title: Compartmentalized gut lymph node drainage dictates adaptive immune responses

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary:
Purpose: The intestine's main function is to digest and absorb dietary nutrients, with help from the absorptive epithelium and underlying vasculature and lymphatic system, as well as the microbiome. The intestine also houses the largest immune cell population in the body, tasked with providing resistance to toxins and invading pathogens while maintaining tolerance to dietary and microbial antigens, either by local action or lymphatic trafficking to the gut-draining lymph nodes (gLNs) to mount adaptive responses. While previous studies revealed the drainage map to various gLNs along the murine gut, and described immunological differences between gLNs, the underlying cellular components and the functional consequences of gut segment-specific drainage have not been systematically addressed. We sought to understand how compartmentalized lymphatic drainage of the intestinal milieu contributes to immune responses towards luminal antigens.

Results: Here we report that gLNs are immunologically unique according to the functional gut segment they drain. Stromal and dendritic cell gene signatures, as well as adaptive T cell polarization against the same luminal antigen, differed between gLNs along the intestine, the proximal small intestine–draining gLNs preferentially giving rise to tolerogenic and the distal gLNs to pro-inflammatory T cell responses. This compartmentalized dichotomy could be perturbed by duodenal infection, surgical removal of select distal gLNs, dysbiosis, or ectopic antigen delivery, impacting both lymphoid organ and tissue immune responses.

Conclusions: Our findings reveal that the conflict between tolerogenic and inflammatory adaptive responses is in part resolved by discrete gLN drainage, and encourage gut segment-specific antigen targeting for therapeutic immune modulation.

overall_design:
Sorted Dendritic cells from  Cecal-Colonic, Duodenum and Ileum Lymph Nodes in four different mice.

Sorted Follicular and Lymphatic Endothelial cells from Cecal-Colonic, Duodenum and Ileum Lymph Nodes in three different mice.

first: Daria

last: Esterházy

first: Maria

last: Canesso

first: Luka

last: Mesin

first: Paul

last: Muller

last: de Castro

first: Ainsley

last: Lockhart

first: Mahmoud

last: ElJalby

first: Ana

last: Faria

first: Daniel

last: Mucida


title: Interrogating histone acetylation and BRD4 as mitotic bookmarks of transcription

status: Public on Apr 10 2019

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

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: Profiling of RNAs downregulated by influenza A virus PA-X ribonuclease

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

type: Expression profiling by high throughput sequencing

summary: The goal of this analysis was to investigate the targets of the influenza A host shutoff ribonuclease PA-X. We profiled the relative levels of cellular RNAs in cells infected with influenza A virus (A/PuertoRico/8/1934 H1N1) comparing wild-type and mutants that make reduced levels of PA-X and/or make a truncated and inactive PA-X. We also profiled relative RNA levels in cells overexpressing wild-type PA-X or a catalytically inactive mutant (D108A).

overall_design: for extopic expression, PA-X (from the A/PuertoRico/8/1934 H1N1 (PR8) strain) was expressed in A549 cells using a doxycyline-inducible transgene for 18 hrs; for infection, A549 cells were infected with the wild-type PR8 strain or mutant strain that carried mutations that reduce PA-X production or activity for 15 hrs. rRNA deplete RNA was subjected to high-throughput sequencing

middle: M

first: Craig

last: McCormick

first: Denys

middle: A

last: Khaperskyy


title: Gene expression analysis of TRuC-T and CAR-T cells in response to tumor antigen stimulation

status: Public on Apr 09 2019

city: Cambridge

first: Jian

last: Ding

state: MA

address: 100 Binney Street, Suite 710

department: Immunology

institute: TCR2 Therapeutics

summary: Analysis of gene expression profile of CD19-specific TRuC and CAR T-cells, before and after co-culture with CD19-positive Raji tumor cells for 4 hours. T cells were generated with T cells from 3 healthy donors. The study was done with NanoString Gene Expression Assay - Human Immunology V2 CodeSet.

overall_design: Non-transduced as well as CD19-specific TRuC, CD28z and 41BBz CAR T cells were generated with T cells from 3 healthy donors. T cells were collected before and after co-culture with tumor cells. NanoString analysis was carried out with cell lysates.

