title: WNT Pathway Signalling in Kidney Transplants with Microvascular Injury

city: Birmingham

middle: Edward

last: Seifert

state: AL

address: 1600 7th Ave S Lowder 516

institute: UAB School of Medicine

summary:
Kidney transplant recipients with biopsy-proven microvascular injury (MVI) have increased risk for allograft failure. MVI is often caused by antibody-mediated injury that is resistant to available treatments. Current diagnostic methods are also inadequate, with interobserver variability in traditional pathology reads, variable assessment of circulating donor-specific antibody between HLA laboratories, and peritubular capillary C4d staining.
Molecular assessments of kidney biopsies can provide improved sensitivity for diagnosing MVI and other allograft pathology, while improving reproducibility and objectivity. Most molecular classifiers have been based on whole genome sequencing to develop diagnostic tests, but have provided limited therapeutic targets. In this study, we pursued a candidate gene approach to measure WNT pathway genes in residual clinical FFPE biopsies with and without MVI. We focused on the WNT pathway because of previous translational studies that implicated this pathway in chronic renal allograft injury as well as vascular injury in native chronic kidney disease.

overall_design: Case-control study of 95 residual FFPE biopsies with MVI (g+ptc score >= 2, n=50) or Stable (g+ptc score < 2 and no other major abnormalities, n=45). Biopsies were retrieved from a biorepository of over 500 kidney transplant biopsies. We compared expression of 180 WNT pathway genes and 30 custom skipe-in targets (derived from previous studies of endothelial injury in transplantation) between MVI and Stable groups, with correction for multiple comparisons using FDR < 5%.

first: Roslyn

last: Mannon


title: Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae

status: Public on Jun 18 2019

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Agaricomycetes produce the most efficient enzyme systems to degrade wood and the most complex morphological structures in the fungal kingdom. Despite decades-long interest in their genetic bases, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known.Here, we perform comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies and enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes of A. ampla and S. commune revealed a high rate of divergence in developmental gene expression, but also several genes with conserved developmental expression, including novel transcription factors and small-secreted proteins, some of the latter might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in a widely distributed family of mushroom-forming fungi.

overall_design: Five development stages of Auriculariopsis ampla sampled, with three biological replicates in each group.

first: Eva

last: Almasi

first: Neha

last: Sahu

first: Krisztina

last: Krizsan

first: Balazs

last: Balint

first: Gabor

middle: M

last: Kovacs

first: Brigitta

last: Kiss

first: Judit

last: Cseklye

first: Elodie

last: Drula

first: Bernard

last: Henrissat

first: Istvan

first: Mansi

last: Chovatia

first: Catherine

last: Adam

first: Kurt

last: LaButti

first: Anna

last: Lipzen

first: Robert

last: Riley

first: Igor

middle: V

last: Grigoriev

middle: G


title: An early Myc-dependent transcriptional program underlies enhanced macromolecular biosynthesis and cell growth during B-cell activation

status: Public on Jun 14 2019

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: An early Myc-dependent transcriptional program underlies enhanced macromolecular biosynthesis and cell growth during B-cell activation [ChIP-seq]

summary: Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size and RNA content. A key regulator in this process is the Myc transcription factor, which is directly induced by activating signals and is required for multiple facets of cell activation, including metabolic reprogramming, chromatin decompaction, RNA and protein accumulation, cell growth and proliferation. However, how Myc activity impacts on those diverse cellular processes remains unclear. We addressed this issue in primary mouse B-cells, based on conditional deletion of the c-myc gene prior to LPS stimulation. Myc was rapidly induced, was recruited to virtually all active promoters and enhancers (a phenomenon known as invasion), but had no direct impact on global transcriptional activity. Instead, Myc contributed to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters were enriched for E-box consensus motifs, bound Myc at the highest levels and showed enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells was also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.

overall_design: Mapping c-Myc and RNAPII genomic distribution during LPS stimulation in primary wt or Myc-deleted (FLOX) B-cells

first: Arianna

last: Sabò


title: RNA sequencing comparing normal and premalignant EuMyc B220+ cells in Max WT and conditional Max KO mice

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

country: USA

institute: Fred Hutch

summary: The goal of this study was to compare expression profiles of B cells in the presence and absence of transcription factor MAX under normal and premalignant settings

overall_design: Each genotype is represented in triplicate (cells isolated from 3 individual mice for each)

middle: N

last: Eisenman


title: An early Myc-dependent transcriptional program underlies enhanced macromolecular biosynthesis and cell growth during B-cell activation [RNA-seq]

overall_design: Total RNA profiling of gene expression  during LPS stimulation in primary wt or Myc-deleted (FLOX) B-cells


title: PlGF and IL6 effect on CD3/CD28-stimulated mouse splenic CD4+ T cell

city: Seoul

first: Saseong

last: Lee

address: Banp-daero

department: Rheumatology

country: South Korea

institute: The catholic university of korea

summary: T-helper (Th) cells actively communicate with adjacent cells by secreting soluble mediators, and yet crosstalk between Th cells and endothelial cells is poorly understood. Placental growth factor (PlGF), originally identified in the placenta, is an angiogenic factor homologous to vascular endothelial growth factor (VEGF)-A. We performed transcriptome analysis to systemically compare the effect of IL6, a key factor in Th cell polarization, and PlGF on T cell functions.

overall_design: Conditioned medium containing PlGF (PlGFCM) was obtained from HEK-293 clones overexpressing PlGF2. Mouse splenic CD4+ T cells were stimulated with anti-CD3 antibody and anti-CD28 antibody in the presence of PlGFCM, control conditioned medium (ConCM), or IL6+ConCM for 12 hours.

first: B

middle: K

last: Hong

first: S

first: W

middle: U

last: Kim


title: The lncRNA Hand2os1/Uph locus orchestrates heart development through regulation of precise expression HAND2

city: Beijing

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

summary: Exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here using multiple knockout mouse models and single-cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2os1/Uph has a key, complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function. Short deletion of the Hand2os1 promoter in mouse diminishes Hand2os1 transcription to 8~32%, but fails to affect HAND2 expression and yields no discernable heart phenotypes. Interestingly, full-length deletion of Hand2os1 in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, leading to profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose that the Hand2os1 locus dampens HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the regulatory complexity of the lncRNA Hand2os1 on HAND2 expression, emphasizing the need for complementary genetic and single-cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.

overall_design: All RNA-seq(s) were designed to reveal the differentially expressed genes between control (heterozygous or wildtype) and homozygous Hand2as KO mice heart tissues. Allele F = full-length KO allele. Allele D = 3' Distal KO allele.

first: Jiejie

last: Zhang

first: Xiaoying

last: Fan

first: Yingjie

last: Luo

first: Fuchou

last: Tang

first: Aibin

last: He

first: Xiaohua

last: Shen


title: RNAseq data of 81 liver cancer cell lines

status: Public on Jun 17 2019

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: A large panel of 81 liver cancer cell models, designated as LIver cancer MOdel REpository (LIMORE) was constructed. These cell lines include 31 public cell lines and 50 new cell models establishend from Chinese liver cancer patients. Whole genome sequencing (WGS), exome sequencing (WES) and RNA sequencing (RNAseq) were performed to obtain the genetic information for these cell lines. These cell lines and associated data provide new models and also a rich resource for liver cancer.

overall_design: RNAseq for 81 liver cancer cell models was performed to analyze the gene expression of these lines. SK-Hep1 was also sequenced, though not considered as HCC cell line.

first: Zhixin

last: Qiu

first: Zhengtao

first: Hong

last: Li


title: MicroRNA data in the hearts from young (8 week-old) and middle-aged (15 month-old) male mice

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

summary:
MicroRNAs have been reported to be involved in the regulation of cellular and organismal aging. However, little is known about the role of microRNAs in cardiac aging.
We used microarrays to examine microRNA profiles in the hearts from young (8 week-old) and middle-aged (15 month-old) male mice.

overall_design: Heart samples from  young (8 week-old) and middle-aged (15 month-old) male mice (n=5 per group) were used for RNA extraction and hybridization on Affymetrix miRNA 4.0.

first: Junjie

last: Xiao

first: Xiaotin

last: Wu

first: Xinli


title: RNA-Sequencing of S. pneumoniae when exposed to the bacteriophage SpSL1

status: Public on Jun 13 2019

city: Leicester

first: Liam

middle: Alexander

last: Crawford

address: Adrian Building, University Road

department: Genetics and Genome Biology

country: United Kingdom

institute: University of Leicester

summary: mRNA was sequenced in triplicate in three time points to determine the global transcriptional response of S. pneumoniae that is susceptible to the bacteriophage SpSL1. Samples were taken from mid log exponential phase in standard glucose contaiing media with an MOI of 0.2 at three time points: 10 minutes, 50 minutes, and 90 minutes post infection.

overall_design: RNA-Seq was used to analyze the global response to the human pathogen S. pneumoniae in response to its bacteriophage SpSL1.

first: Leonardo

last: Furi

middle: A

first: Marco

middle: R

last: Oggioni


title: Gene expression profile analysis of WT and LGP2-/- bone-marrow derived dendritic cells treated with a RIG-I agonist

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

summary: We performed RNAseq analysis on WT and LGP2-/- BM-DCs treated with a RIG-I agonist (HCV Poly-U/C RNA) to understand how LGP2 impacts global transcriptional changes following activation of the RIG-I pathway. Analysis of the transcriptional profiles revealed that LGP2 functions as a negative regulator of RIG-I signaling as early as 1 hours post-RIG-I agonist treatment. This finding led us to study how LGP2 negatively influences RIG-I activation through post-translational modification.

