extraction and gene expression profiling were performed in multiple batches over time using Affymetrix U133A microarrays. Genomic analysis of a subset of this sequentially accrued patient population were reported previously. For each endpoint, the first 130 cases were used as a training set and the next 100 cases were used as an independent validation set.


title: Multifactorial Approach to Predicting Resistance to Anthracyclines

status: Public on Jan 26 2010

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

summary:
PURPOSE: Validated biomarkers predictive of response/resistance to anthracyclines in breast cancer are currently lacking. The neoadjuvant TOP trial, in which patients with estrogen receptor (ER)-negative tumors were treated with anthracycline (epirubicin) monotherapy, was specifically designed to evaluate the predictive value of topoisomerase IIα (TOP2A) and to develop a gene expression signature to identify those patients who do not benefit from anthracyclines.

METHODS: The TOP trial included 149 patients, of which 141 were evaluable for response prediction analyses. The primary endpoint was pathological complete response (pCR). TOP2A and gene expression profiles were evaluated using pre-epirubicin biopsies. Gene expression data from ER-negative samples of the EORTC 10994/BIG 00-01 and MDACC 2003-0321 neoadjuvant trials were used for validation purposes.

RESULTS: A pCR was obtained in 14% of the evaluable TOP patients. TOP2A amplification, but not protein overexpression, was significantly associated with pCR (p=0.001 and 0.22). We developed an “anthracycline-based score (A-Score)” that combines three signatures: a TOP2A gene signature and two previously published signatures related to tumor invasion and immune response. The A-Score was characterized by a high negative predictive value (NPV=0.98 [95% CI: 0.90-1.00]) overall, and in the HER2-negative and HER2-positive subpopulations. Its performance was independently confirmed in the anthracycline-based (FAC/FEC) arms of the two validation trials (BIG 00-01: 0.80 [0.61-0.92] and MDACC 2003-0321: 1.00 [0.80-1.00]).

CONCLUSION: Given its high NPV, the A-Score could become, if further validated, a useful clinical tool to identify those patients who do not benefit from anthracyclines and could therefore be spared the non-negligible side effects.

overall_design:
Predicting the efficacy of anthracyclines (epirubicin) in breast cancer (BC) patients (TOP trial)

120 microarray experiments from primary ER-negative breast tumors of anthracycline-treated patients.

No replicate, no reference sample.

first: C

last: Desmedt

first: A

last: Di Leo

first: E

last: Azambuja

first: D

last: Larsimont

first: B

first: J

last: Selleslags

first: S

last: Duhem

first: JP

last: Kains

last: Carly

first: M

last: Maerevoet

last: Vindevoghel

first: G

last: Rouas

first: F

last: Lallemand

first: V

last: Durbecq

last: Cardoso

first: R

last: salgado

last: Rovere

last: Bontempi

last: Michiels

last: Buyse

first: JM

last: Nogaret

first: Y

last: Symmans

first: L

last: D'Hondt

last: Piccart-Gebhart

last: Sotiriou


title: Clinical and Pathologic Response of the Primary Tumor in Women Receiving Neoadjuvant Docetaxel-Capecitabine (+/- Trastuzumab) Chemotherapy

status: Public on Mar 18 2011

first: Charles

last: Perou

summary: Results: In subjects who completed treatment and surgery, the pCR and near-complete response rates were 15.8% in HER2-negative and 50% in HER2-positive subjects. When stratified by genomic subtype, subjects of the HER2-enriched subtype had the best response (66.7%), the luminal A (11%) and B (4.8%) subtypes the poorest. Of 147 patients tested for p53 mutations using the AmpliChip test, 78 variants were detected; 55 were missense. The response rate among TP53 mutated patients was 30%, significantly higher than the rate in TP53 wild-type patients (10%, P = .0032). Concordance between AmpliChip mutation status versus IHC staining was 65%, with AmpliChip status being predictive of response and IHC status being not being predictive. Conclusion: Capecitabine plus docetaxel in HER2-negative subjects, and with trastuzumab in HER2-positive subjects, provided a good response rate with fewer cycles. p53 mutational analysis using the AmpliChip p53 assay, and genomic subtyping using the PAM50 assay, were promising predictive tests of response.

