title: Genomic Analysis of DNA Repair Genes and Androgen Signaling in Prostate Cancer

status: Public on Sep 30 2018

city: Charlottesville

first: Aakrosh

last: Ratan

state: VA

address: 1335 Lee Street, West Complex

department: Center for Public Health Genomics

institute: University of Virginia

summary: Abstract    Background. The cellular effects of androgen are transduced through the androgen receptor, which controls the expression of genes that regulate biosynthetic processes, cell growth, and metabolism. Androgen signaling also impacts DNA damage signaling through mechanisms involving gene expression and transcription-associated DNA damaging events. Defining the contributions of androgen signaling to DNA repair is important for understanding androgen receptor function, and it also has important translational implications.    Methods. We generated RNA-seq data from multiple prostate cancer lines and used bioinformatic analyses to characterize androgen-regulated gene expression. We compared the results from cell lines with gene expression data from prostate cancer xenografts, and patient samples, to query how androgen signaling and prostate cancer progression influences the expression of DNA repair genes. We performed whole genome sequencing to help characterize the status of the DNA repair machinery in widely used prostate cancer lines. Finally, we tested a DNA repair enzyme inhibitor for effects on androgen-dependent transcription.    Results. Our data indicates that androgen signaling regulates a subset of DNA repair genes that are largely specific to the respective model system and disease state. We identified deleterious mutations in the DNA repair genes RAD50 and CHEK2. We found that inhibition of the DNA repair enzyme MRE11 with the small molecule mirin inhibits androgen-dependent transcription and growth of prostate cancer cells.    Conclusions. Our data supports the view that crosstalk between androgen signaling and DNA repair occurs at multiple levels, and that DNA repair enzymes in addition to PARPs, could be actionable targets in prostate cancer.

overall_design: RNA was extracted from PC3-AR, VCaP, and LNCaP cells under untreated and androgen (2 nM, R1881) treated conditions. A total of 21 samples were sequenced with 3 replicates for each condition.

first: Kasey

last: Jividen

first: Bryce

middle: M

last: Paschal


title: Transcriptome characterization of triple negative breast cancer [Mexico]

status: Public on Aug 31 2018

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: Triple negative breast cancer (TNBC) represents a challenging tumor type due to their poor prognosis and limited treatment options. It is well recognize that clinical and molecular heterogeneity of TNBC is driven in part by mRNA and lncRNAs. To stratify TNBCs, we profiled mRNAs and lncRNA in 158 adjuvant TNBC tumors using  an Affymetrix microarray platform. Lehmann clustering analysis allowed us to identify TNBC subtypes featuring unique lncRNA expression patterns, disease free and overall survival rates and particular gene ontology enrichments (performed with GSEA algorithm).

overall_design: Breast cancer tumors were collected from the archives of the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix microarrays.

first: Fredy

middle: O

last: Betlran-Anaya

middle: L

first: Sergio

last: Rodriguez-Cuevas

first: Verónica

last: Bautista-Pina

first: Antonio

last: Maffuz-Aziz

first: S

last: Baroni

first: Marilena

last: Iorio

first: Alfredo

last: Hidalgo-Miranda


title: Chromatin interaction of ERG and AR in established prostate cancer

status: Public on Mar 28 2019

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

country: USA

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The current study defines the how ERG, PTEN, and AR inteact to regulate the transciptome in established prostate cancers.  Prostate cancer organoids were derived from established prostate cancer in GEM models harboring ERG over-expression and/or loss of PTEN and cultured in vitro using prostate epithelial organoid culture conditions. The established organoids were then isolated as individual clones in triplicate and CRISPR strategies were employeed to knock out ERG and AR.  ChIP seq was performed under standard growth and media conditions.

overall_design: 12 samples with 3 genotype in 4 conditions

first: Brett

middle: S

last: Carver


title: A microRNA signature identifies four subtypes of triple-negative breast cancer I

status: Public on Aug 16 2018

summary: Triple negative breast cancer (TNBC) represents a challenging tumor type due to their poor prognosis and limited treatment options. It is well recognize that clinical and molecular heterogeneity of TNBC is driven in part by post-transcriptional regulators such as miRNAs. To stratify TNBCs, we profiled 1050 miRNAs in 132 adjuvant TNBC tumors and 40 tumors from other immunophenotypes using  an Affymetrix microarray platform. A NMF clustering analysis allowed us to identify 4 TNBC subtypes featuring unique miRNA expression patterns, disease free and overall survival rates and particular gene ontology enrichments (performed with GSEA algorithm). Our agglomerative approach was cross-validated by using two other clustering algorithms (k-means and consensus clustering). TNBC miRNAs subgroups were also correlated with the Lehmann intrinsic subtypes, finding a significant enrichment of immmnomodulartory and basal 1 subtypes in our high risk miRNA subgroups. 3 cell line models (MDA MB 468, MDA MB 231 and HS578T) were classified according to our miRNA signature, recapitulating two different miRNA subgroups. The TNBC tumors were compared against other phenotypes identifying differentially expressed miRNAs that together with the altered miRNAs within the subgroups allowed us to define interesting miRNAs for further functional analysis.

overall_design: Breast cancer tumors were collected from the archives of the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix miRNA microarrays.  Breast cancer tumors were collected from the archives of the Fundación Mexicana de Fomento para la Prevención Oportuna del Cáncer de Mama, A.C., (FUCAM) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix miRNA microarrays.

first: Rosa

last: Rebollar-Vega

first: E

last: D'Ippolito

first: M


title: Transcriptome characterization of triple negative breast cancer [Italy]

overall_design: Breast cancer tumors were collected from the archives of the Fondazione IRCCS Istituto Nazionale dei Tumori of Milan (INT) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix microarrays.


title: Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

status: Public on May 14 2019

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: Myc is a family of regulator genes and proto-oncogenes that code for transcription factors. Gene expression of CTCF in human cancer cells and control uncover the disrupted enhancer-promoter regulation of MYC in human cancer cells.

overall_design: RNA-seq library constructed on genome wide deletion of CTCF cells and control.

first: Judith

last: Hyle

first: Yang

last: Zhang

first: Shaela

last: Wright


title: Genome-Wide DNA Methylation Encodes Cardiac Transcriptional Reprogramming in Human Ischemic Heart Failure [DNA Methylation]

status: Public on Aug 22 2018

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

type: Methylation profiling by genome tiling array

summary:
RNA-sequencing analysis was performed on human ischemic left ventricular tissue obtained from patients with end-stage heart failure, which enriched known targets of the polycomb methyltransferase EZH2 compared to non-ischemic hearts. Combined RNA sequencing and genome-wide DNA methylation analysis revealed a robust gene expression pattern consistent with suppression of oxidative metabolism, induced anaerobic glycolysis, and altered cellular remodeling.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


summary:
Background – Epigenetic alterations are stable modifications to  chromatin structure that occur in response to environmental cues such as hypoxia  or altered nutrient delivery. DNA methylation is a well-established and dynamic DNA modification that contributes to the regulation of gene expression. In the current study, we test the hypothesize that ischemic heart failure is defined by a distinct signature of DNA methylation that corresponds with altered expression of genes involved in cardiac ventricular dysfunction.
Methods and Results – Using a methylation array, we quantified genome-wide DNA methylation of endomyocardial samples acquired from patients  with ischemic (n = 6) or non-ischemic (n = 5) heart failure. RNA-sequencing analysis was performed in the same samples to identify transcriptomic changes (Fold Change > 1.5, Q < 0.05, FPKM > 2) associated with differential methylation (|Percent Change| > 5%, p < 0.05). Of the promoter-associated CpG Islands, which are well-established regions of negative transcriptional regulation, we identified a signature of robust hypermethylation. The methylation changes linked to significantly decreased transcripts included key fatty acid metabolic regulators (e.g. KLF15, AGPAT9, APOA1, and MXD4). Among the few hypomethylated and induced genes was PFKFB3, which encodes for the rate-limiting enzyme of glycolysis. Gene set enrichment analysis  identified TGFβ  as a nodal upstream regulator of the methylation changes, potentially supporting a role of DNA methylation in the increased fibrosis and apoptosis that accompanies ischemic heart failure.
Conclusions – Our data identify  that the DNA methylation signature recapitulates the pathologic hallmarks of ischemic heart failure. Furthermore, we show that differential DNA methylation of CpG islands within the promoter depict alterations in metabolic substrate utilization known to occur in ischemic heart failure, and may govern a return to the fetal-like metabolic program.

