title: Transcriptional profiles of human CD14+ monocytes conditioned with melanoma exosomes [miRNA expression]

summary: We analyzed gene and microRNA expression profiles of purified CD14 monocytes isolated from blood of 5 healthy donors after 24 h of in vitro co-culture with exosomes exosomes isolated from the INT12 melanoma cell line generated in our laboratory from a human melanoma specimen. Differentially expressed genes and miRNAs were identified between treated and untreated monocytes.

overall_design: Gene and microRNA expression profiles of CD14+ monocytes co-cultered with melanoma exosomes (five biological replicates) were compared to those of untreated CD14+ monocytes (five biological replicates).

first: Licia

last: Rivoltini

first: Monica

last: Rodolfo

first: Loris

last: De Cecco


title: Identification of gene signature in human colorectal CD44+ cancer stem cells

status: Public on Nov 09 2018

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University

summary: We prospectively isolated human colorectal CD44+ cancer stem cells (CSCs) from organoids and primary colorectal cancer. The gene expression of CD44+ CSCs are relevant to each other between organoids and primary tissues. The common gene signature in two different modality identifies CSCs' properties with the biological significance shown in original article.

overall_design: Gene expression profiles of primary colorectal cancer cells and organoids, which were purified into CD44- and CD44+ fraction by cell sorting, were analyzed.

first: Kohta

last: Miyawaki


title: USP7 controls the oncogenic transcriptional circuitry and is a novel therapeutic target in T cell leukemia

status: Public on Nov 01 2018

city: Chicago

first: Panagiotis

last: Ntziachristos

state: IL

address: 320 E Superior

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we chemically inhibited the deubiquinating enzyme USP7 and assayed for gene expression changes. This piece of data was further integrated to epigenetic changes using ChIP-Sequencing analysis of H3K27me3, H2AUb, H2BUb, H3K27Ac and H3K79me2 upon inhibition of USP7. These results coupled helped to determine the role of USP7 in stabilizing and promoting T-ALL leukemia. We also compared the gene expression and epigenetic changes of USP7 inhibition with inhibition of NOTCH1 pathway and JMJD3.

overall_design:
[USP7 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against USP7 (Bethyl, A300-033A).
[H3K79me2 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K79me2 (homemade, Ali Shilatifard lab)
[H3K27me3 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K27me3 (Cell Signaling Technology, 9733S).
[H2AUb ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H2AUb (Cell Signaling Technology, 8240S).
[H2BUb ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H2BUb (Cell Signaling Technology, 5546S).
[H3K27Ac ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K27Ac (Cell Signaling Technology, 8173S).
[RNA-Seq]: 1-5 million primary cells from CUTLL1 human T cell leukemia cells treated with the following inhibitor: 1 micromolar USP7 inhibitor, 1 micromolar GSI, 2 micromolar GSKJ4 and 1 micromolar DMSO.
[RNA-Seq]: 1-5 million primary cells from JURKAT human T cell leukemia cells treated with the following inhibitor: 1 micromolar USP7 inhibitor and 1 micromolar DMSO.
[RNA-Seq]: 3-5 million primary cells from JURKAT human T cell leukemia cells treated with shUSP7 or empty vector (PLKO).
[RNA-Seq]: 1-5 million primary cells from JURKAT human T cell leukemia cells treated with the following inhibitors: 1 micromolar GSI, 500 nanomolar JQ1, and 1 micromolar DMSO.

first: Carlos

last: Martinez


status: Public on Oct 26 2018

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

summary: Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after 120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3-ends that can be used by DNA polymerase to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggests a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria.

overall_design: Mapping 5´-ends in mithonchondrial DNA from human cells (healthy fibroblast cells as well as fibroblast cells from RNase H1 patients), via 5´-End-seq (end sequencing of genomic fragments generated) and HydEn-seq (end sequencing of genomic fragments generated by alkaline hydrolysis).

first: Viktor

last: Posse

first: Ali

last: Al-Behadili

first: Jay

middle: P

last: Uhler

first: Anders

middle: R

first: Aurelio

last: Reyes

first: Massimo

last: Zeviani

first: Maria

last: Falkenberg

first: Claes

middle: M

last: Gustafsson


title: Gene expression data of fibroblasts with differential Gli1 expression in the colon.

status: Public on Oct 27 2018

city: Amsterdam

first: Olga

middle: N

last: Karpus

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal research

country: Netherlands

institute: Academic Medical Center

summary:
The morphogen Indian Hedgehog is expressed by the intestinal epithelium and signals in paracrine manner to fibroblasts by activating trascription factor Gli1. ZsGreen is used to track Gli1+ cells.
To describe different fibroblast subpopulations we used gp38 as a general marker and Sca1 as a marker expressed in some of gp38+ cells.

overall_design: Fibroblasts from colon tissue from Gli1CreERT2-ZsGreen mice were isolated and Epcam-CD45-CD31-gp38+ fibroblasts were flow-sorted based on expression of Sca1 and Gli1ZsGreen generating 4 fibroblast subpopulations from 4 different mice: 1.Sca1+Gli1ZsGreenhigh, 2.Sca1+Gli1ZsGreendim, 3.Sca1+Gli1ZsGreen- and 4.Sca1-Gli1ZsGreen-.

first: O

first: G

last: van den Brink


title: Transcriptome analysis of V336Y mutant mitochondrial ribosomal protein in human HEK293 cell line

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: Analysis of HEK293 cells lines expressing V336Y mutant mitochondrial ribosomal protein.

overall_design: mRNA profiles of wild-type and V336Y mutant HEK293 cell culture samples generated by deep sequencing.

first: Dimitri

last: Scherbakov

first: Erik

middle: C

last: Böttger


title: Circadian Clock Regulation of Hepatic Lipid Metabolism by Modulation of m6A mRNA Methylation [Bmal1 KO]

status: Public on Oct 25 2018

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: No. 6, Tongwei Road, Xuanwu District

department: College of Animal Science and Technology

country: China

institute: Nanjing Agricultural University

summary: Circadian transcriptional rhythms are necessary for lipid metabolic homeostasis. Disruptions can lead to metabolic diseases. Whether epigenetic N6-methyladenosine (m6A) mRNA methylation impacts circadian regulation of lipid metabolism is unclear. Here, we show m6A mRNA methylation oscillations in murine liver depend upon a functional circadian clock. Hepatic deletion of Bmal1 increased m6A mRNA methylation, particularly of PPaRα. Inhibition of m6A methylation via knockdown of m6A methyltransferase METTL3 decreased PPaRα m6A abundance and increased PPaRα mRNA lifetime and expression, reducing lipid accumulation in cells in vitro. Our data suggest YTH domain family 2 (YTHDF2, a m6A binding protein) binds to PPaRα, prolonging its lifetime and mRNA expression. Reactive oxygen species accumulation increased PPaRα transcript m6A levels, revealing a possible mechanism for circadian clock disruption on m6A mRNA methylation. These data suggest m6A RNA methylation is important for circadian clock regulation of downstream genes and lipid metabolism that impacts metabolic outcome.

overall_design: Examination of  different m6A mRNA methylation  in WT and Bmal1 KO sample from HepG2 cell.

first: Vanessa

last: Leone

first: Jiayao

last: Yu

first: Xiaocheng

last: Weng

first: Yu

last: Li

first: Candace

last: Cham

first: Kyle

last: Dolan

first: Xiaorong

last: Zhu

first: Nathaniel

last: Hubert

first: Yun

last: Tao

first: Fanfei

last: Lin

first: Kristina

first: Yong

last: Huang

first: Tian

last: Wang

first: Jianzhao

last: Liu

first: Chuan

last: He

first: Eugene

middle: B

last: Chang


title: A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors [Illumina HumanMethylation]

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

type: Methylation profiling by genome tiling array

summary: We have generated and comprehensively characterized 30 patient-derived orthotopic xenograft (PDOX) models and 7 cell lines represeneting subgroups of medulloblastoma, high-grade glioma, atypical teratoid/rhabdoid tumor, ependymoma and pineoblastoma.

overall_design: 82 samples were profiled on IlluminaHumanMethylation450k arrays: 30 PDOX models (30 early passages, 23 late passages), 7 cell lines, 22 matching human tumors

first: Sebastian

last: Brabetz


title: A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors [Affymetrix]

overall_design: 55 samples (34 PDOX samples (30 different models),15 matching human tumors, 6 cell lines) were profiled on the Affymetrix Human Genome U133 Plus 2.0 array.


title: Microglia innatly develop within cerebral organoids

status: Public on Oct 22 2018

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

institute: UMC Utrecht

summary: Here we report that human organoid-grown microglia have transcriptional identity similar to that of human ex vivo adult primary microglia. By performing RNAseq on total coding RNA we show that crucial genes necessary for microglia development and identity are expressed at similar levels between the 2 groups.

overall_design: Comparison of organoid-grown microglia at 2 different time points with ex vivo adult microglia. 3 samples for each group were sequenced each from different donors, without replicates. After sequencing samples were compared with iPSC (n=4 different donors, no replicates) and fibroblast(n=3 different donors, no replicates) datasets containing the same donors used for organoid differentiation.

first: Paul

last: Ormel

first: Renata

last: Vieira de Sá

first: Emma

middle: J

last: van Bodegraven

first: Elly

last: Hol

first: Lot

middle: D

last: Witte


title: Diabetes Mellitus Drives Extracellular Vesicle Secretion and Promotes Increased Internalization by Circulating Leukocytes

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Type 2 diabetes mellitus is a chronic age-associated degenerative metabolic disease that reflects relative insulin deficiency and resistance. Extracellular vesicles (EVs; exosomes, microvesicles and apoptotic bodies) are small (50-400 nM) lipid-bound vesicles capable of shuttling functional proteins, nucleic acids, and lipids as part of intercellular communication systems. Recent studies in mouse models and in cell culture suggest that EVs may modulate insulin signaling. We designed a longitudinal and cross-sectional cohort of euglycemic, pre-diabetic and diabetic participants. Diabetic individuals had significantly higher levels of EVs in their circulation than euglycemic controls. We found that insulin resistance increases EV secretion through an autophagy-dependent mechanism. Furthermore, the levels of several proteins involved in insulin signaling were altered in EVs from individuals with high levels of insulin resistance and β-cell dysfunction. Moreover, EVs from diabetic individuals were preferentially internalized by circulating leukocytes. Microarray of these leukocytes revealed altered gene expression pathways related to cell survival, oxidative stress and immune function. Collectively, these results suggest that insulin resistance increases the secretion of EVs, which are preferential internalized by leukocytes and whose gene expression is subsequently altered by the internalized EVs.

