title: The expression of miRNAs is influenced by the infection of Helicobacter Pylori

first: Gerolamo

last: Lanfranchi

summary: Macrophages are important cells involved in infections responses. They are mediators of gastritis in acute Helicobacter pylori (Hp) Infection and to identify how Hp affects macrophages response to infection we measured miRNA expression after macrophages Hp infection.

overall_design: 16 samples were profiled to identify miRNAs expression. Experiments were performed on macrophages monocytes derived using M-CSF  for 6 days. Experiments with macrophages infected with Hp for 24h were replicated 3 times as well as experiments with 72h of Hp infection. As controls were used macrophages not infected and cultivated for the same time of those infected. Hp volume was substituted by PBS. It was performed 3 replicates for PBS controls at 24h and two for those at 72h. Moreover, monocyte-derived macrophages cultured for 1 d in culture medium without M-CSF  were profiled in 5 replicates.

first: Matteo

last: Pagliari

first: Fabio

last: Munari

first: Silvia

last: Lonardi

last: Chemello

first: Gaia

last: Codolo

first: Caterina

last: Millino

first: Beniamina

last: Pacchioni

first: William

last: Vermi

last: Fassan

first: Marina

last: de Bernard

first: Stefano

last: Cagnin


title: CATaDa chromatin accessiblity data for neural and midgut cell types.

status: Public on Feb 20 2018

city: London

first: Gabriel

last: Aughey

address: Imperial college road

country: United Kingdom

institute: Imperial College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulation of eukaryotic gene expression is coordinated by dynamic changes to chromatin states throughout development. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst the chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic stem cell lineages are not well defined. Here we show that tissue specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting. We have profiled chromatin accessibility in individual cell types of the Drosophila neural and midgut stem cell lineages. Functional cell-type specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding the gene regulatory mechanisms underlying development.

overall_design: Animals were raised at 18 degrees and shifted to 29 degrees at the appropriate developmental stage. 24 hours after temperature shift, tissues were collected and frozen. Genomic DNA was isolated, RNAseA treated and DpnI digested.  Adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of adaptors.Libraries were generated using the illumina TruSeq library kit and sequenced on a HiSeq2500.

middle: N

first: Tony

middle: D

last: Southall


title: A roadmap for early human liver development from pluripotent stem cells

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Embryonic stem cells (ESCs) have the potential to yield new liver cells for regenerative medicine. However it has been challenging to generate homogeneous ESC-derived human liver populations capable of engrafting in vivo and ameliorating liver failure. To overcome this challenge, we define extrinsic signals regulating six consecutive stages of human liver development, including patterning of endoderm into foregut, liver bud specification, and segregation of hepatocyte vs. biliary fates. This knowledge enabled differentiation of human ESCs into 89% pure AFP+HNF4A+TBX3+ liver bud progenitors and subsequently, a >77% uniform ALB+ hepatocytic population. ESC-derived ALB+ human hepatocytic cells engrafted the damaged livers of Fah-/- mice, improving overall mouse survival and reducing liver damage. Interestingly, certain signals that matured hESC-derived hepatocytic cells also sustained primary adult hepatocytes in vitro for one week. Collectively we demarcate extrinsic signaling, mRNA and surface marker dynamics during human liver development, enabling the generation of engraftable liver cells from ESCs.

overall_design: 32 samples consisting of H1 hESCs differentied into D2 definitive endoderm, D6 liver bud and D12 hepatic progenitors with the full base condition, without Notch inhibitor DAPT, without Forskilin, without AAP or without insulin.

first: Lay

middle: T

last: Ang

first: Antson

middle: K

last: Tan

first: Joanne

middle: S

last: Goh

first: Siew

middle: H

last: Choo

first: Kian

middle: L

last: Lee

first: Autio

middle: I

last: Matias

first: Jianmin

first: Isabelle

last: Yeo

first: Chloe

middle: J

last: Wong

first: Jane

first: Jen

last: Lum

first: Chet

last: Loh

first: Ying

middle: Y

last: Lim

first: Ling

last: Oh

first: Pei

last: Chia

first: Say

last: Kong

first: Angela

last: Chen

first: Pang

middle: W

last: Koh

first: Qing

middle: F

first: Irving

last: Weissman

first: Kyle

middle: M

first: Bing


title: Underestimation of inadvertent morpholino RNA targets: evidence from the study of Danio rerio Ser/Arg-rich splicing factors using gene editing tools

status: Public on Feb 22 2018

city: Liège

first: Marine

last: Joris

address: Chemin de la vallée 4 Quartier de la vallée 1

department: Life Sciences

country: Belgium

institute: University of Liège

type: Expression profiling by high throughput sequencing

summary: We used morpholinos and gene editing tools to inactivate the srsf5a gene. In contrast to srsf5a homozygous mutants that did not display any phenotypic traits, microinjection of sMOsrsf5a led to developmental defects. By using RNA sequencing on morphants and control embryos we were able to identify a plethora of morpholino inadvertant target.

overall_design: Two biological replicates were used per conditions. Samples named CtrlMO consist in embryos injected with the control morpholino (5'-CCTCTTACCTCAGTTACAATTTATA-3', Gene Tools). Samples named sMOsrsf5a consist in embryos injected with the morpholino against srsf5a (5'-GGATTCAGTCTCACCTCTCACTGCA-3', Gene Tools).

first: Patrick

last: Motte

first: Marc

last: Muller


title: Influenza and gene expression in lungs and blood of prepubertal vs pubertal mice

status: Public on Feb 21 2018

city: Boston

first: Lester

last: Kobzik

state: MA

address: 665 Huntington Ave

department: Environmental Health

country: USA

institute: Harvard T.H. Chan School of Public Health

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

overall_design: Refer to individual Series


title: Extensive characterization of NMD complexes in yeast

status: Public on Feb 19 2018

city: Paris

last: Dehecq

address: 25 rue du docteur roux

country: France

institute: Institut Pasteur

summary: Nonsense mediated mRNA decay is a translation-dependent surveillance pathway that detects and eliminates RNA harboring premature termination codon. Our NMD complexes analysis led to the description of strong in vivo interaction between Nmd4, Ebs1 and Upf1, the major factor of NMD. We wondered if these proteins affected the degradation of RNA sensitive to NMD and if they could act on a specific class of targets. We performed RNAseq experiments in strains deleted for NMD4, EBS1 or both in comparison with wild type and upf1∆ strains. Our analysis confirmed that Nmd4 and Ebs1 have a role in the degradation of NMD substrates. The effect of Nmd4 or Ebs1 deletion was weak compared to upf1∆, fold change compared with WT was between -1 and 1 in log2. The double mutant had a global stronger effect. We have not detected any target specificity for Nmd4 or Ebs1, their profiles were very well correlated. We have also compared our data with upf1∆ RNAseq results. Among the more stabilized RNA in ebs1 and nmd4∆ strains, the majority were also stabilized in upf1∆. We observed a good correlation between upf1∆ and ebs1∆ profiles. For nmd4∆ the correlation was weaker, probably due to the low effect of the deletion, on NMD substrates stabilisation.  We conclude that Nmd4 and Ebs1 play a specific role in the stabilization of all NMD substrates.

overall_design: body RNAseq of WT and NMD deficient yeast cells (upf1∆, nmd4∆, ebs1∆, nmd4∆/ebs1∆)

first: Caroline

last: Proux

first: Gwenael

last: Badis

first: Alain

last: Jacquier

first: Cosmin

last: Saveanu


title: Expression data of Arabidopsis leaves during extended darkening of the whole plant or an individual leaf

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

summary:
In Arabidopsis, an individually darkened leaf (IDL) initiates senescence much quicker than a leaf from an entirely darkened plant (DP).
In this study, we analysed the transcriptomes of leaves in these two darkening setups, to identify the differing metabolic strategies utilised that lead to such different fates.

overall_design: Samples were harvested at noon, i.e. in the middle of the photoperiod, at 0 days (light D0) and after 3 and 6 days of the respective darkening treatments. For all conditions (i.e. Light D0, DP-D3, DP-D6, IDL-D3 and IDL-D6), three biological replicates were used, each of them being a pool of two leaves from independent plants.

middle: R

first: Daria

last: Chrobok

first: Nicolas

last: Delhomme

first: Pernilla

last: Lindén

first: Bastiaan

last: Brouwer

first: Marta

last: Juvany

first: Abdul

last: Ahad

first: Thomas

last: Moritz

first: Stefan

last: Jansson

first: Per

last: Gardeström

first: Olivier

last: Keech


title: Pre-treatment expression data from neoadjuvant platinum & bevacizumab treated triple negative breast cancer patients

city: Lyngby

first: Nicolai

middle: Juul

last: Birkbak

address: Kemitorvet, Build. 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

summary:
Gene expression data from 21 triple negative breast cancer samples treated with cisplatin & bevacizumab in the neoadjuvant setting as part of a clinical trial.
Gene expression data RMA normalized was used to find predictors of platinum sensitivity

overall_design: Patients were treated in the neoadjuvant setting, RNA was purified from core biopsy pre-treatment and pre-surgery, profiled for RNA expression on Affymetrix U133 Plus 2.0 gene expression array following manufacturers protocol.

first: Andrea

last: Richardson


title: Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors

city: Oxford

first: Christopher

last: Booth

state: Oxfordshire

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus


title: Small RNA profiling in mouse mammary tumor virus (MMTV) infected cell cultures and induced mammary tumors

city: Austin

last: Sullivan

state: Texas

address: 2506 Speedway Stop A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

type: Non-coding RNA profiling by high throughput sequencing

summary: Mouse mammary tumor virus (MMTV) is a complex retrovirus that induces breast cancer in mice in the absence of known virally-encoded oncogenes. Like other non-acute retroviruses, tumorigenesis by MMTV is thought to occur primarily through insertional mutagenesis, leading to the activation of cellular proto-oncogenes and outgrowth of selected cells. In this study, we investigated whether MMTV encodes microRNAs (miRNAs) and/or modulates host miRNAs that could contribute to tumorigenesis. We have applied high throughput small RNA sequencing to the analysis of MMTV-infected cells and MMTV-induced mammary tumors. Our results demonstrate that MMTV does not encode miRNAs. However, MMTV infected cells and MMTV-producing tumors have altered levels of several cellular miRNAs, including increases in the expression of members of the oncogenic miRNA cluster, miR-17-92. Notably, similar changes in levels of these miRNAs have been previously reported in human breast cancers. Combined, our results demonstrate that virally encoded miRNAs do not contribute to MMTV-mediated tumorigenesis, but that changes in specific host miRNAs in infected cells may contribute to virus replication and tumor biology.

