title: Imprinted survival genes preclude loss of heterozygosity of chromosome 7 in cancer cells

status: Public on Jan 01 2019

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

summary: Oncocytic variants of follicular thyroid carcinomas show a near-homozygous genome. Remarkably, homozygosity of chromosome 7 has never been observed which suggests that retention of heterozygosity is essential for cells. We hypothesized that cell survival genes are genetically imprinted on either of two copies of chromosome 7 which thwarts loss of heterozygosity at this chromosome in cancer cells.  We identified 6 genes on chromosome 7 which demonstrated allele-specific expression. Subsequent knockdown of gene expression showed that CALCR, COPG2, GRB10, KLF14, MEST and PEG10 were essential for cancer cell survival resulting in reduced cell proliferation, G1-phase arrest and increased apoptosis. We propose that imprinted cell survival genes provide a genetic basis for retention of chromosome 7 heterozygosity in cancer cells.

overall_design: 7 thyroid carcinoma samples with stable genomic profiles, 7 thyroid carcinomas with near homozygous genomes and 2 adrenal cortical carcinoma samples with near homozygous genomes. Sample selection was based on previous results; sample ID's used here are identical to those used in the previous study (Corver et al., Genes Chromosomes.Cancer, 2014).

first: Tom

last: van Wezel


title: ULMC Plasma and serum exRNA from healthy donors at University of Michigan

status: Public on Oct 27 2018

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Place

department: Computational Medicine and Bioinformatics

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: The potential for extracellular RNA as a potential biomarker for human health and disease is well-established. This study explores how extracellular RNAs vary among healthy individuals and across different sample treatments.

overall_design:
Blood was collected from 8 healthy donors ( 4 male, 4 female ). Plasma was separated for all 8 donors, with matching sera processed from 3. Total extracellular RNA was isolated and treated +/- Tewari PNKQ protocol. Libraries were prepared for each sample in triplicate. Two pooled libaries were generated for 1. Donors with plasma only and 2. Donors with matching plasma and serum. Pooled libraries were sequened on different lanes on the same machine in the same run. Each library was sequenced in three lanes.
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."

first: Ryan

last: Spengler

first: Maria

last: Giraldez


title: Identifying novel small RNA biomarkers unique to patients with gastric cancer

city: Los Angeles

first: David

last: Wong

state: CA

address: 10833 Le Conte, CHS - Box 951668

institute: UCLA

summary: Extracellular RNA (exRNA) is an emerging paradigm as endocrine signals in cellular communication, biomarker development, therapeutic applications and systemic physiology. This project is to test the hypothesis that salivary extracellular RNA (exRNA) can be developed for the clinical detection of human diseases. Our laboratory first reported the existence of a transcriptome and microRNA profile in cell free saliva followed by its scientific characterizations and clinical utilities including biomarker development for molecular oncology applications. Most recently we have performed RNA-sequencing in cell free saliva and reported three major types of RNA in saliva (mRNA, miRNA and snoRNA). This study is to test the hypothesis that salivary exRNA can be developed to detect gastric cancer by performing a biomarker development study to definitively validate salivary exRNA biomarkers for the detection of gastric cancer.

overall_design:
198 total samples from 198 donors were analyzed. The study contains 100 non-gastric cancer controls and 98 gastric cancer patients with no replicates. All samples are saliva.
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."

first: Feng

last: Li


title: DNA methylation profiling of vascular maturation

status: Public on May 11 2018

city: Heidelberg

first: Hellmut

middle: G

last: Augustin

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ Heidelberg

type: Methylation profiling by high throughput sequencing

summary: Endothelial cells line the inside of all blood vessels forming a single layer of quiescent, non-proliferating cells. While the mechanisms of sprouting angiogenesis, network formation and vascular remodelling are molecularly unravelled in increasing detail, the molecular mechanisms of vascular maturation are still poorly understood. We performed whole-genome bisulfite sequencing on endothelial cells isolated from infant and adult mice to establish the epigenetic landscape of vascular maturation.

overall_design: Tagmentation-based Whole-Genome Bisulfite Sequencing of infant and young adult lung endothelial cells. Three independent biological replicates each were analyzed.

first: Katharina

last: Schlereth

first: Dieter

last: Weichenhan

first: Tobias

last: Bauer

first: Roland

last: Eils

first: Christoph

last: Plass


title: Expression profiling of infant and young adult lung endothelial cells by RNA-sequencing.

summary: Endothelial cells line the inside of all blood vessels forming a single layer of quiescent, non-proliferating cells. While the mechanisms of sprouting angiogenesis, network formation and vascular remodelling are molecularly unravelled in increasing detail, the molecular mechanisms of vascular maturation are still poorly understood. We performed comparative transcriptomic analysis of endothelial cells isolated from infant and adult mice to examine the regulation of angiogenic molecules.

overall_design: Total RNA-sequencing of infant and young adult lung endothelial cells. Three independent biological replicates each were analysed.