overall_design: Whole-Genome DNA Methylation analysis of left ventricle samples in 11 subjects with end-stage heart failure.

first: Adam

middle: R

last: Wende

middle: E


title: Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis [RNA-Seq]

status: Public on Nov 07 2019

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: During mammalian spermatogenesis, male germ cells undergo dramatic reorganization of chromatin, whereby 90-99% of histones are evicted and replaced by protamines.  This reorganization prominently features histone acetylation to loosen chromatin structure.  Given the potential role of retained histones in fertility and early embryonic development, the genomic location of retained nucleosomes is of great interest.  However, the ultimate position and mechanisms underlying nucleosome eviction/retention are poorly understood, including several studies utilizing MNase-seq methodologies, but reporting remarkably dissimilar locations. Here, we utilized ATAC-seq to determine the location of retained nucleosomes in mouse sperm and found enrichment at promoters, but also retention at inter- and intragenic regions, and repetitive elements.  We further investigated nucleosome eviction/retention by generating pre-meiotic, germ cell specific, conditional knockout mice for the histone acetyltransferase Gcn5, a key histone acetyltransferase.  Gcn5cKO germ cells exhibited abnormal chromatin dynamics during spermiogenesis, including diminished nucleosome eviction leading to increased histone retention in sperm.  These mice exhibited severe reproductive phenotypes: abnormal sperm production, sperm morphology, and ultimately, male infertility.  Our findings demonstrate Gcn5 mediated histone acetylation promotes chromatin accessibility and nucleosome eviction in spermiogenesis, and that loss of histone acetylation leads to defects that disrupt male fertility and potentially, early embryogenesis.

overall_design: Includes RNA-seq from four stages of spermatogenesis (meiotic spermatid, round spermatid, elongating spermatid, mature sperm) in three separate genetic backgrounds: SV129E mice (1 replicate each), C57BL6 GCN5+/+ mice (2 replicates each) and C57BL6 GCN5-/- mice (Stra8-CRE homozygous flox'd alleles) (2 replicates each)

first: Lacey

middle: J

last: Luense

first: Greg

first: Enrique

last: Shiao

first: Richard

last: Rangel

first: Angela

middle: H

last: Weller

first: Marisa

last: Bartolomei

first: Shelley

last: Berger


title: Genome-Wide DNA Methylation Encodes Cardiac Transcriptional Reprogramming in Human Ischemic Heart Failure [RNA-Seq]

overall_design: RNA Sequencing analysis of left ventricle samples in 11 subjects with end-stage heart failure.

first: David

middle: K

last: Crossman

first: Joseph

middle: P

last: Barchue

first: Salpy

middle: V

last: Pamboukian

first: Steven

last: Pogwizd


title: Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

status: Public on Feb 23 2019

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: These experiments identify the primary response genes of ZNF143 in HEK-293T cells and the transcriptional response that results from treating cells with 500μM auxin.

overall_design: Oryza sativa TIR1 was inserted into all copies of the AAVS1 locus in HEK-293T cells and a single clone was expanded. All subsequent genetic modifications were derived from this progenitor cell line. Genetic modifications include endogenously tagging ZNF143 with an auxin-inducible degron (AID) and insetion of Auxin Response Factor (OsARF16). Cells were treated with 500μM auxin for 90 minutes to degrade ZNF143. Progenitor cells were treated with 500μM Auxin for 3 hours as a control experiment.


title: m6A/m-Seq of mouse adult cortex after acute stress

status: Public on Jul 10 2018

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

country: Germany

institute: Max-Planck-Institute of Psychiatry

type: Methylation profiling by high throughput sequencing

summary: N6-Methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo are currently unknown.  Here, we provide a detailed analysis of the stress-epitranscriptome using m6A/m-Seq of 10-12 w male C57BL/6 mouse cortex of unstressed or acutely stressed mice (4 h after 15 min restraint stress) of 6-7 samples per condition (pooled from 3 mice each). PolyA-RNA-fragments of each sample was processed both as m6A/m-sample (RNA immunoprecipiation RIP with an m6A and m6Am antibody) and RNA-input sample.

overall_design: 7 replicates for basal mouse cortex ("control", "C"), 6 replicates for stressed mouse cortex (4 h after 15 min of restraint stress, "stress", "S"), each samples was processed as m6A/m-immunoprecipitation-sample ("m6A") or as input RNA samples ("RNA"). Additionally, 1 RNA sample (equimolar mixed from all samples) was processed as IgG control.

first: Alon

last: Chen


title: Ribosome profiling Seq of mouse adult cortex after acute stress

summary: N6-Methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo are currently unknown.  Here, we provide ribosome profiling data of 10-12 w male C57BL/6 mouse cortex of unstressed or acutely stressed mice (4 h after 15 min restraint stress) of 6 samples per condition to relate to m6A/m-Seq data of similiar samples.

overall_design: 6 replicates of basal mouse cortex ("Control", "C"), 6 replicates for stressed mouse cortex (4 h after 15 min of restraint stress, "Stress", "S").


title: The role of m6A/m-RNA methylation in stress response regulation

summary:
N6-Methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo are currently unknown.
Here, we provide a detailed analysis of the stress-epitranscriptome using m6A/m-Seq, global and gene-specific m6A/m measurements. We show that stress exposure and glucocorticoids region- and time-specifically alter m6A/m and its regulatory network. We demonstrate that deletion of the methyltransferase Mettl3 or the demethylase Fto in adult neurons alter the m6A/m epitranscriptome, increase fear memory, alter the transcriptome response to fear and synaptic plasticity. Moreover, we report that regulation of m6A/m is impaired in major depressive disorder (MDD) patients following glucocorticoid stimulation.
Our findings indicate that brain m6A/m represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m6A/m-response may contribute to the pathophysiology of stress-related psychiatric disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: m6A/m-Seq of mouse adult cortex of Mettl3 cKO or Fto cKO mice

summary: N6-Methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo are currently unknown.  Here, we investigated the effect of gene deletion of Mettl3, a m6A methyltransferase, and Fto, a m6A and m6Am demethlyase, induced in adulthood in excitatory neurons of the neocortex and hippocampus (Camk2a-Cre Mettl3 or Fto cKO) on the cortical epitranscriptome. PolyA-RNA-fragments from 3-5 replicates per group were processed both as m6A/m-sample (RNA immunoprecipiation RIP with an m6A and m6Am antibody) and RNA-input sample.