sample_organism:
Mus musculus
Mouse mammary tumor virus

platform_organism:
Mus musculus
Mouse mammary tumor virus

overall_design: Six samples each, 2 cell lines, 2 glands, and 2 tumors.

first: Rodney

middle: P

last: Kincaid

first: Jaquelin

last: Dudley

first: Farah

last: Mustafa


title: Differentiation of functional endothelial cells from human iPS cells

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: Endothelial cell (EC) therapy may promote vascular growth or reendothelization in a variety of disease conditions. However, the production of a cell therapy preparation containing differentiated, dividing cells presenting typical EC phenotype, functional properties and chemokine profile is challenging. We focused on comparative analysis of seven small molecule-mediated differentiation protocols of ECs from human induced pluripotent stem cells. Differentiated cells showed a typical surface antigen pattern of ECs as characterized with flow cytometry analysis, functional properties, such as tube formation and ability to uptake acetylated LDL. Gene expression analysis by RNA sequencing revealed an efficient silencing of pluripotency genes and upregulation of genes related to cellular adhesion during differentiation. In addition, distinct patterns of transcription factor expression were identified during cellular reprogramming providing targets for more effective differentiation protocols in the future. Altogether, our results suggest that the most optimal EC differentiation protocol includes early inhibition of Rho-associated coiled-coil kinase and activation of cyclic adenosine monophosphate signaling, and inhibition of transforming growth factor beta signaling after mesodermal stage. These findings provide the first systematic characterization of the most potent signalling factors and small molecules used to generate ECs from human induced pluripotent stem cells. Consequently, this work improves the existing EC differentiation protocols and opens up new avenues for controlling cell fate for regenerative EC therapy.

overall_design:
Comparison of the effects of signalling factors and small molecules on endothelial cell differentiation from induced pluripotent stem cells using RNA-Seq.
Following small molecules and growth factors were used in different combinations and time courses: 10 uM TGFβ-inhibitor SB431542, 10 uM ROCK-inhibitor Y-27632, 20 ng/ml recombinant human BMP-4 and 0,25 mM 8-Br-cAMP. In all groups without TGFβ-inhibitor at day 1 in the differentiation, it was added at day 4. In those groups with BMP-4 at day 1, it was removed at day 4. Differentiating ECs were passaged every 4-6 days using Accutase.

first: Heini

last: Belt


title: Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors [Mouse bone marrow and human cell line ChIP-Seq]

summary: Understanding the specific cell populations responsible for propagation of leukemia is an important step for development of effective targeted therapies. Recently, the lymphoid-primed multipotent progenitor (LMPP) has been proposed to be a key propagating population in acute myeloid leukemia (AML; PMID 21251617). We have also shown that LMPPs share many functional and gene expression properties with early thymic progenitors (ETPs; PMID 22344248). This finding is of particular interest as ETP leukemias have recently been described: a distinct and poor prognostic disease entity with a transcriptional profile reminiscent of murine ETPs, showing co-expression of hematopoietic stem cell (HSC) and myeloid markers (PMID 19147408). Together, this raises the question whether ETPs can act as a leukemia-initiating/propagating cell population; however, relevant disease models to test this hypothesis are currently lacking. Analysis of the genetic landscape of ETP leukemias has revealed frequent coexistence of inactivating mutations of EZH2 and RUNX1 (PMID 22237106). We therefore generated mice with deletions of Ezh2 and Runx1 specifically targeted to early lymphoid progenitors using Rag1Cre (Ezh2fl/flRunx1fl/flRag1Cre+; DKO mice). As anticipated, HSCs lacked significant recombination in DKO mice whereas close to 100% of purified ETPs (Lin-CD4-CD8-CD44+CD25-Kit+Flt3+) showed deletion of Ezh2 and Runx1. Strikingly, despite a 16-fold reduction in thymus cellularity caused by a block in thymocyte maturation at the DN2-DN3 transition, absolute numbers of ETPs within the thymus of DKO mice were markedly expanded (12-fold; p<0.0001). In contrast, Ezh2 or Runx1 deletion alone had no impact on numbers of ETPs. RNA-sequencing of the expanded ETPs in DKO mice revealed upregulation of HSC- and myeloid-associated transcriptional programs, reminiscent of ETP leukaemia e.g. Pbx1 (log2FC=3.0; p<0.0001) and Csf3r (log2FC=1.9; p=0.0038). Single-cell gene expression analysis confirmed co-expression of HSC and myeloid programs with lymphoid genes within individual DKO ETPs. Further, some key regulators of T-cell maturation which are aberrantly expressed in ETP leukemia were also disrupted in DKO ETPs e.g. Tcf7 (log2FC=-9.5; p<0.0001). Gene expression associated with aberrant Ras signalling was also present. However, despite a continued expansion of the ETP population with age, we did not observe leukemia in DKO mice with over 1 year of follow-up. Since ETP leukemias frequently feature activating mutations in genes regulating RAS signaling, we hypothesised that the expanded “pre-leukemic” ETPs in DKO mice would be primed for leukemic transformation by signalling pathway mutation. We therefore crossed DKO mice with a Flt3ITD/+ knock-in mouse line, as internal tandem duplications (ITD) of FLT3 are frequent in ETP leukemias. Ezh2fl/flRunx1fl/flRag1Cre+Flt3ITD/+ (DKOITD) mice showed dramatically reduced survival (median 9.3 weeks) resulting from an aggressive, fully penetrant acute leukemia showing a predominantly myeloid phenotype (e.g. Mac1) but with co-expression of some lymphoid antigens (e.g. intracellular CD3). Crucially, this leukaemia could be propagated in wild-type recipients upon transplantation of the expanded ETPs. DKOITD ETPs were transcriptionally very similar to DKO ETPs, retaining expression of lymphoid alongside HSC- and myeloid-associated genes. Finally, in a lympho-myeloid cell line model (EML cells) we demonstrated that Ezh2 inactivation-induced loss of H3K27me3 is associated with a corresponding increase in H3K27Ac, a transcriptional activating signal that recruits bromodomain proteins. As such, we reasoned that our ETP leukemia model might be sensitive to bromodomain inhibitors such as JQ1. Indeed, we observed high sensitivity of expanded DKOITD ETPs to JQ1, raising the possibility of a new therapeutic approach for ETP leukemias. This novel mouse model of ETP-propagated leukemia, driven by clinically relevant mutations, provides intriguing evidence that leukemias with a predominant myeloid phenotype, but co-expressing lymphoid genes, may initiate within a bona fide early lymphoid progenitor population. Since the functional characteristics of the cell of origin of a leukaemia may direct its progression and response to therapy, these findings could have important implications for future stratification and treatment of both AML and ETP leukemias.

overall_design: H3K27ac and H3K27me3 ChIP-sequencing of bone marrow cells from eight mice, and two human leukemia cell lines

middle: A

first: Wen

last: Neo

first: Sten

middle: E

last: Jacobsen

first: Adam

last: Mead


title: Transcriptome profiles of liver biopsy tissues from patients with various stages of alcoholic liver disease

status: Public on Feb 18 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Corticosteroids are the current standard of care to improve short-term mortality in severe alcoholic hepatitis (AH), although nearly 40% of the patients do not respond and accurate pre-treatment predictors are lacking. We developed 123-gene prognostic score based on molecular and clinical variables before initiation of corticosteroids. Furthermore, The gene signature was implemented in an FDA-approved platform (NanoString), and verified for technical validity and prognostic capability. Here we demonstrated that a Nanostring-based gene expressoin risk classification is useful to predict mortality in  patients with severe alcoholic hepatitis who were treated by corticosteroid

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues.

first: Eric

last: Trépo

first: Nicolas

last: Goossens

first: Naoto

last: Fujiwara

first: Denis

last: Franchimont


title: Prepubertal vs pubertal whole blood gene expression in male and female mice

first: Lester

last: Kobzik

summary:
During the 1918 influenza pandemic, children experienced substantially lower mortality than adults, a striking but poorly understood finding. Whether this was due to enhanced resistance (reduced virus load) or better tolerance (reduced impact of infection) has not been defined. We found that prepubertal mice infected with H1N1 influenza virus also showed greater survival than infected pubertal mice, despite similar virus loads.
To explore mechanisms for the survival differences, we compared gene expression profiles in whole blood leukocytes from normal, uninfected mice of both age groups.

overall_design: Whole blood from male and female C57Bl/6 mice was collected from 3-4 mice per group and RNA isolated for microarray analysis.

first: Suber

last: Freeman

first: Kobzik

last: Lester


title: Regulatory Mechanisms Mediated by DNA methyltransferase 1 link the maternal Environment with the Development of the Embryo

city: Al Ain

first: Ranjit

last: Vijayan

state: Abu Dhabi

address: PO Box 15551

department: Biology

country: United Arab Emirates

institute: United Arab Emirates University

summary: Epidemiological as well as animal model studies have demonstrated the close relationship that exists between the early maternal developmental environment and the risk of developing metabolic diseases in adulthood. Small birth weight has been shown to be an important marker for this although the molecular mechanisms which mediate these changes are not well understood

overall_design: By using average (50th to 75th) and lower (5th to 25th) percentiles of the normal birth weight range of Wistar rat pups, we show here that the growth of embryos is linked to the early maternal developmental environment

first: Ashok

middle: D

last: Prabakaran

first: Jimsheena

middle: V

last: Karakkat

first: Jisha

last: Chalissery

first: Marwa

last: Ibrahim

first: Suneesh

last: Kaimala

first: Ernest

last: Adeghate

first: Ahmed

last: Al-Marzouqi

first: Suraiya

last: Ansari

first: Mensah-Brown

last: EPK

first: Starling

last: David


title: Identification of the RB loss-induced transcriptome and E2F1 cistrome in prostate cancer