overall_design: PBMC-derived monocyes were incubated with PBS (control, N=3) or with extracellular vesicles (EVs) from euglycemic (EU, N=3,samples, 1 technical repeat (TR)) or Type 2 diabetes mellitus (T2DM, diabetic, N=2, 2 TR ) individuals.

first: David

middle: W

last: Freeman

first: Nicole

last: Noren Hooten

first: Erez

last: Eitan

first: Jamal

last: Green

first: Nicolle

middle: A

last: Mode

first: Monica

last: Bodogai

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: Alan

last: Zonderman

first: Arya

last: Biragyn

first: Josephine

last: Egan

first: Kevin

middle: G

last: Becker

first: Mark

last: Mattson

first: Ngozi

last: Ejiogu

first: Michele

middle: K

last: Evans


title: A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors

first: Marcel

last: Kool

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

overall_design: Refer to individual Series


title: Cdk4-inhibitor induces tumor regression of Bladder cancer in vivo

city: Madrid

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

summary: Cdk4/6 inhibitors have shown to increase overall survival in hormone-positive breast tumors, but whether other solid tumors could respond to these inhibitors has not yet defined. Here we show that Palbociclib (a Cdk4/6 specific inhibitor in clinic use) treatment exerts antiproliferative effects in vivo using a bladder cancer cell lines.

overall_design: Gene expression was compared between bladder cancer cell lines with the same cell lines treated with Cdk4-inhibitor (IC50)

first: Carolina

last: Rubio

first: Mónica

last: Martínez-Fernández

first: Cristina

last: Segovia

first: Fernando

middle: F

last: Calderon

first: Marta

last: Dueñas

first: Jesús

last: Paramio


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum with TAP treatment

status: Public on Oct 20 2018

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from S Lycopersicum leafs were created using HD and standard Illumina adapters, with a TAP treatment; the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in M truncatula, without TAP treatment

summary: The sRNA population (sequence identity and distribution of abundances) in M truncatula was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from M truncatula leafs were created using HD and standard Illumina adapters, without a TAP treatment; the resulting libraries were compared side by side.

first: Archana

last: Singh


title: RNA seq analysis of human Fetal and adult derived Enterospheres

status: Public on Oct 17 2018

city: Boston

first: Stefania

last: Senger

state: MA

address: 114, 16th st. Charlestown, Navy Yard

department: Pediatrics

institute: Massachusetts General Hospital

summary: enterospheres (FEnS) from six aborted fetal’ small intestines, ranging in gestational age from 11 to 22.5 weeks ), and from adult duodenum AEnS  were generated based on previously developed protocols for human organoids cultures . We sought to compare the global gene expression profile of FEnS and AEnS by whole transcriptome shotgun sequencing (WTSS) analysis. We evaluated FEnS (N=6) and AEnS (N=3) samples at a low passage, ranging from P6 to P14.

overall_design: Examination of 2 groups of enterospheres (organoids) from human intestine  from Fetal and adult developmental age

first: Alessio

last: Fasano

first: W

last: Walker

first: Laura

last: Ingano

first: Rachel

last: Frere

first: Weishu

last: Zhu

first: Anthony

last: Anselmo

first: Ruslan

last: Sadreyev


title: Major impact of sampling methodology on gene expression in estrogen receptor positive breast cancer

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

summary: To investigate the impact of sampling methodology on gene expression data from primary estrogen receptor positive (ER+) breast cancer biopsies. Analysis of global gene-expression measured in core-cut biopsies at baseline and surgery from patients randomised to receive either 2-week’s presurgical aromatase inhibitor (AI, n=157) or no presurgical treatment (n=56) revealed genes most markedly altered in the AI group (e.g. FOS, DUSP1, RGS1, FOSB) were equally altered in the no-treatment group; some widely investigated genes that were apparently unaffected in the AI group (e.g. MYC) were counter-altered in the Control group masking actual AI-dependent changes. In the absence of a Control group these artefactual changes would likely lead to the most affected genes being the erroneous focus of research. The findings are likely relevant to all archival collections of ER+ breast cancer.

overall_design: Global gene-expression measured in core-cut biopsies at baseline and surgery from patients randomised to receive either 2-week’s presurgical aromatase inhibitor (AI, n=157) or no presurgical treatment (n=112).

first: Qiong


title: Cdk4-inhibitor induces tumor regression of Bladder cancer in vivo using a metastatic mouse model

status: Public on Oct 21 2018

first: Monica

last: Martinez-Fernandez

summary: Cdk4/6 inhibitors have shown to increase overall survival in hormone-positive breast tumors, but whether other solid tumors could respond to these inhibitors has not yet defined. Here we show that Palbociclib (a Cdk4/6 specific inhibitor in clinic use) + cisplatin (CDDP, a chemotherapeutic agent most active in locally or advanced bladder cancer patients) treatment exerts antiproliferative effects in vivo using a bladder cancer mouse model.

overall_design: Gene expression was compared between normal bladders from transgenic CKO mice (Rbf/f, Ptenf/f, Tp53f/f, p107-/- ), tumor bladders from CKO inoculated with Adeno-Cre in the bladder, bladders from CKO treated with Cdk4-inhibitor+CDDP, and metastasis from these mice.

first: Carolina

last: Rubio

first: Mónica

last: Martínez-Fernández

first: Cristina

last: Segovia


title: DNA methylation profiling of primary and metastasis ccRCC tumors

status: Public on Oct 16 2018

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 510 20th Street South

department: Urology

institute: UAB

summary: Current study focus on unraveling the promoter DNA methylation pattern changes in normal kidney, primary ccRCC and metastatic ccRCC tumors

overall_design: DNA methylation profile for 9 normal kidney, 9 primary ccRCC and 26 metastasis ccRCC tumors was analyzed

first: D

middle: S

last: Chandrashekar

first: S


title: N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA

first: Guan-Zheng

last: Luo

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago to exist in simple eukaryotes, yet functional studies have been limited. Recent investigations in multiple eukaryotes suggest 6mA as a potential DNA epigenetic mark that plays regulatory roles in gene regulation. Here we use Tetrahymena thermophila as a model to examine the effects of 6mA on nucleosome positioning. We have employed independent methods to identify genome-wide 6mA distribution, which revealed the enrichment after transcription start sites with a periodic pattern and a mutually exclusive relationship with the positions of nucleosomes. The exclusive distribution pattern of 6mA and nucleosome can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA, but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation revealed that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase disturbs the nucleosome positioning in Tetrahymena, leading to the transcriptome-wide change of gene expression. These findings uncover a new mechanism by which DNA 6mA assists to shape the chromatin topology in order to stabilize gene expression.

overall_design: Determine the 6mA sites in genome wide by using 6mA-IP-seq, 6mA-CLIP-exo and 6mA-RE-seq.Profile the nucleosome positioning by MNase. Measure the gene expression by RNA-seq

first: Chuan

last: He


title: Transcriptome analysis of normal kidney, primary and metastasis ccRCC

summary:
Understanding gene expression changes during transformation from normal tissue to primary RCC and then to metastasis is important. Such analysis is pivotal for undertanding biology in renal cancer and also to unearth novel gene targets.
Hence, we examined global transcriptome profile of normal renal tissue, primary RCC and metastasis RCC tumors, identifying important RCC biomarkers

overall_design: Transcriptiome profiling of normal (n=9), priamry ccRCC (n=9) and metastatic ccRCC (n=26) samples were done.


title: High-fidelity base editing mediated by Cpf1-cytidine deaminase fusion

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: C-to-T base editing mediated by CRISPR/Cas9 base editors (BEs) needs a G/C-rich PAM and the editing fidelity is compromised by unwanted indels and non-C-to-T substitutions. We developed CRISPR/Cpf1-based BEs to recognize a T-rich PAM and induce efficient C-to-T editing with few indels and/or non-C-to-T substitutions. The requirement of editing fidelity in therapeutic-related trials necessitates the development of CRISPR/Cpf1-based BEs, which also facilitates base editing in A/T-rich regions.

overall_design: Examination of indels and base substitutions induced by the CRISPR/Cpf1 base editors

first: Jia

last: Chen

first: Xingxu

last: Huang

first: Bei

first: Ying

last: Wang

first: Xiaosa

last: Li


title: ChIP-Seq in mouse embryonic stem cells of endogenous HA-tagged Tet1

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: R-loops are prevalent three-stranded nucleic acid structures, composed of a DNA:RNA hybrid and a displaced single-stranded DNA loop. Although aberrant R-loop formation is a threat to genome stability, R-loops are enriched at CpG islands (CGI) and are implicated in maintaining CGI promoters unmethylated. Mapping of genomic regions where Tet1 binds in an R-loop dependent manner we here identify almost exclusively CGIs. The results suggest that R-loops are genomic address labels for TET1.

overall_design: ChIP-Seq of endogenous HA-tagged Tet1 in E14TG2a mouse embryonic stem cells  (mESHA-Tet1)  was performed on permeabilized cells incubated with RNase H1 and Nuclease S1 or mock treated. Subsequently the cells were double crosslinked with disuccinimidyl glutarate (DSG) and formaldehyde. Fragmented chromatin was subjected to immunoprecipitation with HA antibody overnight.

first: Khelifa

last: Arab

first: Ingrid

last: Grummt

first: Christof

last: Niehrs


title: Patient-derived xenograft model identifies clinically relevant subtype-specific features of colorectal cancer