first: Stepan

last: Gluck

first: Lin

last: Wu


title: Expression data from human breast cancers pre and post chemothrapy

status: Public on Oct 30 2009

city: Seattle

first: Larissa

last: Korde

state: WA

address: 825 Eastlake Ave, E G30630

department: Division of Medical Oncology

institute: University of Washington

summary: Neoadjuvant chemotherapy has been shown to be equivalent to post-operative treatment for breast cancer, and allows for assessment of chemotherapy response.  In a pilot trial of docetaxel (T) and capecitabine (X) neoadjuvant chemotherapy for Stage II/III BC, we assessed correlation between baseline gene expression and tumor response to treatment, and examined changes in gene expression associated with treatment.  Patients received 4 cycles of TX. Tumor tissue obtained from Mammotome™ core biopsies pretreatment (BL) and post-Cycle 1 (C1) of TX was flash frozen and stored at -70C until processing. Gene expression analysis utilized Affymetrix HG-U133 Plus 2.0 GeneChip arrays. Statistical analysis was performed using BRB Array Tools after RMA normalization. Gene ontology (GO) pathway analysis used random variance t-tests with a significance level of p<0.005.  For gene categories identified by GO pathway analysis as significant, expression levels of individual genes within those pathways were compared between classes using univariate t-tests; those genes with significance level of p<0.05 were reported.

overall_design: The analysis of baseline gene expression included baseline specimens from twenty-eight patients:  11 responders and 17 non-responders.  Analyses of changes in gene expression included paired baseline and post-cycle 1 specimens from 14 patients; of these 6 patients were responders and 8 patients were non-responders.

first: Lara

last: Lusa


title: Gene expression profiling of myelodysplastic CD34+ hematopoietic stem cells treated in vitro with decitabine

status: Public on Dec 23 2009

city: Roma

first: Francesco

last: D'Alò

address: Largo A. Gemelli 8

department: Hematology

country: Italy

institute: Università Cattolica del Sacro Cuore

summary: Epigenetic mechanisms contribute to deregulated gene expression of  hematopoietic progenitors in Myelodysplastic Syndromes (MDS). Hypomethylating agents are able to improve peripheral cytopenias in MDS patients. To identify critical gene expression changes induced by hypomethylating agents, we analyzed gene expression profiling (GEP) of myelodysplastic and normal CD34+ hematopoietic stem cells treated in vitro with or without decitabine. Four MDS and two untreated early stage Hodgkin’s lymphomas were analyzed for GEP. Mock treated CD34+ stem cells segregate according to diagnosis and karyotype. After decitabine treatment, gene expression changes were more consistent on MDS CD34+ cells with abnormal kayotype. Comparing decitabine-induced genes with those found down-regulated in mock-treated MDS cells, we identified a list of candidate tumor suppressor genes in MDS. By real-time RT-PCR we confirmed expression changes for three selected genes CD9, CXCR4 and GATA2 in 12 MDS patients and 4 controls. CD9 was widely repressed in most MDS CD34+ cell samples, although similar levels of methylation were found in both normal and MDS total bone marrows. CXCR4 promoter methylation was absent in total bone marrows from 36 MDS patients. In conclusion, changes in gene expression changes induced by hypomethylating treatment are more pronounced in CD34+ cells from abnormal karyotype.

overall_design: Bone marrow mononuclear cells were obtained by Ficoll gradient centrifugation from 4 patients with intermediate-2/high risk Myelodysplastic Syndromes (MDS) (two with normal and two with abnormal karyotype) and from two patients with untreated early-stage Hodgkin’s lymphoma (HL). CD34+ cells were freshly isolated using immunomagnetic beads (Minimacs, Milteny Biotec GmbH, Germany), according to the manufacturer’s instructions. CD34+ cells were cultured in 24-well-plates with a pool of growth factors, including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), for 24 hours. Decitabine (Sigma Aldrich) was then added to a final concentration of 1 µM for the following 72 hours, while the corresponding amount of solvent was added for the mock treated plates. Three biological replicates were prepared for each patient (for both decitabine- and mock-treated). At the end of the treatment cells were harvested and total RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions. Biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Data were then normalized by GCRMA. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock).