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University


title: The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks

status: Public on Feb 17 2018

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: The p.R482W hotspot mutation in A-type nuclear lamins causes familial partial lipodystrophy of Dunnigantype (FPLD2), a lipodystrophic syndrome complicated by early-onset atherosclerosis. Molecular mechanisms underlying endothelial cell dysfunction conferred by the lamin A mutation remain elusive. However, lamin A regulates epigenetic developmental pathways and mutations could perturb these functions. Here, we demonstrate that lamin A R482W elicits endothelial differentiation defects in a developmental model of FPLD2. Genome modeling in fibroblasts from patients with FPLD2 caused by the lamin A R482W mutation reveals repositioning of the mesodermal regulator T/Brachyury locus towards the nuclear center relative to normal fibroblasts, suggesting enhanced activation propensity of the locus in a developmental model of FPLD2. Addressing this issue, we report phenotypic and transcriptional alterations in mesodermal and endothelial differentiation of induced pluripotent stem cells we generated from a patient with R482Wassociated FPLD2. Correction of the LMNA mutation ameliorates R482W-associated phenotypes and gene expression. Transcriptomics links endothelial differentiation defects to decreased Polycomb-mediated repression of the T/Brachyury locus and over-activation of T target genes. Binding of the Polycomb repressor complex PRC2 to T/Brachyury is impaired by the mutated lamin A network, which is unable to properly associate with the locus. This leads to a deregulation of vascular gene expression over time. By connecting a lipodystrophic hotspot lamin A mutation to a disruption of early mesodermal gene expression and defective endothelial differentiation, we propose that the mutation rewires the fate of several lineages, resulting in multitissue pathogenic phenotypes.

overall_design:
RNA-seq data pertain to examination of expression profiles of 1) iPS cells derived from patients with Familial Partial Lipodystrophy of Dunnigan-type (FPLD2) with the LMNA p.R482W mutation and 2) FPLD2 patient-derived iPS cells in which the LMNA mutation has been repaired -- both during mesodermal differentiation from day 0 to day 4.
ChIP-seq data pertain to ChIP of lamin A/C (LMNA) and lamin B1 (LMNB1) from cultured FPLD2 patient fibroblasts.

first: Akshay

last: Shah

first: Nolwenn

last: Briand


title: Tcf-1 shapes the chromatin landscape of naive T cells

first: Herbert

last: De'Broski

address: 3800 Spruce St

institute: University of Pennsylvania

summary: We investigate the requirement of the transcription factor Tcf-1 for T cell specific accessible elements and gene expression in developing T cells. We examine the impact of Tcf-1 on creating chromatin accessibility related to T cell identity in an unrelated, differentiated cell-type.

overall_design: Examination of chromatin accessibility in developing DP T cells from WT and Tcf-1 KO. Examination of chromatin accessibility, repressive histone modifications, and binding of Tcf-1 after ectopic expression in NIH3T3 fibroblasts.

first: John

last: Johnson

first: George

last: Georgakilas


title: Cry2 is critical for circadian regulation of myogenic differentiation by Bclaf1-mediated mRNA stabilization of cyclin D1 and Tmem176b

city: Minneapolis

first: Nobuaki

last: Kikyo

state: Minnesota

department: Stem Cell Institute

institute: University of Minnesota

summary: Circadian rhythms regulate cell proliferation and differentiation; however, little is known about their roles in myogenic differentiation. Our synchronized differentiation studies demonstrate that myoblast proliferation and subsequent myotube formation by cell fusion occur in circadian manners. We found that one of the core regulators of circadian rhythms Cry2, but not Cry1, is critical for the circadian patterns of these two critical steps in myogenic differentiation. This is achieved through the specific interaction between Cry2 and Bclaf1, which stabilizes mRNAs encoding cyclin D1, a G1/S phase transition regulator, and Tmem176b, a transmembrane regulator for myogenic cell fusion. Myoblasts lacking Cry2 display premature cell cycle exit and form short myotubes due to inefficient cell fusion. Consistently, muscle regeneration is impaired in Cry2-/- mice. Bclaf1 knockdown recapitulated the phenotypes of Cry2 knockdown: early cell cycle exit and inefficient cell fusion. This study uncovers a post-transcriptional regulation of myogenic differentiation by circadian rhythms.

overall_design: mRNA profiles of Cry1 knockdown, Cry2 knockdown and control C2C12 cells at d0, d3 and d5 were generated by using Illumina HiSeq2500.

first: Mathew

last: Lowe

first: Jacob

last: Lage

first: Ellen

last: Paatela

first: Dane

last: Munson

first: Reilly

last: Hostager

first: Ce

last: Yuan

first: Nobuko

last: Katoku-Kikyo

first: Mercedes

last: Ruiz-Estevez

first: Yoko

last: Asakura

first: James

last: Staats

first: Mulan

last: Qahar

first: Michaela

last: Lohman

first: Atsushi


title: New role of ID3 in melanoma adaptive drug-resistance

status: Public on Feb 16 2018

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

summary: Adaptive resistance to targeted therapy such as BRAF inhibitors represents in melanoma a major drawback to this otherwise powerful treatment. Some of the underlying molecular mechanisms have recently been described: hyperactivation of the BRAF-MAPK pathway, of the AKT pathway, of the TGFβ/EGFR/PDGFRB pathway, or the low MITF/AXL ratio. Nevertheless, the phenomenon of early resistance is still not clearly understood. In this report, we show that knockdown of neural crest-associated gene ID3 increases the melanoma sensitivity to vemurafenib short-term treatment. In addition, we observe an ID3-mediated regulation of cell migration and of the expression of resistance-associated genes such as SOX10 and MITF. In sum, these data suggest ID3 as a new key actor of melanoma adaptive resistance to vemurafenib and as a potential drug target. Molecular mechanisms that are responsible for the development of human skin epithelial cells are not completely understood so far. As a consequence, the efficiency to establish a pure skin epithelial cell population from human induced pluripotent stem cells (hiPSC) remains poor. Using an approach including RNA interference and high-throughput imaging of early epithelial cells, we could identify candidate kinases which are involved in skin epithelial differentiation. Among them, we found HIPK4 to be an important inhibitor of this process. Indeed, its silencing increased the amount of generated skin epithelial precursors, increased the amount of generated keratinocytes and improved growth and differentiation of organotypic cultures, allowing for the formation of a denser basal layer and stratification with the expression of several keratins. Our data bring substantial input in the regulation of human skin epithelial differentiation and for improving differentiation protocols from pluripotent stem cells.

overall_design: mRNA isolated from NHM, D1NC, vemurafenib-treated melanoma lines, DMSO-treated melanoma lines, WM266-4 EV cell line and WM266-4 ID3 cell line.

last: Larribère


title: Gene expression data of gdT-derived iPSCs and validated iPS clone for pluritest

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

summary: γδT cells constitute a small proportion of lymphocytes in peripheral blood. Unlike αβT cells, the anti-tumor activities are exerted through several different pathways in a MHC-unrestricted manner. Thus, immunotherapy using γδT cells is considered to be effective for various types of cancer. Occasionally, however, ex vivo expanded cells are not as effective as expected due to cell exhaustion. To overcome the issue of T-cell exhaustion, researchers have generated induced pluripotent stem cells (iPSCs) that harbor the same T-cell receptor (TCR) genes as their original T-cells, which provide nearly limitless sources for antigen-specific cytotoxic T lymphocytes (CTLs). However, these technologies have focused on αβT cells and require a population of antigen-specific CTLs, which are purified by cell sorting with HLA-peptide multimer, as the origin of iPS cells.   In the present study, we aimed to develop an efficient and convenient system for generating iPSCs that harbor rearrangements of the TCRG and TCRD gene regions (γδT-iPSCs) without cell-sorting. We stimulated human whole peripheral blood mononuclear cell (PBMC) culture using Interleukin-2 and Zoledronate to activate γδT cells. Gene transfer into those cells with the Sendai virus vector resulted in γδT cell-dominant expression of exogenous genes. The introduction of reprogramming factors into the stimulated PBMC culture allowed us to establish iPSC lines. Around 70% of the established lines carried rearrangements at the TCRG and TCRD gene locus. The γδT-iPSCs could differentiate into hematopoietic progenitors.   Our technology will pave the way for new avenues toward novel immunotherapy that can be applied for various types of cancer.

overall_design: We extracted total RNAs from two gdT-derived iPSCs (46A1-s3, 46C2-s4) and validated iPS clone (409B2) and performed microarray for pluritest.

first: Mariko

last: Taniguchi-Ikeda

first: Takashi

last: Aoi


title: Therapy-induced hypoxia contributes to AML drug-resistance through BMX Kinase upregulation

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Oncogenic addiction to FLT3 kinase signaling is a hallmark of FLT3-ITD+ acute myeloid leukemia (AML). While FLT3 inhibitors like sorafenib show initial therapeutic efficacy, resistance rapidly develops through mechanisms that are incompletely understood. Here, utilizing RNA-Seq based analysis of patient leukemic cells, we found significant up-regulation of the Tec-family kinase BMX during sorafenib resistance. BMX upregulation was recapitulated in an in vivo FLT3-ITD+ model of sorafenib resistance. Mechanistically, we found that the anti-angiogenic effects of sorafenib led to increased bone-marrow hypoxia, which contributed to HIF-dependent BMX upregulation. In in vitro experiments, hypoxia-dependent BMX up-regulation was observed in both AML and non-AML cell lines. Functional studies in FLT3-ITD+ cell lines showed that BMX is part of a compensatory signaling mechanism that promotes AML cell survival during FLT3 inhibition. Our results demonstrate that hypoxia-dependent up-regulation of BMX contributes to therapeutic resistance through a compensatory pro-survival signaling mechanism. These results also reveal the role of ‘off-target’ drug effects on tumor microenvironment and development of acquired drug resistance. We propose that the bone marrow niche can be altered by anti-cancer therapeutics, resulting in drug resistance through cell non-autonomous microenvironment-dependent effects.