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

institute: AUMC

summary: Colorectal cancer (CRC) is a heterogeneous disease classified into four consensus molecular subtype (CMSs) with distinct biological and clinical features. This study aims to understand the value of patient-derived xenografts (PDXs) in relation to these CMSs. A total of 42 primary tumors, recurrences and metastases were used to develop PDXs. Detailed genetic analyses were performed on PDXs and corresponding patient tumors to determine relationship and PDX heterogeneity. Out of 42 tumors 22 (52%) showed successfully PDX engraftment, which was biased towards metastases and CMS1 and CMS4 tumors. Importantly, gene expression analysis revealed a clinical relevant association between an engraftment gene signature and prognosis for stage II patients. Moreover, this gene signature revealed an association between Src pathway activation and positive engraftment. Src pathway activity co-aligned with CMS4 and the levels of fibronectin in tumors and was confirmed by pSrc immunohistochemistry. From this analysis we further deduced that decreased cell cycle activity is a prognostic factor for successful engraftment and related to patient prognosis. However, this is not a general phenomenon, but subtype specific as decreased cell cycle activity was highly prognostic for recurrence-free survival within CMS2 but not in CMS1 and CMS4, while it showed an inverse correlation in CMS3. These data illustrate that CRC PDX establishment is biased toward CMS1 and CMS4, which impacts translation of results derived from pre-clinical studies using PDXs. Moreover, our analysis reveals subtype-specific features, pSrc in CMS4 and low Ki67 in CMS2, which provide novel avenues for therapy and diagnosis.

overall_design: Gene expression analysis of 34 CRC patient tumors and 37 patient derived xenografts established from those tumors

first: P

last: Prasetyanti

first: N

last: de Vries

first: T

last: van Herwaarden

first: K

last: Kalloe

first: H

last: Rodermond

first: R

last: van Leersum

first: J

middle: H

last: de Jong

first: M

last: Franitza

last: Nürnberg

last: Todaro

first: G

last: Stassi

last: Medema


title: Integrative Epigenetic and Gene Expression Analysis of Renal Tumor Progression to Metastasis

first: Sunil

last: Sudarshan

summary: Renal cell carcinoma (RCC) is among the ten most common malignancies.  By far, the most common histology is clear cell (ccRCC).   The Cancer Genome Atlas and other large scale sequencing studies of ccRCC have been integral to the current understanding of molecular events underlying RCC and its  biology.   However, these data sets have focused on primary RCC which often demonstrates indolent behavior.  In contrast, metastatic disease is the major cause of mortality associated with ccRCC.  However, data sets examining metastatic tumor are sparse. We therefore undertook an integrative analysis of gene expression and DNA methylome profiling of metastatic ccRCC in addition to primary RCC and normal kidney.  Integrative analysis of the methylome and transcriptome identified over 30 RCC specific genes whose mRNA expression inversely correlated with promoter methylation including several known targets of hypoxia inducible factors (HIFs).  Notably, genes encoding several metabolism-related proteins were identified as differentially regulated via methylation. Collectively, our data provide novel insight into biology of aggressive RCC.  Furthermore, they demonstrate a clear role for epigenetics in the promotion of HIF signaling and invasive phenotypes in renal cancer.


title: Epigenetic alterations detected in the genome of very young breast cancer patients: identification of new biomarkers

city: Valencia

first: Sara

last: OLTRA SANCHIS

state: Valencia

address: Avda Menéndez Pelayo, 4 accesorio

department: Medical Oncology

institute: INCLIVA

summary:
Breast cancer in very young women (< 35 years BCVY) presents more aggressive and complex biological features than in their older counterparts. In this study we aimed to identify the key pathways that may cause cancer in this younger age group. EPIC and 450k Illumina methylation arrays were used to identify differences in DNA methylation in 74 breast cancer tumours, including 37 from very young women. Additionally, we analysed copy number variation (CNV) and DNAm age using methylation intensities from Illumina Infinium MethylationEPIC BeadChip.
Although we are able to identify aberrant CNV patterns in breast cancer samples, they were not highly specific to BCVY. However, we identified 2 219 CpG sites that were differently methylated in BCVY vs. older women (false discovery rate < 0.05 beta-value difference ± 0.1), with the general hypomethylation profile affecting genes involved in neuronal-system pathways, cell communication, and extracellular matrix organisation, as confirmed by our experimental data. Additionally, a specific hypermethylation profile comprising 502 CpG sites located mainly in open-sea regions distinguished BCVY from older patients. Pathway enrichment analysis showed that regions implicated in the hypermethylation profile were involved in regulating genes related to Notch signalling pathways, the immune system, DNA repair, and vesicular trafficking. Moreover, BCVY presented age acceleration comparing with older women.
The expression of genes regulated by differentially-methylated CpG sites was validated using both Cancer Genome Atlas genomic data and by qRT-PCR, the latter in an independent sample (n = 40). This validation highlighted that 186 genes were consistently deregulated, including consistent hypomethylation and higher expression of HOXD9, PCDH10, and HDAC5 genes when considering BCVY vs. BC. Thus, we propose HDAC5 hypomethylation as a possible early detection biomarker in BCVY, and moreover, HDAC5 inhibitors, such as LMK-235, may be useful in treating breast cancer tumours in young women

overall_design:
We extracted DNA from 26 samples from BCVY (< 35 years) and 15 samples from older women with breast cancer (BCO) (> 45 years). Normal tissue samples from very young women (NVY) (n = 2) and older women (NO) (n = 3) were also included in the methylation study. All DNA samples were hybridized to the Illumina Infinium MethylationEPIC BeadChip.
This Series represents 21 samples from BCVY (< 35 years) and 13 samples from older women with breast cancer (BCO) (> 45 years). Normal tissue samples from very young women (NVY) (n = 2) and older women (NO) (n = 3) .

last: Oltra

first: Gloria

last: Ribas


title: Dynamic gene expression response to altered gravity in human myelomonocytic U937 cells

first: Cora

middle: S.

last: Thiel

department: Institute of Anatomy


title: H3K79me2 ChIP-seq in cerebellar granular neurons (CGN) and progenitors (CGNP) upon DOT1L inhibition with SGC0946 in vitro

status: Public on Oct 15 2018

city: Freiburg

first: Patrick

middle: Piero

last: Bovio

address: Albertstr. 19

department: Department of Molecular Embryology

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

summary: DOT1L as methyltransferase of H3K79 is implicated in brian development. Here, we further defined  DOT1L function within the granular neurons during cerebellar development using ChIP-seq of H3K79 dimethylation of isolated cerebellar granular neurons and progenitors. Thereby we compared samples treated with a DOT1L inhibitor versus DMSO treated cells. The data sets reveals new important targets of DOT1L, which ensure a correct development of the cerebellum.

overall_design: H3K79me2 ChIP-seq of CGNPs,4 h after DOT1L inhibition and CGNs, 44 h after DOT1L inhibition; compared to DMSO control each. Cells derived from murine cerebellum of P7 NMRI WT mice

first: Fabian

last: Kilpert

first: Ulrike

last: Bönisch

first: Thomas

last: Manke

first: Tanja

last: Vogel


title: Dynamic gene expression response to altered gravity in human myelomonocytic U937 cells [sounding rocket]

summary: We investigated differentially regulated genes in human myelomonocytic U937 cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes.

overall_design: Human myelomonocytic U937 cells  were exposed to altered gravity during a sounding rocket mission.

first: Svantje

last: Tauber

first: Swantje

last: Hauschild

first: Andreas

last: Huge

first: Beatrice

last: Lauber

first: Jennifer

last: Polzer

first: Katrin

last: Paulsen

first: Hartwin

last: Lier

first: Frank

last: Engelmann

first: Burkhard

last: Schmitz

last: Schütte

first: Liliana

middle: E

last: Layer

first: Oliver

last: Ullrich


title: Gene expression analysis of P3 Dot1l conditional knockout mice in the cerebellum and of cerebellar granular neuron progenitors (CGNPs) or cerebellar granular neurons (CGNs) isolated from P7 wt mice upon DOT1L inhibition

last: Bovio

summary: DOT1L as methyltransferase of H3K79 is implicated in brian development. Here, we further defined DOT1L function in gene expression during cerebellar development using Microarrays. For that we generated Dot1l knockout mice using a Atoh-Cre driver line resulting in a Dot1l knockout within the cerebellum. The RNA of cerebellar tissue of the Dot1l knockout animals was thereby compared to controls. Additionally we compared the RNA levels of cultured CGNP and CGN samples treated with a DOT1L inhibitor versus DMSO treated cells. The data sets reveals potential new gene expression targets of DOT1L in vivo and in vitro, which ensure a correct development of the cerebellum.

overall_design: Microarray analysis using Affymetrix (which array?) arrays of the cerebellum of Dot1l conditional knockout mice versus controls. Additionally, CGNPs and CGNs were isolated at P7 of wt mice, treated with the DOT1L inhibitor SGC0946 and than analyzed via Affymetrix Microarrys.

first: Dietmar

last: Pfeifer

first: Henriette

last: Bertemes


title: Dynamic gene expression response to altered gravity in human myelomonocytic U937 cells [parabolic]

first: Cora

last: Thiel

overall_design: Human myelomonocytic U937 cells  were exposed to altered gravity during a parabolic flight


title: Cerebellar granular neurons (CGN) and progenitors (CGNP) upon DOT1L inhibition or cKO

first: Patrick

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

overall_design: Refer to individual Series


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Rat ATAC-Seq]

status: Public on Oct 12 2018

city: New York

first: Xiao

last: Xu

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

summary: Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions.

overall_design: RNA purified from nuclei or cytoplasm from mouse, rat, or human cerebellum. ATAC-seq was also performed using cerebellar nuclei from the three species.

first: X

first: E

middle: I

last: Stoyanova

first: A

last: Lemiesz

first: J

last: Xing

first: D

last: Mash

first: N

last: Heintz


title: Integrated Transcriptomic and Proteomic Dynamics of Rituximab Treatment in Primary B Cells

status: Public on Oct 13 2018

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: The investigation aims to profile the molecular dynamics of Rituximab treatment in cells.  Specifically, primary B cells were treated with Rituximab, and sampled across 6 time points. Treated and untreated cells were processed to extract RNA and protein, that were subsequently used in high-throughput analysis of the transcriptome (RNA-Sequencing) and proteome (mass spectrometry).