first: Robert

last: Hofmeister


title: Effects of the RNA Exosome on damage induced small RNAs in the 28S ribosomal locus

city: Solna

first: Franziska

last: Bonath

state: Stockholm

address: Tomtebodavägen 23A

department: Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories

country: Sweden

institute: Stockholm University

type: Non-coding RNA profiling by high throughput sequencing

summary: The repair of DNA double strand breaks (DSBs) has recently been shown to depend not only on protein function but also on RNA. In particular, the processing of a long damage-induced RNA into small damage induced RNAs (diRNAs) has been a focus of interest. Given that the RNA exosome has been shown in Drosophila and human cells to participate in DSB repair, we investigated whether the catalytic components EXOSC10 and DIS3 have a function in diRNA biogenesis in human cells.

overall_design: EXOSC10 or DIS3 was depleted in Hela cells and the cells subsequently transfected with a plasmid coding for the homing endonuclease I-PpoI that induces a double strand break in the 28S rDNA. After transfection the small RNA fraction was sequenced using standard Illumina sequencing and analyzed for reads mapping to the 28S rDNA.

first: Judit

last: Domingo-Prim

first: Marc

last: Friedländer

first: Neus

last: Visa


title: Avidity Selection of Natural Killer Response to MCMV

first: Endi

middle: K

last: Santosa

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity, such as the ability to recognize specific antigen, among others. In MCMV infection, the engagement of a subset of NK cells expressing an activating receptor Ly49H with MCMV-derived glycoprotein m157 results in a clonal-like expansion and the generation of a small pool of long-lived memory cells with higher Ly49H expression than the naive Ly49H-expressing NK cell pool. In this study, we interrogate the transcriptional differences between NK cells that express high verus low levels of Ly49H early after infection.

overall_design: RNASeq was performed on Ly49Hhi and Ly49Hlow NK cells harvested after 1.5 days post in vivo infection; 4 replicates per group and 50,000 cells per replicate.

first: Joseph

middle: C

last: Sun


title: MiSSEel - MicroRNA Sequencing in Stressed Eels

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

summary: This project aims to study the role played by small non-coding RNAs in the response of aquatic organisms to the presence of micropollutants in the environment. MiRNA were purified from Eels (Anguilla anguilla) sampled from two sites along the Gironde aquatic system with contrasted pollution profiles.

overall_design: 6 yellow eels were sampled in a pristine site (Arcachon Bay) and compared to 6 individuals from a polluted site (Gironde Estuary)

first: Fabien

last: Pierron

first: Tao

last: Ye

first: Patrice

last: Gonzalez

last: Couture

first: Magalie

last: Baudrimont


title: Peripheral whole blood mRNAs and lncRNAs expression analysis in eosinophilic asthmatics

city: Beijing

first: Yu-Jin

last: Zhu

address: FuXing Road, Haidian District

country: China

institute: Chinese PLA General Hospital

summary: Long non-coding RNA (lncRNA) plays roles in many diseases including asthma. Several lncRNAs function in the early differentiation of T-helper cells. lncRNA controls gene transcription, protein expression and epigenetic regulation; As one of the four asthma phenotypes, eosinophilic asthma(EA) occupies the largest proportion in asthma patients; However, lncRNA associated with eosinophilic asthma have not to be identified so far.   We designed the study to identify the circulating lncRNA signature in EA samples. We tested whether any significant changes in lncRNA expression was observed in EA and healthy people (Control) sample’ blood samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed through lncRNA-mRNA co-expression network. lncRNA expression was measured by means of microarray, quantitative real-time PCR.   A total of 41 dysregulated lncRNAs and 271 dysregulated mRNAs (difference ≥2-fold) were found in EA compared to Control samples. GO terms and KEGG pathway annotation data revealed that several lncRNA were significantly associated with EA. By qRT-PCR, lncRNA is confirmed significantly expression between EA and control samples.   The results presented here show several lncRNA may take part in the immune process of EA. Whether these lncRNA can be used as biomarkers need to be further study in future trials

overall_design:
The eosinophilic asthmatics (EA n=9) are included according the accepted standard (induced sputum eosinophil counts >3% and neutrophil<63%)1. Exclusion criteria included recent (past month) respiratory tract infection, recent asthma exacerbation, recent unstable asthma or change in maintenance therapy and current smoking (or past smoking within 6 months of cessation).All of the patients were selected from People's Liberation Army General Hospital. EA samples were subdivided into high expression IgE group (EAH n=6) and low expression IgE group (EAL n=3). Healthy people were selected as Control samples (n=3). The clinical data are provided for individual samples in Table 1. This study was approved by the Ethics Committee of the People's Liberation Army General Hospital. Informed consent was obtained from each donor.
The results presented here show several lncRNA may take part in the immune process of EA. Whether these lncRNA can be used as biomarkers need to be further study in future trials.

first: Yu-jin

first: Hong

last: Hu


title: Differential expression of Hdc-/- VS WT  hematopoietic stem and progenitor cells (HSPC) from bone marrow.