overall_design: Bone-marrow derived dendritic cells were generated from WT (C57BL/6J) and LGP2-/- mice. BM-DCs were treated with a RIG-I agonist (HCV Poly-U/C RNA). At 1, 3 and 6 hours post-treatment, time-matched mock and RIG-I agonist cells were collected for RNAseq analysis.

first: Kendra

last: Quicke

first: Kristin

last: Kim

first: Curt

last: Horvath

middle: S


title: MITF controls the TCA cycle to modulate the melanoma hypoxia response

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: In response to the dynamic intra-tumor microenvironment, melanoma cells adopt different phenotypic states possessing distinct biological properties associated with differential expression of the microphthalmia-associated transcription factor (MITF). The response to hypoxia, a major microenvironmental cue, is underpinned by expression of hypoxia-inducible transcription factors (HIFs) that reprogram metabolism and promote pro-angiogenic VEGF expression. HIF1 indirectly represses MITF via the transcription factor bHLHE40/DEC1, and MITF can activate HIF1 expression. Although HIF and MITF share a highly related DNA-binding specificity, it is unclear whether they share a subset of target genes. Moreover, the genome-wide impact of hypoxia on melanoma, which genes are direct HIF targets, and whether melanoma cell lines representing different phenotypic states exhibit distinct hypoxic responses is unknown. Here we show, that three different melanoma cell lines exhibit widely different hypoxia responses with only a core 23 genes regulated in common after 12 h in hypoxia. Surprisingly, under hypoxia MITF is transiently up-regulated by HIF1 and co-regulates a subset of HIF targets including VEGFA. Significantly, we also show that MITF represses itself and also regulates SDHB to control the TCA cycle and suppress pseudo-hypoxia. Our results reveal a previously unsuspected role for MITF in metabolism and the network of factors underpinning the hypoxic response in melanoma.

overall_design: Melanoma cell lines representing 3 phenotypically distinct states were subjected to time-course hypoxia treatment for transcriptomic analysis

first: Colin

last: Goding

first: Ioanna

last: Ledaki


title: Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Library DR

department: LRBGE

institute: NIH

summary: The binding of the glucocorticoid receptor (GR to GR regulatory elements (GREs) over constant treatment with 600nM corticosterone (Cort) changes over time in a locus-specific manner. We show this by comparing GR binding at 0h, 1h, and 12h after Cort treatment. This finding is further corroborated by the reduced dwell times of GR over time measured by single molecule tracking (SMT) as well as by the reduced RNA bust duration and frequency observed at the GR-mediated mouse mammary tumor promoter (MMTV) transcription sites (TSs).

overall_design: We examined the Cort-mediated effects on GR binding patterns

first: Diana

last: Stavreva

middle: L


title: Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health and disease

status: Public on Jun 12 2019

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Human mononuclear phagocytes comprise phenotypically and functionally overlapping subsets of dendritic cells (DC) and monocytes, but their identification remains elusive. By integrating high-dimensional single-cell protein and RNA expression data, we clearly delineated monocytes from conventional DC2 (cDC2), identifying new markers including CD88/CD89 for monocytes and HLA-DQ/FcRI for cDC2, allowing their unambiguous characterization in blood and tissues. We also show that cDC2 can be subdivided into phenotypically and functionally distinct subsets based on CD5, CD163 and CD14 expression, including a unique subset of circulating inflammatory CD5-CD163+CD14+ cells related to previously defined DC3. These inflammatory DC3 were expanded in systemic lupus erythematosus patients, correlating with disease activity. Unravelling the heterogeneity of DC sub-populations in health and disease paves the way for specific DC subset-targeting therapies.

overall_design: Indexed single cell RNAseq (scRNAseq) of human peripheral blood dendritic cells and monocytes

first: Charles-Antoine

last: Dutertre

first: Etienne

last: Becht

first: Sergio

middle: E

last: Irac

first: Ahad

last: Khalilnezhad

first: Vipin

last: Narang

first: Shabnam

first: Pei

middle: Y

last: Ng

first: Lucas

last: vandenHoogen

first: Jing

last: Leong

first: Bernett

last: Lee

first: Marion

last: Chevrier

first: Xiao

last: Zhang

first: Pearly

middle: J

last: Ai Yong

first: Geraldine

last: Koh

first: Josephine

last: Lum

first: ShanShan

middle: W

last: Howland

first: Esther

last: Mok

first: Jinmiao

last: Chen

first: Anis

last: Larbi

first: Henry

last: Tan

first: Tony

middle: H

last: Lim

first: Panagiota

last: Karagianni

first: Athanasios

last: Tzioufas

first: Benoit

last: Malleret

first: Joshua

last: Brody

first: Salvatore

last: Albani

first: Joel

last: van Roon

first: Timothy

last: Radstake

first: Evan

last: Newell


title: Gene expression analysis of Mtb-infected mouse alveolar macrophages from mice lacking Nrf2 in LysM- or CD11c-expressing cells

first: Aderem

last: Lab

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: The aim of this study was to measure the immune response of alveolar macrophages (AMs) from mice lacking Nrf2 in LysM- or CD11c-expressing cells to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing.

overall_design: To characterize the early macrophage transcriptional response to Mtb infection, we infected mice with 2000-4000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at 24 hours following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice.

first: Alissa

middle: C

last: Rothchild

first: Alan

last: Diercks

last: Aderem


title: RNA-Seq of WT Staphylococcus aureus and dpurR grown to exponential and stationary phase

city: NEW YORK

first: William

middle: E.

last: Sause

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU School of Medicine

summary: We report here that mutants for purR display altered transcriptional profiles compared to WT S. aureus at multiple stages of growth.

overall_design: Examination of the transcriptional profiles of WT S. aureus and the isogenic purR mutant.

first: Victor

last: Torres


title: Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures [RNA-seq]

city: London

first: May

last: Sabry

address: Rowland Hill Street

department: Cancer Institute

institute: University College London

summary: An emerging cellular immunotherapy for cancer is based on the cytolytic activity of natural killer (NK) cells against a wide range of tumors. Although in vitro activation or ‘priming’ of NK cells by exposure to pro-inflammatory cytokines such as interleukin (IL)-2 has been extensively studied, the biological consequences of NK cell activation in response to target cell interactions are less characterized. Herein, we investigate the consequences of co-incubation with K562, CTV-1, Daudi and RPMI-8226 tumor cell lines on the phenotype, cytokine expression profile and transcriptome of human NK cells. We observe the downregulation of several activation receptors including CD16, CD62L, C-X-C chemokine receptor (CXCR)-4, natural killer group 2 member D (NKG2D), DNAX accessory molecule (DNAM)-1 and NKp46 following tumor-priming. Although this NK cell phenotype is typically associated with NK cell dysfunction in cancer, we show upregulation of NK cell activation markers such as CD69 and CD25, secretion of pro-inflammatory cytokines including macrophage inflammatory proteins (MIP-1) α /β and IL-1β/6/8 and overexpression of numerous genes associated with enhanced NK cell cytotoxicity and immunomodulatory functions such as FAS, TNFSF10, MAPK11, TNF and IFNG. Key signaling molecules exclusively affected by tumor-priming include MAP2K3, MARCKSL1, STAT5A, and TNFAIP3, which are specifically associated with NK cell cytotoxicity against tumor targets. Collectively, these findings help define the phenotypic and transcriptional signature of NK cells following their encounter with tumor cells, independent of cytokine stimulation, and provide insight into tumor-specific NK cell responses to inform the transition towards harnessing the therapeutic potential of NK cells in cancer.

overall_design: The mRNA profiles of freshly isolated healthy donor-derived human NK cells after stimulation with tumor cells (K562 or CTV-1 also referred to as INB16) or cytokine (IL-2)  were analyzed through RNA-sequencing and compared to unstimulated controls (NK alone)

first: Agnieszka

last: Zubiak

first: Simon

middle: P

last: Hood

first: Poppy

last: Simmonds

first: Helena

last: Arellano

first: Eily

last: Cournoyer

first: Mashar

last: Meghavi

first: Graham

last: Pockley

first: Mark

last: Lowdell


title: β-catenin activation promotes immune escape and resistance to anti-PD-1 therapy in hepatocellular carcinoma

city: New York

first: Amaia

last: Lujambio

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: We study the role of CTNNB1 in immune escape in HCC.

overall_design: Examination of transcriptional profiles in 4 different tumor genotypes

first: Marina

last: Ruiz de Galarreta


title: Profiling downstream targets of PUCHI in roots of Arabidopsis thaliana

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: Rokko-dai 1-1

country: Japan

institute: Kobe University

summary: Lateral root organogenesis plays an essential role in defining plant root system architecture. In Arabidopsis, the AP2-family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify downstream targets of PUCHI, we engineered a transgenic line with inducible PUCHI activity by expressing a fusion protein of PUCHI and rat glucocorticoid receptor (GR) under the control of its own regulatory region (gPUCHI-GR) in the puchi-1 mutant.

overall_design: PUCHI-Glucocorticoid Receptor (GR) driven by its own regulatory region in puchi-1 mutant was used for PUCHI induction. We collected roots from 5-day-old seedlings of gPUCHI:GR puchi-1 line 4 hours after treatment with/without dexamethazone (DEX), naphthaleneacetic acid (NAA) and cycloheximide (CHX). Two independent sets of mRNA samples for each treatment were used for this analysis

first: Tatsuaki

last: Goh


title: Gene expression analysis of mouse alveolar macrophages infected with Mycobacterium tuberculosis

first: Aderem

last: Lab

summary: The aim of this study was to measure the immune response of alveolar macrophages (AMs) to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing. To determine the effect of the transcription factor Nrf2 on this response we also measured the transcriptional profiles of AMs from mice lacking Nrf2.