overall_design: 5 replicates of WT mice (from both lines) as well as 3 replicates of Mettl3 cKO and 3 replicates of Fto cKO mice (cortex sample from 3 mice pooled per replicate) were processed as m6A/m-immunoprecipitation-sample ("m6A") or as input RNA samples ("RNA"). Additionally, 1 RNA sample (equimolar mixed from all samples) was processed as IgG control.


title: mRNA-Seq of mouse Mettl3 cKO and Fto cKO hippocampus after fear conditioning

summary: N6-Methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo are currently unknown.  Here, we investigated the effect of gene deletion of Mettl3, a m6A methyltransferase, and Fto, a m6A and m6Am demethlyase, induced in adulthood in excitatory neurons of the CA1 and CA3 in the hippocampus (Nex-CreERT2 Mettl3 or Fto cKO) on the transcriptome of CA1 and CA3 as well as the transcriptomic response of the CA1 and CA3 transcriptome to fear conditioning.

overall_design: 5 biological replicates each for CA1/3 of Nex-CreERT2 Mettl3 wild type ("WT") and conditional knock-out mice ("cKO") or Nex-CreERT2 Fto WT and cKO, each at baseline("Box")  or 24 h after fear conditioning ("FC").


title: RNA transcriptome analysis of IRF1 and IRF3 knockout in immortalized primary hepatocytes infected with hepatitis A virus

status: Public on Jun 01 2018

city: Chapel Hill

first: Stanley

last: Lemon

state: NC

address: 8034 Burnett-Womack CB#7292

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

summary: Interferon regulatory factors (IRFs) play key roles in the transactivation of antiviral genes at the step downstream of activated pathogen-associated molecular pattern sensors, such as RIG-I-like receptors or Toll-like receptors. Whereas IRF1 and IRF3 are thought to bind similar DNA elements (ISRE and PRD-III, PRD-I) to activate antiviral gene transcription, genome-wide transcriptome profiling of IRF1 versus IRF3 knockouts in an immortalized primary hepatocyte (PH5CH8) cell line infected with hepatitis A virus (HAV) revealed unexpected disparities in their target genes. IRF1 targets include several anti-HAV effector genes that were not previously recognized to have antiviral functions.

overall_design: mRNA transcriptome profiles of the WT, IRF1, and IRF3 knockout cell lines infected with hepatitis A virus HM-175/18f strain, each in triplicate.

first: Daisuke

last: Yamane

first: Sara

last: Selitsky

first: Praveen

last: Sethupathy


title: A microRNA signature identifies four subtypes of triple-negative breast cancer and correlates miR-342-3p as a regulator of the lactate metabolic pathway through silencing the monocarboxylate transporter 1

status: Public on Aug 17 2018

first: Sandra

last: Romero-Cordoba

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
synthetic construct


title: Transciptomic analysis of cachectic muscles from metastatic allograft models

status: Public on Jul 01 2018

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University

summary: RNA sequencing analysis of muscles comparing normal muscles with cachectic muscles isolated from mice bearing distant metastasis from C26m2 and 4T1 murine colon and breast cancer cell lines, collected at the onset of weight loss five weeks after tumor cell injection in these mice.

overall_design: Transcriptomic analysis of muscles performed by RNA sequencing (RNA seq) isolated from mice bearing metastatic colon cancer cell line, C26m2 or metastatic breast cancer cell line, 4T1 and their respective age-matched healthy controls. Mice bearing distant metastases were compared using the resection-and-relapse approach after 5 weeks post-tumor cell injection.

first: Swarnali

last: Acharyya

first: Gang

last: Wang

first: Anup

last: Biswas

first: Wanchao

last: Ma


title: m6A/m-Seq of human B-lymphocyte cell lines from healthy controls and major depressive disorder patients

summary: N6-Methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the human stress response are currently unknown.  Here, we provide m6A/m-Seq of immortalied cell lines derived from B lymphocytes from male healthy donors or male donors diagnosed with major depressive disorder (MDD), harvested 1 h after treatment with 100 nM cortisol or mock treatment. PolyA-RNA-fragments of each sample was processed both as m6A/m-sample (RNA immunoprecipiation RIP with an m6A and m6Am antibody) and RNA-input sample.

overall_design: 3 biological replicates of cells from healthy male donors and 3 biological replicates of cells from male donors diagnosed with major depressive disorder each split in two treatment samples: mock treatment (ethanol only) or  100 nM cortisol in ethanol for 1 h creating 4 groups with each 3 biological replicates: healthy-mock: H_x_M, healthy-cortisol: H_x_C, MDD-mock: M_x_M and MDD-cortisol: M_x_C.  Each samples was processed as m6A/m-immunoprecipitation-sample ("m6A") or as input RNA samples ("RNA"). Additionally, 1 RNA sample (equimolar mixed from all samples) was processed as IgG control.


title: A microRNA signature identifies four subtypes of triple-negative breast cancer II

overall_design: Breast cancer tumors were collected from the archives of the Fondazione IRCCS Istituto Nazionale dei Tumori of Milan (INT) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain triple negative tumors (ER-, PR- and Her2-) and tumors from other immunophenotype (ER+, PR+ or/and Her2+) by microdissection of tumoral cells for RNA extraction and hybridization on Affymetrix miRNA microarrays.

first: Rosa

last: Rebollar-Vega

first: Sergio

last: Rodriguez-Cuevas

first: Verónica

last: Bautista-Pina

first: Antonio

last: Maffuz-Aziz

first: S

last: Baroni

first: E

last: D'Ippolito

first: M

last: Iorio

first: Alfredo

last: Hidalgo-Miranda


title: Human telomerase requires TCAB1 for catalytic function and for shaping RNA component conformation

status: Public on Jun 24 2018

city: Bethesda

first: Pedro

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

summary: Ribonucleoprotein enzymes require specific and dynamic conformations of their RNA constituents for regulated catalysis. Telomerase RNA components (TRs) rely on two conserved domains, a pseudoknot/template sequence and a three-way junction (CR4/5), each of which binds the telomerase reverse transcriptase protein (TERT). Vertebrate TRs evolved a third element, the H/ACA domain, involved in assembly and trafficking of telomerase through binding telomerase cofactors, dyskerin and TCAB1, respectively. Here, we show that telomerase unexpectedly requires TCAB1 for enzyme catalysis and for shaping the conformation of the TR CR4/5 domain. Human and mouse cells lacking TCAB1 exhibit a marked reduction in telomerase activity, but show no defect in enzyme assembly. Instead, loss of TCAB1 causes specific unfolding of critical RNA helices in TR CR4/5 required for catalysis, and impairs TR-TERT association. CR4/5 mutations derived from patients with the telomere disorder dyskeratosis congenita phenocopy the loss of enzyme activity and disruption of TERT binding observed with TCAB1 deletion. These findings show that the H/ACA element acquired by telomerase during vertebrate evolution serves an unanticipated role in controlling folding of the essential TR CR4/5 domain, facilitating optimal TERT engagement and enabling telomerase catalysis through the action of TCAB1 protein tethered at the H/ACA domain.

overall_design: SHAPE profiles for hsTR isolated from telomerase ribonucleoprotein RNP complexes from Wild Type, TCAB1-KO, TCAB1-KO genetic rescue,  TCAB1-KO with TCAB protein added in vitro and Coilin KO cells.