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary:
The gene expression of bone marrow Hdc-/-  and WT  (LSK, Lin-c-kit+Sca-1+) hematopoetic stem and progenitor cells were isolated from Hdc-/- or WT mice.
Cells were sorted by  the cell surface markers of LSK
total RNA was isolated from sorted 2,000 HSPCs using the ARCTURUS PicoPure RNA isolation kit (Life Technologies). cDNA was amplified and libraries were constructed by using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories) and the Nextera XT DNA Library Preparation kit (Illumina) according to the respective manufacturer’s instructions. Sequencing was performed on the Illumina HiSeq2500 platform.

overall_design:
a. Hdc-/- bone marrow HSPC (n=4)
b. WT bone marrow HSPC (n=4)

first: Xiaowei

last: Chen

first: Alexander

middle: L

first: Richard

last: Friedman

first: Siddhartha

last: Mukherjee


title: Bone marrow niche

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine


title: Genome-wide analysis of gene expression in osteoclast precursor cells cultured for 3 days with either M-CSF or M-CSF + RANKL

status: Public on Apr 05 2019

city: Farmington

last: Lorenzo

state: CT

address: 263 Farmington Avenue

department: Medicine

institute: UConn Health

summary: Genome wide expression analysis of murine bone marrow osteoclast precursor cells that were cultured for 3 days either with macrophage colony stimulating factor (M-CSF) alone to remain as monocytes or M-CSF + receptor activator of NF-kB (RANKL) to differentiate down the osteoclast lineage. Results provide important information on genes that are regulated  by RANKL in order to drive commitment to the osteoclast lineage.

overall_design:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Raw data are unavailable for this series.  The UConn Health core facility where these arrays were processed no longer exists.


title: Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura

overall_design: ChIP-seq, ChIP-nexus or 5' RNA-seq was performed using transfected Drosophila Kc167 cells or Drosphila pseudoobscura ML83-63 cell line. Triptolide (TRI) treatment was used to assay the stability of paused Pol II.

first: Wanqing

last: Shao

first: Sergio

last: Garcia-Moreno Alcantara


title: Genome-wide mining for microRNAs and their targets in a pre-model tree for Betula luminifera using high-throughput sequencing and degradome analyses

status: Public on Apr 08 2019

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

summary: microRNAs (miRNAs) play vital roles in plants regulating a panoply of biological processes, such as development, hormone signaling, and the stress response, by inhibiting target genes at the post-transcriptional level. However, the roles of miRNAs in Betula luminifera remain elusive. To mine for B. luminifera miRNAs and targets, we used a deep sequencing approach to analyze the sRNAs and degradome sequencing of mixed samples, including roots, stems, and leaves. A total of 114 known miRNAs or miRNA*s from 44 families, and 24 novel miRNAs and 17 miRNA*s plus 15 plausible miRNA candidates were identified, of which 36 known miRNAs, 29 miRNA*s, and all novel miRNAs had precursor sequences. Additionally, 49 targets for 19 known miRNA families and seven miRNA*s, and seven targets for novel miRNAs were identified using a high-throughput degradome-sequencing approach. The conserved miRNA targets were mainly transcription factors, whereas the miRNA* targets were mainly protein-coding genes, with preferential propensity to functional enzymes. A Gene Ontology analysis showed that the predicted targets were classified into 62 biological processes, 20 cellular components, and 28 molecular functions, respectively. We found two different targets for 396a* and miR396c*, and the target changed when the miR156d precursor cleavage site was shifted toward the 5′-end by two nucleotides, indicating the diverse regulatory roles of MIRNA genes. Furthermore, three targets identified by degradome sequencing were validated further through 5′ rapid amplification of cDNA ends. The expression patterns of the randomly selected miRNAs varied among different tissues. miR164 expression was induced under nitrogen starvation, with tissue-specific expression patterns, and was negatively correlated with the NAC1 target gene in roots and leaves, but not in stems. This study is a transcriptome-based analysis of miRNAs and the degradome in a B. luminifera pre-model tree and provides useful information to explore the functions of miRNAs and their target genes in B. luminifera.