first: Manuela

last: Giachelia


title: MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD+ consumption

status: Public on Aug 18 2017

city: Badalona

first: Roberto

last: Malinverni

address: Josep Carreras Building, Ctra de Can Ruti,

institute: Josep Carreras Leukaemia Research Institute

summary: The macro domain of the histone variant macroH2A1.1 is an evolutionary conserved ADP ribose-binding module of unknown physiological function. We demonstrate that during myogenic differentiation alternative splicing switches the expression of macroH2A1 from the non-ADP ribose binding to the binding isoform. While differentiation commitment is normal in cells lacking macroH2A1.1, we observe two phenotypes: diminished cell fusion correlating with reduced expression of adhesion and migration genes and reduced mitochondrial capacity. While the integrity of the ADP ribose-binding pocket is dispensable for gene regulation and fusion, it is critical to sustain optimal mitochondrial fatty acid oxidation. Rescue experiments using a pharmacological PARP-1 inhibitor and metabolomics support the idea that loss of macroH2A1.1 leads to PARP-1 activation and accelerated NAD+ consumption. As a consequence, the level of nicotinamide mononucleotide, the key metabolite for mitochondrial NAD+ pool regeneration, is reduced and sirtuins fail to maintain mitochondrial proteins in their hypoacetylated and active form. Our results support the idea that chromatin states containing the histone variant macroH2A1.1 contribute to optimal mitochondrial oxidative capacity by channeling the consumption of NAD+ from the nucleus to mitochondria in a manner largely independent on transcriptional regulation.

overall_design: Examination of  histone variant macroH2A in 2 cell type.

first: Melanija

last: Posavec Marjanović

first: Sarah

last: Hurtado-Bagès

first: Marcus

last: Buschbeck


title: GGI: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial

status: Public on Jul 09 2009

first: Benjamin

last: Haibe-Kains

summary:
Background: We have previously shown that the Gene expression Grade Index (GGI) was able to identify two subtypes of estrogen receptor (ER)-positive tumors that were associated with statistically distinct clinical outcomes in both untreated and tamoxifen-treated patients. Here, we aim to investigate the ability of the GGI to predict relapses in postmenopausal women who were treated with tamoxifen (T) or letrozole (L) within the BIG 1-98 trial.
Methods: We generated gene expression profiles (Affymetrix) and computed the GGI for a matched, case-control sample of patients enrolled in the BIG 1-98 trial from the two hospitals where frozen samples were available. All relapses (cases) were identified from patients randomized to receive monotherapy or from the switching treatment arms for whom relapse occurred before the switch.  Each case was randomly matched with four controls based upon nodal status and treatment (T or L).  The prognostic value of GGI was assessed as a continuous predictor and divided at the median.  Predictive accuracy of GGI was estimated using time-dependent area under the curve (AUC) of the ROC curves.
Results:  Frozen samples were analyzable for 48 patients (10 cases and 38 controls).  Seven of the 10 cases had been assigned to receive L. Cases and controls were comparable with respect to menopausal and nodal status, local and chemotherapy, and HER2 positivity. Cases were slightly older than controls and had a larger proportion of large, poorly differentiated ER+/PgR- tumors.  The GGI was significantly and linearly related to risk of relapse: each 10-unit increase in GGI resulted in an increase of approximately 11% in the hazard rate (p=0.02).  Within the subgroups of patients with node-positive disease or who were treated with L, the hazard of relapse was significantly greater for patients with GGI at or above the median. AUC reached a maximum of 78% at 27 months.
Conclusions: This analysis supports the GGI as a good predictor of relapse for ER-positive patients, even among patients who receive L.  Validation of these results, in a larger series from BIG 1-98, is planned using the simplified GGI represented by a smaller set of genes and tested by qRT-PCR on paraffin-embedded tissues.

overall_design:
Test whether the Gene expression Grade Index (GGI) is a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial.

55 microarray experiments from primary breast tumors of endocrine-treated patients.

No replicate, no reference sample.