overall_design: To characterize the early macrophage transcriptional response to Mtb infection, we infected mice with 2000-4000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at various time points over the first 10 days following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice. As a comparison, we repeated the high-dose infections using an mEmerald-expressing strain of Mtb lacking the RD1 virulence locus (deltaRD1-H37Rv) and using fluorescent 1uM carboxylate-coated latex beads.

first: Alissa

last: Rothchild

last: Diercks


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [ChIP-seq II]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Complete activation of macrophage proinflammatory and antimicrobial phenotype is promoted by combined action of IFN-g and LPS. Synergistic activation of canonical inflammatory NF-kB target genes by IFN-g and LPS is well appreciated, but less is known about whether IFN-g negatively regulates components of the LPS response, and how this affects polarization. A combined transcriptomic and epigenomic approach revealed that IFN-g selectively abrogates LPS-induced feedback and select metabolic pathways by suppressing TLR4-mediated activation of gene enhancers. In contrast to superinduction of inflammatory genes via enhancers that harbor IRF sequences and bind STAT1, IFN-g-mediated repression targeted enhancers with STAT sequences that bound STAT3. TLR4-activated IFN-g-suppressed enhancers comprised two subsets distinguished by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin, and were functionally inactivated by IFN-g. These findings reveal that IFN-g suppresses feedback inhibitory and metabolic components of the TLR response to achieve full macrophage activation and provide insights into mechanisms by which IFN-g selectively inhibits TLR4-induced transcription.

overall_design: ChIP-seq analysis of epigenomic changes in human macrophages that were cultured with or without IFN-γ and then stimulated with LPS

first: Lionel

last: Ivashkiv

first: Kyuho


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [RNA-seq]

summary: Complete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requires combined action of IFN-γ and LPS. Synergistic activation of canonical inflammatory NF-κB target genes by IFN-γ and LPS is well appreciated, but less is known about whether IFN-γ negatively regulates components of the LPS response, and how this affects polarization. A combined transcriptomic and epigenomic approach revealed that IFN-γ selectively abrogates LPS-induced feedback and select metabolic pathways by suppressing TLR4-mediated activation of gene enhancers. In contrast to superinduction of inflammatory genes via enhancers that harbor IRF sequences and bind STAT1, IFN-γ-mediated repression targeted enhancers with STAT sequences that bound STAT3. TLR4-activated IFN-γ-suppressed enhancers comprised two subsets distinguished by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin, and were functionally inactivated by IFN-γ. These findings reveal that IFN-γ suppresses feedback inhibitory and metabolic components of the TLR response to achieve full M1 polarization, and provide insights into mechanisms by which IFN-γ selectively inhibits TLR4-induced transcription.

overall_design: RNA-seq analysis of transcriptional changes in human macrophages that were cultured with or without IFN-γ and then stimulated with LPS


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [ChIP-seq]


title: Expression data of butyrate stimulated epithelial organoid cultures generated from intestinal mucosa

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: In order to investigate the response of epithelium to butyrate, we generated in vitro epithelial organoid cultures from colon samples of non-IBD controls and they were stimulated with different doses of butyrate. The transcriptional signature revealed that butyrate negatively regulated proliferation and cell cycle, induced a protective response to oxidative stress and regulated genes related to the immune response.

overall_design: Colon samples from non-IBD controls (subjects undergoing surgery for colorectal cancer) were collected. Epithelial organoid cultures (EpOCs) were expanded from human colonic crypts and then induced to differentiate (d-EpOCs). Paired first-passage EpOCs and d-EpOCs (n=4) were stimulated with two doses of butyrate (0.5 mM and 5 mM) during 1h, 3h, 6h and 24h. RNA was then extracted and used for hybridization on Affymetrix microarrays.

first: Elena

last: Ferrer-Picón


title: Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures [Nanostring]

first: May

last: Sabry

summary:
An emerging cellular immunotherapy for cancer is based on the cytolytic activity of natural killer (NK) cells against a wide range of tumors. Although in vitro activation or ‘priming’ of NK cells by exposure to pro-inflammatory cytokines such as interleukin (IL)-2 has been extensively studied, the biological consequences of NK cell activation in response to target cell interactions are less characterized. Herein, we investigate the consequences of co-incubation with K562, CTV-1, Daudi and RPMI-8226 tumor cell lines on the phenotype, cytokine expression profile and transcriptome of human NK cells. We observe the downregulation of several activation receptors including CD16, CD62L, C-X-C chemokine receptor (CXCR)-4, natural killer group 2 member D (NKG2D), DNAX accessory molecule (DNAM)-1 and NKp46 following tumor-priming. Although this NK cell phenotype is typically associated with NK cell dysfunction in cancer, we show upregulation of NK cell activation markers such as CD69 and CD25, secretion of pro-inflammatory cytokines including macrophage inflammatory proteins (MIP-1) α /β and IL-1β/6/8 and overexpression of numerous genes associated with enhanced NK cell cytotoxicity and immunomodulatory functions such as FAS, TNFSF10, MAPK11, TNF and IFNG.
Key signaling molecules exclusively affected by tumor-priming include MAP2K3, MARCKSL1, STAT5A, and TNFAIP3, which are specifically associated with NK cell cytotoxicity against tumor targets. Collectively, these findings help define the phenotypic and transcriptional signature of NK cells following their encounter with tumor cells, independent of cytokine stimulation, and provide insight into tumor-specific NK cell responses to inform the transition towards harnessing the therapeutic potential of NK cells in cancer.

overall_design: The mRNA profiles of freshly isolated healthy donor-derived human NK cells after stimulation with tumor cells (CTV-1) or cytokine (IL-2)  were analyzed and compared to unstimulated controls (NK alone).

first: Agnieszka

last: Zubiak

first: Simon

last: Hood

first: Poppy

last: Simmonds


title: The hypoxic landscape of melanoma

first: Pakavarin

last: Louphrasitthiphol

summary: Micro-environment played an important role in the disease progression and overall survival. More recently, hypoxic signature were identified as one of the key signatures of innate anti-PD1 resistance, however, relatively little had been done to identify the key molecular signature of hypoxic response in melanoma and how these may correlated with other know signatures which correlate with poor prognosis. In this study we performed large scale study which integrate ChIP-seq of HIF (in one cell line) and RNA-seq (in three commonly used melanoma cell lines) to identify a common melanoma hypoxic signature. The finding were used to further integrated with our other genome wide which focus on MITF (the master regulator of the melanocyte lineage and a melanoma lineage oncogene, GSE77609) to elucidate the intricate interplay between MITF and HIF and how this interplay define a melanoma specific response to hypoxia.

overall_design: Three melanoma cell lines were subjected to time course hypoxic induction. Triplicate samples were collected in three consecutive weeks.

first: Colin

last: Goding

first: Ioanna

last: Ledaki


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [ATAC-seq]

overall_design: ATAC-seq analysis of epigenomic changes in human macrophages that were cultured with or without IFN-γ and then stimulated with LPS


title: The Molecular Anatomy of Mammalian Upper Lip and Primary Palate Fusion at Single Cell Resolution

status: Public on Jun 11 2019

city: Aurora

first: Hong

last: Li

state: CO

department: Craniofacial Biology

institute: University of Colorado Denver Anschutz Medical Campus

summary: The mammalian lip/primary palate form when coordinated growth and morphogenesis bring the nasal and maxillary processes into contact, the epithelia co-mingle, remodel and clear from the fusion site to allow mesenchyme continuity. Although several genes required for fusion have been identified, an integrated molecular and cellular description of the overall process is lacking. Here we employ single cell RNA sequencing of the developing mouse face to identify ectodermal, mesenchymal, and endothelial populations associated with patterning and fusion of the facial prominences.  This analysis indicated that key cell populations at the fusion site exist within the periderm, basal epithelial cells and adjacent mesenchyme. Overall, these data provide a comprehensive high-resolution description of the various cell populations participating in fusion of the lip/primary palate as well as formation of the nasolacrimal groove, and they furnish a powerful resource for those investigating the molecular genetics of facial development and facial clefting that can be mined for critical mechanistic information concerning this prevalent human birth defect.

overall_design: Single cell RNA sequencing were performed on microdissted regions of the upper face where the nasal and maxillary prominences are juxtaposed, including the lambdoid junction, the nasolacrimal groove, and the nasal fin, from E11.5 Wild-type C57BL/6J and E11.5 Crect; ROSA26-lacZ embryos. We obtined about 8000 cells for the C57BL/6J dataset (C57LJ), and about 7000 cells for the Crect; ROSA26-lacZ dataset (CrectLJ). Cells were sequenced to a depth of about 100,000 reads per cell.

first: Trevor

last: Williams


title: RNA-seq data of PatchSeq dataset from Pvalb-Cre positive interneurons in the mouse hippocamus CA1 region

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: This study takes on the problem of bridging transcriptional data to neuronal phenotype and function by using publicly available datasets characterizing distinct neuronal populations based on gene expression, electrophysiology and morphology. In addition, a non-published PatchSeq dataset of Pvalb-cre positive cells in CA1 was used, which is the dataset submitted here. Taken together, these datasets were used to identify cross-cell type correlations between these data modalities. Detected correlations were classified as “class-driven” if they could be explained by differences between excitatory and inhibitory cell classes, or “non-class driven” if they could be explained by gradient like phenotypic differences within cell classes. Some genes whose relationships to electrophysiological or morphological properties were found to to be specific to either excitatory or inhibitory cell types. The Patch Seq data specifically allowed simultaneous single-cell characterization of gene expression and electrophysiology, showing that the gene-property correlations observed across cell types were further predictive of within-cell type heterogeneity.

overall_design:
Patchseq data was collected from single cells of the mouse hippocampus CA1 in order to investigate correlations between gene expression patterns and electrophysiological properties of various interneuron cell classes
19 individual cells
Re-analysis details included in supplementary file readme.txt.