overall_design: analyze the sRNAs  of mixed samples, including roots, stems, and leaves.

first: Zaikang

last: Tong

first: Junhong

last: Zhang


title: Changes in chromatin accessibility and gene expression induced by overexpression of ONECUT transcription factors

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Stem cell competition orchestrates skin homeostasis and ageing

city: Tokyo

last: Liu

address: 1-5-45 Yushima, Bunkyo-ku

department: Stem Cell Biology

country: Japan

institute: Tokyo Medical and Dental Universtiy

summary:
Stem cells underlie tissue homeostasis, but their dynamics during ageing—and the relevance of these dynamics to organ
ageing—remain unknown. Here we report that the expression of the hemidesmosome component collagen XVII (COL17A1)
by epidermal stem cells fluctuates physiologically through genomic/oxidative stress-induced proteolysis, and that the
resulting differential expression of COL17A1 in individual stem cells generates a driving force for cell competition. In
vivo clonal analysis in mice and in vitro 3D modelling show that clones that express high levels of COL17A1, which
divide symmetrically, outcompete and eliminate adjacent stressed clones that express low levels of COL17A1, which
divide asymmetrically. Stem cells with higher potential or quality are thus selected for homeostasis, but their eventual
loss of COL17A1 limits their competition, thereby causing ageing. The resultant hemidesmosome fragility and stem cell
delamination deplete adjacent melanocytes and fibroblasts to promote skin ageing. Conversely, the forced maintenance
of COL17A1 rescues skin organ ageing, thereby indicating potential angles for anti-ageing therapeutic intervention.

overall_design: RNA from total epidermal cells of young and aged mice was extracted before being hybridized Agillent microarray. We obtained a gene of list by comparing young and aged cells.

first: Hiroyuki

last: Matsumura

first: Emi

last: Nishimura


title: Engineering Patient-Specific Tissue Implants

status: Public on Apr 06 2019

city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

summary: We developed an approach to engineer completely personalized tissue implants that are based merely on the patient’s own materials and cells. Here, an omentum is extracted from the patient in a safe, easy and quick procedure. The cells and the ECM materials of the tissue are separated and while the cells are reprogrammed to become pluripotent, the ECM is processed to become a personalized thermoresponsive hydrogel.  The undifferentiated cells are then encapsulated within the hydrogel and efficiently differentiated to cardiomyocytes, neurons, and endothelial cells.

overall_design: Examination of differentiation of iPSCs iside omentum hydrogel and matrigel

first: Dvir

last: Tal

first: Edri

last: Reuven


title: DNA methylation analysis of human keratoconus corneas using RRBS sequencing

city: Poznań

first: Michal

last: Kabza

address: ul. Fredry 10

country: Poland

institute: Poznan University of Medical Sciences

type: Methylation profiling by high throughput sequencing

summary: Keratoconus (KTCN) is a complex degenerative eye disorder resulting in loss of visual function. It is known, that its development is affected by both genetic and environmental or behavioral components. In order to verify if DNA methylation may also play a role in KTCN development, reduced representation bisulfite sequencing (RRBS) of human corneas obtained from five KTCN and five non–KTCN individuals  was performed.

overall_design: DNA methylation analysis of 5 KTCN and 5 non-KTCN corneas using RRBS

first: Justyna

last: Karolak

first: Malgorzata

last: Rydzanicz

first: Piotr

last: Gasperowicz

first: Rafal

last: Ploski

first: Jacek

middle: P

last: Szaflik

first: Marzena

last: Gajecka


title: Influence of CD200R-deficiency on gene expression in primary murine neutrophils

status: Public on Apr 04 2019

city: Manchester

first: Stefano

last: Rossi

address: Grafton Street

country: United Kingdom

institute: Univeristy of Manchester

summary: RNA-seq analysis at steady state of primary bone marrow neutrophils isolated from WT and CD200R-/- C57BL6 mice. Of the 323 genes that were significantly differentially expressed, one of the major pathways that differed included genes related to reactive oxygen species (ROS) clearance and scavenging.