first: Chrisopher

last: Previti


title: Ex-vivo Human Hematopoietic Stem Cell Expansion Requires Coordination of Cellular Reprogramming with Mitochondrial Remodeling and P53 Activation

status: Public on Oct 10 2018

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: Profiles of Extracellular RNA in Cerebrospinal Fluid and Plasma from Subarachnoid Hemorrhage Patients

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. Fifth Street

institute: The Translational Genomics Research Institute

summary: Brain injury resulting from hemorrhagic stroke is clinically challenging to manage and results in high rates of morbidity and mortality. The pathophysiology of brain damage resulting from aneurysmal subarachnoid hemorrhage (aSAH) is largely unknown, and methods to treat and monitor patients are variable with no meaningful correlations to patient outcome. Prediction of patient risk for serious neurological complications is currently a significant clinical obstacle. An extracellular RNA (exRNA) biomarker to predict onset and severity of brain damage would improve patient outcomes. We sequenced plasma and CSF samples from adult patients with SAH. Samples were collected from post bleed day 1 to day 7. Total exRNA was isolated from each sample. In addition, we prepared a subset of 140 CSF samples, isolating the RNA contained within extracellular vesicles and vesicle-depleted biofluid.

overall_design:
523 total samples from 30 donors were analyzed. All patients suffered subarachnoid hemorrhages (no controls). Samples are either plasma or CSF.
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."

first: Matthew

last: Huentelman

first: P

middle: D

last: Adelson

first: Yashar

last: Kalani


title: AGO2 Plasma exRNA Profiles

status: Public on Dec 22 2018

summary: The Michael J. Fox Foundation (MJFF) collected AGO2 exRNA samples for distribution to interested individuals.

overall_design:
AGO2 small RNA-Seq profiles were isolated using anti-AGO2 immunoprecipitation from plasma from healthy human controls.
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.


title: Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health

city: Boston

first: Saumya

last: Das

state: MA

address: 185 Cambridge Street Suite 3201

department: Cardiovascular Research Center

institute: Massachusetts General Hospital

summary: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry. We found changes in miRNAs and other ex-RNAs with exercise (e.g., y-RNAs, t-RNAs) implicated in cardiovascular disease. In two independent cohorts of acute maximal exercise, we identified miR-181b-5p as a key ex-RNA increased in plasma after exercise, with validation in a separate cohort. In a mouse model of acute exercise, we found significant increases in miR-181b-5p expression in skeletal muscle after acute exercise in young (but not older) mice. Previous work revealed a strong role for miR-181b-5p in vascular inflammation in obesity, insulin resistance, sepsis, and cardiovascular disease. Circulating ex-RNAs altered in plasma after acute exercise target pathways involved in inflammation, including miR-181b-5p. Further investigation into the role of known (e.g., miRNA) and novel (e.g., y-RNAs) is warranted to uncover new mechanisms of vascular inflammation on exercise-mediated benefits on health.

overall_design:
Plasma from samples; collected at baseline and peak exercise
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."


title: A class of GATA3 mutation reprograms the breast cancer transcriptional network through gain and loss of function

status: Public on Oct 16 2017

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A pioneer transcription factor, GATA3, is one of the most frequently mutated genes in breast cancer, yet the impact of these mutations is largely unknown. We generated a GATA3 mutant cell line (T47D wt/R330fs) by CRISPR. Mutation of one allele of GATA3 led to loss of binding and decreased expression at a subset of genes, including Progesterone Receptor.  At other loci, associated with epithelial to mesenchymal transition, gain of binding at a novel sequence motif correlated with increased gene expression. Our results illuminate tumor-promoting functions of specific GATA3 mutations in breast cancer.

overall_design: Genome-wide mapping of chromatin localization of luminal transcription factors in GATA3 mutant cells

first: Motoki

last: Takaku

first: Sara

last: Grimm

first: Wade

last: Paul


title: Identifying novel small RNA biomarkers for electrical and mechanical remodeling post-MI (myocardial infarction)

summary: To identify novel small RNA biomarkers for electrical and mechanical remodeling post-MI

overall_design:
extracellular sRNA protocol optimization and biomarker discovery
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."

first: Kirsty

last: Danielson

first: Yaoyu

last: Wang

first: Ravi

last: Shah


title: Transcriptome profile of rat adrenal evoked by gonadectomy and testosterone or estradiol replacement

status: Public on Jan 18 2017

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Sex differences in rat adrenal cortex are manifested as larger adrenal volume of cortex and higher corticosterone secretion by females compared with males. The molecular bases of these sex related differences are poorly understood.
Therefore we performed microarray studies to demonstrate the effect of testosterone and estradiol on the expression of differentially regulated genes in rat adrenal gland.