first: Claire

last: Bomkamp

first: Shreejoy

last: Tripathy

first: Carolina

last: Bengtsson Gonzales

first: Jens

last: Hjerling-Leffler

first: Ann

middle: M

last: Craig

first: Paul

last: Pavlidis


title: Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures

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

overall_design: Refer to individual Series


title: Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer [ChIP-seq]

city: Salt Lake CIty

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Estrogen receptor alpha (ESR1) mutations have been identified in hormone therapy resistant breast cancer and primary endometrial cancer. Analyses in breast cancer suggests that mutant ESR1 exhibits estrogen independent activity. In endometrial cancer, ESR1 mutations are associated with worse outcomes and less obesity, however experimental investigation of these mutations has not been performed. Using a unique CRISPR/Cas9 strategy, we introduced the D538G mutation, a common endometrial cancer mutation that alters the ligand binding domain of ESR1, while epitope tagging the endogenous locus. We discovered estrogen-independent mutant ESR1 genomic binding that is significantly altered from wildtype ESR1. The D538G mutation impacted expression, including a large set of non-estrogen regulated genes, and chromatin accessibility, with most affected loci bound by mutant ESR1. Mutant ESR1 is unique from constitutive ESR1 activity as mutant-specific changes are not recapitulated with prolonged estrogen exposure. Overall, D538G mutant ESR1 confers estrogen-independent activity while causing additional regulatory changes in endometrial cancer cells that are distinct from breast cancer cells.

overall_design: ChIP-seq was used to study the effects of the D538G ESR1 mutation on genomic binding

first: Zannel

last: Blanchard


title: Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer [RNA-seq]

overall_design: RNA-seq was used to study the effects of the D538G mutation on gene expression


title: Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer [ATAC-seq]

overall_design: ATAC-seq was used to study the effects of the D538G ESR1 mutation on chromatin accessibility


title: Structural basis of specific DNA binding by the transcription factor ZBTB24

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes – the other three being DNMT3B, CDCA7 and HELLS – that are mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a genetic disorder characterized by DNA hypomethylation and antibody deficiency. The molecular mechanisms by which ZBTB24 regulates gene expression and the biological functions of ZBTB24 are poorly understood. Here we identified a 12-bp consensus sequence [CT(G/T)CCAGGACCT] occupied by ZBTB24 in the mouse genome. The sequence is present at multiple loci, including the Cdca7 promoter region, and ZBTB24 binding is mostly associated with gene activation. Crystallography and DNA-binding data revealed that the last four of the eight zinc fingers (ZFs) (i.e. ZF5-8) in ZBTB24 confer specificity of DNA binding. Two ICF missense mutations have been identified in the ZBTB24 ZF domain that alter zinc-binding cysteine residues. We demonstrated that the corresponding C382Y and C407G mutations in mouse ZBTB24 abolish specific DNA binding and fail to induce Cdca7 expression. Our analyses indicate, and suggest a structural basis for, the sequence specific recognition by a transcription factor centrally important for the pathogenesis of ICF syndrome.

overall_design: HA-tagged ZBTB24 was stably expressed in Zbtb24 knockout mouse ES cells, and ChIP-Seq analysis was performed.

first: Ren

last: Ren

first: Swanand

last: Hardikar

first: John

last: Horton

first: Yang

last: Zeng

first: Anup

middle: K

last: Singh

first: Kevin

last: Lin

first: Luis

middle: D

last: Coletta

first: Jianjun

last: Shen

first: Celine

last: Kong

first: Hideharu

last: Hashimoto

first: Xing

last: Zhang

first: Taiping

last: Chen

first: Xiaodong

last: Cheng


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization

first: Keunsoo

last: Kang


title: Genome-wide expression study of macrophage subsets in mouse skin

city: Freiburg

first: Philipp

last: Henneke

address: Breisacher Str. 115

department: CCI

country: Germany

institute: Universitätsklinikum Freiburg


title: Estrogen-independent molecular actions of mutant estrogen receptor alpha in endometrial cancer

first: Jason

last: Gertz


title: PRRX2 and HEY2 double knock-down facilitates ASCL1-induced neuron conversion in human dermal fibroblasts II

city: Buffalo

first: Jian

last: Feng

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

summary: Forced expression of ASCL1, Nurr1, Lmx1a, miRNA-124 and p53shRNA (ANLmp) in fibroblasts reprograms fibroblasts to induced dopaminergic neurons (iDA). While human lung fibroblasts can be converted rapidly and efficiently, iDA of dermal fibroblast is very unefficient and incompleted. To address this issue,  we performed time series RNAseq on both lung and dermal fibroblasts during the first several days of ANLmp induced neuron convertion. Bioinformatics analysis revealed the stable fibroblast gene regulatory network (GRN)  was a potential repressive factor for iDA in human dermal fibroblasts.

overall_design: Time serial comparison of transcriptomes of non-isogenic human skin fibroblasts C002 and human lung fibroblasts MRC5 during their transdifferentiation to dopaminergic neuron induced by ANLmp.

first: Hanqin

last: Li

first: Houbo

last: Jiang


title: PRC2-associated chromatin contacts in the developing limb reveal a possible mechanism for the atypical role of PRC2 in HoxA gene expression

status: Public on Jun 10 2019

city: Montreal

first: Marie

last: Kmita

state: Quebec

address: 110 Pine Ave W

country: Canada

institute: Institut de recherches cliniques de Montreal (IRCM)

summary: Preventing inappropriate gene expression in time and space is as fundamental as triggering the activation of tissue/cell-type specific factors at the correct developmental stage and in the correct cells. Here, we study the impact of Polycomb Repressive Complex 2 (PRC2) function on HoxA gene regulation. We analyze chromatin conformation of the HoxA cluster and its regulatory regions and show that in addition to the well-known role of PRC2 in silencing Hox genes via direct binding, its function is required for the changes in HoxA long-range interactions distinguishing proximal limb from distal limb. This effect stems from the differential PRC2 occupancy over the HoxA cluster and, at least in part, from the ability of PRC2-bound loci to engage in long-range contacts. Unexpectedly, PRC2 also impacts chromatin conformation in a way that promotes enhancer-promoter contacts required for proper HoxA expression, pointing to a dual role of PRC2 in gene regulation.

overall_design: ChIP analysis of SUZ12, RING1B and H3K27ac in proximal and distal limb tissue at E12.5

first: Claudia

last: Gentile

first: Alexandre

last: Mayran

first: Fanny

last: Guerard-Millet


title: A subset of skin macrophages modulates surveillance and regeneration of local nerves

first: Patrice

last: Zeis

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Host-environment interfaces such as the dermis comprise tissue macrophages as the most abundant resident immune cell type. Diverse tasks, i.e. to resist against invading pathogens, to attract bypassing immune cells from penetrating vessels and to aid tissue development and repair require a dynamic postnatal coordination of tissue macrophages specification. Here, we delineated the postnatal development of dermal macrophages and their differentiation into distinct subsets by adapting single cell transcriptomics, fate-mapping and tissue imaging. We thereby identified a small phenotypically and transcriptionally distinct subset of embryo-derived skin macrophages that was maintained and largely excluded from the overall postnatal exchange by monocytes. These macrophages specifically interacted with dermal sensory nerves, surveilled and trimmed the myelin sheets and regulated axon sprouting after mechanical injury. In summary, our data show long-lasting functional specification of macrophages in the dermis that is driven by step-wise adaptation to guiding structures and ensures codevelopment of ontogenetically distinct cells within the same compartment.

overall_design: Single Cell Sequencing was performed on CD45+CD11b+CD64+Lin-(lineage B220, CD3, NK1.1, Siglec-F, Ly6G) CX3CR1 (low, mid, high) macrophage subsets from mouse dermis after enzymatic digestion

first: Julia

last: Kolter

first: Dominic

last: Grün


title: Microbiota-derived short-chain fatty acids promote the memory potential of antigen activated CD8+ T cells

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

country: Australia

institute: Monash University


title: Mapping distinct bone marrow niche populations and their differentiation paths

city: Birmingham

first: Rob

last: Welner

address: 1824 6th Ave S

department: Medicine - Hem/Onc

institute: University of Alabama at Birmingham

summary: The bone marrow microenvironment is composed of heterogeneous cell populations of non-hematopoietic cells with complex phenotypes and undefined trajectories of maturation. Among them, mesenchymal cells maintain the production of stromal, bone, fat and cartilage cells. Resolving these unique cellular subsets within the bone marrow remains challenging. Here, we used single-cell RNA-sequencing of non-hematopoietic bone marrow cells to define specific subpopulations. Furthermore, by combining computational prediction of the cell state hierarchy with known expression of key transcription factors, we mapped differentiation paths to the osteocyte, chondrocyte, and adipocyte lineages. Finally, we validated our findings using lineage-specific reporter strains and targeted knockdowns. Our analysis reveals differentiation hierarchies for maturing stromal cells, determines key transcription factors along these trajectories, and provides an understanding of the complexity of the bone marrow microenvironment.

overall_design: Single-cell mRNA sequencing of stromal cells from mouse bone marrow. Sample Stroma1 represents 948 final filtered single cells. Sample Stroma2 represents 1899 final filtered single cells.

first: Samuel

last: Wolock

first: Indira

last: Krishnan

first: Danielle

last: Tenen

first: Victoria

last: Matkins

first: Virginia

last: Camacho

first: Sweta

last: Patel

first: Puneet

last: Agarwal

first: Ravi

last: Bhatia

first: Daniel

middle: G

first: Allon

last: Klein

first: Robert


title: Genome-wide expression study of macrophage subsets in the adult murine dermis

first: Philipp

last: Henneke

summary: CX3CR1-high dermal macrophages are specifically associated with dermal nerves. The aim of this expression profiling was to identify transcriptional differences in comparison to dermal CX3CR1-low macrophages.

