title: Pharmacological blockade of MYCN in neuroblastoma using orally-bioavailable CDK inhibitors reveals an approach widely applicable to Myc-dependent cancers

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Neuroblastoma (NB) is a paediatric tumor wherein amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN confers clinical and biologic features prototypical of Myc-dependent cancers. TF-dependent cancers like MYCN-amplified NB are difficult to target, but the availability of clinical-candidate transcription inhibitors makes selective blockade of oncogenic TF activity a possibility. Here we investigated whether NB could be controlled via dual targeting of the transcription elongation machinery and cell cycle progression, using an orally bioavailable and selective CDK9/2 inhibitor CYC065. CYC065 blocks nascent transcription and leads to a drastic reduction in steady-state levels of short-lived transcripts. In MYCN-amplified NB, CYC065 rapidly and completely eliminated MYCN mRNA and protein, terminating expression of a MYCN-dependent gene expression programme. This result is phenocopied by multiple clinical-candidate CDK9 chemical inhibitors and genetic manipulation of CDK9. Mechanistically, CYC065 dissociates MYCN from physical proximity of P-TEFb in cells. P-TEFb co-occupies promoters and enhancers of de-differentiating pathway genes highly-occupied by MYCN, and CDK9 inhibition terminates expression of these and other highly transcribed genes. Intriguingly, targeted inhibition of CDK9 alone is insufficient to eradicate MYCN-dependent cells lines as CDK9 loss alone is compensated by upregulation of CDK2. CYC065 targeted MYCN-driven neuroblastoma in vivo, resulted in tumor regression or eradication and prolonged survival in multiple NB models, and was effective against a wide range of Myc-dependent cancer cells lines in vitro. The data establish that combined CDK9/CDK2 inhibition blocks transcriptional dependence induced by MYCN, highlighting a potential clinical strategy by which many Myc-driven cancers could be targeted.

overall_design: ChIP-Seq in KELLY neuroblastoma cell lines for H3K27ac, CDK9

first: Tong

last: Liang

first: Evon

last: Poon

middle: Y

first: Louis

last: Chesler


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [RNA-seq data set 1]

status: Public on Nov 01 2018

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

type: Expression profiling by high throughput sequencing

summary: BOFS is a rare congenital syndrome that arises due to defects during neural crest (NC) development and is thus considered as a human neurocristopathy. All reported BOFS cases are caused by heterozygous mutations within TFAP2A. Here we describe a unique BOFS patient carrying a de novo heterozygous inversion in which one of the breakpoints is located 40 kb downstream of TFAP2A. Using in vitro and in vivo NC developmental models, we uncovered that TFAP2A is located within a large Topologically Associating Domain (TAD) containing enhancers essential for TFAP2A expression in NC cells (NCC). Importantly, using patient-specific hiPSC lines, we showed that the inversion causes a loss of physical interactions between the inverted TFAP2A allele and its cognate enhancers, leading to TFAP2A monoallelic and haploinsufficient expression in human NCC. More generally, our results highlight potential etiological mechanisms for other human neurocristopathies and illustrate how TAD disruption can lead to a loss of enhancer gene-interactions and, consequently, to pathological changes in gene expression.

overall_design: Gene expression profiles were generated in WT p2hNCC (two different cell lines) and BOFS p2hNCC (three different cell lines) using RNA-seq

first: Michaela

last: Bartusel

first: Magdalena

last: Laugsch

first: Alvaro

last: Rada-Iglesias


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [scRNA-seq]

overall_design: Gene expression profiles were investigated in WT d11hNCC and del0.4Mb d11hNCC using single-cell RNA-seq (scRNA-seq).


title: Transcriptional response to PORCN inhibition using a subcutaneous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)

status: Public on Dec 04 2018

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: SRP136970 - PRJNA448481 - RNA-seq of response to PORCN inhibition, using ETC-159,in a subcutanenous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).

overall_design: Drug response in a subcutaneous model of RNF43 mutant PDAC (HPAF-II) following 24 h and 48 h of treatment.

first: Nathan

last: Harmston

first: Babita

last: Madam

first: Enrico

last: Petretto

first: David

middle: M

last: Virshup


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: Genomic regions with accessible chromatin were identified in WT d11hNCC and chicken frontonasal prominences using ATAC-seq.


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [4C-seq data set 2]

overall_design: 4C-seq interaction profiles were generated in human cells (WT hiPSC, WT hNCC and BOFS patient hNCC) using as viewpoints the TFAP2A promoters or different enhancers located within the TFAP2A regulatory domain (Enh100, Enh480).


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [4C-seq data set 1]

overall_design: 4C-seq interaction profiles were generated in human cells (WT hiPSC, WT hNCC and BOFS patient hNCC) and chicken embryonic tissue (Frontonasal prominences (FNP)) using as viewpoints the TFAP2A promoters or different enhancers located within the TFAP2A regulatory domain (Enh100, Enh480).


title: Pharmacologic activation of G protein-coupled estrogen receptor inhibits pancreatic ductal adenocarcinoma

status: Public on Oct 18 2018

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

country: USA

institute: University of Pennsylvania

summary: We examine the effect of GPER activation on murine pancreatic ductal adenocarcinoma cell lines

overall_design: Examination of RNA-seq expression profiles in murine pancreatic ductal adenocarcinoma cell lines treated with the specific GPER agonist G-1 by RNA-seq

first: Todd

last: Ridky


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of E9.5 mouse embryos lacking the lipoprotein receptor SR-B1

status: Public on Sep 21 2018

city: Santiago

first: Dolores

last: Busso

address: Alameda 340 Edificio CIM-Patio 4 piso

department: Nutrition, Diabetes and Metabolism

country: Chile

institute: Pontificia Universidad Católica de Chile

summary: The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early development, SR-B1 is located in the maternal-fetal interface, where it facilitates vitamin E transport towards the embryo. Consequently, embryos lacking SR-B1 are vitamin E-deficient, and around half of them fail to close the neural tube and show neural tube defects (NTD). Here, we studied the transcriptomic profile of mouse embryos lacking SR-B1 to identify the molecular determinants of this phenotypic difference. We used RNA-Seq to analyze the expression of mRNA globally in E9.5 wild-type embryos and embryos lacking SR-B1 with or without NTD, in order to compare expression profiles in those groups and to identify putative genes driving phenotypic differences.

overall_design: We analyzed 3 samples of each group (wild-type, SR-B1 KO normal, SR-B1 KO NTD). Each samples corresponded to a pool of 3 embryos.

first: Nicolas

last: Santander

first: Carlos

last: Lizama


title: ChIP-seq for Spt16 before and after transcription inhibition

status: Public on Sep 26 2018

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

summary: The FACT (FAcilitates Chromatin Transactions) complex is a conserved complex that maintains chromatin structure on transcriptionally active genes. Consistent with this, FACT is enriched on highly expressed genes, but how it is targeted to these regions is unknown. In vitro, FACT binds destabilized nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin through recognition of RNA polymerase-disrupted nucleosomes. In this study, we used high resolution analysis of FACT occupancy in S. cerevisiae to test this hypothesis. We demonstrate that FACT interacts with nucleosomes in vivo and its interaction with chromatin is dependent on transcription by any of the three RNA polymerases. Deep sequencing of micrococcal nuclease (MNase)-resistant fragments shows that FACT-bound nucleosomes exhibit differing nuclease sensitivity compared to bulk chromatin, consistent with a modified nucleosome structure being the preferred ligand for this complex. Interestingly, a subset of FACT-bound nucleosomes may be “overlapping di-nucleosomes”, in which one histone octamer invades the ~147 bp territory normally occupied by the adjacent nucleosome. While the differing nuclease sensitivity of FACT-bound nucleosomes could also be explained by the demonstrated ability of FACT to alter nucleosome structure, transcription inhibition restores nuclease resistance suggesting that it is not due to FACT interaction alone. Collectively these results are consistent with a model in which FACT is targeted to transcribed genes through preferential interaction with RNA polymerase-disrupted nucleosomes.

overall_design: Saccharomyces cerevisiae yeast cells were arrested in G1 with alpha factor and treated with 1,10-phenanthroline for 15 minutes. ChIP-seq was performed for Spt16 from sonicated and MNase-digested lysates.

middle: J

first: LeAnn

last: Howe


title: NTPDase3 antibody targets adult human pancreatic β-cells for in vitro and in vivo analysis

status: Public on Sep 12 2018

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

summary: Identification of cell surface markers specific to human pancreatic β-cells would allow in vivo analysis and imaging. Here we introduce a biomarker – ectonucleoside triphosphate diphosphohydrolase-3 (NTPDase3) – that is expressed on the cell surface of essentially all adult human β-cells, including those from individuals with type 1 or type 2 diabetes (T1D, T2D). NTPDase3 is expressed dynamically during postnatal human pancreas development, appearing first in acinar cells at birth, but several months later its expression declines in acinar cells while concurrently emerges in islet β-cells. Given its specificity and membrane localization, we utilized an NTPDase3 antibody for purification of live human β-cells as confirmed by transcriptional profiling, and, in addition, for in vivo imaging of transplanted human β-cells. Thus, NTPDase3 is a cell surface biomarker of adult human β-cells and the antibody directed to this protein should be a useful new reagent for β-cell sorting, in vivo imaging, and targeting.

overall_design: Total of 5 non-diabetic control donors were analyzed. β-cells were FACS-sorted and RNA was extracted from each of these samples. RNAseq was performed on all 5 samples.

first: Alvin

middle: C

last: Powers

first: Diane

last: Saunders

first: Marcela

last: Brissova

first: Neil

last: Phillips


title: Alport (Col4a3-/-) Mouse Recapitulates Heart Failure with Preserved Ejection Fraction Pathologies Driven by Osteopontin-Mitochondria Axis

status: Public on Oct 23 2018

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

summary: Hearts were snap frozen from 2 month old wild type, Col4a3-/-, or Col4a3-/-OPN-/- mice. RNA was isolated using Mirvana Paris kit.

overall_design: Hearts were snap frozen from 2 month old wild type (n=3), Col4a3-/- (n=3), or Col4a3-/-OPN-/- (n=3) mice. RNA was isolated using Mirvana Paris kit.