first: Christine

last: Desmedt

first: Anita

last: Giobbie-Hurder

first: patrick

last: Neven

first: Robert

last: Paridaens

first: Marie-Rose

last: Christiaens

first: Ann

last: Smeets

first: Françoise

last: Lallemand

first: Giuseppe

last: Viale

first: Richard

last: Gelber

first: Martine

last: Piccart

first: Christos


title: MicroArray Quality Control Phase II (MAQC-II) Project

first: Leming

last: Shi

summary:
The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models

The second phase of the MicroArray Quality Control (MAQC-II) project evaluated common practices for developing and validating microarray-based models aimed at predicting toxicological and clinical endpoints. The purposes of the MAQC-II project were to survey approaches in genomic model development  in an attempt to understand sources of variability in prediction performance, and to assess the  influences of endpoint signal strength in data. Thirty-six teams developed classifiers for 13 diverse  endpoints -- some easy, some difficult to predict, from six relatively large training data sets -- three  preclinical (toxicogenomics) and three clinical. By providing the same data sets to many organizations  for analysis, but not restricting their data analysis protocols (DAPs), the project made it possible  to evaluate to what extent, if any, results depend on the team that performs the analysis. These analyses  collectively produced >18,000 models that were challenged by independent and blinded validation sets  generated for MAQC-II. The cross-validated performance estimates for models developed under good  practices are predictive of the blinded validation performance. The achievable prediction performance  is largely determined by the intrinsic predictability of the endpoint, and simple data analysis methods  often perform as well as more complicated approaches. Multiple models of comparable performance can be developed for a given endpoint and the stability of gene lists correlates with endpoint predictability. Importantly, similar conclusions were reached when >12,000 new models were  generated by swapping the original training and validation sets.

Description of six data sets including 13 prediction endpoints:
(Summarized in GSE16716_MAQC-II_Datasets_Overview.pdf attached as supplementary file. For more details, see the MAQC-II main paper and its references for individual dataset.)

The MAQC-II predictive modeling was limited to binary classification problems; therefore, continuous endpoint values such as overall survival (OS) and event-free survival (EFS) times were dichotomized using a "milestone" cutoff of censor data. Prediction endpoints were chosen to span a wide range of prediction difficulty. Two endpoints, H (CPS1) and L (NEP_S), representing the gender of the patients, were used as positive control endpoints, since they are easily predictable by microarrays. Two other endpoints, I (CPS1) and M (NEP_R), representing randomly assigned class labels, were designed to serve as negative control endpoints, since they are not supposed to be predictable. Data analysis teams were not aware of the characteristics of endpoints H, I, L, and M until their swap prediction results had been submitted. If a data analysis protocol did not yield models to accurately predict endpoints H and L, or if a data analysis protocol claims to be able to yield models to accurately predict endpoints I and M, something must have gone wrong.

The Hamner data set (endpoint A) was provided by The Hamner Institutes for Health Sciences (Research Triangle Park, NC, USA). The study objective was to apply microarray gene expression data from the lung of female B6C3F1 mice exposed to a 13-week treatment of chemicals to predict increased lung tumor incidence in the 2-year rodent cancer bioassays of the National Toxicology Program. If successful, the results may form the basis of a more efficient and economical approach for evaluating the carcinogenic activity of chemicals. Microarray analysis was performed using Affymetrix Mouse Genome 430 2.0 arrays on three to four mice per treatment group, and a total of 70 mice were analyzed and used as the MAQC-II's training set. Additional data from another set of 88 mice were collected later and provided as the MAQC-II's external validation set.

The Iconix data set (endpoint B) was provided by Iconix Biosciences, Inc. (Mountain View, CA, USA). The study objective was to assess, upon short term exposure, hepatic tumor induction by non-genotoxic chemicals, since there are currently no accurate and well-validated short-term tests to identify non-genotoxic hepatic tumorigens, thus necessitating an expensive 2-year rodent bioassay before a risk assessment can begin. The training set consists of hepatic gene expression data from 216 male Sprague-Dawley rats treated for 5 days with one of 76 structurally and mechanistically diverse nongenotoxic hepatocarcinogens and non-hepatocarcinogens. The validation set consists of 201 male Sprague-Dawley rats treated for 5 days with one of 68 structurally and mechanistically diverse non-genotoxic hepatocarcinogens and non- hepatocarcinogens. Gene expression data were generated using the Amersham Codelink Uniset Rat 1 Bioarray (GE HealthCare, Piscataway, NJ). The separation of the training set and validation set was based on the time when the microarray data were collected; i.e., microarrays processed earlier in the study were used as training and those processed later were used as validation.

The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression "compendium" data set was collected from 418 rats exposed to one of eight compounds (1,2- dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). All eight compounds were studied using standardized procedures, i.e. a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes. Briefly, for each compound,  four to six male, 12 week old F344 rats were exposed to a low dose, mid dose(s) and a high dose  of the toxicant and sacrificed at 6, 24 and 48 hrs later. At necropsy, liver was harvested for  RNA extraction, histopathology, and clinical chemistry assessments.