overall_design: eight AML samples from 4 patients, 7 are relapses and 1 is a diagnosis sample

first: Jolieke

middle: G

last: van Oosterwijk

first: Daelynn

last: Buelow

first: Christina

last: Drenberg

first: Aksana

last: Vasilyeva

first: Lie

last: Li

first: Lei

last: Shi

first: Yong-Dong

last: Wang

first: Sheila

last: Shurtleff

first: Laura

last: Janke

first: Stanley

last: Pounds

first: Jeffrey

last: Rubnitz

first: Hiroto

last: Inaba

first: Navjotsingh

last: Pabla

first: Sharyn

last: Baker


title: An integrative transcriptomic and clinical score for mortality prediction in severe alcoholic hepatitis treated with corticosteroids

first: Yujin

last: Hoshida


title: Gene expression profile in node negative breast tumor

city: Milan

first: Marco

last: Silvestri

address: via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: We analyzed gene expression profile in node negative breast tumor for molecular subtype classification

overall_design: Fresh frozen primary tumors were collected at the time of diagnosis from 92 patients with operable breast cancer previously untreated and undergoing radical or conservative surgery at the Istituto Nazionale Tumori of Milano (INTM) between1990 and 1998. All patients were pathologically defined as axillary node negative and were not submitted to any type of adjuvant systemic treatment until relapse.

first: V

last: Cappelletti

first: M

last: Daidone


title: Rescue of Fragile X syndrome by DNA methylation editing of the FMR1

city: CAMBRIDGE

first: Shawn

last: Liu

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Rescue of Fragile X syndrome by DNA methylation editing of the FMR1 [ChIP-seq II]

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

summary: Fragile X syndrome (FXS), the most common genetic form of intellectual disability in male, is caused by the silence of FMR1. Hypermethylation of the CGG expansion mutation in the 5’UTR region of FMR1 in FXS patients was thought to epigenetically silence FMR1. Here, we applied our previously developed DNA methylation editing tool to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/gRNA switched the heterochromatin status of the FMR1 promoter to an active chromatin status and subsequently restored FMR1 expression in FXS iPSCs. Neurons derived from methylation edited FXS iPSCs showed a similar electrophysiological property as wild-type neurons, and maintained FMR1 expression for months after engrafting into the mouse brain. Reactivation of FMR1 can be achieved in FXS neurons with demethylation of the CGG expansion. Lastly, we showed that targeted demethylation of the FMR1 promoter can reactivate FMR1 as well suggesting potential therapeutic approaches for FXS.

overall_design: ChIP-Seq for histone modifications and RNA Polymerase II in human induced pluripotent stem cells

first: X

middle: S

first: Hao

last: Wu

first: Marine

last: Krzisch

first: Xuebing

first: Julien

last: Muffat

first: Denes

last: Hnisz

first: Charles

first: Bingbing

last: Yuan

first: Yun

first: Steven

middle: T

last: Warren

first: Dan

last: Vershkov

first: Nissim

last: Benvenisty

first: Angela

last: Cacace

first: Rudolf

last: Jaenisch


title: Comparison of host gene expression profiles in spleen tissues of genetically susceptible and resistant mice during ECTV infection

city: Lanzhou

first: Wenyu

last: Cheng

state: Gansu

department: State Key Laboratory of Veterinary Etiological Biology

country: China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary:
Ectromelia virus (ECTV) has emerged as a valuable model for investigating the host-orthopoxvirus relationship as it relates to pathogenesis and the immune response. ECTV causes mousepox in most strains of mice, including BALB/c and DBA/2, and these are therefore classified as susceptible mice. Conversely, C57BL/6 and certain 129 strains display limited pathology and a very low mortality, and are thus classified as resistant. To understand the host genetic factors of different mouse strains in response to ECTV infection, we carried out a microarray analysis using Affymetrix Gene-Chip Mouse Genome Arrays of spleen tissues from BALB/c and C57BL/6 mice at 3 and 10 days post-ECTV infection.
Differential Expression of Genes (DEGs) analyses revealed distinct differences in the gene profiles of resistant and susceptible mice infected with ECTV. Gene ontology and KEGG pathway analysis showed that the DEGs of susceptible mice were involved mainly in immunity, apoptosis, spliceosomes and cancer-related pathways, while the DEGs of resistant mice were largely involved in MAPK signaling and leukocyte transendothelial migration. This suggests that the susceptible BALB/c mice have a stronger response than the resistant C57BL/6 mice to ECTV infection. The BALB/c mice showed a strong induction of interferon-induced genes (ISGs), including guanylate binding proteins (GBPs), myxovirus resistance protein (Mx) GTPases, oligoadenylate synthetase (OAS) and IFN-induced protein with tetratricopeptide repeats (IFIT) family proteins, while the C57BL/6 mice upregulated more genes related to metabolic pathways. This suggests that the susceptible BALB/c mice have a stronger response than the resistant C57BL/6 mice to ECTV infection.

overall_design: Five C57BL/6 and BALB/c mice in each group were infected with 104 TCID50/mL ECTV (in 100 µL PBS) and spleen tissues were harvested at 3 day (T1) and 10 day (T2) post infection. The pooled spleen tissues were performed the microarray experiment. The non-infected at 0 hour (T0) biological condition were used as an additional control.

first: Huaijie

last: Jia

first: Xiaobing

last: He

first: Guohua

last: Chen

first: Xiaoxia

last: Wang

first: Zhizhong

last: Jing


title: Rescue of Fragile X syndrome by DNA methylation editing of the FMR1 [ChIP-seq]

city: New York

first: Xuebing

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

overall_design: This series includes two sets of Cas9 ChIP in FX52 iPSCs. The first set includes 3 samples: the input and IP sample from an iPSC line stably expressing dCas9-Tet1 and a guide RNA targeting FMR1 5' UTR repeat, and the IP sample from a mock iPSC line. The second set of samples include Cas9 IP from two additional lines with the same transgene expressed at a lower level, and an input sample from line 3.

first: X

last: Liu


title: The Effect of RBM5 Gene Manipulation on Expression Data from Day In Vitro 6 Primary Rat Cortical Neurons

city: Pittsburgh

first: Travis

middle: C.

last: Jackson

state: Pennsylvania

address: 3550 Terrace Street

department: Critical Care Medicine

institute: University of Pittsburgh

summary:
RNA Binding Motif 5 (RBM5) is a nuclear splicing factor. Prior studies show that RBM5 overexpression in cancer cells alters gene splicing, gene expression, and induces cell death and/or growth arrest.  The role of RBM5 in primary neurons is unknown, and its potential mRNA targets have not been identified. Using lentivirus based approaches we tested if RBM5 knockdown (i.e. by shRNA) or RBM5 overexpression (DDK-tagged rat open reading frame) alters whole genome expression in primary rat cortical neurons.
We used microarrays to examine genes that are up-regulated vs. down-regulation in cortical neurons after RBM5 knockdown vs. overexpression.

overall_design: Brain cortices were collected from Sprague Dawley rat embryos. Primary rat cortical neurons were cultured and maintained using Neurobasal media+B27 supplement. On day in vitro (DIV) zero (i.e. on the day of plating) neurons were transduced with lentivirus. The vector treatment groups were as follows: Group 1: Non-Targeting(NT)/scrambled shRNA control with green fluorescent protein (GFP), Group 2: RBM5 targeting shRNA with green fluorescent protein (GFP), Group 3: Empty vector control, Group 4: DDK-Tagged rat RBM5 open reading frame overexpression vector.  For control vs. treatment comparision groups 1 vs. 2, three biological replicates (per group) were done (i.e. different neuron cultures established from different timed pregnant rats on different days). For control vs. treatment comparision groups 3 vs. 4, four biological replicates (per group) were done. (i.e. different neuron cultures established from different timed pregnant rats on different days). Neurons were harvested on DIV6 with TRIzol for total RNA extraction.  Reverse transcription was performed on 100ng total RNA and dNTP-T7 random primers. Amplified cRNA was made using second strand synthesis and in vitro transcription.  cDNA was produced by a subsequent reverse transcription and then fragmented. Fragments were biotin end-labeled in preparation for hybridization to the RTA. The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used for array processing. 5.2µg biotin-labeled fragmented ss-cDNA was added to 1X hybridization buffer containing oligo B2, hybridization controls, and DMSO.  Following incubation at 95°C and 45°C for 5 minutes each, 200µL hybridization mix was loaded onto each array. Arrays were incubated for 16h in a GeneChip 645 hybridization oven (Affymetrix) at 45°C with rotation at 60rpm. Arrays were scanned using the GeneArray® 3000 scanner (Affymetrix). Results were normalized by robust multi-array average (RMA).

middle: C

first: Shawn

last: Kotermanski

first: Patrick

last: Kochanek


title: Transcriptome analyses of toxoflavin-dependent genes in Fusarium graminearum wild-type GZ03639 and toxoflavin-sensitive mutants

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: Bacterial pathogen Burkholderia glumae and fungal pathogen Fusarium graminearum cause similar disease symptoms and often co-isolated from rice heads, inferring interactions between the two pathogens. F. graminearum is resistant to the bacterial toxin toxoflavin, a strong anti-microbial activity, produced by B. glumae. We isolated toxoflavin-sensitive mutants from transcription factor deletion mutant library of F. graminearum. To understand genome-wide transcriptional profiling, we performed RNA-seq analyses of F. graminearum wild-type strain GZ03639 and toxoflavin-sensitive mutant strains (∆GzZC190, ∆GzC2H008, ∆GzbZIP005) under toxoflavin condition.