overall_design: Dermal macrophages were collected by fluorescence-activated cell sorting (FACS) from digested skin of 3-6 pooled adult Cx3cr1+/GFP C57Bl/6 mice. For each subset, two replicates were purified from 2 independent litters.


title: Genome-wide expression study of macrophage subsets in mouse skin distinguished by differential CX3CR1 expression

summary: Dermal murine macrophages can be subdivided into three subpopulations based on their CX3CR1 expression pattern which differ in longevity, replenishment and localization. The aim of this expression profiling was to identify additional genes which differ in expression  between these populations and find potential functional markers.

overall_design: Dermal macrophages were collected by fluorescence-activated cell sorting (FACS) from digested skin of 4 pooled 2-week old Cx3cr1+/GFP C57Bl/6 mice. For each subset, two replicates were purified from 2 independent litters.


title: The aryl hydrocarbon receptor binds to kynurenine and mediates a signal supports the undifferentiated state in pluripotent stem cells

status: Public on Jun 09 2019

first: Takako

last: Yamamoto

address: Minatojima-minamimachi

institute: foundation for biomedical Research and Innovation at Kobe

summary: Kynurenine is generated from tryptophan by indoleamine 2,3-dioxygenase (IDO1) and binds to the aryl hydrocarbon receptor (AhR). We found that kynurenine generated by human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) stimulated the AhR to bind selectively to the promoters and enhancers of self-renewal genes, thus enhancing their transcription. The kynurenine-AhR complex also directly stimulated the expression of IDO1 and AHR, activating a positive feedback loop. Substantial amounts of kynurenine that were not complexed with AhR were present in the culture medium, providing a paracrine signal for maintenance of the undifferentiated state. Kynurenine was not present in the medium of differentiated ESCs and iPSCs. When cells were induced to undergo ectodermal differentiation, the abundance of kynurenine in the medium was reduced through activation of the main kynurenine catabolic pathway mediated by aminotransferase 2 (KAT2), resulting in the secretion of 2-aminoadipic acid (2-AAA) into the culture medium. Thus, kynurenine in the culture medium is a biomarker for the undifferentiated state, and 2-AAA in the culture medium is a biomarker for ESCs and iPSCs that have committed to differentiate along the ectoderm lineage.

first: T

first: S

last: Kawamata


title: Alternative splicing controls Leucine-rich repeat domain modularity in NOD-like receptors

city: Bonn

first: Florian

last: Hoss

address: Sigmund-Freud-Str. 196

department: Institute of Innate Immunity

institute: University Clinics, University of Bonn

summary: Leucine-rich repeat (LRR) domains are evolutionarily conserved in proteins that function in development and immunity. Somatic recombination of LRR sequences evolved to create diversity in jawless vertebrate adaptive immunity, yet the role repetitive LRR-encoding exons in humans remains unknown.  We performed this RNA Seq study to understand how alternative splicing of NOD-like receptors (NLRs) at the locus encoding a LRR domain can regulate NLRs function, with a focus on NLRP3.

overall_design: RNA Seq of GM-CSF differentiated human monocyte derived macrophages from 5 individuals

first: Francisca

last: Ringeling

first: Stefan

last: Canzar

first: Eicke

last: Latz


title: NET-CAGE Characterizes the Dynamics and Topology of Human Transcribed Cis-regulatory Elements

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

institute: RIKEN, Yokohama

summary: Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell-type-specific transcriptomes is not fully understood. We developed a simple and robust approach to sensitively detect 5’-ends of nascent RNAs (NET-CAGE) in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site (TSS) level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously upon stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell-type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 catalogue of transcribed enhancers, with broad applicability to biomedical research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Our study consists of 144 samples (NET-CAGE: 87 samples, CAGE: 43 samples and RNA-seq: 14 samples). Five ENCODE human cell lines and 2 mouse tissues were used to generate these data sets. A)  NET-CAGE samples for 5 human cell lines: MCF-7 (46 samples: 24 samples for time course experiment which consists of 8 time points with 3 biological replicates for each time point, 6 samples with different cell freezing conditions with 2 biological replicates for each condition, and 16 samples for 6 urea treatment conditions with 2-6 biological replicates for each condition), GM12878 (14 samples for 6 urea treatment conditions with 2-4 biological replicates for each condition), HeLa-S3, HepG2, K562 (6 samples for each cell line, comprising of 3 urea treatment conditions with 2 biological replicates for each condition). B) CAGE samples for 5 human cell lines: MCF-7 (26 samples: 24 samples for time course experiment which consists of 8 time points with 3 biological replicates for each time point, and 2 biological replicates without any treatment), GM12878, HeLa-S3, HepG2, K562 (2 biological replicates for each cell line). C) NET-CAGE samples for mouse tissues: brain (1 sample with 3 technical replicates), kidney (2 biological replicates with 3 technical replicates). D) CAGE samples for mouse tissues: brain (1 sample with 3 technical replicates), kidney (2 biological replicates with 3 technical replicates). E) Nascent RNA-seq samples for MCF-7 (3 urea treatment conditions with 2 biological replicates for each condition). F) Total RNA-seq samples for MCF-7 (2 biological replicates). G) Nascent RNA-seq samples for mouse tissues: brain (1 sample), kidney (2 biological replicates). H) Total RNA-seq samples for mouse tissues: brain (1 sample), kidney (2 biological replicates).

first: Yasuhiro

last: Murakawa

first: Hideya

last: Kawaji

first: Shigeki

last: Hirabayashi

first: Yu

last: Matsuki


title: Back-signaling from CX3CL1 regulates neurogenesis during development and in the adult mouse

status: Public on Jun 08 2019

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: CX3CL1 was discovered as a chemokine, and is best known to function via interaction with its receptor CX3CR1. However, in this study, we report a unique role of CX3CL1 that is independent from this pathway. We show that CX3CL1 is naturally shedded by both α- and β-secretase. The membrane-anchored C-terminal fragment is further cleaved by γ-secretase to release the CX3CL1 intracellular domain (CX3CL1-ICD), which is translocated into the cell nucleus to control gene expression. Among the regulated genes, we noted prominent induction of TGFβ2/TGFβ3 signaling in cultured cells by CX3CL1-ICD. Mice overexpressing only the C-terminal fragment (Tg-CX3CL1-ct) strongly induced TGFβ3 expression, as evidenced by Western and RNAseq analyses. Phenotypically, Tg-CX3CL1-ct mice exhibited enhanced neurogenesis both during development and in adulthood. Enhanced adult neurogenesis was seen in both the subgranular zone and the subventricular zone. Together, we demonstrate that CX3CL1-ct has a back-signaling function by enhancing neurogenesis through TGFβ3 and other genes important for neurogenesis.  Induction CX3CL1 back signaling may be a promising novel mechanism to replenish neuronal loss.

overall_design: NGS RNA-Seq profiling of P0 mouse hippocampi

first: Qingyuan

last: Fan

first: Manoshi

last: Gayen

first: Fan

last: Gao

first: Wanxia

last: He

first: Xiaoyang

last: Luo

first: Xiangyou

last: Hu

first: Riqiang

last: Yan


title: Transcriptomic analysis of hiPSC-derived neurons, pre-treated or not with KU-55933 compound (ATMi), after camptothecin (CPT) exposure and release.

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: The goal of the analysis was to determine the effect of Top1ccs blocking, elicited by CPT, on global transcription in hiPSC-derived neurons, in which ATM was catalytically inhibited or not with KU-55933.  Particular attention was focused on the correlation between CPT-modulated genes and gene length and on the potential involvement of ATM in this phenomenon.

overall_design: The experiment was performed in biological triplicate for each experimental condition, which included the Ctrl hiPSC-derived neurons untreated, treated with CPT and the same but pre-treated with the ATMi KU-55933.

first: Domenico

last: Delia

first: Alessandro

last: Corti

first: Loris

last: De Cecco


title: Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [TAIL-Seq]

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

institute: KAIST

summary: RNA tails play integral roles in the control of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TUT3 (PAPD5) and TUT5 (PAPD7) (TUT3/5) as the enzymes responsible for mRNA guanylation. Purified TUT3/5 predominantly incorporate GTPs to generate a mixed poly(A) tail with intermittent non-adenosine residues. A single guanosine is sufficient to impede the deadenylation complex (CCR4-NOT) which trims the tail and exposes guanosine at the 3′ end. Consistently, the depletion of TUT3/5 leads to a decrease in mRNA half-life and abundance in cells. Thus, TUT3/5 produce a mixed tail which shields the mRNA from rapid deadenylation. Our study unveils the role of mixed tailing, and expands the complexity of post-transcriptional gene regulation.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: HeLa cells and HFF cells were knocked down of control or TUT3/5 with two different siRNAs.

first: Jaechul

last: Lim

first: Dongwan

last: Kim

first: V

middle: N


title: Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation


title: Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [RNA-Seq]

overall_design: HeLa cells were knocked down of control or TUT3/5 with two different siRNAs


title: Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock [S2]

status: Public on Jun 07 2019

city: Ithaca

first: Charles

last: Danko

address: 235 Hungerford Drive

department: Computational Biology

institute: Cornell University

summary: Heat shock (HS) causes dramatic and rapid changes in transcription of thousands of genes in metazoans. We have used insitu Hi-C in Drosophila S2 and human K562 cells to determine the effects of HS upon chromatin conformation. Our study shows that topologically associated domains (TADs), compartments and distal regulatory interactions remain unchanged upon HS.

overall_design: Investigate changes in chromatin conformation upon acute HS in Drosophila S2 and human K562 cells by insitu Hi-C. Two biological replicates were done for Non heat shock (NHS) or HS conditions in each organism.