overall_design: Examination of gene expression dynamics in two sets of: (i) treated Primary B cells and (ii) a parallel untreated control  primary B cells. Both sets  were sampled at 6 timepoints -  (0, 1, 2, 4, 7, and 15 hours, with respect to the start of the experiment). The treated cells, (i), were treated with Rituximab at timepoint 1 (0 hours). Validation was performed using a new repeated experiment over the same time points, including again both treatment and control sets of primary B cells.

first: Lavida

middle: R

last: Brooks


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [RAT RNA-Seq]


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Mouse RNA-Seq]

middle: C


title: Transcriptome profiling reveals anti-inflammatory activity of miR-29b in multiple myeloma associated dendritic cells

status: Public on Oct 10 2018

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

summary:
Dendritic cells (DCs) are among the major components of multiple myeloma (MM)-associated bone-marrow microenvironment and are involved in MM progression, growth and chemo-resistance. We observed that after 24h co-culture with different MM cell lines, DCs downregulate miR-29b expression.
To gain insight on the effects of miR-29b, we performed a transcriptome analysis of DCs after transient transfection of a negative control or miR-29b mimics and 24h co-culture with U266 cell line.

overall_design: total RNA was obtained from dendritic cells obtained from three different healthy donors, transfected with either negative control or miR-29b mimics and co-cultured for 24h with U266 cell line

first: Maria

middle: T

last: Di Martino

first: Pierosandro

last: Tagliaferri

first: Pierfrancesco

last: Tassone


title: Genome-wide mapping of H3K79me2 in EPZ5676-treated lymphatic endothelial cells [RNA-Seq]

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

summary: Proper functioning of the lymphatic system is required for normal immune response, fluid balance and lipid reabsorption. Multiple regulatory mechanisms are employed to ensure correct formation of lymphatic vessels; however, whether epigenetic regulation is involved in this process remains largely unknown. We report that epigenetic priming by the Disruptor of telomeric silencing 1-like (DOT1L) in endothelial cell (EC) is indispensable for generation and function of lymphatic endothelial cells (LECs). Mechanistically, loss function of DOT1L leads to reduction of H3K79 di-methylation and expression of the genes important for LEC development and function. Thus, our study establishes DOT1L-mediated transcriptional regulation in ECs plays an important role in differentiation and function of LECs.

overall_design: We perform RNA-Seq experiment in mouse E15.5 skin LECs (control vs Dot1l KO).

first: H

last: Yoo

first: C

first: Y

last: Zhang

last: Choi

first: K

last: Hong


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia

first: Xiao

last: Xu

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Genome-wide mapping of H3K79me2 in EPZ5676-treated lymphatic endothelial cells


title: Centromeres license the mitotic condensation of yeast chromosome arms

status: Public on Oct 11 2018

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: During mitosis, chromatin condensation shapes chromosomes as separate, rigid and compacted sister-chromatids to facilitate their segregation. Here, we show that unlike wild type yeast chromosomes, non-chromosomal DNA circles and chromosomes lacking a centromere fail to condense during mitosis. Genetics and ChIP-seq experiments establish that the centromere functions in chromosome condensation upstream of the kinases Aurora B and Bub1. Downstream of Aurora B and Bub1, Shugoshin and the deacetylase Hst2 facilitated spreading of the condensation signal from the pericentromeric region to the chromosome arms. Targeting Aurora B to DNA circles or centromere-ablated chromosomes, or releasing Shugoshin from PP2A-dependent inhibition bypassed the centromere requirement for condensation and enhanced the mitotic stability of DNA circles. Our data indicate that yeast cells license in a centromere-dependent manner the chromosome-autonomous condensation of their chromatin, excluding non-centromeric DNA from this process and thereby inhibiting their propagation.

overall_design: Analysis of histone modification in different experimental conditions

first: Tom

last: Kruitwagen

first: Jorrit

last: Enserink

first: Yves

last: Barral


title: Global methylation patterns in Primary Plasma Cell leukemia

city: Rionero in Vulture, PZ

first: Giovanni

last: Calice

address: Via Padre Pio, 1

institute: IRCCS - CROB Centro di Riferimento Oncologico della Basilicata

summary: Primary plasma cell leukemia (pPCL) is a rare and aggressive variant of multiple myeloma (MM), which is associated with a very poor prognosis. Specific molecular patterns distinguish pPCL in comparison to MM and in relation to main genomic alterations. In the present study, a whole-genome methylation profiling analysis by high-density array revealed a global gene hypomethylation profile in pPCL. Lower methylation levels were particularly observed in the promoter and 5’ untranslated regions (5’UTR), whereas higher levels were evidenced in gene body or 3’ untranslated regions (3’UTR).  CpG islands (CGI) resulted largely hypomethylated, whereas higher methylation levels were observed in CGI distal regions. Peculiar differential methylation patterns were identified in association to major chromosomal aberrations and DIS3 mutational status and involved  genes playing roles in cell migration, bone metabolism, transcription regulation or DNA damage response. Finally, decreasing methylation levels were evidenced for few genes in association to MM disease progression, from healthy condition to MM and pPCL. Our data may provide new insights into the molecular characterization of pPCL patients, thus being potentially useful in the prognostic stratification or identification of novel molecular targets.

overall_design: Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip array (Illumina Inc., San Diego, CA, USA)

first: Katia

last: Todoerti

first: Stefania

last: Trino

first: Vittorio

last: Simeon

first: Marta

last: Lionetti

first: Martina

last: Manzoni

first: Sonia

last: Fabris

first: Marzia

last: Barbieri

first: Alessandra

last: Pompa

first: Luca

last: Baldini

first: Valentina

last: Bollati

first: Pellegrino

last: Musto

first: Antonino

last: Neri


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Human RNA-Seq]

first: Xiao

last: Xu

first: X

first: E

last: Stoyanova

first: A

last: Lemiesz

first: J

last: Xing

first: D

last: Mash

first: N

last: Heintz


title: Monitoring Nivolumab binding as a method to clarify the residual therapeutic effects and to characterize the immune profile in antibody bound T cells in previously treated non-small cell lung cancer patients

status: Public on Oct 05 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The goal of this study is to evaluate immune profile in anti PD-1 antibody, Nivolumab, bound CD8 T cells vs Nivolumab unbound CD8 T cells.

overall_design: We performed sorting for IgG4 positive and negative CD8 T cells from five individual patients at the time after one dose treatment and compared transcriptome profile between them.

first: Shohei

last: Koyama

first: Atsushi

last: Kumanogoh


title: The aryl hydrocarbon receptor pathway defines the time frame for restorative neurogenesis

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
In contrast to mammals, zebrafish has high capacity to regenerate tissue architecture and replace lost neurons after traumatic brain injury. The ependymoglia cells react to the injury and generate new neurons, which migrate to the lessoned site and contribute to the tissue restoration. Understanding molecular and cellular mechanisms underlying this regenerative neurogenesis is the crucial step towards achieving regenerative therapies in the mammalian brain. In order to identify molecular pathways governing this mode of restorative neurogenesis, we analysed changes in the transcriptome of ependymoglia cells and their progeny during regeneration process and identified Aryl hydrocarbon receptor (AhR) to be involved in regulation of ependymoglia differentiation towards post-mitotic neurons.
Our in vivo imaging analysis shows that the high AhR signalling promotes direct conversion of newly identified population of ependymoglia into the post-mitotic neurons. In contrast, decrease in AhR signalling promotes ependymoglial proliferation. Interestingly, we observed inactivation of the AhR signalling shortly after the injury and return to the basal levels 7 days post injury (dpi) suggesting the role of AhR in proper timing of the direct conversion of ependymoglia, ensuring the successful repair. Taken together, we identified the role of AhR signalling pathway in regulating differentiation of ependymoglia into the neurons and setting up the proper timing of restorative neurogenesis in zebrafish brain.

overall_design: We performed gene expression microarray analysis from zebrafish from the dorsal subventricular zone and the dorsal parenchyma. We analysed different time points after stab-wound injury and tissues from control animals

first: Rossella

last: Di Giaimo

first: Tamara

last: Durovic

first: Pablo

last: Barquin

first: Anita

last: Kociaj

first: Tjasa

last: Lepko

first: Sven

last: Aschenbroich

first: Christopher

last: Breunig

first: Martin

last: Irmler

first: Filippo

middle: M

last: Cernilogar

first: Gunnar

last: Schotta

first: Joana

last: Barbosa

first: Dietrich

last: Trümbach

first: Emily

middle: V

last: Baumgart

first: Andrea

last: Neuner

first: Wolfgang

last: Wurst

first: Stefan

last: Stricker

first: Jovica

last: Ninkovic


title: Genome-wide mapping of H3K79me2 in EPZ5676-treated lymphatic endothelial cells [ChIP-Seq]

first: Chanhyeok

last: Park

summary: Proper functioning of the lymphatic system is required for normal immune response, fluid balance and lipid reabsorption. Multiple regulatory mechanisms are employed to ensure correct formation of lymphatic vessels; however, whether epigenetic regulation is involved in this process remains largely unknown. We report that epigenetic priming by the Disruptor of telomeric silencing 1-like (DOT1L) in endothelial cell (EC) is indispensable for generation and function of lymphatic endothelial cells (LECs). Loss function of DOT1L leads to reduction of H3K79 di-methylation and expression of the genes important for LEC development and function. Thus, our study establishes DOT1L-mediated transcriptional regulation in ECs plays an important role in differentiation and function of LECs.

overall_design: We perform ChIP-Seq (H3K79me2) in mouse primary skin LECs (DMSO-treated vs EPZ5676-treated).