The human breast cancer (BR) data set (endpoints D and E) was contributed by the University of Texas M. D. Anderson Cancer Center (MDACC, Houston, TX, USA). Gene expression data from 230 stage I-III breast cancers were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. Patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer. Response to preoperative chemotherapy was categorized as a pathological complete response (pCR = no residual invasive cancer in the breast or lymph nodes) or residual invasive cancer (RD), and used as endpoint D for prediction. Endpoint E is the clinical estrogen-receptor status as established by immunohistochemistry. RNA extraction and gene expression profiling were performed in multiple batches over time using Affymetrix U133A microarrays. Genomic analysis of a subset of this sequentially accrued patient population were reported previously. For each endpoint, the first 130 cases were used as a training set and the next 100 cases were used as an independent validation set.

The multiple myeloma (MM) data set (endpoints F, G, H, and I) was contributed by the Myeloma Institute for Research and Therapy at the University of Arkansas for Medical Sciences (UAMS, Little Rock, AR, USA). Gene expression profiling of highly purified bone marrow plasma cells was performed in newly diagnosed patients with MM. The training set consisted of 340 cases enrolled on total therapy 2 (TT2) and the validation set comprised 214 patients enrolled in total therapy 3 (TT3). Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions of bone marrow aspirates in a central laboratory. All samples applied to the microarray contained more than 85% plasma cells as determined by 2-color flow cytometry  (CD38+ and CD45-/dim) performed after selection. Dichotomized overall survival (OS) and eventfree survival (EFS) were determined based on a two-year milestone cutoff. A gene expression model of  high-risk multiple myeloma was developed and validated by the data provider and later on validated in three additional independent data sets.

The neuroblastoma (NB) data set (endpoints J, K, L, and M) was contributed by the Children's Hospital of the University of Cologne, Germany. Tumor samples were checked by a pathologist prior  to RNA isolation; only samples with =60% tumor content were utilized and total RNA was isolated  from ~50mg of snap-frozen neuroblastoma tissue obtained before chemotherapeutic treatment. First, 502 pre-existing 11K Agilent dye-flipped, dual-color replicate profiles for 251 patients were provided. Of these, profiles of 246 neuroblastoma samples passed an independent MAQC-II quality assessment by majority decision and formed the MAQC-II training data set. Subsequently, 514 dyeflipped dual-color 11K replicate profiles for 256 independent neuroblastoma tumor samples were generated and profiles for 253 samples were selected to form the MAQC-II validation set. Of note, for one patient of the validation set, two different tumor samples were analyzed utilizing both versions of the 2x11K microarray (see below). All dual-color gene-expression of the MAQC-II training set were generated using a customized 2x11K neuroblastoma-related microarray. Furthermore, 20 patients of the MAQC-II validation set were also profiled utilizing this microarray. Dual-color profiles of the remaining patients of the MAQC-II validation set were performed using a slightly revised version of the 2x11K microarray. This version V2.0 of the array comprised 200 novel oligonucleotide probes whereas 100 oligonucleotide probes of the original design were removed due to consistent low expression values (near background) observed in the training set profiles. These minor modifications of the microarray design resulted in a total of 9,986 probes present on both versions of the 2x11K microarray. The experimental protocol did not differ between both sets and gene-expression profiles were performed as described. Furthermore, single-color geneexpression profiles were generated for 478/499 neuroblastoma samples of the MAQC-II dual-color training and validation sets (training set 244/246; validation set 234/253). For the remaining 21 samples no single-color data were available, due to either shortage of tumor material of these patients (n=15), poor experimental quality of the generated single-color profiles (n=5), or correlation of one single-color profile to two different dual-color profiles for the one patient profiled with both versions of the 2x11K microarrays (n=1). Single-color gene-expression profiles were generated using customized 4x44K oligonucleotide microarrays produced by Agilent Technologies (Palo Alto, CA, USA). These 4x44K microarrays included all probes represented by Agilent's Whole Human Genome Oligo Microarray and all probes of the version V2.0 of the 2x11K customized microarray that were not present in the former probe set. Labeling and hybridization was performed following the manufacturer's protocol as described.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Molecular Subtype Predicts Response to Neoadjuvant Chemotherapy in Breast Cancer

status: Public on May 25 2010

city: Vienna

first: Dietmar

last: Pils

address: Waehringer Guertel 18-20

department: Dept. of Surgery

country: Austria

institute: Medical University of Vienna

summary: In a prospective cohort study of 32 women with primary invasive breast cancer with a measurable lesion, we obtained a tumor specimen by high speed core biopsy before and after 4 cycles of NAC with epirubicine 90mg/m2 and cyclophosphamide 600mg/m2 every 3 weeks, followed by 4 cycles of docetaxel 100mg/m2. Total RNA was extracted from tumor specimens and the whole transcriptome was quantified with Agilent’s 44K single color microarray interrogating 41000 unique human genes. Tumor lesions were ultrasonographically measured to assess response using Sinn criteria. Genes significant different and significant changing during chemotherapy accompanying and predicting response were searched.