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource [RNA-seq II]

status: Public on Sep 08 2018

city: Cambridge

last: Walker

address: Downing Street

department: Genetics

institute: University of Cambridge

summary: This data release is part of the EU BLUEPRINT reference epignome project (http://www.blueprint-epigenome.eu/) and consists of genome wide gene expression, histone modifications and DNA methylation profiles from murine Naive CD4+ T-cells and Resting B cells.

overall_design:
RNA expression profiled on Naive CD4+ T cells and Resting B cells derived from pooled murine male and female replicates using RNA sequencing

Quantified processed data are not available for these samples.

last: Sjoberg

last: Adams

first: Anne

last: Ferguson-Smith


title: Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [RNA-seq]

status: Public on Jul 18 2018

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

country: China

institute: Chinese Academy of Sciences

summary: The emerging 4D genome project aiming to map the dynamics of genomes in spatial and temporal dimension has put forward to developing the mechanisms of how the nucleus is organized and functions. Therefore, processes like cellular senescence characterized by complex events give rise to understanding the regulation network from 1D genome to dynamically organized 3D structure. Unfortunately, how spatial genome reorganization triggers cellular senescence and how it influences senescence-related downstream transcriptional profile remains unaddressed well. Here, we uncover that re re-orchestration of 3D chromatin architecture has occurred in cellular senescence, accompanied with remodeling of enhancer repertories, which in turn facilicate the recruitment of the chromatin reader C/EBPα to newly activated senescence enhancers (SAEs), leading to the expression of SAEs flanking SASP genes kinetics.

overall_design: Study gene expression using RNA-seq in different passaged MEFs (PD2, PD8, PD14)

first: Wei

last: Tao

first: YiTing

last: Guan


title: Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [ChIP-seq]

overall_design: Study the global enhancer activities using ChIP-seq (H3K27ac, H3K4me1) of different passaged MEFs (PD2, PD8, PD14)


title: Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile


title: Human Pancreatic Islets Expressing HNF1A Variant Have Defective β cell Transcriptional Regulatory Networks

status: Public on Sep 22 2018

summary: Using an integrated approach to characterize the pancreatic tissue and isolated islets from a 33-year-old with 17 years of type 1 diabetes (T1D), we found donor islets contained β cells without insulitis and lacked glucose-stimulated insulin secretion despite a normal insulin response to cAMP-evoked stimulation. With these unexpected findings for T1D, we sequenced the donor DNA and found a pathogenic heterozygous variant in hepatocyte nuclear factor 1 alpha (HNF1A). In one of the first studies of human pancreatic islets with a disease-causing HNF1A variant associated with the most common form of monogenic diabetes, we found that HNF1A dysfunction leads to insulin-insufficient diabetes reminiscent of T1D by impacting the regulatory processes critical for glucose-stimulated insulin secretion and suggest a rationale for a therapeutic alternative to current treatment.

overall_design: Total of 12 samples were analyzed, 10 were non-diabetic control donors and 2 were  HNF1A donors. GEO accession number for non-diabetic controls are GSE116559(β cell controls) and GSE106148 (α cell controls).  α cells and β cells were FACS-sorted and RNA was extracted from each of these samples. RNAseq was performed on all 12 samples

first: Rachana

last: Haliyur


title: WTX overexpression effect on gastric cell line

status: Public on May 16 2018

city: Guangzhou

first: Jian

last: Li

address: 1023-1063，Shatai South Road, Baiyun District

institute: Southern Medical University

summary: We used microarrays to detail the global gene expression in AGS gastric cancer cells overexpressing WTX, a tumor suppressor frequently inactivated in Wilms tumor. Results provide insight into roles for WTX in gastric cancer cells.

overall_design: Two experimental condition : AGS.W cells versus AGS.veh cells (control)

first: Q

first: J

first: D

last: Ye


title: Differential expressed genes in respone to diesel exhaust particle (DEP) on mouse nasal cavity

status: Public on May 22 2018

city: Goyang-si

first: Young Rok

last: Seo

address: Dongguk-ro 32

department: Life science

country: South Korea

institute: Dongguk University

summary: Transcription profiling of mouse nasal cavity comparing control and short-term (4 weeks) or long-term (8 weeks) of DEP-exposed group.

overall_design: Two-condition experiment : 4 weeks and 8 weeks exposure to DEPs. Biological replicates : 4 weeks - 4, 8 weeks - 3

first: Hyun

middle: S

last: Kim

first: Moo

middle: K

last: Park

first: Young

middle: R


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [RNA-seq data set 2]

first: Milos

last: Nikolic

overall_design: Gene expression profiles were investigated in WT d11hNCC and del0.4Mb d11hNCC using RNA-seq.

first: Michaela

last: Bartusel

first: Magdalena

last: Laugsch

first: Alvaro

last: Rada-Iglesias


title: Epigenome-wide association study in peripheral white blood cells: Methyl Epigenome Network Association (MENA) project

status: Public on Jun 05 2018

city: Pamplona

first: Ana

last: Arpón

address: Irunlarrea 1

country: Spain

institute: University of Navarra

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation from peripheral white blood cells (PWBCs) from individuals from different cohorts included in the MENA project. Samples included 474 individuals (DiOGenes-UNAV n=52, OBEPALIP n=29, Food4Me-UNAV n=39, GEDYMET n=57, ICTUS n=7, NUGENOB-UNAV n=22, PREDIMED-UNAV n=116, RESMENA n=44, OBEKIT n=96, and NormoP n=12). The Illumina Infinium 450k Human DNA methylation Beadchip or Infinium MethylationEPIC Beadchip (for OBEKIT) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in these samples.

overall_design: Bisulphite converted DNA from 474 samples from different cohorts were hybridised to the Illumina Infinium 450k Human Methylation Beadchip (DiOGenes-UNAV, OBEPALIP, Food4Me-UNAV, GEDYMET, ICTUS, NUGENOB-UNAV, PREDIMED-UNAV, RESMENA, NormoP) or Infinium MethylationEPIC Beadchip (OBEKIT).

first: Fermín

middle: I

last: Milagro

first: Omar

last: Ramos-Lopez

first: M

middle: L

last: Mansego

first: José

last: Riezu-Boj

last: Martínez


title: Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [Hi-C]

first: Chao

last: Zhang

overall_design:
Study chromatin 3D structures using Hi-C in different passaged MEFs (PD2, PD8, PD14)
Each processed data was generated from both rep1 and rep2 samples together and is linked the corresponding rep1 sample records.

first: Wei

last: Tao

first: YiTing

last: Guan


title: The effect of Abl kinases,or Ponatinib challenging on breast cancer cells' global transcriptome

status: Public on Mar 01 2018

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

summary:
To gain insight into the signaling pathway(s) required for ABL1/ABL2-kinase activity or effected by Ponatinib treatment, we evaluated the consequences of single or double inactivation of ABL1/ABL2 cells, or Ponatinib treated cells on the transcriptome of breast cancer cells. To examine the consequences of depleting the ABL kinases, or Ponatinib treatment on the transcriptome of lung metastatic breast cancer cells we employed next generation sequencing (RNAseq) analysis.
We found that 321 genes were significantly differently expressed in Ponatinib treated LM2 cells, and 73 genes were differently expressed in double inactivation of ABL1/ABL2 LM2 cells. However, only about 3.4 percent of Ponatinib affected genes can also be changed by ABL knocking down.

overall_design: Samples were analyzed by pair of either control (DMSO) versus ABL Kinase inhibitor Ponatinib, Or using scrambled shRNA versus single or double inactivation of ABL1 and ABL2-specific shRNAs.

last: Shao

first: Dong

last: Wang


title: Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

status: Public on Feb 20 2018

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

type: Non-coding RNA profiling by high throughput sequencing

summary: We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4).  Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. Antisense sRNAs were found to overlap both 5’ and 3’ UTRs of mRNAs revealing a hybrid system between Eukarya (3’ UTR) and Bacteria (5’ UTR) sRNA-silencing systems, as well as targeting the coding sequence (CDS) of mRNAs, a unique system to Archaea. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide induced oxidative stress in H. volcanii.  A majority of these sRNAs are lowly expressed compared to mRNAs. The sRNAs could be classified in two populations based on expression patterns: those that are up-regulated and those that are down-regulated during oxidative stress. Targets of antisense sRNAs decreased in expression when sRNAs were up-regulated indicating that sRNAs are likely playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of sRNAs included mRNAs involved in transposons, chemotaxis signaling, peptidase activity, transcription factors, and secondary metabolite regulation.

overall_design: We exposed 5 biological replicates of H. volcanii strain H53 liquid cultures to the oxidative stress agent H2O2. Initially, cultures were grown in 80 mL of Hv-YPC under optimal conditions to an OD of 0.4 (mid exponential phase). To ensure homogeneity, each replicate was subsequently split into two 40 mL cultures, one used for the non-challenged (control) condition and the other for the oxidative stress condition (treatment). For the latter condition, 2 mM H2O2  (80% survival rate, previously determined) was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Total RNA was extracted using the Zymo Quick-RNA Miniprep kit and was split into two pools for total RNA-seq and a custom sRNA-seq protocol. 20 µg of total RNA was size selected from 50-500 nucleotides on a 7% denaturing urea polyacrylamide gel for sRNA-seq. Both the size-selected RNA and total RNA were used to make strand-specific libraries using SMART-seq Ultralow RNA input kit (Takara). Only three replicates (each condition) were sequenced for total RNA-seq thus resulting in a total of 16 libraries (10 sRNA-seq, 6 mRNA-seq).