first: Judhajeet

last: Ray

first: Paul

middle: R

last: Munn

first: Anniina

last: Vihervaara

first: Abdullah

last: Ozer

first: John

middle: T

last: Lis


title: Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

overall_design: Refer to individual Series


title: Systems modeling of developmental vascular toxicity

city: RTP

first: Thomas

last: Knudsen

state: North Carolina

address: 109 T.W. Alexander Drive

institute: U.S. EPA

summary: More than 80,000 chemicals in commerce present a challenge for hazard assessments that toxicity testing in the 21st century strives to address through high-throughput screening (HTS) assays. Assessing chemical effects on human development adds an additional layer of complexity to the screening, with a need to capture complex and dynamic events essential for proper embryo-fetal development. HTS data from ToxCast/Tox21 informs systems toxicology models, which incorporate molecular targets and biological pathways into mechanistic models describing the effects of chemicals on human cells, 3D organotypic culture models, and small model organisms. Adverse Outcome Pathways (AOPs) provide a useful framework for integrating the evidence derived from these in silico and in vitro systems to inform chemical hazard characterization. To illustrate this formulation, we have built an AOP for developmental toxicity through a mode of action linked to embryonic vascular disruption (Aop43). Here, we review the model for quantitative prediction of developmental vascular toxicity from ToxCast HTS data and compare the HTS results to functional vascular development assays in complex cell systems, virtual tissues, and small model organisms. ToxCast HTS predictions from several published and unpublished assays covering different aspects of the angiogenic cycle were generated for a test set of 38 chemicals representing a range of putative vascular disrupting compounds (pVDCs). Results boost confidence in the capacity to predict adverse developmental outcomes from HTS in vitro data and model computational dynamics for in silico reconstruction of developmental systems biology. Finally, we demonstrate the integration of the AOP and developmental systems toxicology to investigate the unique modes of action of two angiogenesis inhibitors.

overall_design: Rat whole embryo cultures were exposed to 5HPP-33 (5, 15, 30 µM), TNP-470 (0.25, 2.5, 25 µM), or culture medium control. At four hours post-culture, the visceral yolk sac (VYS) was separated from the embryo and RNA was extracted from each embryo (n = 8/concentration) or from pooled VYSs ( n = 4/concentration) for RNA-seq analysis.

first: Katerine

middle: S

last: Saili

first: Jill

middle: A

last: Franzosa

first: Nancy

last: Baker

first: Robert

last: Ellis-Hutchings

first: Raja

last: Settivari

first: Edward

last: Carney

first: Richard

last: Spencer

first: Todd

last: Zurlinden

first: Nicole

last: Kleinstreuer

first: Shuaizhang

last: Li

first: Menghang

last: Xia

middle: B


title: Differential gene expression in human RAF1 S257L/+ and isogenic corrected iPSC-derived cardiomyocytes

status: Public on Jun 15 2019

city: New York

first: Fabrice

last: Jaffre

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medicine

summary: Although several studies have uncovered abnormal signaling pathways in RASopathy disorders, little is known about the alterations of the cardiac transcriptome induced by Noonan syndrome (NS) mutations. Hence, to gain insights into the transcriptional alterations induced by the NS-associated RAF1S257L/+ mutation in human iPSC-derived cardiomyocytes, we performed quantitative transcriptome profiling by RNA-sequencing. Since we have found that inhibition of ERK5 and MEK1/2 pathways could normalized hypertrophy and myofibrillar disarray in mutant cardiomyocytes, we also aimed at identifying gene transcriptional profiles that were specifically affected by either MEK5-ERK5 or MEK1/2-ERK1/2 activation in RAF1S257L/+ iCMs.

overall_design: mRNA profiles of  human RAF1 S257L/+ and isogenic corrected iPSC-derived cardiomyocytes were generated by RNA-sequencing, in triplicate, using Ion S5.

last: Jaffré

first: Maria

last: Kontaridis


title: Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock [K562]

first: Charles

last: Danko

first: Judhajeet

last: Ray

first: Paul

last: Munn

first: Anniina

last: Vihervaara

last: Ozer


title: DNA methylation in progeroid syndromes

city: Wuerzburg

first: Tobias

last: Mueller

address: Am Hubland

institute: University of Wuerzburg

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of patients with WRN, LMNA or POLD1 mutations

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip

first: Anna

last: Maierhofer

first: Julia

last: Flunkert

first: Junko

last: Oshima

first: George

last: Martin

first: Martin

last: Poot

first: Indrajit

last: Nanda

first: Marcus

last: Dittrich

last: Müller

first: Thomas

last: Haaf


title: Apical sodium-dependent bile acid transporter inhibition with volixibat improves metabolic aspects and components of non-alcoholic steatohepatitis in Ldlr-/-.Leiden mice

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

summary: Abstract:    Interruption of bile acid recirculation through inhibition of the apical sodium-dependent bile acid transporter (ASBT) is a promising strategy to alleviate hepatic cholesterol accumulation in non-alcoholic steatohepatitis, and improve the metabolic aspects of the disease. Putative disease-attenuating effects of the ASBT inhibitor volixibat (5, 15, and 30 mg/kg) were investigated in  high-fat diet (HFD)-fed Ldlr-/-.Leiden mice over 24 weeks. Plasma and fecal bile acid levels, plasma insulin, lipids, and liver enzymes were monitored. Final analyses included liver histology, intrahepatic lipids, mesenteric white adipose tissue mass, and liver gene profiling. Consistent with its mechanism of action, volixibat significantly increased total bile acid excretion. At the highest dose, volixibat significantly attenuated the HFD-induced increase in hepatocyte hypertrophy, hepatic triglyceride and cholesteryl ester levels, and mesenteric white adipose tissue deposition, while total plasma bile acid levels remained constant. Non-alcoholic fatty liver disease activity score was significantly lower in volixibat-treated mice than in the HFD controls. Gene profiling showed that volixibat reversed the inhibitory effect of the HFD on metabolic master regulators, including peroxisome proliferator-activated receptor-γ coactivator-1β, insulin receptor, and sterol regulatory element-binding transcription factor 2. Volixibat may have beneficial effects on physiological and metabolic aspects of non-alcoholic steatohepatitis pathophysiology.

overall_design: Experimental design:    Mice (N = 75, between 16-18 weeks old) were matched by body weight and plasma cholesterol, triglyceride, and blood glucose levels were divided into five study groups, and maintained on either a chow diet (n = 10), a HFD (n = 20), or a HFD supplemented with volixibat 5, 15, or 30 mg/kg (n = 15 in each dose group) for 24 weeks (Fig 2). Food intake and body weight were monitored throughout the study to ensure accurate volixibat dosing. The schedule of assessments over the 24 weeks is shown in Fig 2, and included measurements of plasma cholesterol triglycerides, insulin, and liver enzymes, and determination of the lipoprotein profile. Bile acid species were measured in plasma and feces. Plasma samples (collected at weeks 0, 4, 8, 12, 16, 20, and 24) were obtained via a tail bleed after 5 hours of fasting (Fig 2). The mice were sacrificed at week 24 and the livers were isolated for histological evaluation of NASH parameters (as described above) [40] and lipid analysis. White adipose tissue depots were also collected and weighed. Gene expression analysis was carried out on liver tissue from eight mice in each group, selected as being representative of the group based on mean values of NASH parameters. All analyses were performed blindly.

first: Kanita

last: Salic

first: Robert

last: Kleemann

first: Cynthia

last: Wilkins-Port

first: John

last: McNulty

first: Melissa

last: Palmer


title: Histone methyltransferase PRDM9 is not essential for meiosis in male mice

city: Bethesda

first: Kevin

last: Brick

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: A hallmark of meiosis is the rearrangement of parental alleles to assure genetic diversity in gametes. These chromosome rearrangements are mediated by the repair of programmed DNA double-strand-breaks (DSBs) as genetic crossovers between parental homologs. In mice, humans, and many other mammals, meiotic DSB occur primarily at hotspots, determined by sequence-specific binding of the PRDM9 protein. Without PRDM9, meiotic DSBs occur near gene promoters and other functional sites. Studies in a limited number of mouse strains showed that functional PRDM9 is required to complete meiosis, but despite its apparent importance, Prdm9 has been repeatedly lost across many animal lineages. Both the reason for mouse sterility in the absence of PRDM9 and the mechanism by which Prdm9 can be lost remain unclear. Here, we explore if mice can tolerate the loss of Prdm9. By generating Prdm9 functional knockouts in an array of genetic backgrounds, we observe a wide range of fertility phenotypes and ultimately demonstrate that PRDM9 is not required for completion of meiosis. Although DSBs still form at a common subset of functional sites in all mice lacking PRDM9, meiotic outcomes differ substantially. We speculate that DSBs at functional sites are difficult to repair as a crossover and that by increasing the efficiency of crossover formation at these sites, genetic modifiers of recombination rates can allow for meiotic progression. This model implies that species with a sufficiently high recombination rate may lose Prdm9 yet remain fertile.

overall_design: DSB hotspots were mapped in two replicates each of B6 Prdm9-/-, PWD Prdm9-/- and (B6xPWD)F7 Prdm9-/- mice.

first: Ondrej

last: Mihola

first: Florencia

last: Pratto

first: Eliska

last: Linhartova

first: Tatyana

last: Kobets

first: Petr

last: Flachs

first: Christopher

first: Radislav

last: Sedlacek

first: Kenneth

last: Paigen

first: Petko

last: Petkov

first: Rafael

last: Camerini-Otero

first: Zdenek

last: Trachtulec


title: Gene expression profiling of cardiac mesenchymal stromal cell during ageing

city: Toulouse

first: Victorine

last: Douin-Echinard

state: 1 avenue du Pr Jean Poulhès

address: Institut Fédératif de Recherche Bio-Médicale de Toulouse (IFR-BMT), Building L4, Room 106

country: France

institute: INSERM

summary:
Our goal is to identify cardiac stromal senescence pathways associated with physiological cardiac ageing
Genome micro-array prolifiling

overall_design: Cardiac mesenchymal cells from young (5 months) and old (20 months) C57BL/6 male mice were cell sorted by flow cytometry (3 mice per sample).