overall_design: Experiment was performed on adult male and female Wistar rats (12-week-old; body weight: 120-150 g). Rats were gonadectomized or sham operated. Orchiectomy (ORX) was performed via scrotal access while ovariectomy (OVX) by two dorso-lateral incisions. Fourteen days after surgery half of ORX rats was replaced with testosterone (s.c. injection of Testoviron-Depot, Schering AG, Berlin, 5 mg/100 g body weight) while half of OVX animals with estradiol (s.c. injection of Estradiol-Depot, Jenapharm, 0.5 mg/100 g body weight). After 2 weeks (4 weeks post surgery) rats were decapitated. Adrenal glands were collected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Karol

last: Jopek

first: Piotr

last: Celichowski

first: Marta

last: Szyszka

first: Marianna

last: Tyczewska

first: Paulina

last: Milecka

first: Ludwik

middle: K

last: Malendowicz


title: Chromatin structure and CTCF across the MCF10 breast cancer progression series (ChIP-Seq)

status: Public on May 23 2017

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Transcription and processing of histone mRNAs occurs at subnuclear domains known as Histone Locus Bodies (HLBs). Although it is known that higher-order chromatin organization is dysregulated in cancer, structural alterations within HLB across breast cancer progression are unclear. Differential expression across known as MCF10, a basal triple negative breast cancer progression model, followed by pathway analysis demonstrated many alterations in signaling cascades known to be related to proliferation. Positional gene enrichment identified the hist1 gene locus at chromosome 6p22 as the most significantly altered cluster of genes from the normal-like MCF10A to premalignant MCF10AT1. The malignant MCF10CA1a had a more varied expression pattern across the hist1 locus. Within this region there are three subclusters of hist1 genes which were generally upregulated while intervening genes were more frequently downregulated. Extending these findings to TCGA breast tumors revealed that normal adjacent tissue had lower expression within the subclusters than their matched tumor samples. Moreover, the expression pattern within the hist1 locus comparing normal versus tumors recapitulated a very similar pattern to that comparing 10A to AT1 or CA1a. Since the hist1 locus is transcribed and processed at a specific subnuclear microenvironment, the higher order chromatin organization of this locus may be a critical component of its regulation. We addressed whether CTCF, a key chromatin organizing protein, may play a role in organizing the hist1 HLB. Immunofluorescence for CTCF along with NPAT, a protein which decorates this locus, identified that CTCF may tether the hist1 HLB to the nuclear matrix. All three subclusters reside within a single topologically associating domain wherein interacting loops are bound by CTCF. Inter-subcluster interactions are lost in the premalignant AT1. Consistent with the varied expression across the hist1 HLB in CA1a, inter-subcluster interactions are regained in the malignant state. These data suggest a transient state in highly proliferative breast cancer cells in which the hist1 HLB is dynamically reorganized.

overall_design: CTCF ChIP-Seq

first: Andrew

last: Fritz

first: Joseph

last: Boyd

first: Coralee

last: Tye

first: Jane

last: Lian

first: Gary

last: Stein


title: Transcriptional and ribosome profiling of Drosophila 3rd instar larvae muscle

status: Public on Nov 06 2017

first: Dion

last: Dickman

state: California

address: 3641 Watt Way, HNB 309

department: Neurobiology

institute: University of Southern California

summary: Presynaptic efficacy can be modulated by retrograde control mechanisms, but the nature of these complex signaling systems remain obscure. Some studies have suggested that retrograde synaptic communication requires new protein synthesis in the postsynaptic compartment, yet the putative translational targets that mediate this signaling are enigmatic. To gain insight into the retrograde mechanisms that stabilize synaptic transmission at the neuromuscular junction, we have developed and optimized a tissue-specific ribosome profiling approach in Drosophila. We first demonstrate the ability of this technology to define genome-wide translational regulations that could not be inferred from transcription, and validate the superior sensitivity of ribosome profiling over conventional translational profiling. We then leverage this technology to test the relative contributions of transcriptional, translational, and post-translational mechanisms in the postsynaptic muscle that orchestrate the retrograde control of presynaptic function. Surprisingly, we find no changes in transcription or translation are necessary to enable retrograde homeostatic signaling. Rather, post-translational mechanisms appear to ultimately gate instructive retrograde communication. Finally, we find that a global increase in translation induces adaptive responses in both transcription and translation of protein chaperones and degradation factors to promote cellular proteostasis. Together, this demonstrates the power of ribosome profiling to define transcriptional, translational, and post-translational mechanisms driving retrograde signaling during adaptive plasticity.

overall_design: Transcriptional (RNA-seq of total RNA) and ribosome profiling were performed in Drosophila muscle tissue. Three genotypes were analyzed: wild type (control sample), GluRIIA mutant and Tor muscle overexpression. In addition, translating ribosome affinity purification (TRAP) based translational profiling was done in wild type sample to assay the difference between ribosome profiling and TRAP translational profiling. Three replicates were performed for each analysis.