first: Jocelyne

last: DiRuggiero


title: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [ChIP-seq]

last: Nikolic

overall_design: Genome-wide binding profiles for TFAP2A and various histone modifications were investigated in WT p2hNCC and BOFS p2hNCC using ChIP-seq.

last: Bartusel


title: Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs

status: Public on Jul 12 2018

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

institute: INIA

summary: One of the most important determinants of meat quality is the intramuscular fat content (IMF). The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the current study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq technique allowed identifying in the samples analyzed around 10,000 of the 25,878 annotated genes. In addition to this, the 42.46% of the identified transcripts corresponded to newly predicted isoforms. The differential expression analyses revealed a total of 221 DE annotated genes and 116 DE newly isoforms. Functional analyses identified an enrichment of overexpressed genes in animals with a higher content of IMF involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC and ADIPOQ) and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB and SEMA4D) in the groups of animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. On the one hand, co-expression networks analyses revealed six lncRNAs (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1 and CIDEC. The computation of the regulatory impact factors (RIFs) revealed a total of 301 transcriptionally regulatory factors involved in the expression differences, some of them have a role in adipogenesis (ARID5B, CREB1, VDR, ATF6 and SP1) and other ones take part of myogenesis and development of skeletal muscle (ATF3, KLF11 and MYF6). The results obtained provide a relevant insight about the knowledge of the genetics mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors is proposed for a further identification of polymorphisms susceptible of integrate in a selection program.

overall_design: Twelve Iberian individuals with divergent breeding values for intramuscular fat content were selected (six per group), samples of Longissimus dorsi were collected after the slaughter, RNA from these samples was extracted, pair-end libraries we

first: Juan

last: García-Casco

first: Carmen

last: Caraballo

first: Miguel

last: Fernández-Barroso

first: Fernando

last: Sánchez-Esquiliche

last: Gómez

last: del Carmen Rodríguez

first: Luis

last: Silió


title: Gene expression profiling of pulmonary arterial hypertension

status: Public on Apr 21 2018

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road East E6-203

institute: Western University

summary:
Pulmonary arterial hypertension (PAH) is the best characterized and most studied type of pulmonary hypertension, classified as Group I according to the international guidelines, and hemodinamically defined as pre-capillary pulmonary hypertension. Our analysis was focused on the role of the osteopontin gene in the transcriptional profile of PAH.
We used microarray to identifiy the gene expression profiles in patients with PAH and in normal controls.

overall_design: Fresh frozen lung samples were obtained from the recipients organs of 15 patients with PAH and 11 normal controls (normal lung tissue obtained from tissue flanking lung cancer resections). The PAH group included 6 patients with idiopathic PAH, 4 patients with PAH secondary to connective tissue disease (CTD), 4 patients with PAH secondary to congenital heart disease (CHD) and 1 patient with chronic thromboembolic pulmonary hypertension (CTEPH). RNA was extracted and hybridized on Affymetrix microarrays.


title: Expression data from LMP1-B cells

status: Public on Feb 14 2018

city: Boston

first: Baochun

last: Zhang

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: In this study, by microarray we analyzed gene expression changes due to LMP1 signaling in B cells, in order to identify candidate co-stimulatory ligands that may account for the ability of LMP1-B cells to induce cytotoxic CD4+ T cell response. The identified candidate co-stimulatory ligands were further validated by other functional assays.

overall_design: In this experiment, two LMP1-expressing B cell samples were analyzed in comparison to two YFP-expressing control B cell samples.


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines (SK-MES, MDA-MB-231, MKN and 786-O)

status: Public on Apr 13 2018

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (lung cancer, breast cancer, gastric cancer and renal cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (SK-MES, MDA-MB-231, MKN and 786-O) were treated with miRNAs (miR-451a, 99a-5p, 99a-3p, 148a-5p and 148a-3p), siRNAs (si-SDC3 and si-SERPINH1).

first: Yasutaka

last: Yamada


title: Transcriptome of the distal late segment of the zebrafish mesonephros

status: Public on Mar 31 2018

city: Charlestown

first: Yuya

last: Sugano

address: 149 13th Street

department: Nephrology

institute: Massachusetts General Hospital

summary: We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim, we obtained transcription profilings in the zebrafish distal late (DL) segment, the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis.

overall_design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.

first: Johannes

last: Loffing

first: Stephan

last: Neuhauss


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource [scRNA-Seq]

status: Public on Dec 15 2017

first: Nicolas

last: Walker

overall_design: RNA expression profiled on Naive CD4+ T cells and Resting B cells derived from pooled murine male and female replicates using RNA sequencing

first: Marcela

last: Sjöberg

first: Catalina

last: Vallejos

first: Martin

last: Del Castillo Velasco Herrera

first: John

last: Marioni

first: David

last: Adams

first: Anne

last: Ferguson-Smith


title: Synectin Promotes Fibrogenesis by Regulating PDGFR Isoforms Through Distinct Mechanisms

status: Public on Dec 31 2017

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: The scaffold protein synectin plays a critical role in the trafficking and regulation of membrane receptor pathways.   As the platelet derived growth factor receptor (PDGFR)  pathway is essential for hepatic stellate cell (HSC) activation and liver fibrosis, we sought to determine the role of synectin on the PDGFR pathway in HSC.  To study the role of synectin in the development of liver fibrosis,  mice with selective deletion of synectin from HSC were generated and found to be protected from fibrosis.  RNAseq revealed that knockdown of synectin in HSC demonstrated reductions in the fibrosis pathway of genes including PDGFR-β, but not PDGFR-α.  Chromatin Immunoprecipitation assay of the PDGFR-β promoter upon synectin knockdown revealed a pattern of histone marks associated with decreased transcription, dependent on p300.  In contradistinction, synectin was found to regulate PDGFR-α through an alternative mechanism: protection from autophagic degradation.  Site directed mutagenesis revealed that ubiquitination of specific PDGFR-α lysine residues is responsible for its autophagic degradation.  Furthermore, functional studies showed decreased PDGF dependent proliferation and migration after synectin knockdown.  Finally, human cirrhotic livers demonstrated increased synectin expression.  This work provides insight into differential transcriptional and post-translational mechanisms of synectin regulation of PDGFRs, which are critical to fibrogenesis.

overall_design: To gain insight into molecular mechanisms by which the genetic inactivation of synectin impacts on liver fibrosis, we performed next generation sequencing of mRNA isolated from HSC in which the levels of this protein were significantly reduced using shRNA-mediated knock down.

first: Usman

last: Yaqoob

first: S

last: Cao

first: V

middle: H

last: Shah


title: Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [expression]

status: Public on Jan 24 2018

city: Munich

first: Roland

last: Rad

state: Bavaria

address: Ismaninger Str. 22

institute: Center for Translational Cancer Research (TranslaTUM)

summary: Primary cell cultures were isolated from KrasG12D-driven, PiggyBac transposon-transposase pancreatic cancer cell cultures and subjected to microarray-based expression profiling for the investigation of expression profiles.

overall_design: Gene expression analysis. Investigated mouse genotype is KrasG12D-Panc;PB-Panc (PK-PB, 17 samples).

first: Sebastian

last: Mueller

first: Thomas

last: Engleitner

first: Roman

last: Maresch

first: Dieter

last: Saur


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource. [Whole Genome Bisulfite-Seq_OX]

type: Methylation profiling by high throughput sequencing

overall_design: DNA methylation profiled on Naive CD4+ T cells and Resting B cells derived from pooled murine male and female replicates using whole genome oxidative/bisulfite sequencing


title: Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes [aCGH]

type: Genome variation profiling by genome tiling array

summary: Primary cell cultures were isolated from different KrasG12D-driven mouse models of pancreatic cancers and subjected to array comparative genomic hybridization (aCGH) for the investigation of copy number profiles.

overall_design: We generated primary pancreatic cancer cell cultures from the following mouse genotypes: KrasG12D-Panc (PK, 54 samples); KrasG12D-Panc;PB-Panc (PK-PB, 17 samples); KrasG12D-Panc;Cdkn2a-∆HOM-Panc (PKC, 16 samples); KrasG12D-Panc;Trp53-∆HOM-Panc (PKP, 16 samples) and Kras-G12D-Panc;Tgfbr2-∆HET/HOM-Panc (PKT, 12 samples).