first: H

last: Yoo

first: C

first: Y

last: Zhang

last: Choi

first: K

last: Hong


title: Comparative study of mRNAs and lncRNAs in endothelial and non-endothelial cells

status: Public on Oct 08 2018

city: New Orleans

first: Shusheng

last: Wang

state: LA

address: 2000 Percival Stern Hall, 6400 Freret Street

department: Cell and Molecular Biology

institute: Tulane University

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

summary: To identify lncRNAs enriched in ECs, a microarray was performed to profile ~30,000 lncRNAs and ~26,000 coding transcripts using an Arraystar human LncRNA microarray v3.0 system (Arraystar, Rockville, MD).  Three primary human EC lines and two non-EC lines at low passages, namely, human umbilical vein EC (HUVEC), human retinal EC (HREC), human choroidal EC, human dermal fibroblast cell (HDF) and human retinal pigment epithelial (RPE) cell lines, were used in the array. Purity of EC lines was confirmed by acetyl-LDL uptake and EC marker staining

overall_design: The expression of long noncoding RNAs and mRNAs was studied using Arraystar human LncRNA microarray v3.0 system using five cell types: human umbilical vein endothelial cells (HUVEC), human retinal endothelial cells (HREC), human choroidal endothelial cells (HCEC), human dermal fibrsolast cells (HDEF) and ARPE-19 cells. The goal of the design is to find endothelial specific lncRNAs and mRNAs.

first: Qinbo

last: Zhou


title: Signal integration in lymphocytes via convergent genomic actions of NFATs with IRF4 and  IRF8

status: Public on Oct 06 2018

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: Lymphocyte activation and effector state differentiation critically depend on integration of  multiple signals, including those from antigen, co-stimulatory ligand and cytokine receptors.  Thus, discovery of molecular components and mechanisms underlying signal integration is vital  for the understanding and control of adaptive immune responses. Stimulation of antigen  receptors in lymphocytes leads to the activation of NFAT family transcription factors (TFs) as  well as the inducible expression of the immune-selective IRFs, IRF4 and IRF8; the latter are  differentially controlled by co-stimulatory ligand and cytokine receptor signaling. Despite their  major overlapping functions in lymphocyte activation and differentiation, it has remained  enigmatic if NFATs can perform signal integration with IRF4 and IRF8, via their cooperative  assembly on composite genomic regulatory elements. Composite elements (CEs) provide a  powerful means of signal integration by inducible TFs and despite their clear importance, CEs  arguably remain the least explored elements within cis-regulomes. To test the above  hypothesis, we deployed a generalizable computational strategy, which revealed a stereospecific  NFAT-IRF composite element (NICE) motif that was enriched within active chromatin regions  (H3K27Ac) of activated B and T lymphocytes. NICE containing DNA sequences promoted  cooperative binding of NFATs with IRF4 or IRF8. Genomic analyses in activated B cells  revealed co-dependent genes that undergo activation or repression and contain NICE motifs in  their regulatory regions. Notably, NFATc2 and IRF8 form a positive feedforward loop and  coordinately repress the Prdm1 gene by binding a NICE motif in a phylogenetically conserved  region, thereby inhibiting extrafollicular plasma cell differentiation and promoting the germinal  center fate of activated B cells. The NICE motif is also enriched in DNA sequences located in  accessible chromatin of human lymphocytes, suggesting evolutionary conservation of its  function. The cooperative assembly of NFAT family members with IRF4 and IRF8 on NICE  motifs reveals a new genomic control mechanism that enables signal integration during  lymphocyte activation and differentiation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For ChIP-Seq, B  cells were stimulated with F(ab’) 2 fragment goat anti–mouse IgM, a-CD40, IL-2,IL-4 and IL-5. Naïve CD4 T cells were stimulated with plate coated a-CD3 and a-CD28.  Human T cells were stimulated with anti-CD3/28 beads. For RNA-seq, B cells were stimulated in the absence or presence of 11R-VIVT.

first: Ankur

last: Saini

first: Jeremy

last: Riddell

first: Masashi

last: Yukawa

first: Artem

last: Barski

first: Matthew

last: Weirauch


title: MYC interacts with the G9a histone methyltransferase to control transcriptional repression in cancer

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

summary: MYC is a master regulator of transcriptional activation and repression that mediates diverse physiological and disease functions, including hematopoiesis, aging, and oncogenesis, yet its essential co-regulators remain unclear. We demonstrate that MYC interacts with and regulates the G9a H3K9 methyltransferase complex to control transcriptional repression in cancer. Inhibiting G9a hinders MYC binding, shifts repressive epigenetic locales to an active state, and de-represses gene expression to antagonize MYC-dependent cellular processes. MYC requires MYC Box II region for its interaction with G9a, providing a mechanism for this region essential for transcriptional repression. In treatment models of MYC-dependent basal breast cancer, genetically inhibiting G9a decreases tumour growth. Anti-proliferative sensitivity to G9a small molecule inhibitors correlates with sensitivity to MYC knockdown and associates with the basal subtype. Our findings illustrate an epigenetic model of MYC-mediated transcriptional repression in driving oncogenesis and establishes G9a as a therapeutic vulnerability in MYC-driven cancers.

overall_design: Genome-wide analysis comparing the effect of G9a knockdown (using two independent shRNAs) versus scramble control (shSCR) on MYC transcription factor binding in MCF10A breast epithelial cells transformed with ectopic PI3KH1047R and MYC (MCF10A.PM). ChIP-seq of three biological replicates immunoprecipitated with a MYC-specific antibody (N262) and respective DNA input for each shRNA condition was performed.

first: William

middle: B

last: Tu

first: Paul

last: Boutros

first: Linda

middle: Z

last: Penn


title: TGFb signaling hyperactivation-induced germ cell-like tumorigenicity during ESC-derived neural progenitors

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

summary: Despite the therapeutic promise for pluripotent stem cells (PSCs)-based transplantation, a crucial challenge for PSC implementation is the frequent development of teratomas or tumors in animal models or clinical patients. Therefore, clarifying the mechanism of cell therapy-derived carcinogenesis is of great importance to reduce the risk of tumorigenicity in stem cell therapy. Here we differentiate Oct4-GFP mouse embryonic stem cells (mESCs) into neural progenitor cells (NPCs) or neurons and find that a minority of Oct4+ cells are sustained at an undifferentiated state. These cells are enriched and proliferated in standard ESC medium. Interestingly, the differentiation potential of these enriched cells is tightly restricted with much higher tumorigenic activity, so defined as differentiation-resistant ESCs (DR-ESCs). Transcriptome and epigenomic analysis shows that DR-ESCs are characterized by primordial germ cell-like gene signatures (Dazl, Rec8, Stra8, Blimp1, etc) and specific histone modification patterns distinct from mESCs. Moreover, the DR-ESCs possess the germ cell potential to generate Sycp3+ haploid cells and are able to reside in sperm-free spermaduct induced by busulfan. Finally, we find that TGFβ signaling is over-activated in DR-ESCs, and inhibition of TGFβ signaling induces the fully differentiation of DR-ESCs and eliminates the tumorigenicity of mESC-derived NPCs. These data demonstrate that these TGFβ hyperactivated germ cell-like DR-ESCs are the main contributor for the tumorigenicity of ESCs-derived target cell therapy and that inhibition of TGFβ signaling in ESC-derived NPC transplantation can help to drastically reduce the risk of tumor development.

overall_design: To fully analyze the molecular mechanisms of carcinogenesis of pluripotent stem cells, we enriched the differentation-resistant cells from mouse neural progenitor cells which are derived from Oct4-GFP mouse embryonic stem cell neural differentiation system by sorting GFP positive cells. Transcriptional analyses by RNA sequencing and epigenetic analyses by chromatin immunoprecipitation followed by sequencing for H3K4me3 (Abcam 8580), H3K4me1 (Abcam 8895), H3K27me3 (Millipore 07-449) and H3K27ac (Active Motif 39133) were performed.

first: Xianfa

last: Yang

first: Ran

first: Xiongjun

first: Yunbo

last: Qiao


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival

status: Public on Oct 04 2018

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

institute: University of Gothenburg


title: Global and targeted microRNA expression profiling in clear cell renal cell carcinoma tissues potentially links miR-155-5p and miR-210-3p to both tumorigenesis and recurrence [discovery phase]

city: Houston

first: Yuanqing

last: Ye

state: TX

address: 1155 Pressler st

department: Epidemiology

institute: UT MD Anderson Cancer Center

summary: About 30% of renal cell carcinoma (RCC) patients undergoing nephrectomy experience disease recurrence. This study aimed to profile microRNAs (miRNAs) that are dysregulated in clear cell RCC (ccRCC) tumor tissues and predictive of recurrence. The expression levels of 800 miRNAs were assessed in paired tumor and normal tissues from a discovery cohort of 18 ccRCC patients via the NanoString assay platform. MiRNAs found to be differentially expressed were further examined in a validation set of 205 patients using quantitative real-time PCR. Tumor-normal data from 64 patients in The Cancer Genome Atlas were used for external validation. Results showed 28 miRNAs were consistently dysregulated in tumor tissues. Dichotomized analyses indicated patients with high levels of miR-155-5p and miR-210-3p displayed increased risk of ccRCC recurrence (HR, 2.64; 95% CI, 1.49-4.70; P=0.0009 and HR, 1.8; 95% CI, 1.04-3.12; P=0.036, respectively) and shorter median recurrence-free survival times than patients with low levels (log rank test P<0.01). A risk score was generated based on expression levels of miR-155-5p and miR-210-3p, and the trend test was significant (P for trend=0.005). Pathway analysis revealed target genes regulated by miR-155-5p and miR-210-3p were mainly enriched in inflammation-related pathways. In summary, we identified and validated multiple miRNAs dysregulated in ccRCC tissues. MiR-155-5p and miR-210-3p were predictive of ccRCC recurrence pointing to potential utility as biomarkers and underlying biological mechanisms.