overall_design: Whole genome expression of breast cancer tissues were measured before and after four cycles neoadjuvant chemotherapy

first: Elmar

last: Stickeler

first: Clemens

last: Tempfer


title: Integrated genomic and function characterization of the 8q22 gain

status: Public on Jan 05 2010

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

summary:
Integrated DNA and expression array analysis in primary human breast tumors identified chromosome 8q22 copy number gain and a suite of over-expressed genes in this region highly relevant to subsequent recurrence.
8q copy gain is associated with increased risk of distant metastasis despite adjuvant chemotherapy and multiple genes from 8q22 are overexpressed and have pleiotropic effects, contributing to tumor growth, survival, and reduced killing of tumor cell by chemotherapy.

overall_design: Affymetrix U133plus2 from 115  tumor patients

first: Charles

last: Wang

first: Lihua

last: Zou

first: Andrea

last: Richardson


title: Identifying Significant Temporal Variation in Time Course Microarray Data Without Replicates

status: Public on Aug 04 2008

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

summary:
An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently  available methods for performing such significance tests required replicates of individual time points. This paper describes a replicate-free method that was developed as part of a study of the estrous cycle in the rat mammary gland in which no replicate data was collected.

Keywords: developmental time course (time series) throughout the estrus cycle in rat mammary gland  singlet data

overall_design: Key points are examined in a time series over the four day estrus cycle of rat mammary gland in virgin (null parous).  Singlet rats at each time point were used for mathematical analysis in this study for a total of 31 individual arrays.

first: Stephen

last: Billups

first: Margaret

last: Neville

first: Weston

last: Porter

first: Pepper

last: Schedin


title: Prediction of breast cancer pathological complete response to anthracycline/taxane chemotherapy.

status: Public on Nov 23 2007

city: Bordeaux

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

country: France

institute: University of Bordeaux

summary:
EORTC 10994 phase III breast cancer clinical  trial comparing FEC (5-fluorouracil, cyclophosphamide, epirubicin)  with ET (epirubicin, docetaxel). 161 needle biopsies of locally  advanced or large operable breast  tumours were hybridised to  Affymetrix X3P chips. The array data from the ER negative tumours  (28/65  pathological CR in the FEC arm, 27/59 pathological CR in the  ET arm) were used to validate the cell line-based chemotherapy  response predictors developed by the Potti/Nevins group at Duke  University (doi:10.1038/nm1491).
Keywords: Tumour profiling

overall_design: We analyzed 161 arrays of breast carcinoma.

first: P

last: Farmer

first: H

last: Bonnefoi

first: R


title: Key stages in mammary gland development.

status: Public on Jun 21 2007

summary:
The transition from pregnancy to lactation is a critical event in the survival of the newborn since all the nutrient requirements of the infant are provided by milk. While milk contains numerous components, including proteins, that aid in maintaining the health of the infant, lactose and milk fat represent the critical energy providing elements of milk. Much of the research to date on mammary epithelial differentiation has focused upon expression of milk protein genes, providing a somewhat distorted view of alveolar differentiation and secretory activation. While expression of milk protein genes increases during pregnancy and at secretory activation, the genes whose expression is more tightly regulated at this transition are those that regulate lipid biosynthesis. The sterol regulatory element binding protein (SREBP) family of transcription factors is recognized as regulating fatty acid and cholesterol biosynthesis. We propose that SREBP1 is a critical regulator of secretory activation with regard to lipid biosynthesis, in a manner that responds to diet, and that the serine/threonine protein kinase Akt influences this process, resulting in a highly efficient lipid synthetic organ that is able to support the nutritional needs of the newborn.
Keywords: developmental time course (time series) throughout pregnancy, lactation and involution.

overall_design: Key points are examined in a time series of FVB mouse mammary gland development, secretory activation, lactation and involution.  Quadruplicate mice (four biological replicates) at each time point were used for statistical power totalling 40 individual arrays in this study.  Mice were as staged pregnant day 1 the day that post coital plug was observed, and similarly, lactation day 1 was the first day after birth.  Involution day 2 is a forced weening model, where day 9  lactating dams had their litters removed for two days and then the dams were killed.