overall_design: 3 WT and 3 CD200R-/- samples

first: Joshua

last: Casulli

first: Mark

middle: E

last: Fife

first: Stephanie

last: Houston

last: Dow

first: Diane

last: Williamson

first: Graeme

last: Clark

first: Tracy

last: Hussell

first: Riccardo

middle: V

last: D'Elia

last: Travis


title: Gene expression response in mouse model of inflammatory bowel disease to ionizing radiation

first: Sanjay

last: Mukherjee

address: 630 W 168th street

institute: Columbia University

summary:
Background: Ionizing Radiation (IR) is a known pro-inflammatory agent and in the process of development of biomarkers for radiation biodosimetry a chronic inflammatory disease condition could act as a confounding factor. Hence, it is important to develop radiation biodosimetry that can distinguish between IR-induced inflammatory responses and pre-existing disease. In this study, we compared the gene expression response of a genetically modified mouse model of inflammatory bowel disease (Il10-/-) with that of a normal wild-type mouse to potentially develop transcriptomic based biodosimetry markers for individual susceptibility to radiation.
Results: Wild-type (WT) and Il10-/- mice were exposed to whole body irradiation of 7Gy (LD50/30 for IL10-/-) X-rays. Gene expression responses were studied using high throughput whole genome microarrays in peripheral blood after 24h post-irradiation. Analysis resulted in identification of 1962 and 1844 genes differentially expressed (p < 0.001, FDR < 10%) after radiation exposure in Il10-/- and WT mice respectively. A set of 155 genes were also identified as differentially expressing between WT and Il10-/-  mice at the baseline pre-irradiation level. Gene ontology analysis revealed that the baseline differentially expressing genes (155) were mainly involved in Inflammatory response, Glutathione metabolism and fibrosis. Analysis of radiation responsive genes revealed commonality of immune function genes between WT and Il10-/- mice. Gene ontology analysis revealed that innate immune response and p53 signaling processes were strongly associated with up-regulated genes whereas, B-cell development process was found to be significant amongst downregulated genes in response to radiation in the two genotypes. However, specific immune response pathways like MHC class I antigen presentation and response to viral/bacterial infection were particularly associated with radiation responsive genes of Il10-/-  mice but not with WT mice. Further analysis of activation status of specific canonical pathways and upstream regulators using IPA-prediction tool revealed significant difference in the activation status of T-cell and hormone mediated signaling as well as regulators of inflammation between WT and Il10-/-  after irradiation.

overall_design: Mouse model of inflammatory bowel disease (Il10-/-) and the respective wild type strain on C57BL/6 background were either exposed to a LD50/30 dose of x rays, or were sham-irradiated as controls, and then sacrificed 24h later. 5 replicates, representing individual mice, were used for each condition.

first: S

last: Amundson


title: RNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

city: San Francisco

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

summary:
We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+).
For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples from 17 of the 30 patients.

overall_design: Bone Marrow aspirates where taken from EBC patients. Patients were considered positive (DTC≥1 cell/ml) via immunomagnetic enrichment followed by flow cytometry (IE/FC). When a sample was determined positive, the remainder of the bone marrow was processed and sorted via IE/FACS. 36 aspirates where sorted for RNA analysis. Quality control (QC) measures were implemented as follow: Sorted cells ≥10, expression of house keeping genes RPS18 and ACTB (Ct value ≤26 and ≤36 respectively), and detection rate ≥ 20% of 64 gene panel. 31 samples from 30 patients passed all QC.

first: Louai

last: Hauranieh

first: Eduardo

last: Sosa

first: Ritu

last: Roy

first: Lauren

last: Eisenbud

first: Janet

middle: H

last: Scott

first: Adam

last: Olshen

first: Dan

last: Pinkel


title: RNA sequencing of control and CTCF-null embryonic day 14 telencephalon

city: London

first: Nathalie

last: Berube

state: Ontario

address: 800 Commissioners Road East

country: Canada

institute: Children's Health Research Institute

summary: The goals of this study are to evaluate differences in transcriptome profiles of E14 mouse telencephalon when the CTCF chromatin organizer is absent.