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource [RNA-seq]


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource. [Whole Genome Bisulfite-Seq]


title: α Cell Function and Gene Expression Are Compromised in Type 1 Diabetes

status: Public on Dec 12 2017

city: Huntsville

first: Nripesh

last: Prasad

state: Alabama

address: 601 Genome way

institute: Hudson Alpha Institute for Biotechnology

summary: Many patients with type 1 diabetes (T1D) have residual beta cells producing small amounts of C-peptide long after disease onset, but develop an inadequate glucagon response to hypoglycemia following T1D diagnosis. The features of these residual beta cells and alpha cells persisting in the islet endocrine compartment are largely unknown due to difficulty of comprehensive investigation. By studying the T1D pancreas and isolated islets, we show that remnant beta cells appeared to maintain several aspects of regulated insulin secretion. However, the function of T1D alpha cells was markedly reduced and these cells had alterations in transcription factors constituting and alpha and beta cell identity. In the native pancreas and after placing the T1D islets into a non-autoimmune, normoglycemic in vivo environment, there was no evidence of alpha-to-beta cell conversion. These results suggest a new explanation for the disordered T1D counterregulatory glucagon response to hypoglycemia.

overall_design: Total of 8 samples were analyzed, 5 were non-diabetic control donors and 3 were T1D donors. α cells were FACS-sorted and RNA was extracted from each of these samples. RNAseq was performed on all 8 samples

first: Alvin

last: Powers

last: Brissova

first: Rachana

last: Haliyur

first: Diane

last: Saunders

first: Shristi

last: Shrestha


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource

first: Nicolas

last: Walker

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

overall_design: Refer to individual Series


title: The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD complex

status: Public on Dec 01 2017

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary:
Background: circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about the role of circular RNAs in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become useful for diagnostic and therapeutic strategies in HNSCC.
Results: Using samples from 115 HNSCC patients, we find that circPVT1 is over-expressed in tumors compared to matched non-tumoral tissues, with particular enrichment in patients with TP53 mutations. The circPVT1 up- and down-regulation determine, respectively, an increase and a reduction of the malignant phenotype in HNSCC cell lines. We show that circPVT1 expression is transcriptionally enhanced by the mut-p53/YAP/TEAD complex. CircPVT1 acts as an oncogene modulating the expression of miR-497-5p and genes involved in the control of cell proliferation.
Conclusions: This study shows the oncogenic role of circPVT1 in HNSCC, extending the current knowledge about the role of circular RNAs in cancer.

overall_design: We show here Affymetrix profiling of 23 normal and 24 tumor tissues. To select miRNA-497-5p targets, we performed a correlation analysis between miRNA-497-5p expression [1] and mRNA expression analysis of 14 patients with TP53 mutations and 9 normal matched patients.  [1] Ganci F, Sacconi A, Bossel Ben-Moshe N, Manciocco V, Sperduti I, Strigari L, et al. Expression of TP53 mutation-associated microRNAs predicts clinical outcome in head and neck squamous cell carcinoma patients. Ann Oncol. 2013;24:3082-088.

first: Giovanni

last: Blandino

first: Andrea

last: Sacconi


title: The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource [ChIP-seq]

summary: This data release is part of the EU BLUEPRINT reference epignome project (http://www.blueprint-epigenome.eu/) and consists of genome wide gene expression, histone modifications and DNA methylation profiles from murine Naive CD4+ T-cells and Resting B cells.

overall_design: Histone modification profiled over Naive CD4+ T cells and Resting B cells derived from pooled murine male and female replicates using ChIP-seq

first: Marcela

last: Sjöberg

first: Hui

last: Shi

first: David

last: Adams

first: Anne

last: Ferguson-Smith


title: Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

first: Roland

last: Rad


title: TET1 (HUES8 WT hESCs) and DNMT3B (HUES8 WT and HUES8 TET TKO hESCs) ChIP-Seq

city: New York

first: Nipun

last: Verma

state: NY

address: 430 East 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit preferential hypermethylation at bivalent promoters without corresponding gene expression changes in undifferentiated hESCs. In the absence of the TET proteins, abnormal accumulation of DNMT3B at bivalent promoters results in hypermethylation and impaired gene activation upon differentiation. Broadly, the competitive balance between the TET proteins and de novo methyltransferases at bivalent promoters could facilitate rapid changes of their methylation state to either activate or silence transcription in a cell-lineage and gene dependent manner.

overall_design: ChIP-Seq was performed for TET1 (WT hESCs) and DNMT3B (WT and TKO hESCs). WT and TKO hESCs were cultured in standard hESC media, as described above. ~5 × 107 cells were fixed, washed and snap-frozen according to the Cell Fixation protocol from Active Motif (http://www.activemotif.com/documents/1848.pdf). Immunoprecipitation and DNA sequencing was done by Active Motif.

first: Dore

last: Louis

first: Pan

last: Heng

first: Verma

last: Nipun


title: 5-hydroxymethylcytosine (5hmC) Profiling of HUES8 WT and HUES8 TET1/2/3 TKO hESCs

overall_design: For 5hmC profiling genomic DNA was isolated from HUES8 WT using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer's guidelines.

first: Louis

last: Dore

first: Heng

last: Pan


title: Whole Genome Bisulfite Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs

overall_design: For whole genome bisulfite sequencing genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. One replicate was done for each sample.


title: RNA Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs

overall_design: For RNA-Sequencing total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136) from HUES8 WT and TKO hESCs


title: Human CD26high T cells elicit tumor immunity against multiple malignancies via enhanced migration and persistence

status: Public on Nov 11 2017

city: Charleston

first: Chrystal

last: Paulos

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: MUSC

summary: CD8+ T lymphocytes mediate potent immune responses against tumor, but the role of human CD4+ T cell subsets in cancer immunotherapy remains ill-defined. Herein, we exhibit that CD26 identifies three T helper subsets with distinct immunological properties in both healthy individuals and cancer patients. Although CD26neg T cells possess a regulatory phenotype, CD26int T cells are mainly naive and CD26high T cells appear terminally differentiated and exhausted. Paradoxically, CD26high T cells persist in and regress multiple solid tumors following adoptive cell transfer. Further analysis revealed that CD26high cells have a rich chemokine receptor profile (including CCR2 and CCR5), profound cytotoxicity (Granzyme B and CD107A), resistance to apoptosis (c-KIT and Bcl2), and enhanced stemness (β-catenin and Lef1). These properties license CD26high T cells with a natural capacity to traffic to, regress and survive in solid tumors. Collectively, these findings identify CD4+ T cell subsets with properties critical for improving cancer immunotherapy

overall_design: Herein, we exhibit that CD26 identifies three T helper subsets with distinct immunological properties in healthy individuals.

first: Bailey

last: Stefanie

first: Paulos

last: Chrystal


title: Trascriptome of thyroid cancer-induced macrophages

status: Public on Jun 12 2017

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: RNA sequencing data of macrophages after differentiation in the presence of TPC1 thyroid cancer cell line

overall_design: Co-incubation in trans-well system between TPC1 cell lines and human primary macrophages

first: Rob

last: Arts

first: Theo

last: Plantinga

first: Sander

last: Tuit

first: Thomas

last: Ulas

first: Bas

last: Heinhuis

first: Mirela

last: Petrulea

first: Marika

last: Tesselaar

first: Yvette

last: Sloot

first: Gosse

last: Adema

first: Leo

last: Joosten

first: Carmen

last: Georgescu

first: Johannes

middle: W

last: Smit

first: Mihai

middle: G

last: Netea

first: Romana

middle: T

last: Netea-Maier


title: A genome-wide CRISPR/Cas9 screen to identify genes required for transgene silencing in human cells

status: Public on May 29 2017

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: A population of KBM7 cells harboring epigenetically-repressed GFPdim transgenes was mutagenized using a genome-wide CRISPR sgRNA library, and GFPbright cells containing relevant gene disruption events isolated by two rounds of FACS.

overall_design: Genome-wide CRISPR screen

first: Richard

last: Timms

first: Paul

last: Lehner


title: Identifying genomic loci exhibiting chromatin decompaction upon loss of MORC2

summary: We used the Differential Viral Integration (DIVA) technique to compare chromatin accessibility in wild-type versus MORC2 knockout HeLa cells.

overall_design: DIVA analysis of wild-type HeLa cells compared to MORC2 knockout HeLa cells.


title: Assessing the impact of loss of MORC2 and SETDB1 on the global distribution of H3K9me3

summary: By comparing HeLa cells lacking MORC2 or SETDB1 generated through CRISPR/Cas9-mediated gene disruption to wild-type HeLa cells, the goal of the experiment was to determine the effect of loss of MORC2 on the distribution of the repressive H3K9me3 histone modification.

overall_design: H3K9me3 ChIP-seq analysis of wild-type HeLa cells compared to MORC2 knockout and SETDB1 knockout HeLa cells.


title: Next Generation Sequencing (NGS) of miRNAs in human hippocampal tissues

status: Public on Nov 30 2017

city: Brno

first: Jiri

last: Baloun

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary: We carried out Next Generation Sequencing (NGS) to reveal miRNA expression profiles of 16 patients with mTLE+HS and 8 post mortem controls (with median coverage of 10.8 million of unprocessed reads per sample). The sequencing platform identified 1962 miRNA species, out of which 422 miRNAs were present with the coverage of more than 500 reads altogether in all samples. We discovered 9 miRNAs potentially related to mTLE+HS that have not yet been associated with epilepsy.

overall_design: Examination of 16 samples from patients suffering from mesial temporal lobe epilepsy with hippocampal sclerosis.

first: Petra

last: Bencurova

first: Sarka

last: Pospisilova

first: Milan

last: Brazdil


title: Assessing the impact of the R252W Charcot-Marie-Tooth disease mutation in MORC2 on HUSH-mediated repression

summary: HeLa cells lacking MORC2 generated through CRISPR/Cas9-mediated gene disruption were reconstituted with either wild-type or R252W mutant MORC2, and re-repression of HUSH target genes assessed by RNA-seq

overall_design: Total RNA-seq of MORC2 knockout cells, either 1) mock transduced, 2) transduced with lentiviral vector encoding wild-type MORC2 or 3) transduced with lentviral vector encoding R252W MORC2.


title: Hyper-activation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2


title: Hyper-repression of HUSH target genes by over-expression of the R252W Charcot-Marie-Tooth disease mutant MORC2

summary: By comparing wild-type SK-N-SH neuroblastoma cells to cells over-expressing either wild-type or R252W mutant MORC2, the goal of the experiment was to assess the effect of MORC2 over-expression on the transcriptome.

overall_design: Total RNA-seq of SK-N-SH cells in triplicate, either 1) mock transduced, 2) transduced with lentiviral vector encoding wild-type MORC2 or 3) transduced with lentviral vector encoding R252W MORC2.


title: Assessing the genome-wide occupancy of MORC2

summary: By comparing HeLa cells expressing V5 epitope-tagged MORC2 constructs, the goal of the experiment was to determine the genome-wide localisation of MORC2 in the presence or absence of the HUSH complex and upon inactivation of the CW domain. The occupancy of V5-MORC2 was also compared to that of endogenous TASOR.

overall_design: ChIP-seq analysis of endogenous TASOR and IgG control in wild-type HeLa cells. ChIP-seq analysis of V5 epitope-tagged wild-type MORC2 and the CW domain mutant W505A expressed in MORC2 knockout HeLa cells generated through CRISPR/Cas9-mediated gene disruption. In parallel, ChIP-seq analysis of V5 epitope-tagged MORC2 in HUSH tirple knockout cells was also carried out.


title: Assessing the impact of loss of MORC2 on the transcriptome

summary: By comparing HeLa cells lacking MORC2 generated through CRISPR/Cas9-mediated gene disruption to wild-type HeLa cells, the goal of the experiment was to determine the effect of loss of MORC2 on the transcriptome.

overall_design: Total RNA-seq of three independent knockout HeLa clones lacking MORC2.


title: Human lung MPC

status: Public on Mar 23 2017

city: Nashville

first: Susan

last: Majka

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

summary:
A comparison of gene expression between control versus IPF human lung MPC using human Affy 1.0st chips.