overall_design: Four samples examined: Fusarium graminearum wild-type strain GZ03639 and three toxoflavin-sensitive mutant strains (∆GzZC190, ∆GzC2H008, ∆GzbZIP005). Two conditions: fungal cultures under toxoflavin condition and minimal media condition.

first: Boknam

last: Jung

first: Jungkwan

last: Lee

first: Young-su

last: Seo


title: RNA-Seq of polysome profiling fractions and whole cell lysates of UVB-irradiated N-TERT keratinocytes

city: Indianapolis

first: Ann

last: Collier

state: IN

address: 635 N Barnhill Dr MS4067

institute: Indiana University School of Medicine

summary: In response to UVB irradiation, human keratinocytes transiently block cell cycle progression to allow ample time for DNA repair and cell fate determination. These cellular processes are important for evading the initiation of carcinogenesis in skin. We previously showed that repression of mRNA translation initiation through phosphorylation of eIF2α (eIF2α-P) protects keratinocytes from UVB-induced apoptosis. In this study, we elucidate the mechanism of eIF2α-P cytoprotection in response to UVB. Loss of eIF2α-P induced by UVB diminished G1 arrest, DNA repair rate, and cellular senescence coincident with enhanced cell death in human keratinocytes. Genome-wide translation analyses revealed that the mechanism for these critical changes directed by eIF2α-P involved induced expression of CDKN1A encoding p21 protein. p21 is a major regulator of the cell cycle, and we show that human CDKN1A mRNA splice variant 4 is preferentially translated by eIF2α-P during stress in a mechanism mediated in part by upstream ORFs situated in the 5’-leader of CDKN1A mRNA. We conclude that eIF2α-P is cytoprotective in response to UVB by a mechanism featuring translation of a specific splice variant of CDKN1A that facilitates G1 arrest and subsequent DNA repair.

overall_design: Untreated and irradiated N-TERT keratinocytes are split into 3 groups: monosome fraction, polysome fraction, and whole cell lysate. N=3.

first: Ronald

last: Wek

first: Dan

last: Spandau


title: Inhibition of AKT-signaling uncouples cellular differentiation from expansion for receptor-engineered T cells

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: Adoptive immunotherapies using genetically-redirected T cells expressing a chimeric antigen receptor (CAR) or T cell receptor (TCR) are poised to enter mainstream clinical practice. Despite encouraging results, some patients fail to respond to current therapies. In part, this phenomenon has been associated with infusion of a reduced number of early memory T cells. Herein, we report that pharmacologic disruption of AKT-signaling (AKTi) is compatible with the transduction of both CARs and TCRs into human T cells and promotes a minimally differentiated CD62L-expressing phenotype. Critically, this intervention did not compromise cell yield. Mechanistically, disruption of AKT-signaling preserved MAPK activation and promoted the intra-nuclear accumulation of FOXO1, a key transcriptional regulator of T-cell memory. Consequently, AKTi synchronized the T-cell transcriptional profile for FOXO1-dependent target genes across multiple donors. Expression of an AKT-resistant FOXO1 mutant phenocopied the influence of AKTi while addition of AKTi to T cells expressing mutant FOXO1 failed to further augment the frequency of CD62L-expressing cells. Finally, CD19 CAR-modified T cells transduced and expanded in AKTi treated established B-cell acute lymphoblastic leukemia superiorly to conventionally grown T cells in a murine xenograft model. Thus, inhibition of AKT-signaling represents a generalizable strategy to generate large numbers of receptor-modified T cells with an early memory phenotype.

overall_design: PBMCs from 3 patients (Patients C, M, and P) were enriched for CD8+ T cells using Miltenyi kit. 1e6 cells per sample. Time 0 represents start of culture. Whole PBMCs (not CD8-enriched) were activated with anti-CD3 and retrovirally-transduced with CD19 CAR and expanded in presence or absence of pharmacologic inhibitor of Akt. Veh denotes cells expanded in conventional conditions. Akt denotes conditions expanded in 1uM Akt inhibitor. At day 10, were enriched for CD8+ T cells using Miltenyi kit and 1e6 cells per sample were preserved in 40ul RNA later and stored in -80C. N=33 samples.

first: Christopher

last: Klebanoff

first: Joseph

last: Crompton

first: Anthony

middle: J

last: Leonardi

first: Tori

middle: N

last: Yamamoto

first: Madhusudhanan

last: Sukumar

first: Robert

last: Eil

first: Suman

middle: K

last: Vodnala

first: David

last: Clever

first: Mary

last: Black

first: Devikala

last: Gurusamy

first: Michael

last: Kruhlak

first: Ping

last: Jin

last: Stroncek

first: Luca

last: Gattinoni

first: Steven

last: Feldman

first: Nicholas

last: Restifo


title: iMEF SDHC-loss ChIP-seq

status: Public on Feb 15 2018

city: Rochester

first: John

middle: Andrew

last: Smestad

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We have developed a tet-inducible immortalized mouse embryonic fibroblast (iMEF) cell culture system  for studying the cross-talk between TCA cycle metabolism and the epigenome, in which silencing gene rearrangement of the Sdhc floxed allele is driven by doxycycline-dependent expression of cre-recombinase from a tet-inducible promoter (R26M2rtTA/+;TetOcre;Sdhcfl/fl).  Using this model and an isogenic Sdhc wt control line (R26M2rtTA/+;TetOcre;Sdhcfl/wt), we have characterized differences in H3K4me3, H3K27me3, and chromatin succinylation that occur genome-wide in response to SDHC loss.  For these experiments, both cell lines were grown in standard DMEM media containing 10% FBS at 37˚C and 5% CO2.  16 days after induction of Sdhc gene rearrangement by doxycycline induction, chromatin from the respective lines was prepared and patterns of H3K4me3, H3K27me3, and chromatin succinylation were studied via ChIP-seq.

overall_design: Included in this dataset are duplicate ChIP-seq experiments and input chromatin for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at day 16 after induction with doxycycline.

first: Louis

last: Maher


title: HOXB4 expression in iRUNX embryoid bodies

city: Essen

first: Stefan

last: Heinrichs

address: Virchowstr. 179

department: Institute of Transfusion Medicine

institute: University Hospital Essen

summary: HOXB4 was retrovirally expressed in differentiating mouse embryonic stem cells. Through the use of Runx1(-/-) ESCs containing a Doxycycline-inducible Runx1 coding sequence (iRUNX ESCs), we uncovered the HOXB4-dependent, Runx1-independent gene expression changes.

overall_design: Total RNA was prepared from sorted Flk1+PDFGRα- cells in 3 independent, replicate experiments at the same time point (day 4) upon EB differentiation.

first: Hannes

last: Klump


title: Expression data from acutely damaged stomachs

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

summary: Tamoxifen injection injures the mouse stomach, triggering a plastic regenerative response termed Spasmolytic Polypeptide Exressing Metaplasia. We are probing how tamoxifen treated stomachs differ from healthy controls, and also how injected rapamycin affects this process

overall_design: Affyetrix microarrays were run on RNA isolated from full stomach tissue as well as from stomachs with the parietal cells isolated from the rest of the cells

first: Spencer

last: Willet

first: Joseph

last: Burclaff


title: Genome-wide biding assay of GTL1 and DF1

city: Yokohama

first: Michitaro

last: Shibata

state: Kanagawa

address: 1-7-22 Suehirocho Tsurumi

department: CSRS

institute: RIKEN

type: Genome binding/occupancy profiling by genome tiling array

summary: We performed a chromatin immunoprecipitation-based microarray experiment (ChIP chip) in order to identify GTL1 and DF1 direct target genes

overall_design: GTL1 and DF1 ChIP was performed with a GFP antibody for two independent biological replicates for each genotype. On each array of GTL1/DF1 and control samples were hybridized in different colors. Moreover, a dye swap was perfomed.

first: Christian

last: Breuer

first: Ayako

last: Kawamura

first: Natalie

middle: M

last: Clark

first: Bart

last: Rymen

first: Luke

last: Braidwood

first: Kengo

last: Morohashi

first: Wolfgang

last: Bruch

first: Pilip

last: Benfey

first: Rossangela

last: Sozzani

first: Keiko

last: Sugimoto


title: Root hair specific transcriptome analysis of gain-of-function and loss-of-function of GTL1 and DF1

summary: How plants determine the final size of growing cells is an important, yet unanswered question. Root hairs provide an excellent model system to study this question since their final cell size is remarkably constant under given environmental conditions. In this study we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by orchestrated actions of opposing transcription factors.

overall_design: Seedlings were grown for 5 days.  Nuclear of root hairs were isolated by GFP fluorecent (pEXPA7:NLS-GFP, pEXPA7:GTL1-GFP, or pEXPA7:DF1-GFP). Subsequently, total RNA was extracted from the isolated nuclear.


title: Wild type and Zbtb7b knockout mouse brown adipose tissue

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

summary:
Zbtb7b is a zinc finger and BTB domain containing transcription factor that activates the thermogenic gene program during brown and beige adipocyte differentiation. Zbtb7b interacts with the long noncoding RNA Blnc1 and hnRNPU to form a ribonucleoprotein transcriptional complex
We used microarray to determine how Zbtb7b regulates brown fat gene expression at ambient room temperature and following cold exposure

overall_design: Wild type and Zbtb7b knockout mice of 10 weeks of age were kept at ambient room temperature (22C) or following cold exposure at 4C for 4 hrs. Brown adipose tissue was harvested for total RNA isolation and microarray analysis.

first: Siming

last: Li


title: Affymetrix SNP array data for wild Dutch great tits (Parus major)

city: Wageningen

first: Veronika

last: Laine

address: Droevendaalsesteeg 10

department: Animal Ecology

country: Netherlands

institute: NIOO-KNAW

summary: The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.

overall_design: Thousands of Dutch great tits were genotyped, including wild and captive samples. This dataset allowed studies on genomic structure and association with phenotypes on this species.