overall_design: RNA sequencing in 2 pairs of control and Ctcf-null embryonic day 14 telencephalon

middle: G

last: Watson

first: Adrienne

last: Elbert

first: Michael

last: Levy


title: Deoxycholate induces biofilm formation by Clostridium difficile while repressing sporuation and toxin production

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: The objective of our study was to characterize the response of C. difficle to deoxycholate. When C. difficile was grown in the presence of deoxycholate, we observed an increase in biofilm formation. We then analyzed the transcriptome of the DCA-induced biofilm and cells grown in the absence of deoxycholate. The transcriptome analysis was then confirmed using phenotypic assays and gene-deletion strains.

overall_design: Total RNA was extracted from 3 independent biological replicates of 630 C. difficile strains at 2 conditions with and without Deoxycholate 240 µM (6 samples).

first: Yannick

last: Tremblay

first: Marc

last: Monot


title: Parallel DNA and RNA profiling of EpCAM-positive cells in bone marrow and primary tumor tissue with positive disseminated tumor cell count via immunomagnetic Enrichment/Flow Cytometry of metastatic breast cancer patients confirm their malignant nature

first: Mark

type:
Expression profiling by RT-PCR
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: DNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

summary:
Parallel DNA and RNA profiling of EpCAM-positive cells in bone marrow and primary tumor tissue with positive disseminated tumor cell (DTC) count via immunomagnetic Enrichment/Flow Cytometry (IE/FC)  of metastatic breast cancer (MBC) patients confirm their malignant nature
We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+).
For DNA profiling, sorted cells were subjected to BAC array comparative genomic hybridization analysis following whole genome amplification. For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples.

overall_design: Bone marrow aspirates were collected from early breast cancer patients. Disseminated tumor cells (DTCs) were enumerated via immunomagnetic enrichment followed by flow cytometry (IE/FC). For patients considered positive for DTCs, the remaining volume of bone marrow sample was subjected to IE/FACS to isolate DTCs for gene expression (QPCR) and copy number analysis. Differential gene expression analysis between EPCAM-positive cells and matched leukocytes confirmed the up-regulation of EPCAM and other genes including MUC1 (adjusted p <0.05). In addition, EPCAM-positive cells showed a significant down-regulation of the leukocyte-specific marker PTPRC (encodes CD45). Matched primary tumor samples from a subset of patients were subjected to copy number analysis. Genomic profiling of DTCs revealed fewer aberrations compared to matched primary tumors.

first: Hope

middle: S

last: Rugo

first: John

middle: W

last: Park


title: Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

status: Public on Apr 03 2019

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

summary: Difference in RNA content of different cell types introduces bias to gene expression deconvolution methods. If ERCC spike-ins are introduced into samples, predicted proportions of deconvolution methods can be corrected

overall_design: Two cell types of distinctly different sizes and RNA per cell content: HEK cells and Jurkat cells were mixed in different proportions ensuring that each mixture contained total of one million cells. We sequenced RNA of the samples (including ERCC spike-in controls to 382 be able to control for the absolute RNA-concentration).

first: Zaitsev

last: Konstantin

first: Monika

last: Bambouskova

first: Amanda

last: Swain

middle: N


title: microRNA expression profiles in Idiopathic Pulmonary Fibrosis (IPF)

status: Public on Apr 02 2019

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by enhanced fibroblast proliferation, collagen synthesis, extracellular matrix deposition. We obtained 28 IPF patient lung tissue samples from the Lung Tissue Research Consortium (LTRC). Here we determined the miRNA expression profiles in these IPF lung samples.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: IPF patient lung tissue RNAs were hybridized with a common reference containing total RNAs pooled from 20 normal human tissues was purchased from Ambion (Grand Island, NY). A dye swap was performed to eliminate dye bias for each sample (as indicated in the raw data file names).

first: Chaoqun

last: Huang

first: Lin

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of  mRNA lifetime of Wild Type and Mettl3-/- mice

city: Beijing, China

first: Huamin

last: Wang

address: Three N0. 5 dongdan street, Dongcheng District, Beijing

department: Department of Immunology

institute: Peking Union Medical College, Chinese Academy of Medical Sciences,

summary: Considering m6A modification in mRNA was reported to be intensively correlated with RNA decay, for example, T cells and neurone cells. We wondered whether deleting Mettl3, the main catalzing enzyme, affect the RNA stability of mouse dendritic cells.