This work was funded by grants to S.M. Majka from the NIH R01HL091105 and NIH R01HL11659701. Additional funding was also provided by PPG-5P01HL108800-04 (PI:J. Loyd). Experiments were performed using the University of Colorado Cancer Center Microarray core (NCI P30 CA 46934-14). The project was supported in part by the National Center for Research Resources, Grant UL1 RR024975-01, and is now at the National Center for Advancing Translational Sciences, Grant 2 UL1 TR000445-06.

overall_design: Human lung MPC were isolated from explanted tissue, expanded and characterized as previously published in Marriott et al. 2014. ABCG2(pos) lung mesenchymal stem cells are a novel pericyte subpopulation that contributes to fibrotic remodeling. American Journal of Physiology - Cell Physiology.C684-C698. 5 controls and 4 IPF cell lines from independent patients were used. RNA was isolated using a Qiagen kit and chips run by the University of Colorado Gene Expression Core facility. Data Analysis was performed by Swapna Menon, AnalyzeDat, India.


title: mRNA-seq analysis of B3 pre-B cell line from STATegra Project

status: Public on Feb 28 2017

city: Valencia

first: Ana

last: Conesa

state: Valencia

address: C/ Eduardo Primo Yúfera 3

department: Computational Genomics Program

institute: Centro de Investigaciones Príncipe Felipe (CIPF)

summary: The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations.  STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells.   The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest.   On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods.

overall_design:
The STATegra experimental design consists of a 6 point, time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hours period. The differentiation was sampled at 0h, 2h, 6h, 12h, 18h and 24h after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches.
Paired-end strand-specific RNA-seq analysis was performed using total RNA of 3 biological batches (1, 2 and 4) for time 0h and total RNA of 3 biological batches (1, 3 and 4) for times 2h, 6h, 12h,18h and 24h. There were two experimental conditions (C=Control, IK=Ikaros) and the 3 biological replicates per condition and time point were numbered as 1, 2 and 3. For some of these biological replicates, also technical replicates were generated in order to measure the variability between batches and afterwards correct the potential batch effect.

first: Matthias

last: Merkenschlager

first: Isabel

last: Ferreiros

first: Ziwei

last: Liang

first: Lee

last: Cooper

first: Jesper

last: Tegnér

first: David

last: Gómez-Cabrero

first: Sunjay

last: Fernandes

first: Peri

last: Noori

first: Gilad

last: Silderberg


title: CHARGE and Kabuki syndromes: Gene-specific DNA methylation signatures

status: Public on May 03 2017

city: Toronto

first: Rosanna

last: Weksberg

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Epigenetic dysregulation has emerged as mechanism in the etiology of neurodevelopmental disorders. Two such disorders, CHARGE and Kabuki syndromes, result from loss of function mutations in chromodomain helicase DNA-binding protein 7 (CHD7LOF) and lysine (K) methyltransferase 2D (KMT2DLOF), respectively. We expected that epigenetically driven developmental pathways regulated by CHD7 and KMT2D would overlap and that DNA methylation (DNAm) alterations downstream of the mutations in these genes would identify common target genes, elucidating a mechanistic link between these conditions, as well as specific target genes for each. Genome-wide DNAm profiles in individuals with CHARGE and Kabuki syndromes with CHD7LOF or KMT2DLOF identified distinct sets of DNAm differences in each of the disorders, which were used to generate two unique, highly specific and sensitive DNAm signatures. These DNAm signatures were able to differentiate pathogenic mutations in these two genes from controls and from each other. Analysis of each gene-specific DNAm signature identified common gene targets which could account for some of the clinical overlap in these syndromes, as well as distinct gene targets. Our findings demonstrate how characterization of the epigenome can contribute to our understanding of disease pathophysiology for epigenetic disorders, paving the way for explorations of novel therapeutics.

overall_design: Bisulphite converted DNA samples were hybridized to the Illumina Infinium Human Methylation450 Beadchip.

first: Darci

last: Butcher

first: Sanaa

last: Choufani

first: Andrei

last: Turinsky


title: miRNA-seq analysis of B3 pre-B cell line from STATegra Project

overall_design:
The STATegra experimental design consists of a 6 points time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hours period. The process was sampled at 0h, 2h, 6h, 12h, 18h and 24h after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches.
Small RNA-seq analysis was performed using Trizol-extracted total RNA of 3 biological batches (4, 5 and 6) for time 0h and total RNA of 3 biological batches (1, 2 and 3) for times 2h, 6h, 12h,18h and 24h. There were two experimental conditions (C=Control, IK=Ikaros) and the 3 biological replicates per condition and time point were numbered as 1, 2 and 4. For some of these biological replicates, also technical replicates were generated in order to measure the variability between batches and afterwards correct the potential batch effect.

first: Esteban

last: Ballestar

first: Javier

last: Rodriguez-Ubreva

first: Carlos

last: Company

first: Roser

last: Vento-Tormo

first: Sonia

last: Tarazona


title: Methyl-seq analysis of B3 pre-B cell line from STATegra Project

first: Ana

last: Conesa

overall_design:
The STATegra experimental design consists of a 6 points time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hours period. The process was sampled at 0h, 2h, 6h, 12h, 18h and 24h after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches.
Methyl-seq analysis was performed using 3 biological batches (1, 2 and 4) for time 0h and 3 biological batches (1, 3 and 4) for times 2h, 6h, 12h,18h and 24h.

first: Matthias

last: Merkenschlager

first: Isabel

last: Ferreiros

first: Francesco

last: Marabita


title: DNase-seq analysis of B3 pre-B cell line from STATegra Project

overall_design:
The STATegra experimental design consists of a 6 points time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hours period. The process was sampled at 0h, 2h, 6h, 12h, 18h and 24h after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches.
For each DNAse-seq sample, 3 biological replicates (R4, R5 and R6) were generated and sequenced as paired-end on the NextSeq 500 Illumina platform. Additionally, some Ikaros samples (corresponding to R4)  were re-sequenced in order to improve the coverage.

first: Ali

last: Mortazavi

first: Ricardo

last: Ramírez

first: Weihua

last: Zeng

first: Nicole

last: El-Ali

first: Jesper

last: Tegnér

first: David

last: Gómez-Cabrero


title: Recruitment of the histone acetyltransferase Nu3A is independently promoted by histone H3K4 and H3K36 methylation in S. cerevisiae

status: Public on Jan 15 2017

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

institute: UBC

summary: Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In S. cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14, which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9 respectively.  However the relative in vivo contributions of these histone PTMs in targeting NuA3 is unknown. Here we show that in vivo H4K4 and H3K36 methylation, but not acetylated or crotonylated H3K9, recruit NuA3 to transcribed genes. Through genome-wide colocalization and by mutational interrogation, we demonstrate that the PHD finger of Yng1, and the PWWP domain of Pdp3 independently target NuA3 to H3K4 and H3K36 methylated chromatin respectively. In contrast, we find no evidence to support the YEATS domain of Taf14 functioning in NuA3 recruitment. Collectively our results suggest that the presence of multiple histone-PTM binding domains within NuA3, rather than restricting it to nucleosomes containing distinct combinations of histone PTMs, can serve to increase the range of nucleosomes bound by the complex. Interestingly however, the simple presence of NuA3 is insufficient to ensure acetylation of the associated nucleosomes, suggesting a secondary level of acetylation regulation that does not involve control of HAT-nucleosome interactions.

overall_design: MNase-based ChIP-seq for Sas3-6HA, H3K23ac and H3K4me3

first: Kristina

last: McBurney

first: Julie

last: Brind'Amour

first: LeAnn

last: Howe


title: Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa

status: Public on Jan 01 2017

city: Portland

first: Michael

last: Rountree

state: OR

address: 3429 NE Sandy Blvd. #330

institute: Nzumbe, Inc.

summary:
Whole-Genome Bisulfite Sequencing of HCHC mutants
To extend our understanding of the role of the HCHC complex in Neurospora, we carried out whole-genome bisulfite sequencing (WGBS) of cdp-2, chap, and hda-1 mutants.  Consistent with prior analyses, the WGBS revealed both hypomethylated and hypermethylated regions in the three HCHC mutants while the ; sequences with a lower Combined RIP Index (CRI) tend to show reduced methylation in the mutants, while sequences with higher CRI scores show increased methylation.  Analysis of the WGBS data also demonstrated that shorter methylated regions, regardless of their degree of methylation in wild type, commonly have reduced methylation in the HCHC mutants, while longer methylated sequences tend to have elevated methylation.  In addition, the borders of normally methylated regions typically lose methylation and show a contraction of boundary methylation in the HCHC mutants.  Sequences near telomeres that are normally methylated were found to lose methylation in the mutants, while most of the increased DNA methylation of the three HCHC mutants is found at centromeres.