overall_design: Study consists of a dual-phase design for discovery and validation. In the discovery phase, total RNA was isolated from paired tumor and adjacent normal tissues from 18 ccRCC patients (9 with disease recurrence and 9 without recurrence) and then subjected to NanoString miRNA profiling. MiRNAs dysregulated in tumors were selected for further validation using the quantitative real-time PCR approach. During the validation phase, total RNA isolated from paired tumor/normal tissues from additional 205 ccRCC patients (63 with disease recurrence and 142 without recurrence) was subjected to Fluidigm real-time PCR quantification. MiRNAs dysregulated in tumors in both discovery and validation phases were identified and analyzed for their association with risk of ccRCC recurrence. The results of altered miRNAs in tumor tissues were further validated using the ccRCC miRNA dataset in The Cancer Genome Atlas. Cumulative effect of altered miRNAs was assessed by developing a risk score, and pathway analysis was conducted to identify potential target genes and enriched pathways.

first: Xifeng

last: Wu


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [ARRAY]

summary: Ovarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (I, II) ovarian carcinomas (n=96) in relation to clinicopathological characteristics and clinical outcome, thereby identifying novel genetic features of ovarian carcinomas. Furthermore, mutation frequencies of specific genetic variants and/or their gene expression patterns were associated with histotype and overall survival, e.g. SLC28A2 (mucinous ovarian carcinoma histotype), ARCN1 (low expression in 0-2 year survival group), and tumor suppressor MTUS1 (mutation status and overall survival). The long non-coding RNA MALAT1 was identified as a highly promiscuous fusion transcript in ovarian carcinoma. Moreover, gene expression deregulation for 23 genes was associated with tumor aggressiveness. Taken together, the novel biomarkers identified here may improve ovarian carcinoma subclassification and patient stratification according to histotype and overall survival.

overall_design: Genome-wide SNP genotyping was performed for nine early-stage primary invasive ovarian carcinomas.

first: Toshima

last: Parris

first: Elisabeth

last: Werner Rönnerman

first: Elin

last: Söderberg

first: Jana

last: Biermann

first: Claudia

last: Mateoiu

first: Karin

last: Sundfeldt

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Global organization of the B cell genome by the transcription factor Pax5 [Hi-C]

status: Public on Oct 07 2018

city: Parkville

first: Rhys

last: Allan

state: Victoria

address: 1G Royal Parade

department: Molecular Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: We used genome-wide in situ Hi-C to show that different immune cell populations display distinct chromatin architecture and that the transcription factor Paired box 5 (Pax5) is critical for the lineage-specific architecture of B cells.

overall_design: Hi-C was undertaken for mouse CD4+ T cells, transitional & marginal zone (Tr/MZ) B cells, granulocytes, LSKs, MEFs, pro-B cells, Pax5-/- pro-B cells, follicular B cells, activated B cells and plasmablasts. Also used was a Pax5-/- pro-B cell line with a Pax5:ER fusion construct allowing Pax5 to be reintroduced to the nucleus. The Pax5:ER cells were either untreated, treated with b-estradiol to reintroduce Pax5, or treated with both b-estradiol and a-amanitin to reintroduce Pax5 but prevent further transcription. Two biological replicates were conducted for each cell type and each treatment condition, except for pro-B cells and Pax5-/- prob-B cells, for which three replicates were performed.

first: Timothy

last: Johanson

first: Hannah

middle: D

last: Coughlan

first: Gordon

last: Smyth


title: RNA-seq transcriptional profiling of wildtype and Pax5 knockout mouse pro-B cells

summary: Total RNA was isolated from wild type and Pax5-/- pro-B cells. Samples were sequenced on an Illumina Hiseq 2000 at the Beijing Genomics Institute to produce 90bp paired-end reads. Reads were aligned to the mm10 genome using Subread with unique alignment. The number of read pairs mapped to each gene in the NCBI RefSeq annotation was counted using the featureCounts function of the Rsubread package.

overall_design: Two independent Pax5-/- samples were prepared and one wild type.

first: Aaron

last: Lun

first: Tania

last: Tan

middle: K

first: Stephen

middle: L

last: Nutt


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (Barcode)

status: Public on Oct 03 2018

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The KDM5B histone H3 lysine 4 (H3K4) demethylase has been implicated in therapy resistance in multiple cancer types including breast cancer, but the underlying mechanism is poorly defined. Here we show that inhibition of KDM5B activity increases sensitivity to anti-estrogens by modulating estrogen-receptor (ER) signaling. Conversely, acquired resistance to KDM5 inhibitors leads to gain of ER chromatin binding and estrogen-independent growth. Sequencing of barcoded cell populations and mathematical modeling demonstrate selection for pre-existent genetically distinct endocrine-resistant cells, while resistance to KDM5 inhibitors is a switch to an acquired epigenetic state. Rare resistant cells can already be detected by single cell RNA-seq prior to treatment. Inhibition of KDM5B in luminal ER+ cells increases H3K4me3 broad domains at promoters and decreases cellular transcriptional heterogeneity. Higher transcriptome heterogeneity is associated with higher KDM5B levels and poor prognosis in ER+ luminal breast tumors.

overall_design: Barcoding analyses of parental and multiple resistant breast cancer cell lines

first: Kunihiko

last: Hinohara

first: Hua-Jun

last: Wu

first: Franziska

last: Michor


title: Cardiac transcriptomic effects of atorvastatin and pravastatin

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

institute: Charite University Hospital

summary:
Treatment with statins lowers low-density lipoprotein cholesterol for prevention of cardiovascular disease.
We hypothesized major cardiac effects of statins.

overall_design: Male mice with atorvastatin and pravastatin by oral gavage for seven months


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (ChIP-Seq)

overall_design: ChIP-Seq of parental and multiple resistant breast cancer cell lines


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (RRBS)

type: Methylation profiling by high throughput sequencing

overall_design: Reduced representation bisulfite sequencing (RRBS) was performed on parental and multiple resistant breast cancer cell lines


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (inDrop)

overall_design: Single cell transcriptome of parental and multiple resistant breast cancer cell lines


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance (RNA-Seq)

overall_design: RNA-Seq of parental and multiple resistant breast cancer cell lines


title: HDAC3 ChIP sequencing of L4-L6 Dorsal Root Ganglia upon spinal or sciatic axonal injury

status: Public on Oct 01 2018

city: Miami

first: Matt

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: A) compare the response to an axonal injury in the peripheral vs central nervous system B) clarify the role of HDAC3 in axonal regeneration
Results: we found that after peripheral axonal injury there is a higher number of differentially expressed genes regulated by HDAC3 with respect to central injury with a number of genes associated with regenerative pathways

overall_design: Method:HDAC3 ChIP-seq from sciatic L4-L6 DRG tissue 24 hours after the following treatments: a) spinal cord dorsal column injury b) laminectomy c) sciatic nerve injury  d) sham. Pool of sciatic DRGs from 20 mice were used for each sample. DRG were collected and flash frozen.

first: Ilaria

last: Palmisano

first: Eilidh

last: McLachlan

first: Arnau

middle: A

last: Hervera

first: Simone

last: Di Giovanni


title: Unraveling cis-regulatory elements by mapping structural changes in mRNAs

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: mRNA molecules are generally thought to be messengers of genetic information in the cell. Stretches of RNA that are complementary in sequence have a propensity to pair, forming elements of secondary structure within RNA molecules. Although these structures will exist in every mRNA molecule, the role they play in gene regulation is not well understood. Currently two techniques are available to profile the cell RNA structure, in-vivo, in an unbiased manner. We applied one of those techniques, DMS-seq, for probing the human mRNA structure in primary foreskin fibroblasts (HFFs) along human cytomegalovirus (HCMV) infection. As a proof of concept, using DMS-seq, we managed to predict the already solved human 28S rRNA structure with high accuracy. Using our data, we are able to show for the first time in-vivo, that human coding sequences (CDSs) are less structured relative to UTRs. Additionally, we provide systematic in-vivo evidences for unwinding of the mRNA by the ribosomes during translation. Intriguingly, we also found structural changes in human CDSs around the start and stop codon, and also in 3’UTRs. The combination of accurate measurements of translation regulation and mapping changes in mRNA structure along a dynamic process can be used as a platform for deciphering cis-regulatory elements that control gene expression in various cell types, organisms and biological processes.

overall_design: in-vivo DMS treatment, neutralization, RNA extration,linker ligation, reverse transcription , circulization, PCR and deep sequencing

first: Orel

last: Mizrahi

first: Alina

last: Shitrit

first: Idit

last: Gilbert

first: Aharon

last: Nachshon


title: ACC-MESO1 cells: Control shRNA vs USP22 shRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: USP22 plays oncogenic role and in order to study molecular mechanism of USP22 to promote tumorigenesis, microarray analysis was performed on USP22 knockdowned cells.

overall_design: MESO1 cells were transfected with USP22 shRNA. After USP22 was knocked down, total RNA was isolated and subjected to microarray analysis.

first: T

last: Okamoto

first: C

last: Morimoto


title: KDM5B links cellular transcriptome heterogeneity to therapy resistance

first: Kornelia

last: Polyak

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

overall_design: Refer to individual Series


title: mRNA expression of cytokine treated KYSE410 cells

city: Beijing

first: Jie

last: Chen

address: No. 52 Fucheng Road Haidian District Beijing

institute: Peking University Cancer Hospital

summary:
KYSE410 cells were treated with PBS, TNFα, IL1β, and LPS respectively and mRNA expression profiles were assayed by Nimblegen gene expression  microarray human HG18 (12x135K)
Investigation of the critical gene participating various inflammatory stimuli in the process of ESCC progression.

overall_design: We designed this experiment to screen for mRNA whose expressions are responsive to inflammatory stimuli.

first: Qimin

last: Zhan


title: ATAC-seq and RNA-seq from mouse mandible during distraction osteogenesis

status: Public on Oct 02 2018

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: During development and tissue regeneration, changes in chromatin structure driven by master transcription factors lead to stimulus-responsive transcriptional programs. A thorough understanding of how stem cells in the skeleton interpret mechanical stimuli and enact regeneration will also shed light on how mechanical forces are transduced in other embryonic and regenerative processes. Here we employ a rigorous mandibular distraction model in mice that is genetically dissectable, allowing for detailed examination of the fundamental principles regulating de novo bone formation. Using lineage tracing, we show that regions of new bone are clonally derived, indicating a stem/progenitor cell origin in regeneration. We go on to profile the distraction-specific response of skeletal stem cells (d-SSC) within the facial skeleton and track their downstream progenitors, revealing that this lineage gives rise to the regenerate. Using the assay for transposase accessible chromatin (ATAC-seq), we show that these stem cell populations have a distinct pattern of chromatin accessibility during distraction, including within the FAK pathway. Inhibiting the FAK pathway blocks bone formation and reverts the chromatin accessibility profile back to that of a fractured bone with suboptimal healing. Mechanotransduction and FAK-responsiveness in skeletal stem cells activates regulatory elements and retrotransposons normally active only in primitive neural crest cells; this reversion of chromatin state may allow robust developmental tissue growth that facilitates regeneration.