first: Vinicius

middle: H

last: da Silva

first: Mirte

last: Bosse

first: Kees

last: van Oers

first: Bert

last: Dibbits

first: Marcel

last: Visser

first: Richard

last: Crooijmans

first: Martien

last: Groenen


title: Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS)

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

summary: Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. This study aims to compare genome-scale DNA methylation between core biopsies (in this GEO accession) and surgical specimens (previously published in GSE66313; see Overall Design below). Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P < 2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P < 0.05). Between patient-matched core biopsy and surgical specimens, < 0.6% of CpGs measured had changes in median DNA methylation > 15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.

overall_design: We compared genome-scale DNA methylation of 13 breast DCIS core biopsy samples (this accession) with previously published, matched surgical specimens (GSE66313).


title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

first: Frederique

last: Ruf-Zamojski

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center


title: Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development [mouse]

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

summary: In this study, we compared the genome-wide transcriptome of mouse and human placentas across gestation to identify species-specific signatures of early development. We also compared human placental signatures to purified primary cytotrophoblasts (CTB) isolated from placentae at different gestational age.

overall_design: In order to characerise the human trophobalst stem cells niche, we performed genome-wide expression profiling of mouse placentas from E7.5 to E18.5 and compared these profiles to those of human placenta specimen from week 4 to term. CD-1 mice were time-mated with the morning of the plug referred to as E0.5. Extraembryonic tissue was dissected and collected at E7.5 and E8.5. Placentas were dissected out of maternal decidua, and halves were collected at E9.5, E10.5, E11.5, E12.5, E14.5, E16.5, and E18.5. At least 6 samples from 2 different litters were collected per time point.

first: Francesca

last: Soncin

first: Marwa

last: Kather

first: Cuong

last: To

first: Donald

last: Pizzo

first: Anna

last: Wakeland

first: Katharine

last: Nelson

first: Ching-Wen

last: Chang

first: David

middle: R

last: Natale

first: Louise

middle: L

last: Laurent

first: Omar

last: Farah

first: Kanaga

last: Arul Nambi Rajan

first: Matteo

last: Moretto Zita


title: Comparative analysis of mouse and human placentas across gestation reveals species-specific regulators of placental development [human]

overall_design: In order to characerise the human cytotrophoblast (CTB) cells niche, we performed genome-wide expression profiling of human placental specimen from week 4 to term and compared these profiles to those of mouse placentas from E7.5 to E18.5. Three to five biological replicates were chosen for each week of gestation from week 4 to week 12; seven second trimester (week 14-16) and five term placental samples were also included. Sample gestational age was defined according to the completed week of gestation (i.e. placentas at week 4 day 0, through week 4 day 6 were defined as “week 4”). For placentas from pre-viable gestations, “normal” is defined as a singleton pregnancy without any detectable fetal abnormalities on ultrasound; for term placentas, “normal” is defined by a non-hypertensive, non-diabetic singleton pregnancy, where the placenta is normally grown and shows no gross or histologic abnormalities.


title: The AP-1 Transcription Factor JunB Is Required for Th17 Cell Differentiation

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

summary: Interleukin (IL)-17-producing T helper (Th17) cells are crucial for host defense against extracellular microbes and pathogenesis of autoimmune diseases.  Here we show that the AP-1 transcription factor JunB is required for Th17 cell development.  Junb-deficient CD4+ T cells are able to develop in vitro into various helper T subsets except Th17.  The RNA-seq transcriptome analysis reveals that JunB is crucial for the Th17-specific gene expression program.  Junb-deficient mice are completely resistant to experimental autoimmune encephalomyelitis, a Th17-mediated inflammatory disease, and naive T helper cells from such mice fail to differentiate into Th17 cells.  JunB appears to activate Th17 signature genes by forming a heterodimer with BATF, another AP-1 factor essential for Th17 differentiation.  The mechanism whereby JunB controls Th17 cell development likely involves activation of the genes for the Th17 lineage-specifying orphan receptors RORt and ROR and reduced expression of Foxp3, a transcription factor known to antagonize RORt function.

overall_design: Naïve T cell, Th0 and Th17 mRNA profiles of wild type (WT) and Junb-/- mice were generated by deep sequencing, using Illumina HiSeq2500

first: Soh

last: Yamazaki

first: Yoshihiko

last: Tanaka

first: Akira

last: Kohda

first: Fumiyuki

last: Sanematsu

first: Tomoko

last: Arasaki

first: Xuefeng

last: Duan

first: Fumihito

last: Miura

first: Takashi

last: Ito

first: Yoshinori

last: Fukui

first: Shogo

last: Endo

first: Hideki

last: Sumimoto


title: Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development

first: Mana

last: Parast

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression response to eupolauridine-9591 (E9591) and liriodenine methiodide (LMT) in Saccharomyces cerevisiae

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

summary: Eupolauridine and liriodenine are plant-derived aporphinoid alkaloids that exhibit potent inhibitory activity against the opportunistic fungal pathogens Candida albicans and Cryptococcus neoformans. However, the molecular mechanism of this antifungal activity is unknown. In this study, we show that eupolauridine 9591 (E9591), a synthetic analog of eupolauridine, and liriodenine methiodide (LMT), a methiodide salt of liriodenine, mediate their antifungal activities by disrupting mitochondrial iron-sulfur (Fe-S) cluster synthesis. Several lines of evidence supported this conclusion. First, both E9591 and LMT elicited a transcriptional response indicative of iron imbalance, causing the induction of genes that are required for iron uptake and for the maintenance of cellular iron homeostasis. Second, a genome-wide fitness profile analysis showed that yeast mutants with deletions in iron homeostasis–related genes were hypersensitive to E9591 and LMT. Third, treatment of wild-type yeast cells with E9591 or LMT generated cellular defects that mimicked deficiencies in mitochondrial Fe-S cluster synthesis, including an increase in mitochondrial iron levels, a decrease in the activities of Fe-S cluster enzymes, a decrease in respiratory function, and an increase in oxidative stress. Collectively, our results demonstrate that E9591 and LMT perturb mitochondrial Fe-S cluster biosynthesis; thus, these two compounds target a cellular pathway that is distinct from the pathways commonly targeted by clinically used antifungal drugs. Therefore, the identification of this pathway as a target for antifungal compounds has potential applications in the development of new antifungal therapies.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Cultures of S. cerevisiae strain S288C were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with eupolauridine-9591 (E9591), liriodinine methiodide (LMT), 1,10-phenanthroline (PHEN), or 2,2'-bipyridyl (BIPR) at their respective IC50 concentrations (0.053 uM, 2.6 uM, 6.2 uM, and 65.9 uM respectively).  Control cultures were simultaneously treated with 0.25% DMSO. PHEN and BIPR served as reference compounds for iron deficiency response. When OD600 of 0.5 was reached (~4 h), cells were harvested and frozen.  For the long-term exposure experiment, all experimental conditions were the same except cells were exposed to compound treatments for 4.5 doublings (~ 15 h). In all experiments, three biological replicate cultures were grown for each treatment, and RNA from each replicate was hybridized to an independent array.


title: Cell-type-specific Brain Methylomes Profiled via Ultralow-input Microfluidics

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Methylomic studies require substantial amounts of DNA samples and this restriction hinders applications involving scarce animal or patient samples with direct biomedical relevance. Here we report a microfluidics-based reduced representative bisulfite sequencing protocol, MIcrofluidic Diffusion-based RRBS (MID-RRBS), that permits methylomic profiling with sub-1 ng starting DNA. Using this technology, we studied DNA methylation in NeuN+ and NeuN- fractions isolated from mouse cerebellum, revealing cell-type specific methylomic patterns. We also studied the DNA methylation in NeuN+ nuclei isolated from clozapine or vehicle treated mouse frontal cortex.

overall_design: We examined genome-wide DNA methylation profiles of GM12878 cell line (with starting DNA sample amounts in the range of 0.3-10 ng and of single cells), NeuN+ and NeuN- fractions from mouse cerebellum (with starting DNA sample amounts of 0.5 or 10 ng) using MID-RRBS. We generated RNA-seq data on NeuN+ and NeuN- nuclei from mouse cerebellum. We also included MID-RRBS and RNA-seq data obtained on homogenates from mouse cerebellum. Finally, we generated MID-RRBS and RNA-seq data on NeuN+ nuclei isolated from clozapine or vehicle treated mouse frontal cortex.

first: Sai

last: Ma


title: Cell-type specific sequencing of microRNAs from complex animal tissues III

status: Public on Feb 14 2018

city: Vienna

first: Chiara

last: Alberti

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies linking miRNA-function to the biology of distinct cell types within complex tissues remain challenging, partly due to the difficulties in achieving cellular resolution using available miRNA-profiling methods. Here, we report an in vivo small RNA-tagging approach that enables high-throughput sequencing of tissue- and cell type-specific miRNAs in animals, which we call microRNome by methylation-dependent sequencing, or mime-seq. The method combines orthogonal, cell-type-specific 3´ terminal 2’-O-methylation of animal miRNAs by the plant-specific methyltransferase HEN1, with oxidation-sensitive small RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of rare cells within C. elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes the current challenges in tissue- and cell-type-specific small RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.

overall_design: 6 small RNA libraries from adult (2-5 days old) female Drosophila melanogaster. For all of the samples (3+3 libraries) there are two conditions (untreated and treated with sodium periodate):  2 libraries for wild-type, non-transgenic flies; 2 libraries for MHC-Gal4; UAST::AthHEN1 flies; and 2 libraries for Act88F-Gal4; UAST::AthHEN1 flies.

first: Raphael

last: Manzenreither

first: Ivica

last: Sowemimo

first: Thomas

last: Burkard

first: Jingkui

last: Wang

first: Luisa

last: Cochella

first: Stefan

last: Ameres


title: Cell-type specific sequencing of microRNAs from complex animal tissues IV

overall_design: 3 small RNA libraries from Drosophila melanogaster S2 cells. For the sample from S2 hen1KO cells expressing Arabidopsis thaliana HEN1-WT (wild type) there are two conditions (untreated and treated with sodium periodate, i.e. unoxidized, -ox; and oxidized, +ox) and for the sample from S2 hen1KO cells expressing Arabidopsis thaliana HEN1-CM (catalytic mutant) there is one condition: untreated (unoxidized, -ox).