first: Xun

last: Chen


title: Ex-vivo Human Hematopoietic Stem Cell Expansion Requires Coordination of Cellular Reprogramming with Mitochondrial Remodeling and P53 Activation [bulk]

first: Yongchao

last: Ge

summary: Ex-vivo culture conditions used to expand the numbers of hematopoietic stem cells (HSCs) present within an umbilical cord blood (UCB) unit create cellular stresses leading to loss or at best maintenance of the primitive HSCs. Recently, we have shown that treatment with a histone deacetylase inhibitor, valproic acid (VPA), increases substantially the numbers of transplantable HSCs from UCB-CD34+ cells. In this report, we demonstrate that VPA treatment orchestrates cellular mechanisms that drive UCB-CD34+ cells into a primitive state in which they acquire and retain phenotypic, transcriptomic and primitive mitochondrial profiles, all of which characterize long-term HSCs. Remarkably, our data link the acquisition of the HSC phenotype to the remodeling of the mitochondrial network and p53 activation and establish both as critical regulators of ROS and therefore of HSC fate. VPA treatment leads to restructured mitochondria with reduced mass, membrane potential and ROS levels. p53 activity is critical for the activation of antioxidant defense mechanisms, which rely on magnesium superoxide dismutase (MnSOD) activity. Failure to activate the p53-MnSOD axis compromises both the acquisition and the maintenance of the HSC phenotype. These studies indicate that suppression of ROS through the coordination of p53 activity and mitochondrial remodeling determines the fate of ex-vivo expanded human HSCs

overall_design: Examination of transcriptome of Cord blood isolated CD34+ culture in stemline media + cytokine or stemline media + cytokine + Valproic acid at 2 different days of culture.

first: Luena

last: Papa

first: Mansour

last: Djedaini

first: Stuart

last: Sealfon

first: Ronald

last: Hoffman


title: EIN2 mediates histone H3K14 and non-canonical histone H3K23 acetylation in the nucleus in ethylene response [RNA-seq]

status: Public on Oct 05 2016

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: We report that ENAP1 interacts with EIN3CEND and histone H3, and enhances histone acetylation. We examined the gene expression in ENAP1ox lines, compared with that in COL lines.

overall_design: Whole seedling mRNA profiles of 3-day old wild type (COL) and ENAP1ox (in COL background) were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

first: Fan

last: Zhang

first: Likai

last: Wang


title: EIN2 mediates histone H3K14 and non-canonical histone H3K23 acetylation in the nucleus in ethylene response [ChIP-seq]

summary: We report that ethylene specifically elevated acetylation of histone H3 at K14 and the non-canonical acetylation of histone H3 at K23. We perform Chip-sequencing of H3K14Ac, H3K23Ac and H3K9Ac using chromatins isolated from 3-day old etiolated Col-0 seedlings treated with ethylene or air gas. Results show that ethylene specifically elevates H3K14Ac and non-canonical H3K23Ac in EIN3 targeted genes that are regulated at the transcriptional level by ethylene.

overall_design: Examination of 3 different histone modifications in 2 Arabidopsis lines which under 2 different treatment.


title: EIN2 mediates histone H3K14 and non-canonical histone H3K23 acetylation in the nucleus in ethylene response

status: Public on Oct 04 2016


title: RNA Sequencing of CSF Samples from Patients with Intraventricular Hemorrhage and Neural Tube Defects

first: Kendall

last: Van Keuren-Jensen

summary: Intraventricular hemorrhage (IVH) is a significant complication of premature infants. With improved preterm infant survival, there is increased incidence of severe IVH, and the potential for lifelong neurodevelopmental deficits. Neurological complications are high in babies that develop hydrocephalus as a result of IVH and require a permanent ventriculoperitoneal (VP) shunt. Spina bifida is a congenital disorder caused by the incomplete closure of the neural tube.  Hydrocephalus is also a common complication of spina bifida, presenting in 15 to 25% of cases. Often, when spina bifida is identified and surgically repaired, CSF shunting mechanisms are placed in a high percentage of cases.  A better understanding of the events leading to the development of hydrocephalus will help clinicians make more informed decisions about the need for CSF shunting and other interventions. Extracellular RNAs (exRNAs) may be indicators of the multiple pathological events surrounding the development of hydrocephalus in subjects with intraventricular hemorrhage or spina bifida. exRNAs may also be indicators for the presence and magnitude of neurodevelopmental outcomes. Under that premise, we sequenced the total exRNA in CSF from children that had IVH or spina bifida, some of which developed hydrocephalus and/or had reported developmental delays.

overall_design:
CSF collected from 35 IVH patients, no controls, some samples collected on multiple days
--------------------------------
Submitter states "We are currently working on submitting the data for these protected datasets to dbGaP, but wanted to submit the processed data to GEO in the mean time."

first: Yashar

last: Kalani

first: Matthew

last: Huentelman

first: P

last: Adelson


title: Prognostic classifier based on genome-wide DNA methylation profiling in well differentiated thyroid tumors

status: Public on Oct 20 2017

city: Vejle

first: Mariana

last: Bisarro dos Reis

address: Kabbeltoft 25

country: Denmark

institute: Vejle Hospital

type: Methylation profiling by genome tiling array

summary: Methylome analysis of different histological thyroid lesions and clinical features, aiming to better understand the DNA methylation deregulation of TC and to identify a prognostic epigenetic signature in well differentiated thyroid carcinomas.