first: S

last: Anderson

first: M

first: J

last: McManaman


title: A stroma-related gene signature predicts sensitivity to epirubicin-containing neoadjuvant chemotherapy in breast cancer.

status: Public on Dec 19 2008

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

institute: Swiss Institute of Bioinformatics

summary: The goal of the study was to identify a gene expression signature capable of predicting a pathological complete response following neoadjuvant anthracycline-based chemotherapy of breast cancer. The samples were taken from the FEC arm (5-fluorouracil, epirubicin, cyclophosphamide) of the EORTC 10994 trial. EORTC 10994 is a phase III clinical trial comparing FEC with ET (epirubicin, docetaxel) in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 200 ng total RNA per chip was amplified using the Affymetrix small sample protocol (IVT then Enzo). 102 tumours were tested on Affymetrix X3P chips. Single biopsies were tested per tumour. The CEL files were quantile normalised using rma. The clinical response measure was pathological complete response (pCR, disappearance of the tumour after chemotherapy with at most scattered invasive cells detected by histology).

overall_design: 102 tumors


title: Gata2 is a master regulator of endometrial function and progesterone signaling [ChIP-Seq]

status: Public on Jan 01 2014

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

summary: The role of Gata2 in regulating uterine function including fertility, implantation, decidualization and P4 signaling in the mouse was investigated by the conditional ablation of Gata2 in the uterus using the (PR-cre) mouse and ChIP-seq for in vivo GATA2 binding sites in the murine uterus upon acute P4 administration.

overall_design: Gata2 gene ablation was confirmed by real-time PCR analysis in the PR-cre; Gata2fl/fl (termed Gata2d/d) uterus. While littermate controls are fertile, Gata2d/d females are completely infertile. Analysis of the infertility indicates that implantation does not occur, and the uterine stroma is incapable of undergoing the decidual reaction to support further embryonic development. Measure of P4 target genes including PR itself indicate a block in P4 target gene induction and that Gata2 regulates PR expression directly. Microarray analysis demonstrates that ablation of Gata2 leads to specific gene changes, including disruption of the Wnt signaling pathway, Progesterone receptor (PR) signaling, and Ihh signaling pathway. In addition we identified 46,183 GATA2 binding sites in P4 treatment conditions with 7,954 binding sites overlapping that of the PR.Taken together, these data demonstrate that Gata2 is a critical regulator of gene expression and function in the murine uterus.

first: Cory

last: Rubel

first: Rainer

middle: B

last: Lanz

first: Heather

last: Franco

first: Ertug

last: Kovanci

first: Sally

last: Camper

first: Qiang

last: Tong

first: Jae-Wook

last: Jeong

first: John

middle: P

last: Lydon

first: Francesco

last: DeMayo


title: RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver

status: Public on Jan 08 2009

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

summary:
The role of chronic hepatitis C virus (HCV) in the pathogenesis of HCV-associated hepatocellular carcinoma (HCC) is not completely understood, particularly at the molecular level.
We studied gene expression in normal, pre-malignant (cirrhosis), and tumor (HCC) liver tissues using Affymetrix GeneChips.

Keywords: cross-sectional

overall_design: Liver tissue samples were obtained from patients waiting for liver transplantation at one of the GR2HCC Centers. Additionally, normal liver and tumor samples were also obtained from the Liver Tissue Cell Distribution System. For each sample, RNA was extracted and hybridized to an Affymetrix GeneChip.

first: Valeria

middle: R

last: Mas

first: Daniel

middle: G

last: Maluf

first: Kenneth

last: Yanek

first: Xiangrong

last: Kong

first: Laura

last: Kulik

first: Chris

last: Freise

first: Kim

last: Olthoff

first: Rafik

last: Ghobrial

first: Paula

last: McIver

first: Robert

last: Fisher


title: Metabolic regulation in the lactating mammary gland:A lipid synthesizing machine

status: Public on Feb 10 2006

first: Michael

last: Rudolph

summary:
The mammary gland of the lactating mouse synthesizes and secretes milk lipid equivalent to its entire body weight in a single 20 day lactation cycle, making it one of the most active lipid synthetic organs known.  To test the hypothesis that multiple metabolic control points and potential regulatory mechanisms are involved in activating lipid and lactose synthesis at the onset of lactation we compared the mammary transcriptome of 130 genes involved in glucose metabolism between late pregnancy and early lactation and in response to dietary fat.  We utilized data obtained from microarray analysis of mammary glands from quadruplicate FVB mice at pregnancy day 17, and lactation day 2.  Diets containing 8% or 40% lipid were fed from lactation days 5 to 10 and mammary glands and livers of triplicate FVB mice prepared for microarray analysis.  We also compared the metabolome obtained from magnetic resonance spectroscopy of flash frozen glands of the mammary gland at day 17 of pregnancy with that at day 2 of lactation.  The results provide a global picture of the multiple metabolic strategies utilized to turn a quiescent organ into an incredibly efficient machine for massive but balanced lipid and lactose synthesis and implicate the transcription factor SREBP-1c in regulation of part of the pathway.
Keywords: Timecourse and dose response to dietary fat