CHAP in vitro DNA-affinity purification HT-seq and CHAP DamID-Seq
To test whether the CHAP AT-hook motifs bind AT-rich RIP’d DNA, we performed in vitro DNA-affinity purification with the recombinant CHAP-N-terminus (1-274 residues) containing the two AT-hook motifs and analyzed the purified DNA with high throughput sequencing (HT-Seq). To complement this approach, we also assessed binding of CHAP in vivo with DamID-seq using the CHAP-Dam strain. Together, these techniques gave us a detailed genomic view of the specific localization and binding of CHAP to AT-rich RIP’d DNA, which is nearly coincident with methylated DNA regions.

overall_design:
Whole Genome Bisulfite-Seq and analysis of Neurospora crassa's four HCHC mutants (hda-1, cdp-2, chap, and hpo) and a wild type control strain.

In vitro DNA-affinity purification using the amino terminus of the CHAP protein followed by high-throughput sequencing.  DamID-seq analysis of CHAP-Dam in vivo binding.

The CHAP AT-hook motifs specifically bind highly RIP?d/AT-rich DNA

first: Eric

middle: U

last: Selker

first: Vincent

last: Bicocca


title: CHD7 controls cerebellar development via Reelin

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

institute: King's College London

summary: Mutation of the gene encoding the ATP-dependent chromatin remodeler CHD7 causes CHARGE syndrome. The mechanisms underlying the neurodevelopmental deficits associated with the syndrome, which include cerebellar hypoplasia, developmental delay, coordination problems and autistic features, are not known. CHD7 is expressed in neural stem and progenitor cells, but its role in neurogenesis during brain development remains unknown. Here we show that deletion of Chd7 from cerebellar granule cell precursors (GCps) in the mouse results in reduced GCp proliferation, cerebellar hypoplasia, developmental delay and motor deficits. Genome-wide expression profiling revealed downregulated Reln gene expression in Chd7-deficient GCps. Recessive RELN mutations is associated with severe cerebellar hypoplasia in humans. We provide molecular and genetic evidence that reduced Reln expression contributes substantially to the GCp proliferative defect and cerebellar hypoplasia in GCp-specific Chd7 mouse mutants. Finally, we show that CHD7 is necessary for the maintenance of an open, accessible chromatin state at the Reln locus. Taken together, this study shows that Reln gene expression is regulated by chromatin remodeling, identifies CHD7 as a previously unrecognized upstream regulator of Reln and provides the first evidence that a mammalian CHD protein controls brain development by modulating chromatin accessibility in neuronal progenitors in vivo.

overall_design:
Examination of the chromatin profile by ATACseq in 3 replicates of control and 3 replicates of Chd7-deficient cerebellar granule cell precurosers (GCps).
Examination of the mRNA profile by RNA-seq in 2 replicates of control and 2 replicates of  Chd7-deficient cerebellar granule cell precurosers (GCps).
Investigation of H3K4me1 binding events throughout the genome by ChIP-seq of Control cells.

first: Danielle

middle: E

last: Whittaker

first: Kimberley

last: Riegman

first: Sahrunizam

last: Kasah

first: Conor

last: Mohan

first: Tian

last: Yu

first: Blanca

middle: P

last: Sala

first: Husam

last: Hebaishi

first: Angela

last: Caruso

first: Ana

last: Marques

first: Caterina

last: Michetti

first: María

last: Smachetti

first: Apar

last: Shah

first: Mara

last: Sabbioni

first: Omer

last: Kulhanci

first: Wee-Wei

last: Tee

first: Danny

last: Reinberg

first: Maria

last: Scattoni

first: Holger

last: Volk

first: Imelda

last: McGonnell

first: Fiona

last: Wardle

first: Cathy

last: Fernandes

first: M


title: Molecular classification of Crohn’s disease reveals two clinically relevant subtypes

status: Public on Dec 11 2016

city: Chapel Hill

first: Shehzad

last: Sheikh

state: NC

address: 5023A Genetic Medicine Building

institute: University of North Carolina - Chapel Hill

summary: Objective: The clinical presentation and course of Crohn’s disease (CD) is highly variable. We sought to better understand the cellular and molecular mechanisms that guide this heterogeneity, and characterize the cellular processes associated with disease phenotypes. Design: We examined both gene expression and gene regulation (chromatin accessibility) in non-inflamed colon tissue from a cohort of adult CD and control patients. To support the generality of our findings, we analyzed previously published expression data from a large cohort of treatment-naïve pediatric CD and control ileum. Results: We found that adult CD patients clearly segregated into two classes based on colon tissue gene expression—one that largely resembled the normal colon and one where certain genes showed expression patterns normally specific to the ileum. These classes were supported by changes in gene regulatory profiles observed at the level of chromatin accessibility, reflective of a fundamental shift in underlying molecular phenotypes. Further, gene expression from the ilea of the treatment-naïve pediatric CD patient cohort could be similarly subdivided into colon- and ileum-like classes. Finally, expression patterns within these CD subclasses highlight large-scale differences in the immune response and aspects of cellular metabolism, and were associated with multiple clinical phenotypes describing disease behavior, including rectal and perianal disease and need for colectomy.  Conclusion: Our results strongly suggest that these molecular signatures define two clinically relevant forms of CD irrespective of tissue sampling location, patient age or treatment status.

overall_design:
Gene expression and chromatin accessibility in macroscopically uninflamed biopsies of the colonic mucosa in Crohn's disease and non-IBD controls.

Submitter states that due to patient privacy concerns, all raw data will be submitted to dbGaP (controlled access).

first: Jeremy

middle: M

last: Simon

first: Matthew

last: Weiser

first: Terrence

last: Furey

middle: Z


title: Genome-Wide Transcriptional Profiling of Salmonella Typhimurium Epiphytically Colonizing Tomato Points to Anaerobic Respiration, and Nitrosative and Oxidative Stress Responses

status: Public on Sep 17 2016

city: Wan-Ju-Goon

first: Sanghyun

last: Han

address: 166 Nong-Saeng-Myung-Ro

institute: RDA-NAAS

summary: Foodborne illness from contaminated fresh produce has increased over the past decade, with the enteric human pathogen Salmonella enterica being frequently implicated in foodborne illness outbreaks associated with tomato consumption. Our previous work demonstrated that Salmonella responds to tomato cultivar differences, but knowledge of the underlying genetic responses is limited. To identify the mechanisms permitting this human pathogen-plant commodity association, a genome-wide transcriptomic analysis of Salmonella on tomato shoots and roots was conducted using an RNA-seq approach. Expression signal for 4,556 out of 4,745 annotated chromosomal and plasmid genes was obtained, indicating >96% coverage of the whole S. Typhimurium transcriptome. Identified key signals of differential expression related to cellular processes preserving viability while dealing with multiple biotic stresses and limited nutrient availability, compared to growth in nutrient-rich medium. Data suggest that sulfur metabolism, anaerobic respiration, nitrosative and oxidative stress tolerance and biofilm formation may be crucial functions for Salmonella survival on tomato.  Some effector protein genes from pathogenicity island-2 were expressed, though their function in this niche is largely unknown. A large proportion of up-regulated genes remain uncharacterized, pointing to as yet undescribed strategies that allow enteric pathogens to associate with plants during transit in the environment to herbivorous hosts.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: mRNA profiles of Salmonella Typhimurium while epiphytically colonizing tomato plants were generated by RNA-seq, in triplicate, using Illumina HiSeq 100bp-PE.

first: Angela

last: Ferelli

first: Shih-Shun

last: Lin

first: Shirley

middle: A

last: Micallef


title: Gene expression of dysfunctional CD8+ T cells from the tumor microenvironment

status: Public on Apr 05 2016

city: Chicago

first: Jason

middle: B

last: Williams

state: Illinois

address: 929 E. 57th St GCIS W423H

department: Pathology

institute: University of Chicago

summary: Although the presence of tumor-infiltrating lymphocytes (TILs) indicates an endogenous anti-tumor response, immune regulatory pathways can subvert the effector phase and enable tumor escape.  Negative regulatory pathways include extrinsic suppression mechanisms but also a T cell-intrinsic dysfunctional state.  A more detailed study has been hampered by a lack of cell surface markers defining dysfunctional TILs, and it is clear that PD-1 alone is not sufficient.  Recently, we identified the transcription factor Egr2 as a critical component in controlling the anergic state in vitro.  In the current study we show that the Egr2-driven cell surface proteins, LAG-3 and 4-1BB, identify dysfunctional tumor antigen-specific CD8+ TIL.  Co-expression of 4-1BB and LAG-3 was seen on a majority of CD8+ TIL but not in lymphoid organs. Functional analysis revealed defective IL-2 and TNF-α production yet retained expression of IFN-γ and Treg-recruiting chemokines. Transcriptional and phenotypic characterization revealed co-expression of multiple additional co-stimulatory and co-inhibitory receptors.  Administration of anti-LAG-3 plus anti-4-1BB mAbs was therapeutic against tumors in vivo, which correlated with a reversal of TIL dysfunction and restored effector phenotype.  Our results indicate that co-expression of LAG-3 and 4-1BB characterize dysfunctional T cells within tumors, and that targeting these receptors has therapeutic utility.

overall_design: 10 female mice purchased from Taconic farms were engrafted on both flanks with 2 million B16.SIY.dsRed tumor cells. After 14 days tumors were pooled, dissociated through a 50μm filter and washed with PBS 3-4 times.  TILs were further enriched by layering Ficoll-Hypaque beneath the cell suspension followed by centrifugation without breaks for 30 min at 400 x g.  The buffy-layer was isolated and washed twice with PBS before staining.  Cells were sorted into RLT (QIAGEN) buffer and directly transferred to dry ice. RNA was isolated using the RNAeasy Micro RNA isolation Kit (QIAGEN) and submitted for QC and subsequent microarray analysis at the University of Chicago Genomics Core.