overall_design: Whole DNA methylation profile was evaluated in 50 non-neoplastic adjacent tissues, 17 benign lesions, 60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated and 3 anaplastic carcinomas. The prognostic classifier was developed and applied in a cross-study validation using a external database (TCGA).

middle: B

last: dos Reis

first: Mateus

middle: C

last: Barros-Filho

first: Fabio

last: Marchi

first: Caroline

middle: M

last: Beltrami

first: Hellen

last: Kuasne

first: Clóvia

last: Pinto

first: Srikant

last: Ambatipudi

first: Zdenk

last: Herceg

first: Luiz

middle: P

last: Kowalski

first: Silvia

middle: R

last: Rogatto


title: Mouse transcriptomics reveals extracellular matrix organization as a major pathway involved in inflammatory and neuropathic pain

status: Public on Apr 04 2019

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

country: Canada

institute: McGill University

summary: Chronic pain is a debilitating and poorly-treated condition. The mechanisms underlying the development of chronic pain are not well understood. Nerve injury and inflammation cause alterations in gene expression in tissues associated with transmission of pain, supporting molecular and cellular mechanisms that maintain painful states. Previous studies in animal models and human patients suffering from different chronic pain conditions have examined changes in transcriptome associated with chronic pain. However, in most studies, the analyses were restricted to a single tissue or pain condition. In the current study, we performed next-generation sequencing of dorsal root ganglia, spinal cord, brain and blood in mouse models of nerve injury and inflammation-induced chronic pain. Comparative analyses of differentially expressed genes (DEG) across these tissues in two pain models identified the extracellular matrix organization (ECMO) pathway as the most commonly affected pathway. Interestingly, examination of GWAS datasets revealed an over-representation of DEGs within the ECMO pathway in SNPs most strongly associated with human back pain. Remarkably, manipulation of the extracellular matrix in the mouse significantly affected the development of pain hypersensitivity following nerve injury, supporting our gene expression findings. In summary, our comprehensive analysis of transcriptional landscape across different mouse pain models and tissues as well as human GWAS datasets identified extracellular matrix organization as a central molecular pathway in the development of chronic pain.

overall_design: Complete Freund's Adjuvant (CFA) and Spared Nerve Injury (SNI) were performed on mice. CFA is surrogate for inflammation pain, while SNI for neuropathic pain. Untreated mice were used as controls. Mice tissues were collected. Transcriptomes were compared, in a tissue-based and pain-related manner.

first: Alexander

last: Samoshkin

first: Shannon

middle: N

last: Tansley

first: Marjo

middle: H

last: Piltonen

first: Loren

last: Martin

first: Jeffrey

middle: S

last: Mogil

first: Arkady

last: Khoutorsky

first: Luda

last: Diatchenko


title: DNA methylation adds prognostic value to minimal residual disease status in pediatric T-cell acute lymphoblastic leukemia

status: Public on Mar 30 2016

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

summary:
Background: Despite increased knowledge about genetic aberrations in pediatric T-cell acute lymphoblastic leukemia (T-ALL), no clinically feasible treatment-stratifying marker exists at diagnosis. Instead patients are enrolled in intensive induction therapies with substantial side effects. In modern protocols, therapy response is monitored by minimal residual disease (MRD) analysis, and used for post-induction risk group stratification. DNA methylation profiling is a candidate for subtype discrimination at diagnosis and we investigated its role as a prognostic marker in pediatric T-ALL.
Procedure: Sixty-five diagnostic T-ALL samples from Nordic pediatric patients treated according to the NOPHO-ALL2008 protocol were analyzed by HumMeth450K genome wide DNA methylation arrays. Methylation status was analyzed in relation to clinical data and early T-cell precursor (ETP) phenotype.
Results: Two distinct CpG Island Methylator Phenotype (CIMP) groups were identified.  Patients with a CIMP negative profile had an inferior response to treatment compared to CIMP positive patients (3-year cumulative incidence of relapse (CIR3y) rate: 29% vs. 6%, p=0.01).  Most importantly, CIMP classification at diagnosis allowed subgrouping of high risk T-ALL patients (MRD ≥0.1% at day 29) into two groups with significant differences in outcome (CIR3y rates:  CIMP negative 50% vs CIMP positive 12%; p=0.02). These groups did not differ regarding ETP-phenotype, but the CIMP negative group was younger (p=0.02) and had higher white blood cell count at diagnosis (p=0.004) compared with the CIMP positive group.
Conclusions: CIMP classification at diagnosis in combination with MRD during induction therapy is a strong candidate for further risk classification and could confer important information in treatment decision-making.