first: Lu

last: Chen

first: Caitlin

last: Roake

first: Adam

last: Freund

first: Siqi

last: Tian

first: Chandresh

last: Gajera

first: Shengda

last: Lin

first: Byron

last: Lee

first: Andrew

last: Venteicher

first: Rhiju

last: Das

first: Howard

middle: Y

last: Chang

first: Steven

last: Artandi


title: Decrease in DNA methylation 1(DDM1) is required for the establishement of CHH islands in maize

status: Public on Oct 24 2017

city: Beijing

first: Jincheng

last: Long

state: Beijing

address: Hai Dian district ,Yuanmingyuan Road.Beijing

department: National Maize improvement center

country: China

institute: China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is required for the formation of m CHH islands. In addition, ZmDDM1 is indispensable for the presence of 24-nt siRNA, suggesting its involvement in the RdDM pathway. Our results provide novel insight into the role of ZmDDM1 in regulating the formation of m CHH islands, via the RdDM pathway maize, suggesting that, in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating m CHH.

overall_design: Characterize the function of chromatin remodeling factor DDM1 on DNA methylation in zea mays

first: Yan

last: He


title: LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies in acute myeloid leukemia

status: Public on Mar 12 2018

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory


title: E. coli ATCC 8739 transcriptomics under culture medium optimization and adaptive laboratory evolution for glycerol consumption

status: Public on Nov 23 2019

city: Bogotá

first: Albert

middle: Enrique

last: Tafur Rangel

address: Cra 1 Nº 18A - 12 Edificio ML

department: Chemical and Food Engineering

country: Colombia

institute: Universidad de Los Andes

summary: Biotechnology suggests that microorganisms can be used as chemical factories that transform renewable feedstock into value-added chemicals. Conversion of glycerol, using direct transformation or fermentation, into valuable products such as polymers, surfactants, solvents, and chemical intermediates has attained growing interest in recent years due to the dramatic growth of the biodiesel industry. However, the use of cell factories could be limited by low growth and uptake rates under certain environmental conditions, thus understanding microbial nutritional requirements is a critical point to use them as cell factories. Here, we compared E. coli ATCC 8739 transcriptomic responses to glycerol under aerobic conditions in an optimized culture medium (Condition 3) and one evolved strain in glycerol using as a reference a glycerol-based medium (Condition 11). Our analyses revealed 478 and 431 differentially expressed genes (DEGs) with log2 fold change (FC) > |2| and p Adjusted value < 0.05, for the bacteria growing in the optimized culture medium and the evolved strain, respectively. Among the DEGs, glp operon was found to be up-regulated as a response to glycerol uptake. Interestingly, between them, it was found genes that requires the use of phosphorous to ovoid the toxicity during glycerol consumption. Previously, we identified using a computational approach that phosphorous and nitrogen are essential compound that support high glycerol consumption in E. coli.

overall_design: Here, we compared E. coli transcriptomic responses to glycerol as carbon source under aerobic conditions for an optimized culture medium and adaptive laboratory evolution. 3 biological replicates were carried out for each condition, respectively.

first: Luis

last: Reyes

first: Ross

last: Carlson

first: Jorge

last: Gomez Ramirez

first: Andrés

last: González Barrios


title: LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies in acute myeloid leukemia (RNA-Seq)

summary: Transcriptome analysis by high throughput sequencing

overall_design: Gene expression profiles in AML with gene knockout or inhibitor treatment

first: Christopher

last: Vakoc


title: PAX3-FOXO1 requires BRD4 to drive oncogene addiction in RMS cells [RNA-seq]

status: Public on Apr 27 2017

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: The fusion transcription factor PAX3-FOXO1 drives oncogenesis in a subset of rhabdomyosarcomas, however the mechanisms by which it remodels chromatin are unknown.  We find PAX3-FOXO1 reprograms the cis-regulatory landscape by inducing super enhancers (SEs), in collaboration with master transcription factors MYOG, MYOD and MYCN.  This myogenic SE circuitry is consistent across cell lines and primary tumors. Deregulation of PAX3-FOXO1 itself occurs by translocation-induced chromatin loops bringing the PAX3 promoter under the control of FOXO1 enhancers.   Protein targets induced by, or bound to, PAX3-FOXO1 occupied SEs, were selectively sensitive to small molecule inhibition. PAX3-FOXO1 co-binds BRD4 at SEs, and BET bromodomains are required for PAX3-FOXO1-dependent transcription and cancer cell growth.

overall_design: RNA-seq in FP-RMS cells exposed to either DMSO or JQ1 treatment, and RNA-seq of fibroblast cells stably transduced with either empty vector or PAX3-FOXO1 vector.

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Developmental programs in chicken early embryos by whole transcriptome analysis.

status: Public on Dec 11 2017

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: Temporal regulation of gene expression is essential for early embryonic development. With the development of next-generation sequencing technologies, transcriptional profiling of early developmental processes in various vertebrates are already revealed. However, overall transcriptome analysis of early embryonic development in avian have never been investigated. In this study, to our knowledge, we provide comprehensive profiling of pre-oviposited embryos in chicken by whole-transcriptome RNA-seq for the first time. We demonstrated the presence of avian-specific mechanism of first- and second-wave of zygotic genome activation (ZGA). Chicken early embryo have distinct developmental programs between cleavage and area pellucida formation period. Additional speculation of epigenetic dynamics indicate that maternal-to-zygotic transition (MZT) in chicken is promoted after second-wave of ZGA, through EGK.VI to EGK.X stages. These extensive results contribute to understanding avian early embryogenesis and comparative studies with other species with many developmental aspects.

overall_design: Chicken early embryo (Oocyte to EGK.X) samples were investigated based on the whole transcriptome sequencing approach.

first: Jaeyong

last: Han


title: Gene expression profiling of inputs to the mesolimbic dopamine circuit

status: Public on Mar 20 2017

city: New York

first: Lisa

last: Pomeranz

address: 1230 York Avenue, Box 305

department: Molecular Genetics

institute: Rockefeller University

summary: PRV-Circuit-TRAP of DAT-cre mice injected with PRV-Introvert-GFP in the nucleus accumbens These studies identify important inputs to the mesolimbic dopamine pathway and further show that PRV circuit-directed translating ribosome affinity purification (PRV-Circuit-TRAP) can be broadly applied to identify molecularly defined neurons comprising complex, multisynaptic circuits.

overall_design: The current study combined neuroanatomical tracing and molecular profiling of inputs to the mesolimbic dopamine pathway using pseudorabies virus whose replication and exression of GFP are dependent on Cre recombinase (PRV-Introvert-GFP).  To molecularly profile this circuit, we mated DAT-Cre to SYN-NBL10 mice and injected PRV-Introvert-GFP into the NAc. GFP expressed from PRV-Introvert-GFP binds to the NBL10-tagged polysomes and is then precipitated using anti-GFP monoclonal antibodies. Immunoprecipitated RNA was purified (IP RNA) along with total RNA collected before immunoprecipitation (Input RNA) was purified and sequenced with an Illumina HiSeq 2000 system. The differential expression of transcripts in our IP fraction was calculated. Final values for fold enrichment were weighted for the effects of PRV infection on transcript abundance.