first: Brendan

last: Horton

first: Thomas

middle: F

last: Gajewski


title: Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 diabetic donors.

status: Public on Jul 05 2016

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

summary: We successfully sequenced and annotated more than 400 cells from child, adult control, type 1 diabetes and type 2 diabetes donors. We detect donor-type specific transcript variation. We also report that cells from child donors have less defined gene signature. Cells from type 2 diabetes donors resemble juvenile cells in gene expression.

overall_design: Cells from three adult controls (56, 74, 92), one donor with type 1 diabetes (91), two donors with type 2 diabetes (75, 143), and two child donors (40, 72) were sequenced. Numbers in parathesis indicates number of cells sequenced.

first: Yue

middle: J

last: Wang

first: Maria

last: Golson

first: Kyoung-Jae

last: Won

first: Chengyang

last: Liu

first: Ali

last: Naji

first: Dana

last: Avrahami

first: Klaus

last: Kaestner


title: Tight Junction Protein 1 is a Modulator and Biomarker of Proteasome Inhibitor Sensitivity in Multiple Myeloma

status: Public on Dec 31 2015

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Proteasome inhibitors are important chemotherapeutics in the treatment of multiple myeloma, but they are currently used empirically as no markers of sensitivity have been validated.  We have identified expression of tight junction protein (TJP) 1 as being associated with sensitivity of plasma cells in vitro and in vivo to proteasome inhibitors.  TJP1 suppressed expression of genes in the major histocompatibility class II region, including two catalytically active immunoproteasome subunits, thereby decreasing proteasome activity, a critical determinant of proteasome inhibitor sensitivity.  This occurred through suppression by TJP1 of signaling through the epidermal growth factor receptor/Janus kinase 1/signal transducer and activator of transcription 3 pathway.  In the clinic, high TJP1 expression in myeloma patients was associated with a significantly higher likelihood of responding to bortezomib, and with a longer time-to-progression after treatment.  Taken together, these data support the use of TJP1 as a biomarker of sensitivity and resistance to proteasome inhibitors.

overall_design: To further elucidate mechanisms of bortezomib resistance, we developed human-derived multiple myeloma cell lines with a 4-fold or greater resistance to bortezomib. Then total RNA for bortezomib resistant (BR) and wild type (WT) was extracted and used for comparison by gene expression profiling.

first: Deborah

last: Kuhn

first: Zhiqiang

first: R

last: Davis

first: Xingding

last: Zhang

first: Robert

last: Orlowski


title: Exon array of heart samples of myotonic dystrophic patients

status: Public on Jan 21 2016

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary: Analysis of alternative splicing of left ventricles heart samples of 3 DM1 adult versus 3 adult controls

overall_design: PolyA RNA from left ventricles (heart) of 3 controls and 3 DM1 patients were analysed on Exon Array (Affymetrix)

first: Nicolas

last: Charlet-Berguerand

first: Masanori

last: Takahashi

first: Christelle

last: Thibault-Carpentier


title: Furin deficiency effect on T cells

status: Public on Aug 05 2015

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

summary: Analysis of T-cells lacking the proprotein convertase furin. Proprotein convertases promote the proteolytic maturation of proproteins. Furin is induced in activated T-cells. Results provide insight into the function of furin in T-cells.

overall_design: CD4+CD62L+CD44- naive, CD4+CD62L-CD44+ memory and CD4+CD25+FoxP3+ regulatory T cells were isolated from Fur flox/flox and CD4 cre Fur flox/flox mice. Naive T cells were activated via TCR. Total RNA was extracted from all cells and hybridized to Affymetrix microarrays.

first: Marko

last: Pesu

first: Wendy

last: Watford

first: Lai

last: Wei

first: Lili

last: Xu

first: Ivan

last: Fuss

first: Warren

last: Strober

first: John

last: Andersson

first: Ethan

last: Shevach

first: Martha

last: Quezado

last: Bouladoux

first: Anton

last: Roebroek

first: Yasmine

last: Belkaid

last: Creemers

last: O´Shea

first: Zsuzsanna

last: Ortutay

first: Anna

last: Oksanen

first: Saara

last: Aittomäki

first: Csaba


title: Gene Expression Profile of Pulpitis

status: Public on Feb 03 2016

first: Asma

last: Khan

address: 1170 Old Dental Building CB 7450

department: Division of Endodontics

institute: UNC School of Dentistry

summary: This study was aimed to identify the genetic contributors to pulpal pain and inflammation. Inflamed pulps were collected from patients diagnosed with irreversible pulpitis (n=6). Normal pulps from teeth extracted for various reasons served as controls (n=6). Pain level was assessed using a visual analog scale (VAS). Genome-wide microarray analysis was performed using Affymetrix GeneTitan Multichannel Instrument. The difference in gene expression levels were determined by the Significance Analysis of Microarray program using a false discovery rate (q-value) of 5%.  Genes involved in immune response, cytokine-cytokine receptor interaction and signaling, integrin cell surface interactions, and others were expressed at relatively higher levels in the pulpitis group. Moreover, several genes known to modulate pain and inflammation showed differential expression in asymptomatic and mild pain patients  compared to those with moderate to severe pain(>30mm on VAS). This exploratory study provides a molecular basis for the clinical diagnosis of pulpitis. With an enhanced understanding of pulpal inflammation, future studies on treatment and management of pulpitis and on pain associated with it can have a biological reference to bridge treatment strategies with pulpal biology.

overall_design:
12 samples were analyzed;
Inflamed pulps were collected from patients diagnosed with irreversible pulpitis (n=6).
Normal pulps (controls; n=6) from teeth extracted for various reasons (i.e. not from patients diagnosed with irreversible pulpitis)

first: Johnah

middle: C

last: Galicia

first: Brett

middle: R

last: Henson

first: Joel

middle: S

last: Parker


title: Identification of oral carcinoma miRNA involved in Wnt/b-catenin signaling

status: Public on Jan 07 2015

city: Zhunan

first: Shine-Gwo

last: Shiah

state: Miaoli County

address: No. 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary: MicroRNAs (miRNAs) participate in many biological processes and have emerged as key players in carcinogenesis. In order to identify changes in miRNAs specific for betelquid-associated oral squamous cell carcinoma (OSCC), we investigated the expression profiles of 858 miRNAs in a panel of 40 pairs of OSCC specimens and their matched non-tumorous epithelial counterparts. Eighty-four miRNAs were differentially expressed in the OSCC specimens compared to the matched tissue. Among these miRNAs, 19 downregulated miRNAs located in the chromosome 14q32.2 miRNA cluster region were analyzed. This miRNA cluster resides within a parentally imprinted region known to be important in development and growth. The re-expression of miR-329 and miR-410from this cluster significantly reduced OSCC cell proliferation and invasion and downregulated Wnt-7b, an activator of the Wnt/b-catenin pathway. Furthermore, the expression of those 2 miRNAs was restored by 5-aza-2′-deoxycytidine treatment and the expression levels of the 2 miRNAs were inversely correlated with the hypermethylation of the Meg-3 promoter in OSCC cells. Specifically, arecoline, a major betel nut alkaloid, reduces miR-329 and miR-410 expression. Our results thus provide a novel molecular insight into how betel quid may contribute to oral carcinogenesis through the epigenetic silencing of tumor suppressor miRNAs targeting the Wnt/b-catenin signaling pathway.

overall_design: Total RNA was obtained  from 40 pairs of OSCC patients with tumor specimens and their adjacent non-tumorous epithelia.

first: Jenn-Ren

last: Hsiao

first: Jang-Yang

last: Chang


title: Transcriptomic analysis of Primary duck hepatocyte with differential susceptibility

status: Public on Mar 09 2016

city: Shanghai

first: LIANG

last: YAN

address: NO 131, Dongan Road

institute: Fudan University

summary:
Our aim was to classify and quantify transcripts in primary duck hepatocytes cultured in medium with 5% FBS or 1.5% DMSO for 8 days.
Methods: The transcriptome of PDHs under different conditions was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters.

overall_design: The transcriptome of PDHs under different culture conditions were analyzed by the paired-end sequencing on the Illumina Solexa platform.

first: Liang

last: Yan

first: Di

last: Qu


title: SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

status: Public on Dec 26 2014

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Specification of primordial germ cells (PGCs) marks the beginning of the totipotent state. However, without a tractable experimental model, the mechanism of human PGC (hPGC) specification remains unclear. Here, we demonstrate specification of hPGC-like cells (hPGCLCs) from germline competent pluripotent stem cells. The characteristics of hPGCLCs are consistent with the embryonic hPGCs and a germline seminoma that share a CD38 cell-surface marker, which collectively defines likely progression of the early human germline. Remarkably, SOX17 is the key regulator of hPGC-like fate, whereas BLIMP1 represses endodermal and other somatic genes during specification of hPGCLCs. Notable mechanistic differences between mouse and human PGC specification could be attributed to their divergent embryonic development and pluripotent states, which might affect other early cell-fate decisions. We have established a foundation for future studies on resetting of the epigenome in hPGCLCs and hPGCs for totipotency and the transmission of genetic and epigenetic information.