overall_design: Bisulphite converted DNA from T-ALL samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Magnus

last: Borssén

first: Zahra

last: Haider

first: Mattias

last: Landfors

first: Ulrika

last: Nyström

first: Kjeld

last: Schmiegelow

first: Ann

middle: E

last: Åsberg

first: Jukka

last: Kanerva

first: Hans

middle: O

last: Madsen

first: Hanne

last: Marquart

first: Mats

last: Heyman

last: Hultdin

first: Göran

last: Roos

first: Erik

last: Forestier


title: GATA3-mediated chromatin reprogramming in breast cancer cells

status: Public on Jan 27 2016

first: Paul

last: Wade

summary: Pioneer transcription factors bind to silent chromatin, and initiate cell fate conversion. One potential pioneer factor, GATA3, is a critical component for multiple cellular programs. GATA3 is of particular interest as it regulates gene expression in breast cancers, and low expression correlates with poor prognosis. Here we demonstrate the pioneering activity of GATA3 utilizing a cellular reprogramming system (the mesenchymal-epithelial transition) in breast cancer cells. During the epithelial transition, GATA3 catalyzes chromatin reprogramming by inducing chromatin opening, active enhancer modifications, and nucleosome remodelling. We determined that the transactivation domain is required for this chromatin reprogramming. Importantly, a mutant lacking the transactivation domain possessed the chromatin binding ability but failed to create open chromatin, suggesting binding alone is not sufficient to induce open chromatin. These data illustrate a fundamental mechanism of GATA3-mediated gene regulation, and provide evidence for a pre-engagement state of closed chromatin bound by a pioneer factor.

overall_design: Genome-wide mapping of chromatin state in GATA3-mediated mesenchymal-epithelial transition

first: Motoki

last: Takaku

first: Sara

last: Grimm

first: Shimbo

last: Takashi

first: Wade

last: Paul


title: Genome-wide maps of primary and processed start-sites of transcripts revealed mechanism controlling in vivo stoichiometry of protein complex in bacteria

status: Public on Apr 27 2015

city: Qingdao

first: Jian

last: Xu

state: Shandong

address: No.189 Songling Road, Laoshan District

country: China

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

summary: Here a differential mRNA-sequencing (dRNA-Seq) strategy was employed to distinguish transcriptional start-sites (TSs) and post-transcriptional processed sites (PSs) of transcripts in the cellulolytic mesophile Clostridium cellulolyticum.  PS-harboring genes usually  encode heteromultimeric complexes such as flagella, ribosomes, F-type ATPases, and cellulosomes. Intriguingly, PSs located in intergenic reigons (iPSs) were appear to be associated with a particular set of operons that expressed as a complex ratio, in which stem-loops were often  found at upstream and/or downstream of highly-expressed processed transcripts; among operons, the folding free energy (deltaG) of the stem-loops is negatively correlated with polarity in transcript level of the operon.

overall_design: mRNA profiles of C. cellulolyticum H10 grown under three carbon sources in two RNA treatments were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000

first: Chenggang


title: Gene expression profiling of Drosophila S2R+ cells following RNAi-mediated knockdown of transcription factors

status: Public on Sep 24 2016

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: In order to study the effect of transcription factor knockdown, we selectively depleted mRNA products from 483 different genes that are known or predicted to encode transcription factors. We treated Drosophila S2R+ tissue culture cells with double strand RNAs designed to be specific for these loci. Following RNAi treatment, we isolated poly A+ RNA from the cells, and performed stranded high-throughput RNA-Seq analyses to determine knockdown efficiency and propagating transcriptional consequences.

overall_design: We started with a curated list of transcription factors and related proteins compiled for production of a reagent library at the DRSC (http://www.flyrnai.org/supplement/TranscriptionFactorGenes.xls). We ranked genes on this list as follows - Rank 1: experimental evidence of TF activity and DNA binding, Rank 2: experimental evidence of TF activity and predicted DNA binding, Rank 3: predicted/unknown TF activity and experimental evidence of DNA binding, Rank 4: predicted/unknown TF activity and/or predicted DNA binding, Rank 5: experimental evidence of TF cofactor, Rank 6: predicted TF cofactor, Rank 7: chromatin regulation, Rank 8: little or indirect annotation, Rank 9: no evidence for any TF activity. We then excluded genes with a rank of 8 or 9. We additionally restricted the list to the subset of 483 genes with expression levels higher than signal from intergenic regions in an Drosophila S2R+ RNA-Seq study (Lee et al., 2014. PMID: 25262759). We generated a panel of double strand RNA (dsRNA) for knockdown reagents (Ramadan et al., 2007. PMID: 17853882). For 387 loci we used two different dsRNA reagents, which target different regions of the mRNAs. Only one dsRNA reagent was used for the remaining 96 loci. As a control for general effects of dsRNA treament, we used dsRNA against the E. coli LacZ gene as a sham. We performed RNAi treatments and library preparations in 96 well format, and we placed one LacZ control in each plate. On each plate, there were also wells that we used to estimate dsRNA uptake after depletion of Death-associated inhibitor of apoptosis 1 (Diap-1, or thread. Flybase ID:  FBgn0260635) and ensured that cells underwent cell death. RNA-Seq libraries from wells with such high proportions of dead cells were not informative and are not part of this submission. We performed all dsRNA treatments in biological duplicate. We performed RNA-sequencing on Illumina platform after polyA+ selection of mRNA. We prepared libraries in strand-specific manner, using the Uracil-DNA glycosylase method (Parkhomchuk et al., 2009. PMID: 19620212). RNA-Seq libraries were sequenced to generate single-end, 50 bp reads.