overall_design: Two sets representing WT and KO dendritic cells were analyzed, each set contains three samples indicating three different treatment with Actinomycotoxin D for 0, 3, or 6h. No replicate was included.

first: Xuetao

last: Cao

first: Xiang

last: Hu


title: Next Generation Sequencing Facilitates Quantitative Analysis of  mRNA translation efficiency of Wild Type and Mettl3-/- mice

summary: Considering m6A modification in mRNA was reported to be intensively corelated with RNA metabolism like RNA decay and RNA translation, we wonderd whether deleting Mettl3, the main catalzing enzyme, affect the RNA translation efficiency of mouse dendritic cells.

overall_design: Two sets representing WT and KO dendritic cells were analyzed, each set contains sucrose gradient centrifuged sample and input indicating. No replicate was incluced.


title: Next Generation Sequencing Facilitates Quantitative Analysis of  mRNA expression of Wild Type and Mettl3-/- mice

summary: Considering m6A modification in mRNA was reported to be important in many biology processes, like cell fate decision and embryonic development and was closely connected to human diseases such as metabolic diseases, neuron disorders and cancer. We wondered how Mettl3 affect dendritic cell development.

overall_design: Replicate representing WT and KO dendritic cells stimulated with LPS  were analyzed


title: Identification of LRH1-driven transcription factor circuitry for hepatocyte identity using cistromic analysis of super-enhancers

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: The gene expression circuitry that controls maintenance of normal liver physiology is poorly understood. Super-enhancers are known to contribute to mammalian cell identity. The injured liver loses normal functions, with concomitant decreased expression of key identity genes. Here, we identified core transcriptional regulators that are highly active in hepatocytes, using genome-wide analysis and hierarchical ordering of super-enhancer distribution. Using network analysis of super-enhancer-associated gene interactions and human GEO databases for liver diseases of various etiologies, we identified a super-enhancer-associated network, with core TFs of LRH1, HNF4a, PPARa and RXRa. In a mouse model, expression of core TFs was robustly inhibited by single or multiple challenge(s) with liver toxicant. Levels of LRH1 and PPARa were greatly diminished, whereas other TFs were moderately altered. In hepatocytes, overexpression of each core TF promoted induction of other core TFs, with recovery of hepatocyte identity. Particularly, LRH1 overexpression caused recovery of super-enhancer-associated signalling circuitry in liver-toxicant challenged mice, protecting against liver injury. Hepatic stellate cells showed a unique super-enhancer signature. Using cistromic analysis of gene expression, we identified a novel hepatocyte-specific transcriptional network, and found that LRH1 drives the positive feed-forward expression circuitry and expression of hepatocyte identity genes, improving our understanding of liver pathophysiology and identifying novel disease targets.

overall_design: Examination of RNA expression in mouse livers treated with vehicle, APAP, or LRH1.

first: Min-Sung

last: Joo

first: Ja-Hyun

last: Koo

first: Sang-Geon


title: Methylated RNA Immunoprecipitation Sequencing of dendritic cells in different development stages

summary: Using m6A immunoprecipitation together with high-throughput sequencing (meRIP-seq), we potrayed the dynamic distribution pattern of m6A modification in the mRNA transcripts of immature DC, mature DC and regulatory DC, aiming to explored the funcion and mechanisms of m6A during DC maturation, activation and differentiation , or maybe other important processes like migration and antigen presentation. This may shed light on the function of m6A in innate and adaptive immune system in an epigenic transcriptome level.

overall_design: Total six samples were  prepared and analyzed  for imDC, maDC and DCreg, each have a replicate.