overall_design: RNA-Seq analysis to investigate transcriptomes of hPGC-like cells (hPGCLCs), fetal hPGCs, TCam-2 and hESCs

first: N

last: Irie

first: L

last: Weinberger

first: W

last: Tang

first: T

last: Kobayashi

first: S

last: Viukov

first: Y

last: Manor

first: J

last: Hanna

first: M

last: Surani


title: Neurospora crassa genome organization requires subtelomeric facultative heterochromatin

status: Public on Oct 27 2016

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

summary: Facultative heterochromatin in the filamentous fungus Neurospora crassa is identified by the repressive histone mark H3K27me3 and is primarily subtelomeric, while constitutive heterochromatin, marked by the DIM-5-catalzyed H3K9me3, is found at centromeres, telomeres, and smaller dispersed regions. In strains lacking constitutive heterochromatin (e.g., Δdim-5), H3K27me2/3 relocalizes to the regions formerly marked by H3K9me3. H3K27me3 is catalyzed by the SET-7 histone methyltransferase subunit of the Polycomb Repressive Complex 2 (PRC2); another PRC2 member, Neurospora p55 (NPF) regulates subtelomeric H3K27me2/3. Despite the de-repression of >70 genes, a Δset-7 strain has no distinguishable phenotype. To investigate the facultative heterochromatin contribution to genome organization, we performed high-throughput “chromosome conformation capture” (Hi-C) on mutants with impacted H3K27me2/3 deposition. A Δset-7 strain has decreased inter-/intra-subtelomeric contacts among others; this pattern is mirrored in a Δnpf strain, which lacks subtelomeric H3K27me3. In a Δset-7 strain, telomere bundles were often uncoupled from the nuclear membrane and de-repressed genes were subtelomeric. The chromosome conformation of a Δset-7;Δdim-5 double mutant was similar to Δset-7, suggesting that facultative heterochromatin relocalization does not compensate for H3K9me3 loss and rescue the Neurospora genome organization in strains with defective constitutive heterochromatin.

overall_design:
Hi-C: We analyzed a total of three strains of Neurospora crassa by chromatin conformation capture followed by high throughput sequencing (Hi-C).  Each strain has two replicates. Strains were grown from conidia ~4 hours, crosslinked, and conidia were made into spheroplasts. Genomic DNA from spheroplasts was digested with HindIII, ends were filled in with dNTPs (including biotin-conjugated dCTP), blunt ends were ligated, crosslinks were reversed, DNA was soniciated, ligation products were purified with streptavidin beads, and libraries were prepared for sequencing. The datasets of wild type strain, NMF39 - deposited in GEO sebmission GSE71024, serves as the reference for the mutants deficient in facultative heterochromatin formation (N4718 delta set-7, N4721 delta npf, and N5542 delta set-7;delta dim-5).

ChIP-seq: We analyzed two strains of Neurospora crassa (control strain: WT N3752, test strain delta npf N4721) by Chromatin Immunoprecipitation for the histone mark H3K27me3. Strains were grown, crosslinked, lysed, the histone mark H3K27me3 was immunopurified, and associated DNA was sequenced).

RNA-seq: We analyzed a total of five strains (four different genetic backgrounds) by poly-A+ mRNA-sequencing for gene expression changes by monitoring poly-adenylated messenger RNA levels. A wild type strain (N3752) serves as the reference strain, and the strains N4718 and N4730 (delta set-7), N4721 (delta npf), and N5916 (delta set-7;delta dim-5) served as the test strains.

Please note that all python scripts (".py.txt" files) are provided as series supplementary file.

middle: D

first: Tereza

last: Ormsby

first: Jonathan

last: Galazka

first: Miki

last: Uesaka

first: Neena

last: Leggett

first: Shinji

last: Honda

first: Michael

last: Freitag

first: Eric

last: Selker


title: Gene expression analysis of human seminoma samples

status: Public on Feb 21 2014

city: Munich

last: Abend

address: Neuherbergstr. 11

institute: Bundeswehr Institute of Radiobiology

summary:
Purpose:
The aim of the present study was to examine the biological differences between seminomas with occult and clinically apparent metastases at the time of diagnosis of the primary tumor to gain insight into the biology of these tumors and facilitate the identification of novel predictors of seminoma metastasis.
Materials and Methods:
Total RNA including small RNAs was isolated from testicular tumors of patients with pure seminoma presenting with lymphogenic metastasis (n=5, clinical stage IIb/c) and occult metastasis (n=5, clinical stage I). The regulation of biological processes was examined (1) throughout the mRNA transcriptome (whole genome microarrays, 8x60K Array, Agilent and 4 samples per group) and (2) the miRNA transcriptome employing small RNA next generation sequencing (SOLID, Life Technologies). Protein coding genes (mRNAs) and small RNAs showing a significant (> 2-fold) difference between the groups were identified. Finally (3), we examined 95 candidate miRNAs in 36 apparent metastasized and another 5 occult metastasized seminoma using logistic regression analysis.
Results:
Among 19,596 genes, on average 12,894 mRNAs appeared expressed (65.8%, SD +/- 2.4; range, 62.0–69.3%) and 16.99×106/13.94×106 small RNA reads were identified for apparent/occult metastasized seminoma. These reads on average convert into 9,901/9,675 small RNAs including 422/404 mature microRNAs. None of these mRNAs/small RNAs met our selection criteria for candidate genes. From 95 candidate miRNAs 44 appeared expressed, with 3 of them showing weak but significant (p=0.047-0.049) differences among both groups.
Conclusions:
Occult and apparent metastasized seminomas are biologically almost indistinguishable and probably represent no separate tumor entities. These findings may simplify future research on seminoma metastasis.

overall_design:
Regarding the genome-wide expression profiling we analyzed gene expression changes in human seminoma samples with occult or lymphatic metastasis using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays in 8x60K format in combination with a one-color based hybridization protocol. Microarray signals were detected using the Agilent DNA Microarray Scanner. Differential RNA expression was assessed by applying appropriate biostatistics to the data set. GeneSpring GX12.6 analysis software was used to normalize and analyze the raw data. Different filtering approaches were applied to identify up- and downregulated transcripts in the comparisons of interest. Identified differentially expressed genes were further characterized for their involvement in biological pathways and processes based on the Panther database.
For mRNA transcriptome analysis we used 4 samples per group. Only significant and > 2-fold differences in gene expression between the two groups were considered for comparisons, and unadjusted p-values and those adjusted for multiple comparisons (false discovery rate) were calculated. All gene candidates underwent gene set enrichment analyses using PANTHER pathway software (http://www.pantherdb.org/), which groups genes with similar biological functions based on their annotation.

first: C

last: Ruf

last: Port


title: liver cancer tissues: tumor tissues vs. non-tumor tissues

status: Public on May 29 2014

city: guangzhou

first: Chuanhui

last: Cao

state: guangdong

address: 1838 guangzhoudadaobeiroad

department: Department of Radiation Oncology

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China

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

summary: lncRNAs and mRNAs profiling of tissues from HCC patients comparing tumor tissues with non-tumor tissues.

overall_design: Two-condition experiment, tumors vs. non-tumors. Biological replicates: 7 tumor replicates, 7 non-tumor replicates.

first: Li

last: Liu


title: Identification of a gene expression signature in colorectal adenoma in comparison with normal mucosa

status: Public on Aug 27 2013

city: Brest

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

institute: INSERM U1078-ECLA

summary: We showed that a large number of genes were deregulated in colorectal adenomas in comparison with colorectal normal mucosae.

overall_design: 37 colorectal adenoma and 9 colorectal normal mucosa samples were analyzed. We generated a comparison between adenomas and normal mucosae.

first: Marine

last: Pesson

first: Alain

last: Volant

first: Kilian

last: Trillet

first: Pierre

last: De La Grange

first: Mélanie

last: Daoulas

first: Michel

last: Robaskiewicz

first: Gérald

last: Le Gac

last: Morel

first: Brigitte

last: Simon


title: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

status: Public on Nov 14 2014

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: We used mouse ENCODE data along with complementary data from other laboratories to study the dynamics of occupancy and the role in gene regulation of the transcription factor TAL1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation. We combined ChIP-seq and RNA-seq data in six mouse cell types representing a progression from multilineage precursors to differentiated erythroblasts and megakaryocytes. We found that sites of occupancy shift dramatically during commitment to the erythroid lineage, vary further during terminal maturation, and are strongly associated with changes in gene expression. In multilineage progenitors, the likely target genes are enriched for hematopoietic growth and functions associated with the mature cells of specific daughter lineages (such as megakaryocytes). In contrast, target genes in erythroblasts are specifically enriched for red cell functions. Furthermore, shifts in TAL1 occupancy during erythroid differentiation are associated with gene repression (dissociation) and induction (co-occupancy with GATA1). Based on both enrichment for transcription factor binding site motifs and co-occupancy determined by ChIP-seq, recruitment by GATA transcription factors appears to be a stronger determinant of TAL1 binding to chromatin than the canonical E-box binding site motif. Studies of additional proteins lead to the model that TAL1 regulates expression after being directed to a distinct subset of genomic binding sites in each cell type via its association with different complexes containing master regulators such as GATA2, ERG, and RUNX1 in multilineage cells and the lineage-specific master regulator GATA1 in erythroblasts.

overall_design:
Combined ChIP-seq and RNA-seq data in six mouse cell types representing a
progression from multilineage precursors to differentiated erythroblasts and megakaryocytes.

first: Weisheng

last: Wu

first: Christapher

last: Morrissey

first: Cheryl

last: Keller

first: Tejaswini

last: Mishra

first: Maxim

last: Pimkin

first: Gerd

last: Blobel

first: Mitchell

last: Weiss

first: Ross

last: Hardison


title: Identification of a gene expression signature in colorectal adenocarcinoma in comparison with normal mucosa

first: Laurent

last: Corcos

summary: We showed that a large number of genes were deregulated in colorectal adenocarcinomas in comparison with colorectal normal mucosae.

overall_design: 9 paired tumor-normal colorectal samples were analyzed. We generated a comparison between adenocarcinomas and normal mucosae.

first: Marine

last: Pesson

last: Volant