first: H

last: Lee

first: M

last: Buckner

first: Q

last: Gilly

first: Y

last: Hu

first: SE

last: Mohr

first: N

last: Perrimon

first: B


title: Gene expression signature that predicts early molecular response failure in chronic phase CML patients on frontline imatinib

status: Public on May 29 2019

city: Adelaide

first: Chung

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

summary: In chronic phase chronic myeloid leukemia (CP-CML) patients treated with frontline imatinib, failure to achieve early molecular response (EMR failure: BCR-ABL1 >10% (IS) at 3 months) is predictive of inferior outcomes. Identifying patients at high-risk of EMR failure at diagnosis provides an opportunity to intensify frontline therapy and potentially avoid EMR failure. We studied blood samples from 96 CP-CML patients at diagnosis and identified 365 genes that were aberrantly expressed in 13 patients who subsequently failed to achieve EMR, with a gene signature significantly enriched for stem cell phenotype (e.g. Myc, b-catenin, Hoxa9/Meis1), cell cycle, and reduced immune response pathways. We selected a 17-gene panel to predict EMR failure and validated this signature on an independent patient cohort. Patients classified as high-risk with our gene expression signature (HR-GES) exhibited significantly higher rates of EMR failure compared to low-risk (LR-GES) patients (78% vs 5%; p<0.0001) with an overall accuracy of 93%. Furthermore, HR-GES patients who received frontline nilotinib had a relatively low rate of EMR failure (10%). However HR-GES patients still had inferior deep molecular response achievement rate by 24 months compared to LR-GES patients. This novel multi-gene signature may be useful for selecting patients at high risk of EMR failure on standard therapy, who may benefit from trials of more potent kinase inhibitors or other experimental approaches.

overall_design: Total RNA obtained from isolated TIDEL-II PBMNCs CP-CML samples (n=96) at the time of diagnosis. All the samples were sent to AGRF for QC, and hybridisation. The raw data was obtained from AGRF for subsequent analysis. The comparison was performed between EMR failure (n=13) vs. EMR achieved (n=83) samples using limma analysis bioconductor package. The interactive gene expression plots can be assessed through shinyapps.io provided in the weblink.

first: David

middle: T

last: Yeung

first: Liu

last: Lu

first: Dale

last: Watkins

first: Tamara

last: Leclercq

first: Phuong

last: Dang

first: Verity

last: Saunders

first: John

last: Reynolds

first: Deborah

middle: L

last: White

first: Timothy

last: Hughes


title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2 [01_fibroblasts_patientAndcarrier]

status: Public on Sep 15 2014

first: Brent

last: Fogel

address: 710 Westwood Plaza

summary: Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4.

overall_design:
Total RNA samples obtained from 1) an AOA2 patient and carrier fibroblast cell lines, 2) 2 biological replicates of haploinsufficient SETX fibroblast cell lines transfected with one of 4 different wild-type and mutant SETX constructs, 3) peripheral blood from 33 patients and carriers across 12 families, and 4) 2 tissues from 2 Setx knockout and 2 control mice were analyzed using expression microarray.

This submission represents the microarray component of study.

first: Fuying

last: Gao

first: Olivier

middle: J

last: Becherel

first: Martin

middle: F

last: Lavin

first: Daniel

last: Geschwind

first: Giovanni

last: Coppola


title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2 [03_AOA2_patient_blood_2011]


title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2 [02_fibroblasts_transfected]


title: Transcriptional profiling of tumor-associated blood vessels in invasive bladder cancer

status: Public on Mar 08 2013

city: Zurich

first: Filip

last: Roudnicky

address: Langwiesstrasse 25

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology

summary:
Tumor-associated blood vessels differ from normal vessels at the morphological and molecular level. Proteins that are only present on tumor vessels may serve as biomarkers and as therapeutic targets for inhibition of angiogenesis in cancer. Comparing the transcriptional profiles of blood vascular endothelium from human invasive bladder cancer and from normal bladder tissue, we found several markers that could serve as novel biomarkers or therapeutic targets.
In this dataset, we include the expression data obtained from laser capture microdissected (LCM) vessels isolated from tumor and bladder normal tissue.

overall_design: 10 samples were analyzed. We compared expression of tumor associated blood vessels with expression of vessels in the normal bladder tissue using Genespring GX 12.

first: Cedric

last: Poyet

first: Michael

last: Detmar


title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2 [04_Cerebellun_and_brain]

institute: UCLA


title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: In vitro antiplasmodial activity of Dicoma anomala subsp. gerrardii (Asteraceae): identification of its main active constituent and gene expression profiling.