first: Hélène

last: Martini

first: Lise

last: Lefèvre

first: Yannick

last: Lippi

first: Claire

last: Naylies


title: IL-1β induces the rapid secretion of the antimicrobial protein IL-26 from Th17 cells

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: We investigated how IL-1β and anti-CD3/CD28 stimulation affected gene expression in IL-1RI+ and IL-1RI- Th17 cells by RNA sequencing.

overall_design: IL-1RI+ and IL-1RI- Th17 cells were sorted from three donors and treated with media as a control, IL-1β, or anti-CD3/CD28 antibody complexes for a total of 18 samples.

first: David

middle: I

last: Weiss

first: Matteo

last: Pellegrini

first: Robert

middle: L

last: Modlin


title: ANKRD31  regulates  spatiotemporal  patterning  of  meiotic  recombination  initiation  and    ensures recombination between heterologous sex chromosomes in mice

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

institute: CNRS

summary:
Orderly  segregation  of  chromosomes  during  meiosis  requires  that  crossovers  form  between  homologous  chromosomes  by  recombination.  Programmed  DNA  double-strand  breaks  (DSBs)  initiate  meiotic  recombination.  We  identify  ANKRD31  as  a  critical  component  of  complexes  of  DSB-promoting   proteins   which   assemble   on   meiotic   chromosome   axes.   Genome-wide,   ANKRD31  deficiency  causes  delayed  recombination  initiation.  In  addition,  loss  of  ANKRD31  alters  DSB  distribution  owing  to  reduced  selectivity  for  sites  that  normally  attract  DSBs.  Strikingly,  ANKRD31  deficiency  also  abolishes  uniquely  high  rates  of  recombination  that  normally   characterize   pseudoautosomal   regions   (PARs)   of   X   and   Y   chromosomes.
Consequently,  sex  chromosomes  do  not  form  crossovers  leading  to  chromosome  segregation failure in ANKRD31-deficient spermatocytes. These defects are accompanied by a genome-wide delay  in  assembling  DSB-promoting  proteins  on  axes  and  a  loss  of  a  pecialized  PAR-axis  domain  that  is  highly  enriched  for  DSB-promoting  proteins.  Thus,  we  propose  a  model  for  spatiotemporal  patterning  of  recombination  by  ANKRD31-dependent  control  of  axis-associated  complexes of DSB-promoting proteins.

overall_design: H3K4me3-ChIP-seq and DMC1-SSDS experiments were performed on testis from different mouse lines

first: Frantzeskos

last: Papanikos

last: Clément

first: Erika

last: Testa

first: Ramya

last: Ravindranathan

first: Corinne

last: Grey

first: Ihsan

last: Dereli

first: Anastasiia

last: Bondarieva

first: Sarai

last: Valerio-Cabrera

first: Marcello

last: Stanzione

first: Alexander

last: Schleiffer

last: Jansa

first: Diana

last: Lustyk

first: Fei

last: Jifeng

first: Jiri

last: Forejt

first: Marco

last: Barchi

first: Bernard

last: de Massy

first: Attila

last: Toth


title: Transcriptome analysis of thymic epithelial cells and thymic non-epithelial stromal cells from young, middle-aged and castrated middle-aged male mice

status: Public on Jun 06 2019

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

summary:
The thymus is primarily responsible for generating naïve, self-tolerant T cells from hematopoietic precursors. Thymic epithelial cells (TECs) together with other stromal cells create a specialized microenvironment which orchestrates the major selection processes for T cell development. Thymic function progressively deteriorates as part of the aging process, with a dramatic loss in TECs and T cell production, and this ultimately constrains the host immune repertoire.
We have previously demonstrated the role of sex steroids in thymic involution in male mice, with surgical castration of middle-aged (9-12 month) male mice resulting in thymus regeneration, peaking around day 28. We have also demonstrated phenotypic alterations in TEC subsets within one week following castration that may contribute to this transient thymus regeneration effect.
In this study, we aimed to examine genetic alterations in TEC and non-TEC stromal cell subsets (predominantly fibroblasts and endothelial cells) during age-related thymic involution (5-6 week old young adults compared to 9-12 month middle aged); and genetic changes in TEC and non-TEC at several timepoints following castration, to identify factors that may be involved in thymus regeneration.

overall_design:
The aim was to investigate gene changes in thymic celll during ageing and following castration when the thymus transiently regenerates.
The thymus was extracted from young (5-6wk old), middle-aged (9-12mo old) , or castrated middle-aged C57Bl/6 mice at day 4, day 7 or day 20 post castration or sham-castration, then digested into single cell suspensions. Thymic epithelial cells (CD45-,EpCAM+) and non-epithelial stromal cells (CD45-EpCAM-) were then FACS purified.

first: Ann

last: Chidgey


title: Sequence diverse miRNAs converge to induce mesenchymal-to-epithelial transition in ovarian cancer cells through direct and indirect regulatory controls

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary:
Epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) are reciprocal molecular processes essential in early embryonic development that have been co-opted by cancer cells to facilitate tumor metastasis. Recent studies have demonstrated that both EMT and MET can be induced by modulations in cellular levels of microRNAs (miRNAs), a well-studied class of small regulatory RNAs. Our laboratory has been particularly interested in the ability of members of the sequentially homologous miR-200 family of miRNAs to induce MET when ectopically over-expressed in mesenchymal-like ovarian cancer (OC) cells. Given that even a single nucleotide substitution within the highly conserved seed region of miRNAs can dramatically change the spectrum of regulated mRNA targets, it is remarkable that families of miRNAs sequentially divergent from one another can similarly regulate the EMT/MET process in a diversity of cancer cells. For example, miR-205, although sequentially highly divergent from members of the miR-200 family, has been reported to display a similar ability to induce MET in mesenchymal-like lung, prostate cancer cells. We report here that although miR-205 has little to no sequence homology with members of the miR-200 family of miRNAs, it induces morphological transitions in mesenchymal OC cells that are morphologically indistinguishable from those induced by members of the sequentially divergent miR-200 family.
We present evidence that the vast majority of the molecular changes underlying these morphological transitions are not brought about by the direct targeting of the same suite of genes but rather by indirect regulatory changes that converge to generate a similar molecular phenotype.

overall_design: Ovarian cancer HEY cells were transfected with miR-200 and miR-205 for 48 hrs. After transfection, RNA were extracted and microarray gene expression analysises were conducted.

first: Neda

last: Jabbari

first: Minati

last: Satpathy

first: Lilya

middle: V

last: Matyunina

first: Yuehua

last: Wang

first: Lila

last: McDonald

first: John

middle: F


title: Ex vivo screen identifies CDK12 as a metastatic vulnerability in osteosarcoma

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

summary: Despite progress in intensification of therapy, outcomes for patients with metastatic osteosarcoma (OS) have not improved in thirty years. We developed a system that enables preclinical screening of compounds against metastatic OS cells in the context of the native lung microenvironment.  Using this strategy to screen a library of epigenetically-targeted compounds, we identified inhibitors of CDK12 to be most effective, reducing OS cell outgrowth in the lung by >90% at sub-micromolar doses. CDK12 inhibition led to defects in transcription elongation in a gene length- and expression-dependent manner. These effects were accompanied by defects in RNA processing and altered the expression of genes involved in transcription regulation and the DNA damage response. We further identify OS models that differ in their sensitivity to CDK12 inhibition in the lung and provide evidence that upregulated MYC levels may mediate these differences. Our studies provide a framework for rapid preclinical testing of compounds with anti-metastatic activity and highlight CDK12 as a potential therapeutic target in osteosarcoma.

overall_design: H3K27ac, RNA Pol 2, RNA Pol 2 Ser2, and CDK12 CHIP-seq were done for DMSO and E9 treated MG63.3-GFP and 143B-GFP osteosarcoma cells. Whole Genome Sequencing  was done for the MG63.3-GFP and 143B-GFP cell lines.  Finally, RNA-seq was done on DMSO or E9 treated MG63.3-GFP and 143B-GFP cells in triplicate.

first: Ian

last: Bayles

first: Alina

last: Saiakhova

middle: C


title: Choroid Plexus Releases miR-204 Regulating the Number of Neural Stem Cells in the Adult Brain

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

institute: LMU Munich

summary: We compared transcriptomes changes in murine quescent neural stem cells after the interference with the function of mu-miR204

overall_design: quiscent neural stem cells were isolated 3 days after intraventricular injection of either aCSF or miR204 specific antagomers using described protocol (Fischer et al., 2011) and their transcriptome was analyzed

first: Tjasa

last: Lepko


title: EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits (ATAC-Seq)

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Memory CD8 T cells have a unique ability to provide lifelong immunity against pathogens. Although memory features generally arise after a challenge with foreign antigen, naïve CD8 single positive (SP) thymocytes may already acquire phenotypic and functional characteristics of memory cells in response to cytokines such as interleukin-4. This process is associated with the induction of the T-box transcription factor Eomesodermin (EOMES). However, the underlying molecular mechanisms remain ill-defined. Using epigenomic profiling, we show that these “innate memory” CD8SP cells acquire only a portion of the active enhancer repertoire of conventional memory cells. This reprograming was secondary to EOMES recruitment, mostly to RUNX3-bound enhancers. Furthermore, we identified direct interaction between EOMES and BRG1 and showed that in vivo acquisition of EOMES-dependent program by CD8SP thymocytes was dependent on this chromatin remodeling factor. In conclusion, our results support a strong epigenetic basis for EOMES-driven establishment of CD8 T cell unconventional memory program.