title: Spatiotemporal role of the lncRNA Evx1as in embryonic patterning

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

summary: We performed spatial transcriptome analysis on cryosections of gastrulating embryos from E6.5 to E7.5 by low-input RNA sequencing (Geo-seq). Careful spatial transcriptomic analysis revealed that the lncRNA Evx1as plays a transient spatiotemporal role in regulating embryonic patterning during gastrulation, yet is dispensable for overall development and survival. Altogether, these results suggest that many lncRNAs are generally dispensable for normal development and survival, but may be selectively required in a particular context in vivo.

overall_design: All RNA-seq(s) were designed to reveal the spatiotemporal role of lncRNA Evx1as in embryonic patterning.

last: Luo

first: Guangdun

last: Peng

first: Guizhong

last: Cui

first: Jinlong

first: Naihe

last: Jing

first: Xiaohua

last: Shen


title: Cell-type specific sequencing of microRNAs from complex animal tissues I

overall_design: 46 small RNA libraries from L1-staged C. elegans. For most of the samples (40/46 libraries) there are two conditions (untreated and treated with sodium periodate) and two biological replicates: 4 libraries for wild-type, non-transgenic worms; 4 libraries for rab-3:Ath-HEN1, henn-1(0) worms; 4 libraries for unc-31:Ath-HEN1, henn-1(0) worms; 4 libraries for rgef-1:Ath-HEN1, henn-1(0) worms; 4 libraries for elt-2:Ath-HEN1, henn-1(0) worms; 4 libraries for myo-2:Ath-HEN1, henn-1(0) worms; 4 libraries for ASE:Ath-HEN1, henn-1(0) worms; 4 libraries for ASE:Ath-HEN1 worms; 4 libraries for myo-3:Ath-HEN1, henn-1(0) worms; 4 libraries for myo-3:Ath-HEN1 worms. For the remaining samples (6/46 libraries) there are two conditions (untreated and treated with sodium periodate) and three biological replicates: 6 libraries for rps-5-3:Ath-HEN1, henn-1(0) worms.


title: Cell-type specific sequencing of microRNAs from complex animal tissues

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster
Mus musculus


title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone [ATAC-Seq]

city: New York

first: Frederique

last: Ruf-Zamojski

summary: The LβT2 mouse pituitary cell line has many characteristics of a mature gonadotrope and is a widely used model system for studying developmental processes and the response to gonadotropin-releasing hormone (GnRH). The global epigenetic landscape, which contributes to cell-specific gene regulatory mechanisms, and the single-cell transcriptome response variation of LβT2 cells have not been previously investigated. Here, we integrate the transcriptome and genome-wide chromatin accessibility state of LβT2 cells during GnRH stimulation. Additionally, we examine cell-to-cell variability in the transcriptional response to GnRH using gel-in-emulsion Drop-seq technology. Analysis of a bulk RNA-seq dataset obtained 45 minutes after exposure to either GnRH or vehicle identified 112 transcripts that were regulated > 4-fold by GnRH (FDR < 0.05). The top regulated transcripts constitute, as determined by Bayesian massive public data integration analysis, a human pituitary-relevant coordinated gene program. Chromatin accessibility (ATAC-seq) datasets generated from GnRH-treated LβT2 cells identified more than 58,000 open chromatin regions, some containing notches consistent with bound transcription factor footprints. Study of the most prominent open regions showed that 75% were in transcriptionally active promoters or introns, supporting their involvement in active transcription. Lhb, Cga, and Egr1 showed significantly open chromatin over their promoters. While Fshb was closed over its promoter, several discrete significantly open regions were found at -40 to -90 kb, which may represent novel upstream enhancers. Chromatin accessibility determined by ATAC-seq was associated with high levels of gene expression determined by RNA-seq. We obtained high quality single-cell gel-in-emulsion Drop-seq transcriptome data, with an average of >4000 expressed genes/cell, from 1992 vehicle- and 1889 GnRH-treated cells. While the individual cell expression patterns showed high cell-to-cell variation, representing both biological and measurement variation, the average expression patterns correlated well with bulk RNA-seq data. Computational assignment of each cell to its precise cell cycle phase showed that the response to GnRH was unaffected by cell cycle. To our knowledge, this study represents the first genome-wide epigenetic and single-cell transcriptomic characterization of this important gonadotrope model. The data have been deposited publicly and should provide a resource for hypothesis generation and further study.

overall_design: ATAC-seq was performed on two replicate samples of LβT2 cells treated with 2 nM GnRH pulses every 2 h for a duration of 6 h and 45 min (4 pulses in total; cells harvested 45 min after last pulse) in a high throughput GnRH pulse system.

first: Miguel

last: Fribourg

first: Yongchao

last: Ge

first: Venugopalan

last: Nair

first: Hanna

last: Pincas

first: Elena

last: Zaslavsky

first: German

last: Nudelman

first: Stephanie

last: Tuminello

first: Hideo

last: Watanabe

first: Judith

last: Turgeon

first: Stuart

last: Sealfon


title: Aged gut microbiota contributes to systemical inflammaging after transfer to germ-free mice

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Advanced age is associated with chronic low-grade inflammation, which is usually referred to as inflammaging. Elderly are also known to have an altered gut microbiota composition. However, whether inflammaging is a cause or consequence of an altered gut microbiota composition is not clear. In this study gut microbiota from young or old conventional mice was transferred to young germ-free mice. Four weeks after gut microbiota transfer immune cell populations in spleen, Peyer’s patches, and mesenteric lymph nodes from conventionalized germ-free mice were analyzed by flow cytometry. In addition, whole-genome gene expression in the ileum was analyzed by microarray. Gut microbiota composition of donor and recipient mice was analyzed with 16S rDNA sequencing. Here we show by transferring aged microbiota to young germ-free mice that certain bacterial species within the aged microbiota promote inflammaging. This effect was associated with lower levels of Akkermansia and higher levels of TM7 bacteria and Proteobacteria in the aged microbiota after transfer. The aged microbiota promoted inflammation in the small intestine in the germ-free mice and enhanced leakage of inflammatory bacterial components into the circulation was observed. Moreover, the aged microbiota promoted increased T cell activation in the systemic compartment. In conclusion, these data indicate that the gut microbiota from old mice contributes to inflammaging after transfer to young germ-free mice.

overall_design: Gut microbiota from young or old conventional mice was transferred to young germ-free mice. Four weeks after gut microbiota transfer whole-genome gene expression in the distal ileum was analyzed by microarray.

first: Floris

last: Fransen

first: Adriaan

middle: A

last: van Beek

first: Theo

last: Borghuis

first: Sahar

last: El Aidy

first: Floor

last: Hugenholtz

first: Christa

last: van der Gaast-de Jongh

first: Huub

middle: F

last: Savelkoul

first: Marien

middle: I

last: de Jonge

first: Mark

last: Boekschoten

first: Hauke

last: Smidt

first: Marijke

last: Faas

first: Paul

last: de Vos


title: A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

summary: Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2–Zip4–Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF–ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals.

overall_design: 10 samples total: 2 independent replicates of Zip2-Flag, Zip3-Flag, Zip4-Flag ChIP at 4 h in meiosis; one utagged ant-Flag ChIP at 4 hr in meiosis; 2 independent relicates of Spo16-Myc ChIP at 4 h in meiosis; one untagged anti-Myc ChIP at 4 h in meiosis.

first: Arnaud

last: De Muyt

first: Valérie


title: Gene expression differences between leukemic cells from Mx1-Cre, Cbfb+/56M and Chd7f/f, Mx1-Cre, Cbfb+/56M mice by microarray

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Results showed that Chd7 deficiency delay Cbfb-MYH11 induced leukemia, to explore the mechanism, We also performed microarray analysis on c-Kit+ leukemic cells to determine gene expression differences between Mx1-Cre, Cbfb+/56M and Chd7f/f, Mx1-Cre, Cbfb+/56M leukemic cells.

overall_design: Total RNA was extracted from c-Kit+ leukemia cells with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN). Three independent samples were obtained for each genotype. RNA quality was assessed using the Agilent BioAnalyzer 2100 (Agilent). Genome-wide RNA expression profiling was performed using Affymetrix GeneChip mouse Gene 2.0 ST Array (Affymetrix) according to the manufacturer’s instructions.

first: Abdel

first: Zhen

last: Tao


title: Identification of KhpA/B-associated RNAs in Brucella suis by deep sequencing in Streptococcus pneumoniae

city: Bloomington

first: Ram

last: Podicheti

institute: Indiana University

summary: We report the identification of  RNAs in Streptococcus pneumoniae D39 that are associated to the KhpA/B proteins

overall_design: Coimmunoprecipitation using Flag-tagged KhpA or KhpB as bait

first: Jiaqi

last: Zheng

first: Ho-Ching

last: Tsui

first: Douglas

middle: B

last: Rusch

first: Malcolm

middle: E

last: Winkler


title: The olfactory molecular snapshot in aged Tg2576 Alzheimer´s disease mouse model

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

summary: Olfaction is often deregulated in Alzheimer´s disease (AD) patients, being also impaired in transgenic Tg2576 AD mouse model, which overexpress the Swedish mutated form of human amyloid precursor protein (APP). However, little is known about the molecular mechanisms that accompany the neurodegeneration of olfactory structures in Tg2576 mice. For that, we have applied proteome- and transcriptome-wide approaches to probe molecular disturbances in the olfactory bulb (OB) dissected from aged Tg2576 mice (18 months of age) respect to age matched wild-type (WT) littermates.