status: Public on Nov 01 2011

city: Brummeria

middle: van Wyk

last: Becker

state: Gauteng

address: Meiring Naude Road

department: Biosciences

country: South Africa

institute: Council for Scientific and industrial Research

summary:
To determine the transcriptional effects of a novel plant-based compound, dehydrobrachylaenolide, on P. falciparum, parasite cultures were treated with the compound over time. Samples were taken for analysis 2, 6, and 12 hours post-invasion of human red blood cells. Control cultures were treated simultaneously with DMSO, and samples isolated at 2, 6, and 12 hours for transcriptional analysis.
Background  Antimalarial drug resistance threatens to undermine efforts to eliminate this deadly disease. The resulting omnipresent requirement for drugs with novel modes of action prompted a national consortium initiative to discover new antiplasmodial agents from South African medicinal plants. One of the plants selected for investigation was Dicoma anomala subsp. gerrardii, based on its ethnomedicinal profile.     Methods  Standard phytochemical analysis techniques including solvent-solvent extraction, thin-layer and column chromatography, were used to isolate the main active constituent of Dicoma anomala subsp. gerrardii. The crystallised pure compound was identified using nuclear magnetic resonance spectroscopy, mass spectrometry and X-ray crystallography. The compound was tested in vitro on Plasmodium falciparum cultures using the parasite lactate dehydrogenase assay. The effects of treatment on the P. falciparum transcriptome were subsequently investigated by treating ring-stage parasites (alongside untreated controls) with the pure compound, followed by oligonucleotide microarray and data analysis.     Results  The main active constituent was identified as dehydrobrachylaenolide, a eudesmanolide-type sesquiterpene lactone. The compound demonstrated an in vitro IC50 of 245.6 nM, which was comparable to the IC50 of chloroquine, against a chloroquine-resistant strain (K1) of P. falciparum. Microarray data analysis identified a cluster of unique genes that were differentially expressed as a result of the treatment and gene ontology analysis identified various biological processes that were significantly affected. Comparison of the dehydrobrachylaenolide treatment transcriptional dataset with a published artesunate (also a sesquiterpene lactone) dataset revealed little overlap. This suggests differentiated modes of action between the two compounds.    Conclusions  Dehydrobrachylaenolide could play a valuable role as a drug candidate to generate new antimalarial compounds with novel modes of action and favourable ADMET properties.

overall_design: Reference design. Transcriptional analysis was performed as described in GSE18075 with the following modification. Profiles from parasite cultures isolated 2hrs after drug treatment during early ring-stage development were contrasted against untreated control cultures isolated at this timepoint. Profiles from parasites isolated 6 and 12 hours following drug treatment were contrasted to against untreated control cultures isolated at 6 hours. A detailed description of the statistical methodology used for this dataset is outlined in the accompanying manuscript.    A reference design was employed for array hybridisation, utilising the URR pool described previously in the NCBI GEO Series GSE18075 dataset. All solvent-control and drug-treated samples were hybridised to Operon slides, along with the URR. In contrast to the hybridisation protocol described in GSE18075, 40 pmoles of each dye was hybridised to each array, utilising Cy3 (sample) and Cy5 (reference) dyes from GE Healthcare (#RPN5661), specifically optimised for nucleic acid labelling. A total of nineteen slides were processed in the study. Two independent cDNA samples (biological replicates) were prepared for each untreated and drug-treated sample at each time point. One of the biological replicate cDNA samples were additionally hybridised to a third slide (representing the technical replicate). In the case of the 2 hour DMSO treated control culture, an additional technical microarray replicate was included for quality control purposes. GenePix results (gpr) files were generated using GenePix 6.0 (Molecular Devices) software, without normalization. For clustering analyses, results files were normalized with DNMAD (Diagnosis and Normalization for MicroArray Data) using print-tip loess. The normalized values were subsequently downloaded and analyzed with the Multiexperiment Viewer (MeV) in the TM4 software suite. Hierarchical Clustering (HCL, average linkage) was performed to estimate technical and biological variation between samples and at which point cytostasis most likely occurred for comparative purposes in downstream analyses. Intensity data for individual slides were imported into LIMMA (linear models for microarray data) in the R computing environment. Pre- and post-normalization diagnostic plots were performed using MARRAY. Data from each microarray slide was normalized using print-tip loess. Data between microarrays was normalized using R-Quantile normalisation. Pearson correlations were computed in MS Excel to estimate variation between technical and biological replicates. Spots excluded from slide correlations and normalisation were those weighted by the limma script or flagged in the genepix results file (gpr). Additionally, spots termed Alien, Empty, Null and Operon Use Only were excluded from the correlation analyses. These spots were similarly excluded for correlations between untreated and treated samples at each time point following normalisation. Results from biological and slide replicates within each of the time points were collated, and linear models were computed to contrast gene expression between time points. A two-fold change in gene expression was used as cut-off, in conjunction with correction for false discovery (false discovery rate (FDR) = 5%). Analysis of differentially expressed genes was performed in MADIBA (Micro Array Data Interface for Biological Annotation).

middle: V

first: Marina

last: van der Merwe

first: Pamisha

last: Pillay

first: Anna

last: Van Brummelen

first: Bridget

last: Crampton

first: Chris

last: Parkinson

first: Fanie

last: van Heerden

first: Neil

last: Crouch

first: Peter

last: Smith

first: Dalu

last: Mancama

first: Vinesh

last: Maharaj