first: Jeffrey

middle: M

last: Friedman

first: Mats

middle: I

last: Ekstrand

first: Kaamashri

middle: N

last: Latcha

first: Gregory

middle: A

last: Smith

first: Lynn

middle: W

last: Enquist


title: Chromatin looping evidence between PAX3-FOXO1 bound super enhancer and MYOD1 promoter [4C-seq]

summary: Circular chromatin confirmation capture in rhabdomyosarcoma cells was performed with viewpoints at the PAX3-FOXO1 bound super enhancer upstream of MYOD1, and also at the MYOD1 promoter, to find support for looping between these two genetic elements almost 80 thousand base pairs apart.

overall_design: 4C-seq was performed on fixed cells, which were exposed to 4-bp cutter DpnII for the primary restriction enzyme, re-ligated in dilute conditions, followed by reversal of crosslinks and purification.  Csp6I was used to reduce template to sizes amenable to inverse PCR for viewpoint amplification.  4C samples of RMS cell line (RH4) were amplified at anchors within the viewpoint.


title: REPROGRAMMING IDENTIFIES FUNCTIONALLY DISTINCT STAGES OF CLONAL EVOLUTION IN MYELODYSPLASTIC SYNDROMES

status: Public on Apr 17 2019

city: Seattle

first: Sergei

last: Doulatov

state: WA

address: 1795 NE Pacific Street

institute: University of Washington

summary: As part of this study, we isolated induced pluripotent stem cells (iPSCs) from a patient with TP53-mutant MDS and identified loss of chromosome 5q as a cooperating genetic event. Using RNA sequencing we found that loss of chromosome 5q dysregulates genes that maintain chromosome stability, predisposing TP53-mutant cells to chromosomal rearrangements and progression to complex karyotype.

overall_design: Hematopoietic progenitors were derived from induced pluripotent stem cells heterozygous for the TP53 R209fs mutation (TP53+/-) with or without the deletion on chromosome 5q (TP53+/-;del5q). Gene expression was compared between TP53+/- and TP53+/-;del5q HPCs by RNAseq to identify genes significantly downregulated as a result of 5q loss.

first: Jasper

last: Hsu

first: Andreea

last: Reilly

first: Brian

last: Hayes

first: Courtnee

last: Clough

first: Eric

middle: Q

last: Konnick

first: Beverly

last: Torok-Storb

first: Suleyman

last: Gulsuner

first: David

last: Wu

first: Pamela

middle: S

last: Becker

first: Siobán

middle: B

last: Keel

first: Janis

middle: L

last: Abkowitz


title: A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (RNA-seq)

status: Public on Jan 08 2018

first: Yali

last: XU

summary: Targeting of general coactivators, such as BRD4, is an emerging strategy to interfere with oncogenic transcription factors (TFs) in cancer. However, coactivator perturbations have the potential to influence the function of numerous TFs, thereby resulting in biological pleiotropy. Here we identify TAF12, an 18 kilodalton subunit of TFIID/SAGA coactivator complexes, as a selective requirement for acute myeloid leukemia (AML) progression. We trace this AML-specific dependency to a direct interaction between the TAF12/TAF4 histone-fold heterodimer and the transactivation domain of MYB, a TF with established roles in leukemogenesis. Ectopic expression of a histone-fold domain fragment of TAF4 can efficiently squelch TAF12 in cells, suppress MYB, and regress AML in mice. Our study reveals a strategy for potent MYB inhibition in AML and highlights how an oncogenic TF can be selectively neutralized by targeting a general coactivator complex.

overall_design: For RNA-seq in cells transduced with control shRNAs/sgRNAs/empty vector, two technical repeats were performed. For RNA-seq in cells transduced with experimental shRNAs/sgRNAs/cDNA, two independent shRNAs/sgRNAs/tagged cDNAs were treated as repeats.

last: Xu

first: Christopher

middle: R

last: Vakoc


title: Tissue engineered colorectal cancer metastasis

status: Public on Jan 28 2017

first: Andrew

last: Wang

address: 101 Manning Dr

department: Radiation Oncology

summary: To confirm that the biology of engineered liver and lung metastases are similar to in vivo metastases, we compared the global gene expression profiles of the engineered liver and lung metastases of HT-29 cells to that of standard tissue culture (plastic), Matrigel culture and in vivo liver metastasis (splenic injection).

overall_design: HT-29 cells were grown on plastic culture dish (plastic), matrigel coated culture dish, liver biomatrix coated culture dish, lung biomatrix coated dish, or in vivo liver metastasis tumor through splenic injection. HT-29 gene expression was measured through microarray. Four different experiments were performed at each culture condition.


title: Integrated Omic Analysis of a Guinea Pig Model of Heart Failure and Sudden Cardiac Death

status: Public on Dec 02 2016

city: Baltimore

first: D.

middle: Brian

last: Foster

address: 720 Rutland Avenue Ross 847

department: Division of Cardiology

institute: Johns Hopkins University School of Medicine

summary: Sudden cardiac death (SCD) associated with heart failure (HF) is a multifactorial problem requiring a systems level approach applied to suitable experimental animal models with features of the human disease. Here we examine key regulatory pathways underlying the transition from compensated hypertrophy (HYP) to decompensated HF and SCD by integrated analysis of the transcriptome, proteome and metabolome. In a guinea pig model of acquired long QT syndrome and HF/SCD, relative protein abundances from sham-operated, HYP and HF hearts were assessed using isobaric tags for relative and absolute quantification (iTRAQ), prior to liquid chromatography and tandem mass spectrometry (LC-MS/MS). Metabolites were quantified by LC-MS/MS or gas chromatography coupled to MS (GC-MS). Transcriptome profiles were obtained using DNA microarrays. The guinea pig HF proteome exhibited classic biosignatures of cardiac HYP, left ventricular dysfunction, fibrosis, cellular degeneration, inflammation and extravasation. Fatty acid metabolism, mitochondrial transcription/translation factors, antioxidant enzymes, and other mitochondrial processes, were downregulated in HF, but not HYP. Proteins upregulated in HF are consistent with extracellular matrix remodeling, cytoskeletal remodeling, and acute phase inflammation markers. Among metabolites, downregulation of acyl-carnitines was observed in HYP, while fatty acids accumulated in HF. Levels of the tricarboxylic acid (TCA) cycle metabolite, citrate, and the potent inhibitor, 2-methylcitrate, increased upon transition from HYP to HF. Correlation of the magnitude of transcript and protein changes in HF is weak (R2=0.23), indicating that targeting transcript/proteome may reveal inform post-transcriptional gene regulation in HF. Proteome/Metabolome integration suggests metabolic bottlenecks in fatty acyl-CoA processing by carnitine palmitoyl transferase (CPT1B) as well as TCA cycle inhibition. We present a model in which hallmarks of acute signaling in HF, including Ca2+ dysregulation and low cAMP levels, are coupled to mitochondrial metabolic and antioxidant defects, through a CREB/PGC1-alpha transcriptional axis.

overall_design: 18 total samples were analyzed. The experiment consisted of 3 treatment groups: 1) HYP (ACi-2wk), 2) HF (ACi-4w) 3) SHAM (Shami-4w). Each group consisted of 6 samples. Samples were compared, pairwise using an ANOVA to obtain an estimate of variance, followed by unpaired two-sample t-test using PARTEK Genomics Suite (Genomics Solutions). Specifically comparisons were HYP vs. Sham, HF vs. Sham and HF vs. HYP. False discovery was assessed for named genes by the method of Story  (Journal of the Royal Statistical Society: Series B (Statistical Methodology). 2002;64(3):479-98.)