overall_design: Olfactory bulbs from 3 WT mice vs olfactory bulbs from 3 Tg2576 transgenic mice

first: Enrique

last: Santamaría


title: Characterization and selective incorporation of small non-coding RNAs in non-small cell lung cancer exosomes

city: Wuhan

first: Mingxiong

last: Guo

address: Luojia Hill

institute: Wuhan University

summary: Exosomes play important roles in intercellular communication through the delivery of their cargoes, which include proteins, lipids, and RNAs. Increasingly, multiple studies have reported the association between exosomal small non-coding RNAs and cancer, due to their regulatory functions in gene expression. Hence, analysis of the features of small non-coding RNA expression and their incorporation into exosomes is important for cancer research. Here, we performed deep sequencing to investigate the expression of small RNAs in plasma exosomes from lung adenocarcinoma patients, lung squamous cell carcinoma patients, and healthy controls. We found that 5’ YRNA hY4-derived fragments are significantly upregulated in non-small cell lung cancer (NSCLC) exosomes, and may serve as a novel class of circulating biomarkers for NSCLC diagnosis. We also identified that the RNY4P7 gene on chromosome 2 may not be a pseudogene, because the corresponding transcript hY4 reverse fragment was detected in exosomes and cells. Further, we demonstrated that a panel of small RNAs, including miR-451a and miR-122-5p, may be selectively sorted into NSCLC exosomes. Overall, our studies have indicated a wider range of biological effects in NSCLC that may be mediated by exosomal small RNAs than previously known.

overall_design: The small RNA in the plasma exosomes from 28 lung adenocarcinoma patients (ADC), 13 lung squamous cell carcinoma patients (SQCC), and 13 healthy individuals (CTRL) were analyzed by high through-put RNA Sequencing. All patients were characterized by clinical stage, and peripheral blood samples were collected before treatment. To minimize differences between individuals, RNA samples from same group were pooled together in a fixed ratio before deep sequencing. All the sequencing data was normalized as RPM (mapped reads per million clean reads).

first: Chuang

last: Li

first: Fang

last: Qin

first: Fen

last: Hu

first: Hui

last: Xu

first: Guihong

last: Sun

first: Guang

last: Han

first: Tao

last: Wang


title: Profiling of expression data in melanoma cells with mutant DOT1L or treated with DOT1L inhibitor

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: DOT1L-dependent H3K79 methylation is associated with telomere silencing, meiotic checkpoint control, DNA repair, modulation of constitutive heterochromatin, and transcriptional activation.

overall_design: We used microarrays to detail the global program of gene expression in C021 melanoma cells (DOT1L wild type) and C025 melanoma cells (DOT1L mutant) treated with DMSO vehicle control, and in C021 cells treated with the DOT1L inhibitor EPZ-5676.

first: Bo

last: Zhu

first: Rutao

last: Cui


title: Profiling of expression data in melanoma cells following DOT1L shRNA knockdown

overall_design: We used microarrays to detail the global program of gene expression in C021 melanoma cells following treatment with shRNA against DOT1L or scrambled control.


title: IL-36/LXR axis modulates cholesterol metabolism and immune defense to Mycobacterium tuberculosis

city: Berlin

first: Fadhil

last: Ahsan

address: Cahriteplatz 1

department: Immunology

institute: Max Planck Institute for Infection Biology

summary: Mycobacterium tuberculosis (Mtb) is a life-threatening pathogen in humans. Bacterial infection of macrophages usually triggers strong innate immune mechanisms, including IL-1 cytokine secretion. The newer member of the IL-1 family, IL-36, was recently shown to be involved in cellular defense against Mtb. To unveil the underlying mechanism of IL-36 induced antibacterial activity, we analyzed its role in the regulation of cholesterol metabolism, together with the involvement of Liver X Receptor (LXR) in this process. Here we report that, in Mtb-infected macrophages, IL-36 signaling modulates cholesterol biosynthesis and efflux via LXR. Moreover, IL-36 induces the expression of cholesterol-converting enzymes and the accumulation of LXR ligands, such as oxysterols. Ultimately, both IL-36 and LXR signaling play a role in the regulation of antimicrobial peptides expression and in Mtb growth restriction. These data provide novel evidence for the importance of IL‑36 and cholesterol metabolism mediated by LXR in cellular host defense against Mtb.

overall_design: THP-1 macrophages (scramble and IL36R knockdown) were infected with Mycobacterium tuberculosis for 24 hour and RNA from the sample lysates were extracted for further microarray analyses. Three independent experiments were included.

first: Jeroen

last: Maertzdorf

first: Ute

last: Guhlich-Bornhof

first: Stefan

last: Kaufmann

first: Pedro

last: Moura-Alves


title: Profiling of expression data in melanoma cells with mutant DOT1L, DOT1L inhibitor or shRNA knockdown

overall_design: Refer to individual Series


title: micro RNA (miR) expression profile of developing fly eye in different Ago-1 expressing condition

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: As miRs are one of the crucial regulators of various cellular processes, our interest was to see whether any change in their expression occurs under Ago-1 overexpression. miRNA microarray analysis was carried out using total RNA extracted from control (GMR-GAL4), Ago-1 overexpressed (UAS Ago-1/GMR GAL4) and Ago-1 mutant (Ago-1^72/ Ago-1^45) adult eye. Several miRNAs were upregulated and several showed down regulation. miRs, which has shown significant fold change in there expression, were selected for further study.

overall_design: Organism : Drosophila melaongaster, Agilent's Drosophila miRNA Expression  8x15k Array (AMADID: 075826)

first: Tanmoy

last: Mondal

first: Manika

last: Pal Bhadra


title: Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance [ChIP-seq]

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

institute: Seoul National University

summary: Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. The direct target genes were related to transmembrane/transporter activity, vesicle, plant hormone, carbohydrate metabolism, and transcription factors. The direct targets of each OsNAC are in a range of 4.0 to 8.7% of the genes up-regulated in RNA-Seq data sets. Thus, each OsNAC up-regulates of corresponding direct target genes that alters root system architectures of RCc3:OsNACs for drought tolerance. Our results provide valuable resources for functional dissection of the molecular mechanisms for plant drought tolerance.

overall_design: ChIPseq using roots of NT and RCc3:6xmyc-OsNAC5, RCc3:6xmyc-OsNAC6, RCc3:6xmyc-OsNAC9, RCc3:6xmyc-OsNAC10 transgenic plants

first: Pil

first: Ju-Kon

last: Kim


title: Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance


title: Expression Profiling of MicroRNAs in Relation to EGFR Mutation status in Japanese Smoker Male with Lung Adenocarcinoma [adinocarcinoma tissue]

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The lung adenocarcinoma has an increased incidence in smokers. The molecular target therapy has been developed for lung adenocarcinoma patients harboring EGFR gene mutation. However, the treatment options for the patients without mutation are currently limited. Thus, analysis of EGFR gene mutation status at early stage is important strategy to classify patients for effective treatments and improving prognosis. This study aimed to identify microRNA (miRNAs) signature in relation to mutation status in EGFR gene in early stage of lung adenocarcinoma male patients with smoking history. MiRNA profiles were assessed by microarray in paired plasma and tissue pooled from 10 EGFR wild type (EGFR-wt) and 10 EGFR mutated (EGFR-mut) patients.

overall_design: Total RNA containing small RNA was pooled equally for each 10 lung adenocarcinoma tissues from EGFR-wt and EGFR-mut patients respectively for microarray analysis. MiRNA profiling was examined using a Toray 3D-Gene® miRNA oligo chip Human miRNA version 21 (Toray, Tokyo, Japan) on which 2,565 probes were mounted. The expression level of each miRNA was normalized using the median signal strength for the entire gene in each chip.

first: Sachio

last: Ito


title: Expression Profiling of MicroRNAs in Relation to EGFR Mutation status in Japanese Smoker Male with Lung Adenocarcinoma [blood plasma]

overall_design: The blood plasmas were pooled from 10 EGFR-wt patients and 10 EGFR-mut patients respectively for microarray analysis. MiRNA profiling was examined using a Toray 3D-Gene® miRNA oligo chip Human miRNA version 21 (Toray, Tokyo, Japan) on which 2,565 probes were mounted. The expression level of each miRNA was normalized using the median signal strength for the entire gene in each chip.


title: Cell-type specific sequencing of microRNAs from complex animal tissues II

first: Chiara

last: Alberti

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: two replicates with 12 libraries each: 12 libraries of 10-fold decreasing dilution series of RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 into RNA from Mmu ES cells:  2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:1 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:10 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:100 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:1000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:10,000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated. 2 libraries with RNA from S2-S cells (DmHen1-KO) expressing AthHEN1 mixed in 1:100,000 ratio with RNA from Mmu ES cells, one subjected to periodate treatment (ox+) and one left untreated.

first: Raphael

last: Manzenreither

first: Ivica

last: Sowemimo

first: Thomas

last: Burkard

first: Jingkui

first: Luisa

last: Cochella

last: Ameres


title: PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

sample_organism:
Mus musculus
Anolis carolinensis

platform_organism:
Mus musculus
Anolis carolinensis


title: PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets [ChIP-Seq]

summary: The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. In addition, we have analyzed PITX1 binding sites in hindlimbs of Anolis lizards to identify ancient PITX1 regulatory targets. We find that PITX1-bound regions in both mouse and Anolis hindlimbs are strongly associated with genes implicated in limb and skeletal system development. Gene expression analyses reveal a large number of misexpressed genes in the hindlimbs of Pitx1-/- embryos. By intersecting misexpressed genes with genes that have neighboring mouse PITX1 binding sites, we identified 440 candidate targets of PITX1. Of these candidates, 68 exhibit ultra-conserved PITX1 binding events that are shared between mouse and Anolis hindlimbs. Among the ancient targets of PITX1 are important regulators of cartilage and skeletal muscle development, including Sox9 and Six1. Our data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.

overall_design: Examination of PITX1 binding sites in Anolis carolinensis hindlimbs

middle: S

first: Carlos

last: Infante

first: Sungdae

last: Park

first: Douglas

last: Menke