overall_design: CD8SP thymocytes: Innate Memory, Naïve, WT, and Eomes-TG

first: Nicolas

last: Istaces

first: Marion

last: Splittgerber

first: Viviana

last: Silva

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Aurore

last: Le

first: Younes

last: Achouri

first: Emilie

last: Calonne

first: Matthieu

last: Defrance

first: François

last: Fuks

first: Abdulkader

last: Azouz


title: Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

summary: Organisms use endogenous clocks to adapt to the rhythmicity of the environment and to synchronize social activities. Although circadian rhythms have been implicated in multiple aspects of aging, it remains uncertain whether evolutionary selection of circadian cycle gene variants contributes to changes in longevity and aging traits within animal populations. We have sequenced the genomes of Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds of selection for reduced senescence from a parental strain. Preservation of youthful muscle gene expression and function is seen during aging in these strains and is primarily due to intergenic polymorphisms rather than to mutations in coding sequences. Expression of transcriptional regulators of the circadian machinery is highly modulated, with higher period and timeless and lower cycle expression in strains with delayed aging compared to the parental strain. These changes in the expression of circadian core components associate with changes in the amplitude and specificity of the circadian transcriptome. Moreover, a muscle-specific increase in timeless expression to levels similar to long-lived lines extends lifespan. Altogether, these findings indicate that circadian clock gene variants contribute to shaping aging traits and to the evolutionarily divergence in longevity within a species.

overall_design: Muscle samples of 3 strains, 2 of which show delayed aging (O1 and O3, O for old) relative to the parental strains (B3, B for Base) showing divergence at 1 and 6 weeks of age. Also included are data from transgenic lines with muscle specific expression of timeless (Mhc>timeless) and a control set (mhc, for Mhc-Gal4 transgene) showing divergent circadian rhythms when measured at 0, 6 12 and 18 hrs.

first: Liam

last: Hunt

first: Jianqin

last: Jiao

first: Yong

last: Wang

first: Deepti

last: Rao

first: Michelle

last: Curly

first: Maricela

last: Robles-Murguia

first: Vishwajeeth

last: Pagala

first: Junmin

last: Peng

first: Yiping

last: Fan

first: Fabio

last: Demontis


title: EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits

first: Stanislas

last: Goriely

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


title: Transcriptional profiling of the zebrafish proximal tubule

status: Public on Jun 05 2019

city: Auckland

first: Veronika

last: Sander

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

summary: The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney, the pronephros, represents a simplified form of the mammalian organ, yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here, we establish a high-resolution expression profile of isolated, GFP-labelled proximal tubules from 3-day-old zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation, proximal tubules from Hnf1b-depleted larvae were analysed in parallel and differential expression analysis was performed.

overall_design: Examination of wild-type and Hnf1b-depleted proximal tubule tissue

first: Dharani

last: Sontam

first: Justin

middle: M

last: O’Sullivan

first: Alan

middle: J

last: Davidson

first: William

last: Schierding

first: Richard

middle: W

last: Naylor

last: Salleh


title: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary:
We utilized the Nematostella vectensis to quantify gene expression differences and loss during light:dark cycling and immediately after light cue removal through comparisons of 136 transcriptomes
Organismal responses to light:dark cycles can result from two general processes: (i) direct response to light or (ii) a free-running rhythm (i.e., a circadian clock). Previous research in cnidarians has shown that candidate circadian clock genes have rhythmic expression in the presence of diel lighting, but these oscillations appear to be lost quickly after removal of the light cue. Here, we measure whole-organism gene expression changes in 136 transcriptomes of the sea anemone Nematostella vectensis, entrained to a light:dark environment and immediately following light cue removal to distinguish two broadly defined responses in cnidarians: light entrainment and circadian regulation. Direct light exposure resulted in significant differences in expression for hundreds of genes, including more than 200 genes with rhythmic, 24-hour periodicity. Removal of the lighting cue resulted in the loss of significant expression for 80% of these genes after one day, including most of the hypothesized cnidarian circadian genes. Further, 70% of these candidate genes were phase shifted. Most surprisingly, thousands of genes, some of which are involved in oxidative stress, DNA damage response, and chromatin modification, had significant differences in expression in the 24 hours following light removal, suggesting that loss of the entraining cue may induce a cellular stress response. Together, our findings suggest that a majority of genes with significant differences in expression for anemones cultured under diel lighting are largely driven by the primary photoresponse rather than a circadian clock when measured at the whole animal level. These results provide context for the evolution of cnidarian circadian biology and help to disassociate two commonly confounded factors driving oscillating phenotypes.

overall_design: ntotal = 136. 17 time points (4 replicates at each) for 2 conditions. (17*4*2 = 136)

first: Adam

last: Reitzel


title: EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits (RNA-Seq)

first: Nicolas

last: Istaces

first: Marion

last: Splittgerber

first: Viviana

last: Silva

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Aurore

last: Le

first: Younes

last: Achouri

first: Emilie

last: Calonne

first: Matthieu

last: Defrance

first: François

last: Fuks

first: Abdulkader

last: Azouz


title: Cell cycle dependent regulation and function of Argonaute 1 in plants [RNA-Seq]

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: The RNA silencing (RNAi) is a biological process, which plays a key role in a wide range of eukaryotes, such as gene expression regulation, transposable elements control and antiviral defense. In human, several studies showed that miRNAs and AGO2 are involved in the regulation of the cell cycle. Indeed, many cell cycle regulators such as cyclins, CDKs, CDK inhibitors, RBR proteins or E2F transcription factors have been identified as miRNA targets. Transcriptional data suggest that these cell cycle miRNAs are differentially accumulated during cell cycle progression and that misregulation of some could lead to proliferative diseases. However, in plants, almost nothing is known about the cell cycle regulation through miRNAs. Unpublished datas from the lab suggest that the Arabidopsis AGO1, which is the most important Argonaute for miRNA-mediated gene regulation, is essential for cell proliferation. In order to investigate the role of AGO1 during cell cycle, we set up a system based on cell cycle synchronization of tobacco BY-2 cell suspensions expressing a GFP-fused AGO1. We sequenced small RNAs from S, G2, M and G1 phases of synchronized cells from total RNA extract and GFP-AGO1 co-purified small RNAs, and investigate whether putative cell cycle specific miRNAs can be highlighted.

overall_design: 3 replicates of stranded RNA seq from total RNA are included in this study. They correspond to 4 different phases of the cell cycle

last: Baldrich

first: Adrien

last: Trolet

first: Marie-Claire

last: Criqui

last: Clavel

first: Pascal

last: Genschik

first: Blake

last: Meyers


title: Inhibition of Hepatocellular Carcinoma Progression by Forced Metabolic Re-Programming

city: Pittsburgh

first: Edward

last: Prochownik

state: PA

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

summary: Using two different mouse models of liver cancer, we have recently shown that the commonly observed metabolic  switch from oxidative phosphorylation to glycolysis known as the Warburg effect is inevitably accompanied by a marked decrease in fatty acid oxidation (FAO) and an increase in the activity of pyruvate dehydrogenase, the enzyme linking glycolysis to the TCA cycle. We now show that the short-term implementation of either medium-chain or long-chain high fat diets (HFDs) just prior to the induction of c-Myc oncoprotein-driven hepatocellular carcinoma (HCC) nearly doubled survival. Mechanistically, HFDs forced tumors to become more reliant on fatty acids as an energy source, thus normalizing FAO and PDH activities. We extended these findings to eighteen different cancer cohorts patients by showing that some tumors with high ratios of FAO-related:glycolysis-related transcripts were associated with more favorable prognoses than those with low ratios. We also used t-SNE, a machine learning-based dimensionality reduction technique, to show in other human tumors that the expression patterns of transcripts encoding FAO-related proteins and enzymes involved in cholesterol biosynthesis were also predictive of survival. Collectively, our results support the idea that tumors which are either forced to utilize fatty acids as an energy source or those which are already predisposed to doing so show significantly less aggressive behaviors. These findings suggest that short-tern dietary manipulation, either alone or in conjunction with more traditional chemotherapeutic regimens, might be employed as a relatively non-toxic and inexpensive means of enhancing survival in certain cancer types.

overall_design: Total 6 groups Samples: Normal diets Liver( 5 samples), medium-chain (MC) high-fat diets Liver( 5 samples), long-chain (LC) high-fat dietsLiver( 5 samples), Normal diets Tumors(4 samples), medium-chain (MC) high-fat diets Tumors( 5 samples), long-chain (LC) high-fat diets tumors ( 5 samples),

first: Huabo

last: Wang


title: Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility

status: Public on Jun 04 2019

city: New Haven

first: Martina

last: Brueckner

state: CT

address: 789 Howard Ave

department: Pediatrics

institute: Yale University

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: Refer to individual Series


title: Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [ChIP-Seq]

summary: Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD are unknown. Histone H2B mono-ubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40 and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment=6.01, p=1.67x10-03), some of whom had abnormal laterality associated with cilia dysfunction. In Xenopus, knockdown of rnf20 and rnf40 results in abnormal heart looping, defective development of left-right asymmetry and impaired cilia motility. Rnf20, Rnf40 and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level in Xenopus embryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and non-ciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factor Rfx3.  Rnf20 knockdown results in decreased levels of rfx3 mRNA in Xenopus, and exogenous rfx3 can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at the Rfx3 locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.

overall_design: Examination of histone 2B monoubiquitination in 2 cell types in duplicate: oviduct and liver