first: D

first: C

middle: C

last: Talbot Jr

last: O'Rourke


title: Aberrant overexpression of TGF-β2 induces epithelial-mesenchymal transition in adenomyosis with β-catenin activation.

status: Public on Oct 19 2016

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary:
Aberrant activation of TGF-β2 plays an important role in the pathogenesis of adenomyosis.
We used microarrays to detail the machanism underlying aberrant activation of TGF-β2 in adenomyosis

overall_design: Uteri of control and Mutant (Pgr cre/+ Ctnnb1f(ex3)/+) mice were selected at 4 weeks of age for RNA extraction and hybridization on Affymetrix microarrays.

first: Tae

middle: H

last: Kim


title: Expression profiling and H3K79me2 ChIP-seq in Prostate cancer cells treated with DOT1L inhibitor

status: Public on Aug 09 2019

first: Rajita

last: Vatapalli

state: IL

address: 303 E SUPERIOR, 6-250

overall_design: Refer to individual Series


title: Gene Expression of Mexican Patients with Breast Cancer

status: Public on Dec 04 2015

city: Monterrey

first: Hugo

last: Gomez

state: Nuevo Leon

address: Garza Sada

department: Bioinformatics

institute: ITESM

summary:
Gene expression of tumor sample of mexican patients with breast cancer.
Samples obtained from the Hospital San Jose Tec de Monterrey.

overall_design: The experiments were with one color per patient, gene expression profile is from a tumor sample of mexican patients with breast cancer.

first: Victor

last: Trevino


title: PAX3-FOXO1 establishes myogenic super enhancers [RMS Chip-seq]

first: Javed

last: Khan

overall_design: Genome-wide profiles for histone marks, DNase hypersensitivity, transcription factors, coactivators and architectural proteins in Rhabdomyosarcoma (RMS) cell lines and tissues

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Ezh2 Inhibition is Bone-anabolic and Osteoprotective in Skeletally Mature Mice

status: Public on Oct 01 2016

city: Rochester

first: Andre

middle: J

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We report genome-wide effects of Ezh2 inhibition (GSK126) in MC3T3 sc4 pre-osteoblasts by ChIP-Seq (H3K27me3) and mRNA-Seq (transcriptome). Treatment of cells for 24 hours with GSK126 suppresses genome-wide H3K27me3, most notably near the transcriptional start sites (TSSs). Genes that exhibit suppression of H3K27me3 near TSSs as a result of GSK126 tend to be up-regulated at the mRNA levels (mRNA-Seq) as well. The mRNA-Seq analysis demonstrates that osteogenic genes are up-regulated after the administration of GSK126. These pro-osteogenic effects are seen 3, 6, and 10 days after the initial GSK126 treatment.

overall_design: MC3T3 cells were seeded in maintenance medium (10,000 cells/cm2). The following day, maintenance medium was replaced with osteogenic medium (50 µg/ml ascorbic acid and 4 mM beta glycerol phosphate) containing vehicle or Ezh2 inhibitor (5µM GSK126).  Three days later, vehicle or Ezh2 inhibitors were added again along with osteogenic medium. On day 6, Ezh2 inhibitor and vehicle were removed and fresh osteogenic medium was added with media changes scheduled every three days. 24 hours after the first drug/DMSO administration, ChIP assay was performed using a H3K27me3 (17-622, Lot 2213948, Millipore) antibody. The resulting DNA along with input DNA was submitted for ChIP-Seq analysis. RNA-seq was performed using RNA isolated at days 3, 6, and 10 from cells treated with vehicle or GSK126 in the presence of osteogenic differentiaiton.

first: Amel

last: Dudakovic


title: RNA-seq performed on FFPE sarcoma blocks

status: Public on Mar 03 2016

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

summary: We validated the technological and material transfers of the CINSARC signature.

overall_design: We performed both microarray and RNA-seq analysis and compared prognostic values based on the CINSARC classification. We measure significant metastasis-free survivals with both approaches. Additionally, depending on RNA degradation, transcriptomic analysis from FFPE blocks show similar CINSARC classification.

first: Tom

last: Lesluyes

first: Gaëlle

last: Pérot


title: Mexican Patients with Breast Cancer

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


title: Disease-stabilizing treatment based on all-trans retinoic acid and valproic acid in acute myeloid leukemia

status: Public on Oct 25 2017

city: Bergen

first: Hakon

last: Reikvam

address: Jonas Lies vei 65

department: Department of Clinical Science

country: Norway

institute: University of Bergen

summary: Acute myeloid leukemia (AML) is an aggressive malignancy that can only be cured by intensive therapy. However, many elderly and unfit patients cannot receive such treatment due to an unacceptable risk of treatment-related morbidity and mortality. Disease-stabilizing therapy is then the only possible strategy, one alternative being treatment based on all-trans retinoic acid (ATRA) combined with the histone deacetylase inhibitor valproic acid and possibly low-toxicity conventional chemotherapy.

overall_design: Primary AML cells were derived from patients included in two clinical studies of treatment based on ATRA plus valproic acid; low toxicity chemotherapy (low-dose cytarabine, hydroxyurea, 6-mercaptopurin) was also allowed. Pretreatment leukemic cells were analyzed by mutation profiling of 54 genes frequently mutated in myeloid malignancies and by global gene expression profiling before and during in vivo treatment.

first: Håkon

first: Øystein

last: Bruserud


title: Stratification of Leiomyosarcoma molecular subtypes by 3' end RNA-sequencing: Toward precision medicine

status: Public on May 19 2015

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary: Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation.  Little is known about its molecular heterogeneity and no targeted therapy currently exists for LMS.  We demonstrate the existence of 3 molecular subtypes in a cohort of 99 cases and an independent cohort of 82 LMS.  Two new FFPE tissue-compatible diagnostic immunohistochemical markers are identified: LMOD1 for subtype I LMS and ARL4C for subtype II LMS. Subtype I and subtype II LMS are associated with good and poor prognosis, respectively.  The LMS subtypes show significant differences in expression levels for genes for which novel targeted therapies are being developed.

overall_design: Gene expression profiling was performed by 3' End RNA Sequencing (3SEQ), a next generation sequencing approach that does not rely on frozen tissue but can be performed on archival FFPE tissue. Samples included 99 LMS, 6 Undifferentiated Pleomorphic Sarcomas (UPS), 3 leiomyomas, 4 normal myometrium samples, and 1 case of Lymphangioleiomyomatosis (LAM). This study only includes the 99 LMS Samples. After gene expression levels were quantified by 3SEQ analysis pipeline, Consensus Clustering with bootstrap method was used to determine that the dataset contained three robust subtypes, and Silhouette analysis was performed to validate the subtype assignments. Two class SAM analysis (Significance Analysis of Microarrays) was performed to identify genes expressed differentially between each subtype of LMS with FDR of 0.05. Immunohistochemical staining was used to validate the potential diagnostic and prognostic markers from 3SEQ data on a tissue microarray.

first: Shirley

middle: X

last: Zhu

first: Vickie

middle: Y

last: Jo

first: Jonathan

last: Fletcher

first: Cheng-Han

last: Lee

first: Inigo

last: Espinosa

first: Santosh

last: Gupta

first: Sushama

last: Varma

first: Alayne

last: Brunner

first: Robert

last: West

first: Matt

last: van de Rijn


title: RNA-seq performed on sarcomas to identify various alterations

first: Frédéric


title: The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [human gene expression array]

status: Public on Nov 28 2017

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

summary: T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. To address its incomplete molecular concept, we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identified novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor / cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM towards a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.