overall_design: ATAC-seq was performed on skeletal stem and progenitor cells from the mouse mandible during bone regeneration in the context of bone lengthening (distraction osteogenesis) or fracture and compared to these cell types in an uninjured, homeostatic state. RNA-seq was performed in distracted and fractured SSCs, pre-bone cartilage and stromal progenitors (BCSPs), and osteogenic progenitors (OPs) during a timecourse from POD5 to POD15.

first: Ava

last: Carter

first: Ryan

last: Ransom

middle: Y

first: Michael

last: Longaker


title: Gene Expression Profiling of SPOP Knocked Down Cell

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: SPOP is one of the most frequent mutated genes in prostate cancer. In the current study, we identified CCNE1 as its substrate. SPOP directly interacts with CCNE1, poly-ubiquitinates CCNE1 in vivo and in vitro, and represses cancer-related phenotypes induced by CCNE1 expression. Thus, we reveal a new mechanism for SPOP in repressing prostate cancer tumorigenesis.

overall_design: SPOP was knocked down by siRNA in DU145 and 769-P, the gene expression profile was studied by RNA sequencing

first: Lin-Gao

last: Ju

first: Yuan

last: Zhu


title: Expression data of synchronised primary human fibroblasts (NHDF, Data Set 3)

city: Edinburgh

first: Tom

last: Freeman

address: Easter Bush Campus, Midlothian

department: Genetics and Genomics

institute: Roslin Institute

summary:
Transcriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.
We used gene expression microarrays to analyse the global programme of gene expression of human primary fibroblasts from a quiescence state (G0) to a synchronised cell proliferation

overall_design: Primary human fibroblasts (NHDF) were firstly synchronised by limiting nutrients (from 10% to 0.1% of faetal calf serum) in the medium for 48 h. Samples were collected at 0 h (after 48 h of starvation but before full medium replacement), 1 h and every 2 h  up to 28 h. From t = 12 to t = 24 samples were collect every hour.

first: Bruno

last: Giotti

first: Mark

middle: W

last: Barnett

first: David


title: Neo-Adjuvant Oncolytic Virotherapy Prior to Surgery Sensitizes Triple-Negative Breast Cancer to Immune Checkpoint Therapy

city: Ottawa

first: Adrian

last: Pelin

address: 501 Smyth Rd.

institute: Ottawa Hospital Research Institute

summary:
Triple-negative breast cancer (TNBC) is an aggressive disease for which treatment options are limited and associated with severe toxicities.
In this experiment we evaluated the response of 2 murine TNBC models to oncolytic Maraba virus infection.

overall_design: Monolayers of 4T1 or EMT6 cells were treated at an MOI of 3 for 24h with either Maraba or UV-inactivated Maraba.

first: M-C

last: Bourgeois-Daigneault

first: John

last: Bell


title: Expression data of synchronised mouse embryonic fibroblasts (MEF) and synchronised primary human fibroblasts (NHDF)


title: Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.

city: Tokyo

first: Takuji

last: Ohyama

address: 1-1-1 Sakuragaoka, Setagaya-ku

department: Department of Applied Biology and Chemistry

institute: Tokyo University of Agriculture

summary: To dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodules from three plants were pooled with three biological replications, and total RNA was extracted.

overall_design: Gene expressions in soybean roots and nodules inoculated with Bradyrhizobium diazoefficiens were analyzed after 24 hours of 5 mM nitrate treatment compared with control with N free medium. Three independent experiments were performed at each inoculation.

first: Shinji

last: Ishikawa

first: Yuki

last: Ono

first: Norikuni

last: Ohtake

first: Kuni

last: Sueyoshi


title: Expression data of synchronised primary human fibroblasts (NHDF, Data Set 2)

overall_design: Primary human fibroblasts (NHDF) were firstly synchronised by limiting nutrients (from 10% to 0.1% of faetal calf serum) in the medium for 48 h. Samples were collected at 0 h (after 48 h of starvation but before full medium replacement), 1 h and every 2 h thereafter up to 24 h. Two biological replicas for controls were collected (unsynchronised).

last: Chen


title: The 3’UTR of ArgR regulates the arc operon

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

institute: university of Groningen

summary: ArgR and the sRNA from its 3’UTR, ArgX, both regulate the arc operon by influencing transcription and RNA stability/translation respectively

overall_design: Two strains, two conditions.

first: S

last: Van der Meulen

first: A

last: Hesseling-Meinders

last: de Jong

first: J

last: Kok


title: Expression data of synchronised mouse embryonic fibroblasts (MEF)

last: Freeman

summary:
Transcriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.
We used gene expression microarrays to analyse the global programme of gene expression of mouse embryonic fibroblast from a quiescence state (G0) to a synchronised cell proliferation

overall_design: Mouse embryonic fibroblasts (MEF) were firstly synchronised by limiting nutrients (from 10% to 0.1% of faetal calf serum) in the medium for 48 h. Samples were collected at t = 0 h (after 48 h starvation but before full medium replacement), t = 0.5 h, t = 1 h, t = 2 h and every 2 h up to 30 h. Biological duplicas were collected for time points 0 h, 12 h, 18 h, 24 h and controls (unsynchronised).


title: The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development [RNA-seq]

city: Memphis

first: Lance

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: MicroRNAs inhibit gene expression by recruiting the RNA-induced silencing complex (RISC) to mRNAs in a process termed RNA interference (RNAi). While it is generally accepted that RNAi modulates gene expression pervasively, the number of mRNAs bound and repressed by miRNAs in vivo in individual cell types remains unknown, with estimates ranging from a few hundred genes to many thousands. We examined microRNA activities in primary cells by combining genetic loss of function with RNA-sequencing, quantitative proteomics and High-Throughput Sequencing of RNA isolated by Crosslinking Immunoprecipitation (HITS-CLIP), focusing on miR-144/451, the most highly expressed microRNA locus during red blood cell (RBC) formation. We show that Argonaute (Ago) protein binds over one thousand different mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs are stabilized in RBC precursors after ablation of the miR-144/451 locus. Thus, Ago-miRNA complexes destabilize only a small subset of bound mRNAs, probably no more than a few hundred in erythroblasts under physiological conditions. Our integrated approach identified more than 50 new miR-144/451 target mRNAs, including Cox10, which facilitates assembly of the mitochondrial cytochrome c oxidase (COX) electron transport complex. Loss of miR-144/451 resulted in increased Cox10 expression, accumulation of the COX complex, and increased mitochondrial membrane potential with no change in mitochondrial mass. Thus, miR-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting Cox10.

overall_design: HITS-CLIP analysis of 3 WT mice fetal livers vs 3 miR-144/451 KO mice fetal livers

first: Vikram

last: Paralkar

first: Peng

last: Xu

first: Christophe

last: Lechauve

first: Guowei

last: Zhao

first: Yu

last: Yao

first: Jing

last: Luan

first: Anastasios

last: Vourekas

last: Scheutz

first: Zissimos

last: Mourelatos

first: Gang

last: Wu

first: Mitchell

middle: J

last: Weiss


title: The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development

middle: E


title: Expression data of synchronised primary human fibroblasts (NHDF, Data Set 1)

first: Tom

overall_design: Primary human fibroblasts (NHDF) were firstly synchronised by limiting nutrients (from 10% to 0.1% of faetal calf serum) in the medium for 48 h. Samples were collected at t= 0 (after 48 h starvation but before full medium replacement), t = 6 h, t = 12 h, t = 18 h, t = 24 h, t = 30 h, t = 36 h, t = 42 h, t = 48 h. Three techincal replica were collected for time points 0 h, 24 h, 30 h, and controls (unsynchronised).

first: Bruno

last: Giotti

first: Mark

last: Barnett

first: David

last: Chen


title: Long-term in vitro expansion of epithelial stem cells enabled by pharmacological inhibition of PAK1-ROCK-Myosin II and TGF-β signaling (MRE-seq)

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

summary: Despite substantial self-renewal capability in vivo, epithelial stem and progenitor cells located in various tissues expand for a few passages in vitro in feeder-free condition before they succumb to growth arrest. Here we describe the EpiX™ method that utilizes small molecules that inhibit PAK1-ROCK-Myosin II and TGF-β signaling to achieve over one trillion-fold expansion of human epithelial stem and progenitor cells from skin, airway, mammary and prostate glands in the absence of feeder cells. Transcriptomic and epigenomic studies show that this condition helps epithelial cells to overcome stresses for continuous proliferation. EpiX-expanded basal epithelial cells differentiate into mature epithelial cells consistent with their tissue origins. Whole genome sequencing reveals that the cells retain remarkable genome integrity after extensive in vitro expansion without acquiring tumorigenicity. EpiX technology provides a solution to exploit the potential of tissue-resident epithelial stem and progenitor cells for regenerative medicine.

overall_design: MRE profiles of human foreskin keratinocytes in different culture conditions were generated by deep sequencing, in duplicate, using Illumina NextSeq.

first: Chengkang

last: Zhang

first: Ting

last: Wang


title: Long-term in vitro expansion of epithelial stem cells enabled by pharmacological inhibition of PAK1-ROCK-Myosin II and TGF-β signaling


title: Pseudomonas syringae pv. tomato DC3000 exploits light signals to optimize virulence and colonization of leaves

city: Pozuelo de Alarcon

first: Emilia

last: López Solanilla

state: Madrid

address: Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38

institute: CBGP-Universidad Politécnica de Madrid (UPM)

summary: To explore the effect of light perception on Pseudomonas syringae pv. tomato DC3000 at a global level, we carried out microarray hybridization experiments. We hybridize custom-designed microarrays (Agilent Technologies) with probes isolated from PsPto after a 10 min treatment with either 20 μE/m2s blue light, 20 μE/m2s red light, 70 μE/m2s white light, or cells kept in the darkness.