overall_design: FVB control time-series mice were on normal lab chow diets and mammary tissue was taken at Pregnant days 12 and 17, plus lactation days 1, 2, and 9 in those animals. the time-points were taken as quadruplicates for each developmental stage. for the dietary component, triplicate FVB dams were fed normal lab chow diets until lactation day 5, when they were converted to diets containing either 8% or 40% Kcal from soy oils (see supplementary table to publication for further detail) for 5 days.  At lactation day 10, mammary and liver tissues were taken from these animals and preparred for microarray analysis.  All tissues were stabilized for RNA content in RNALater and were then isolated and cleaned up following manufacturer's instructions (Qiagen).

middle: C

first: James

middle: L

last: McManaman

first: Tzulip

last: Phang

first: Tanya

middle: D

last: Russell

first: Douglas

last: Kominsky

first: Natalie

last: Serkova

first: Steven

last: Anderson

first: Margaret

last: Neville


title: Complex Disease Subtypes Identified by Network-Based Clustering of Gene Expression Data:  Application to COPD

status: Public on Jan 12 2016

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

type:
Expression profiling by array
Third-party reanalysis

summary:
One of the most common smoking-related diseases, chronic obstructive pulmonary disease (COPD), results from a dysregulated, multi-tissue inflammatory response to cigarette smoke. We hypothesized that systemic inflammatory signals in genome-wide blood gene expression can identify clinically important COPD-related disease subtypes, and we leveraged pre-existing gene interaction networks to guide unsupervised clustering of blood microarray expression data. Using network-informed non-negative matrix factorization, we analyzed genome-wide blood gene expression from 229 former smokers in the ECLIPSE Study, and we identified novel, clinically relevant molecular subtypes of COPD. These network-informed clusters were more stable and more strongly associated with measures of lung structure and function than clusters derived from a network-naïve approach, and they were associated with subtype-specific enrichment for inflammatory and protein catabolic pathways. These clusters were successfully reproduced in an independent sample of 135 smokers from the COPDGene Study.
Briefly, gene expression was derived from whole blood samples in ECLIPSE subjects and peripheral blood mononuclear cells (PBMCs) for the COPDGene subjects. Gene expression profiling was performed using the Affymetrix Human U133 Plus2 array. Gene expression data were log-transformed, and background correction and normalization were performed for the merged ECLIPSE and COPDGene samples using robust multi-array averaging and quantile normalization as implemented in the affy Bioconductor package[27]. Of the 136 COPDGene subjects reported in a previous publication[13], one self-reported African-American subject was removed from analysis, which was conducted on the remaining 135 non-Hispanic white subjects. To identify a set of genes associated with COPD, we performed differential expression analysis for 38,519 probesets in ECLIPSE that passed quality control measures. Normalized probeset intensities were related to measures indicative of two primary dimensions of pulmonary impairment in COPD airway obstruction as indicated by two measures of spirometric lung function (FEV1 (% of predicted) and FEV1/FVC) and lung parenchymal destruction, i.e., emphysema (as quantified by the percentage of low attenuation area less than -950 Hounsfield units on lung computed tomography, %LAA-950). The analysis was conducted using the limma Bioconductor package, and the false discovery rate was controlled at 5%. The following covariates were included in the differential expression analysis age, pack-years of cigarette smoke exposure, and gender.

overall_design:
After standardizing gene expression data from 229 ECLIPSE subjects by the variance of each probe set, we applied NMF[29] and NBS[6] to identify meta-patients (i.e. subtypes or subject clusters) and meta-genes (i.e. representative subtype expression profiles).

Cross-sectional study of smokers. 229 subjects from the ECLIPSE study were analyzed in the model discovery phase. 135 subjects from the COPDGene Study (GSE42057) were used for replication.

Please note that the entire data set for total 364 samples including the re-analyzed samples is provided in the *364samples.txt files.