overall_design: Purified T-cells from 98 T-PLL patients (Supplementary Data1 for additional information) were analyzed using various high-throughput profiling platforms (overlap indicated): Illumina HumanHT‑12 v4 BeadChip arrays (n=70 cases) for gene expression profiling (GEP). CD3+ pan T-cells isolated from peripheral blood (PB) of healthy donors with a similar age-median were used as “normal” controls for GEP (n=10). The isolation strategy of PB tumor cells and matched same-sample germline controls from PB mononuclear cells (PBMCs) of T-PLL patients employed a two-step magnetic separation (MACS columns) process: (1) Positive enrichment of T-PLL tumor cells: magnetic beads bound to anti-CD4 or anti-CD8 antibodies (Microbeads, Miltenyi Biotec) and LS Columns (Miltenyi Biotec) were used. The specificity of beads was selected according to the individual immunophenotype. (2) Depletion of residual T-PLL cells from the flow-through designated as normal control: Depletion Columns (LD, Miltenyi Biotec) were used to remove residual CD4 or CD8 positive cells from the flow-through obtained from step 1. For further details, see Methods section.


title: Expression data (micro-array and RNA-seq, frozen tumors and FFPE blocks) from various sarcomas

last: Chibon


title: Long Noncoding RNA HNF1A-AS1 Regulates Proliferation and Migration in Esophageal Adenocarcinoma  Cells

status: Public on Oct 21 2013

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
Objectives: Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of cancer. However, functional lncRNAs and their downstream mechanisms are largely unknown in the molecular pathogenesis of esophageal adenocarcinoma (EAC) and its progression.
Design: lncRNAs that are abnormally upregulated in EACs were identified by RNA-seq analysis, followed by quantitative RT-PCR (qRTPCR) validation using tissues from 31 EAC patients. Cell biological assays in combination with siRNA-mediated knockdown were performed in order to probe the functional relevance of these lncRNAs.
Results: We discovered that a lncRNA, HNF1A-AS1, is markedly upregulated in human primary EACs relative to their corresponding normal esophageal tissues (mean fold change 7.2, p<0.01). We further discovered that HNF1A-AS1 knockdown significantly inhibited cell proliferation and anchorage independent growth, suppressed S-phase entry, and inhibited cell migration and invasion in multiple in vitro EAC models (p<0.05). A gene ontological analysis revealed that HNF1A-AS1 knockdown preferentially affected genes that are linked to assembly of chromatin and the nucleosome, a mechanism essential to cell cycle progression. The well-known cancer-related lncRNA, H19, was the gene most markedly inhibited by HNF1A-AS1 knockdown. Consistent to this finding, there was a significant positive correlation between HNF1A-AS1 and H19 expression in primary EACs (p<0.01).

overall_design: In order to identify novel oncogenic lncRNAs in esophageal adenocarcinogenesis, we carried out RNA-seq of a matched NE-BE-EAC tissue pair

first: Xue

last: Yang

first: Yuriko

last: Mori

first: Stephen

last: Meltzer


title: Identification of genes involved in aromatic amino acid metabolism

status: Public on Sep 09 2015

city: West lafayette

first: Natalia

last: Dudareva

state: IN

address: 175 S.University Street

department: Biochemistry

institute: Purdue University

summary: To accurately detect and quantify low abundant transcripts no represented in current EST databases we generated an RNA-seq dataset based on RNA isolated from Petunia hybrida corolla tissue harvested at 8 PM at two developmental stages, day -1 (bud) and day 2 postanthesis (the tissues containing the lowest and highest levels of phenylalanine, respectively).

overall_design: Total RNA samples were obtained from corollas of at least eight wild-type petunia flowers per biological replicate at the two developmental stages using an RNeasy plant mini kit from Qiagen.

first: Jyothi

last: Thimmapuram


title: Airway epithelial gene expression in asthma versus healthy controls

status: Public on Apr 01 2015

city: San Francisco

first: Stephanie

last: Christenson

state: California

address: 513 PARNASSUS AVENUE, HSE1305

department: Pulmonary and Critical Care

institute: University of California, San Francisco

summary: Airway epithelial brushings were obtained for microarray analysis by research bronchoscopy in 62 subjects with mild-to-moderate asthma not on inhaled steroids and 43 healthy controls. Asthma subjects were stratified into 2 subgroups, Th2 high and Th2 low asthma, based on their expression of a three-gene signature of Type 2 inflammation: POSTN, SERPINB2, and CLCA1.

overall_design: Gene expression comparisons were made between: 1. asthmatics and healthy controls, and 2. Th2 high asthma and Th2 Low asthma/Healthy controls. The gene expression alterations most associated with asthma were then used in gene set enrichment analyses and gene signature development to compare this asthma dataset to COPD gene expression datasets.

first: Joseph

last: Arron

first: Katrina

last: Steiling

first: Maarten

last: van den Berge

first: Kahkeshan

last: Hijazi

first: Pieter

last: Hiemstra

first: Dirkje

last: Postma

first: Marc

last: Lenburg

first: Avrum

last: Spira

first: Prescott

middle: G

last: Woodruff


title: RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli

status: Public on Oct 10 2015

city: Dublin

first: David

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms.

overall_design: Whole-transcriptome analysis of M. bovis- and non-infected alveolar macrophages from ten calves (n = 10) at 2, 6, 24 and 48 hours (h) post-infection using RNA-sequencing (RNA-seq).

first: Nicolas

last: Nalpas

last: Magee

first: Kevin

middle: M

last: Conlon

first: John

last: Browne

first: Claire

last: Healy

first: Kirsten

last: McLoughlin

first: Kévin

last: Rue-Albrecht

first: Paul

last: McGettigan

first: Kate

last: Killick

first: Eamonn

last: Gormley

middle: V

last: Gordon


title: A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD

status: Public on Aug 11 2014

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool


title: Interphase condensins regulate ligand-depedent enhancer activation

status: Public on Jul 15 2015

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD


title: Expression data (micro-array, frozen tumors) from various sarcomas

first: Frédéric

last: Chibon

first: Tom

last: Lesluyes

first: Gaëlle

last: Pérot


title: Interphase condensins regulate ligand-depedent enhancer activation (ChIP-seq)

summary: An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-β-estradiol-induced preferential recruitment to oestrogen receptor α (ER-α)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α distinct from classic cofactors. Condensins prove to positively regulate ligand-dependent gene and eRNA transcription by modulating a binding equilibrium of enhancer-associated coactivators/corepressors, including p300 and RIP140. This activity was achieved by the condensin-dependent recruitment of an E3 ubiquitin ligase, HECTD1, to active enhancers, where it polyubiquitinates and dismisses corepressor RIP140 to stimulate eRNA transcription. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating enhancer activation, providing new insights into enhancer function in the regulated transcriptional programs

overall_design: The ChIP-seqs in this study measure the binding landscapes of condensin subunits, master transcription regulator of estrogen signaling - ERα, histone marks including H3K27ac and transcription coactivators such as p300  in MCF7 cells. The details of each dataset was indicated in each file.

first: Wenbo

last: Li

first: M

last: Rosenfeld


title: Gene expression in response to AGL15 during somatic embryogenesis

status: Public on Sep 18 2009

city: Lexington

first: Sharyn

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

summary:
Transcript accumulation was measured using the Affymetrix Arabidopsis ATH1 Genome Array [ATH1-121501] to document changes in response to the MADS-domain transcription factor AGAMOUS-Like 15 during somatic embryogenesis.