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: Four different replicates of each light treatment were performed.

first: Saray

last: Santamaria-Hernando

first: Jose

last: Rodriguez-Herva

first: Pedro

last: Martinez-Garcia

first: Isabel

last: Rio-Alvarez

first: Pablo

last: Gonzalez-melendi

first: Jaime

last: Zamorano

first: Carlos

last: Tapia

last: Rodríguez-Palenzuela

last: Lopez-Solanilla


title: Effects of miR-149-3p overexpression as compared to the effects of DAB2IP depletion.

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: PC3 are a metastatic prostate cancer cell line. Microarray analysis was performed to evaluate the impact of miR-149-3p overexpression or DAB2IP depletion in PC3.

overall_design: PC3 cells were transfected with control or DAB2IP siRNA, or with miR-149-3p mimic, for 48 hours before analysis. The study comprises three experimental points, each in duplicate.

first: Licio

last: Collavin

first: Arianna

last: Bellazzo


title: Antagonistic action of PHYA and PHYB is involved in FR-dependent leaf senescence in Arabidopsis accessions

status: Public on Sep 30 2018

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Sensing environmental changes is important for survival of plants, as sessile organisms, in habi-tat. Recently, latitudinal clines in leaf senescence have been reported to be influenced by tem-perature and photoperiod. However, the relationship of light quality with latitudinal response of leaf senescence is still unclear. Here, we found that Arabidopsis accessions in far-red (FR) showed a strong negative correlation of leaf senescence with the latitude of their origin. phyto-chrome A (phyA) and B (phyB) mutants showed early and delayed senescence in FR, respec-tively, suggesting that PHYA and PHYB are involved in FR-dependent leaf senescence. Tran-scriptomic analysis identified genes oppositely regulated by PHYA and PHYB, and they were mainly associated with phytohormone, temperature, and defense, suggesting their associations with FR-dependent antagonistic effects of PHYA and PHYB on leaf senescence. Among these genes, the expression of WRKY6 in Arabidopsis accessions showed the highest correlation with latitude of their origin. Consistently, wrky6 mutant exhibited delayed senescence phenotype in FR. In conclusion, we propose that PHYs-regulated genes, including WRKY6, are involved in latitudinal leaf senescence in FR and this regulatory mode may contribute to latitudinal adapta-tion by responding FR, as a piece of geographical information.

overall_design: We measured gene expression in phyA-211 and phyB-9 mutants, and Col-0 before and after Far-red light treatment (730 nm, 1μmol m-2s-1; 0 and 4 days). We used biological duplicates for each condition

first: Junhyun

last: Lim

first: Seok-Jun

last: Jung

first: Souk

last: Seo

first: Gyochang

last: Hong

first: Daehee

last: Hwang

first: Hong-Gil

last: Nam

first: Sunghyun


title: The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development (HITS-CLIP)

first: Lance

last: Palmer

first: Vikram

last: Paralkar

first: Peng

last: Xu

first: Christophe

last: Lechauve

first: Guowei

last: Zhao

first: Yu

last: Yao

first: Jing

last: Luan

first: Anastasios

last: Vourekas

first: John

last: Scheutz

first: Zissimos

last: Mourelatos

first: Gang

last: Wu

first: Mitchell

last: Weiss


title: Expression data from different levels of ANA in HIV+ people

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

summary:
Different focal adhesions, gap junction, adherens junction, and tight junction, TLR signaling pathway were seen when compared the HIV+ high ANA (anti-nuclear antibodies) group with low ANA group
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: HIV+ subject received the influenza vaccine, we draw the blood at the D0 and D7 of vaccination. Total RNA from purified B cells of PBMC was extracted using RNeasy Micro kit . Affymetrix Human GeneChip U133 Plus 2.0 Array was used for RNA hybridization and labeling assay. We used the gene expression to compare the gene expression of high ANA HIV+ subjects versus and low ANA subjects.

first: Wei

last: Jiang


title: Long-term in vitro expansion of epithelial stem cells enabled by pharmacological inhibition of PAK1-ROCK-Myosin II and TGF-β signaling (MeDIP-seq)

first: Hyung Joo

last: Lee

overall_design: MeDIP profiles of human foreskin keratinocytes in different culture conditions were generated by deep sequencing, in duplicate, using Illumina NextSeq.

first: Chengkang

last: Zhang

first: Ting

last: Wang


title: Long noncoding RNA NKX2-1-AS1 inhibits cell migration and regulates cell-adhesion independent of NKX2-1 in human lung carcinoma cells

status: Public on Sep 28 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The long noncoding RNA NKX2-1-AS1 is highly expressed in primary lung adenocarcinomas compared to squamous carcinomas, similar to its adjacent protein-coding gene NKX2-1, but its contribution to lung tumorigenesis is not well understood. In this study we knockdown NKX2-1-AS1 by siRNA transfection and analyze the effect on gene expression in the lung carcinoma H441 cell line.

overall_design: This study is comprised of two independent knock-down experiments, each containing 6 Human Gene 2.0 ST arrays profiling H441 lung carcinoma cells treated with control siRNA or a pool of three siRNAs (A, B and D) targeting the lncRNA NKX2-1-AS1 (n=3 per group in each experiment). TRIzol RNA extraction was used to prepare samples for the first experiment (Experiment 1), while spin-column RNA extraction was used to prepare samples for second experiment (Experiment 2).

first: Maria

middle: I

last: Ramirez


title: RNA-seq analysis of uveal melanoma cells treated with FR900359

city: Saint Louis

first: Michael

last: Onken

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

summary: FR900359 is an allosteric inhibitor of Gq. 92.1 uveal melanoma cells, which are driven by constitutively active Gq, were treated with 100 nM FR900359 or vehicle for 1 day and 3days. RNA-seq was performed.

overall_design: Samples represent two independent experiments; treated and vehicle control; 1 day and 3 day time points.

first: Kendall

last: Blumer


title: Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow I

status: Public on Sep 27 2018

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

summary: Today’s diagnostic tests for multiple myeloma (MM) reflect the criteria of the updated WHO classification based on biomarkers and clinicopathologic heterogeneity. To that end, we propose a new subtyping of myeloma plasma cells (PC) by B-cell subset associated gene signatures (BAGS), from the normal B-cell hierarchy in the bone marrow (BM). To do this, we combined FACS and GEP data from normal BM samples to generate classifiers by BAGS for the PreBI, PreBII, immature (Im), naïve (N), memory (M) and PC subsets. The resultant tumor assignments in available clinical datasets exhibited similar BAGS subtype frequencies in four cohorts across 1302 individual cases. The prognostic impact of BAGS was analyzed in patients treated with high dose melphalan as first line therapy in three prospective trials: UAMS, HOVON65/GMMG-HD4 and MRC Myeloma IX with Affymetrix U133 plus 2.0 microarray data available from diagnostic myeloma PC samples. The BAGS subtypes were significantly associated with progression free (PFS) and overall survival (OS) (PFS, P=3.05e−06 and OS, P=1.06e−11) in a meta-analysis of 926 pts. The major impact was observed within the PreBII and M subtypes conferred with significant inferior prognosis compared to the Im, N and PC subtypes. Cox proportional hazard meta-analysis documented that the BAGS subtypes added significant and independent prognostic information to the TC classification system and ISS staging. BAGS subtype analysis identified transcriptome differences and a number of novel differentially spliced genes. We have identified hierarchal subtype differences in the myeloma plasma cells, with prognostic impact. This observation support an acquired reversible B-cell trait and phenotypic plasticity as a hallmark, also in MM.

overall_design: Gene expression profiles of multiple myeloma  cell lines used as validation in the article

first: Julie

middle: S

last: Bødker

middle: F

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Hans

last: Johnsen


title: Placental gene expression profiling for the identification of subtypes of human fetal growth restriction

city: Toronto

first: Brian

last: Cox

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

type:
Expression profiling by array
Third-party reanalysis

summary: Fetal growth restriction (FGR) is a heterogeneous disorder of pregnancy associated with pathologically low fetal and neonatal weights. We hypothesized that FGR consists of multiple placental subtypes, similar to what we have observed in preeclampsia. To address this hypothesis, we assembled a fetal growth-focused human placental microarray data set (N=97) consisting of 20 new normotensive suspected FGR samples (below), in addition to term controls (N=26) and hypertensive suspected FGR samples (N=51) from GSE75010.

overall_design: FGR was defined as an SGA infant (birthweight <10th percentile for gestational age and sex based on a Canadian growth reference) with signs of placental insufficiency, and 20 normotensive suspected FGR placentas were purchased from a biobank. Genome-wide mRNA expression was assessed by Affymetrix Human Gene 1.0 ST Array chips and aggregated with samples from GSE75010. Unsupervised clustering analysis was applied to the combined dataset (N=97), followed by pathway enrichment analysis and correlative analysis with clinical information and histological lesions in these placentas.

first: Isaac

last: Gibbs

first: Katherine

last: Leavey

first: Shannon

last: Bainbridge


title: Modeling of the Response to a Multiple Vaccination Schedule Using the Adjuvant Neisseria meningitidis Porin B

status: Public on Sep 26 2018

summary:
Vaccine adjuvants enhance the immune response to vaccines, resulting more robust and durable immune responses. Although extensive work has been done on the response to a single vaccination over time, here we seek to characterize the response over the course of multiple vaccinations.
In particular we modeled the changes in expression of mouse splenocytes after each of three vaccinations with and without antigen (chicken egg white ovalbumin) and adjuvant (N. meningitidis PorB). We also fitted the regulated genes into enriched gene sets to better characterize the response.

overall_design: 2x2 factorial design (+/- antigen, +/- adjuvant) over 3 time points, with a single universal control (PBS), n=3

first: Andrew

last: Platt

first: Lee

last: Wetzler