A somatic embryo system was used where mature seed is allowed to complete germination in liquid MS media containing 2,4-D and seedlings produce somatic embryos from the shoot apical meristem (SAM) region. The frequency with which these embryos are produced directly correlates with AGL15 accumulation.

overall_design: Wild type Arabidopsis (Columbia ecotype) with normal amounts of AGL15 were compared to (1) 35S:AGL15 that constitutively expresses AGL15 and produces more somatic embryos from the shoot apical region than wild type and (2) agl15 agl18 double loss-of-function mutants that produce less somatic embryos from the shoot apical region than wild type.

first: Y

last: Zheng

first: S


title: Genome-Wide Binding Sites of the MADS-domain protein AGAMOUS-Like 15 (AGL15) in Arabidopsis

type: Genome binding/occupancy profiling by genome tiling array

summary:
The MADS domain transcriptional regulator AGAMOUS-Like 15 promotes somatic embryogenesis by binding DNA and controlling downstream gene expression. Chromatin immunoprecipitation (ChIP) has been used to identify DNA fragments with which AGL15 is associated in vivo and a low-throughput approach to identify these fragments and determine regulatory consequences has revealed a role for AGL15 in GA catabolism that is relevant to embryogenesis. However, to understand more globally the gene networks in which AGL15 is involved, higher throughput methods to identify direct and indirect targets are needed.

Here we report mapping of AGL15 in vivo binding sites using a ChIP-chip approach with Affymetrix tiling arrays for Arabidopsis and find that ~2000 sites represented in three biological replicates of the experiment are annotated to nearby genes.

overall_design: Three independent biological replicates of the ChIP experiment using anti-AGL15 specific antiserum (I) or preimmune (PI) serum as a control were performed.


title: Expression data of human CD4 T cells with chronic or acute simian immunodeficiency virus (SIV) infection

status: Public on Aug 27 2014

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary:
We compared gene expression profiles of a human CD4+ T-cell line 24 h after infection with a cell line of the same origin permanently releasing SIVmac251/32H. A new knowledge-based-network approach (Inter-Chain-Finder) was used to identify subnetworks leading to resistance to SIV-induced cell death. Notably, the method can identify not only differentially-expressed key hub genes but also non-differentially expressed, critical, ‘hidden’ regulators.
6 out of the 13 predicted major hidden key regulators were among the landscape of proteins known to interact with HIV. Several subnetworks were dysregulated upon chronic infection with SIV. Most prominently, factors engaged in early stages of viral infection were affected, e.g. entry,   integration and provirus transcription or cellular responses like apoptosis and proliferation.

overall_design: Human CD4 T cells with different types of SIV infection were used for RNA extraction and hybridization on Affymetrix HG_U133A  microarrays.  Our aim is to identify subnetworks in T cells leading to resistance to SIV-induced cell death. To the end, we compared acute infection with chronic infection and mock control infection. Each pair (including three types of infection) was done in duplicate.

last: He

first: Ulrike

last: Sauermann

first: Christiane

last: Beer

first: Silke

last: Winkelmann

first: Zheng

last: Yu

first: Sieghart

last: Sopper

first: An-Ping

last: Zeng

first: Manfred

last: Wirth


title: Integrative Molecular Profiling in Leiomyosarcoma

status: Public on Nov 12 2009

first: Andrew

last: Beck

state: CA

address: Stanford

type:
Expression profiling by array
Genome variation profiling by array

summary:
Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We employed integrative molecular profiling to discover and characterize molecular subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering demonstrated 3 reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and demonstrated that the molecular subtypes defined by gene-expression showed distinct genomic changes. Tumors from the "muscle-enriched" cluster showed significantly increased copy number changes (p=0.04). Most muscle-enriched cases showed loss at 16q24 which contains FANCA, known to play an important role in DNA repair, and loss at 1p36 which contains PRDM16, whose loss promotes muscle differentiation. Immunohistochemistry was performed on LMS tissue microarrays (n= 377) for five markers with high levels of mRNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP,CFL2, MYLK) and demonstrated significantly correlated expression of the 5 proteins (all pairwise p < 0.005).  Expression of the 5 markers was associated with improved disease-specific survival (DSS) in a multivariate Cox regression analysis (p < 0.04).  In this analysis that combined gene expression profiling, aCGH and immunohistochemistry, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers. This set contains microarray slides from expression studies.

VARIABLES:
Phenotype: Tumour morphology
Age: age at the time of the primary lesion diagnosis (*:Age of diagnosis at the time of tumor resection)
Individual
Compound Based Treatment: Patient received treatment (CT: exposure to chemotherapy, RT: exposure to radiation therapy)
Organism Part: Primary tumour site (UT: uterine origin, ST: soft tissue origin; **:clinically most likely anatomic origin of the tumor)
Disease State: Tumour status (P: primary tumor, M: metastatic tumor, LR: local recurrence, N/A: information not available.)
Sex/Mating type: M(ale)/F(emale)
Experiment type: aCGH or Expression type II

overall_design: A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.

first: Matt

last: Van De Rijn


title: trf4, trf5, and trf4-DADA mutant cells gene expression; Trf4p X-RIP-Chip

status: Public on Jul 15 2009

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

type:
Expression profiling by array
Other

overall_design: Refer to individual Series


title: Interphase condensins regulate ligand-depedent enhancer activation (GRO-seq)

first: Qi

last: Ma

summary: An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-?-estradiol-induced preferential recruitment to oestrogen receptor ? (ER-?)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-? distinct from classic cofactors. Condensins prove to positively regulate ligand-dependent gene and eRNA transcription by modulating a binding equilibrium of enhancer-associated coactivators/corepressors, including p300 and RIP140. This activity was achieved by the condensin-dependent recruitment of an E3 ubiquitin ligase, HECTD1, to active enhancers, where it polyubiquitinates and dismisses corepressor RIP140 to stimulate eRNA transcription. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating enhancer activation, providing new insights into enhancer function in the regulated transcriptional programs

overall_design: The GRO-seq measures the trancription of nascent RNAs in the genome. From MCF7 cells treated with veichle or estrodial, we could identify estrogen-regulated eRNAs and subsequently could study their functions.


title: Intrasite and Intersite expression analysis of Mytilus californianus

status: Public on Dec 25 2011

first: Sean

middle: P

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

summary:
Transcriptional analysis of the effects of natural environmental variation across the vertical distribution of Mytilus californianus within a single mussel bed

Keywords: Environmental Response

overall_design: 30 Biological replicates from plots sampled at 3 different verticle tide heights above the MLLW at Strawberry Hill Oregon. 15 mussels were sampled after a mid-day emmersion event and 15 mussels were sampled after a 1 hour recovery at ambient seawater temperatures. 1 replicate per array, compared using a common reference sample. 50 Biological replicates for 5 plots sampled at 2 different verticle tide heights above the MLLW at Boiler Bay Oregon. 25 mussels were sampled after a mid-day emmersion event and 25 mussels were sampled after a 1 hour recovery at ambient seawater temperatures. Pooled RNA from 5 biological replicates from each plot per array, compared using a common reference sample.

first: Gretchen

last: Hofmann


title: Global identification of targets of the Arabidopsis MADS-domain protein AGAMOUS-Like 15

first: Sharyn

last: Perry