title: RNA-seq of MDA-MB-231 siCt and siAXL

status: Public on Apr 01 2019

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: Triple-Negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is associated with poor prognosis due to its propensity to form metastases. Unfortunately, the current treatment options are limited to chemotherapy such that identification of actionable targets are needed. The receptor tyrosine kinase AXL plays a role in the tumor cell dissemination and its expression in TNBC correlates with poor patients? survival. Here, we explored whether exploiting an AXL knockdown gene signature in TNBC cells may offer an opportunity for drug repurposing. To this end, we queried the PharmacoGx pharmacogenomics platform with an AXL gene signature which revealed Phenothiazines, a class of Dopamine Receptors antagonists (Thioridazine, Fluphenazine and Trifluoperazine) typically used as anti-psychotics. We next tested if drugs may be active to limit growth and metastatic progression of TNBC cells, similarly to AXL depletion.  We found that the Phenothiazines were able to reduce cel  l invasion, proliferation and viability, and also increased apoptosis of TNBC cells in vitro. Mechanistically, these drugs did not affect AXL activity but instead reduced PI3K/AKT/mTOR and ERK signaling. When administered to mice bearing TNBC xenografts, these drugs showed were able to reduce tumor growth and metastatic burden. Collectively, these results suggest that these antipsychotics are novel anti-tumor and anti-metastatic agents that could potentially be repurposed, in combination with standard chemotherapy, for use in TNBC.

overall_design:
RNA-seq of the Triple Negative Breast Cancer cell line MDA-MB-231 treated with siCt or siAXL
Differential gene expression profile between MDA-MB-231 siCt and siAXL by RNA sequencing (Illumina HiSEq 2000)

first: Jean-François

last: Côté


title: Identification of transcriptional targets of a network of Drosophila core promoter factors in neural stem cells

city: Seattle

first: Alexandre

last: Neves

state: WA

address: 1100 Fairview Av N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

summary: The transcriptional mechanisms that allow neural stem cells (NSC) to balance self-renewal with differentiation are not well understood. We identify here a unique subset of TATA -binding protein associated factors (TAFs) as NSC identity genes in Drosophila. We found that depletion of any one of nine TAFs or the TBP-related factor 2 (TRF2), resulted in fewer NSCs exhibiting delayed cell cycle progression without impacting NSC survival. In contrast, depletion of TBP led to a delay in NSC cell cycle progression without loss of self-renewal.  An integrated RNA-seq and DamID analysis revealed that TAFs function with both TBP and TRF2, and that TAF-TBP and TAF-TRF2 shared targets genes encode different subsets of transcription factors and RNA-binding proteins with established or emerging roles in NSC identity and brain development. Taken together, our results demonstrate that core promoter factors are selectively required for NSC identity in vivo by promoting cell cycle progression, NSC cell polarity and by preventing premature differentiation. Because pathogenic variants in TAF1, TAF2, TAF6, TAF8 and TAF13 have all been linked to human neurological disorders, this work may stimulate and inform future animal models of TAF-linked neurological disorders.

overall_design: Comparison of transcriptomes of Drosophila melanogaster control, TBP, TRF2, TAF5 and TAF9 RNAi larval brain type I neural stem cell lineages

first: Robert

last: Eisenman


title: Identification of genomic binding sites of a network of core promoter factors in developing Drosophila brains

overall_design: Comparing and contrasting in vivo genomic binding sites of Drosophila TBP, TRF2S and TAF5 using targeted DamID-seq (TaDa).


title: Single cell RNA-seq of CRX+ cells obtained at day 90 of retinal organoid differentiation

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

summary: Death of photoreceptors and/or Retinal Pigment Epithelium (RPE) cells is a common cause of age related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a well sought therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate into all key retinal cell types either in isolation or as part of three dimensional retinal organoids. Photoreceptor precursors have been isolated from differentiating human pluripotent stem cells either through application of cell surface markers or fluorescent reporter approaches and shown to share a transcriptional profile akin to foetal photoreceptors. In this study we investigated the transcriptional profile of CRX+ photoreceptor precursors derived from human embryonic stem cells (hESC) using single cell RNA sequencing and their engraftment capacity in an animal model of retinitis pigmentosa (C3H/rd1). Single cell RNA seq analysis revealed the presence of dominant cell cluster which displayed the hallmarks of early cone photoreceptor expression. When transplanted subretinally into the C3H/rd1 mice, the Crx positive cells settled next to the inner nuclear layer of host retina, matured into cone photoreceptors and made connections with the inner neurones of the host retina. Cellular transfer between the host retina and donor photoreceptors was investigated and shown to be minimal. Together our data provide valuable molecular insights into the transcriptional profile of human pluripotent stem cells derived CRX+ photoreceptor precursors and indicate their usefulness as a source of transplantable cone photoreceptors.

overall_design: CRX-GFP human ESC line was differentiated to retinal organoids. At day 90 CRX+ and CRX- cells were purified by flow activated cell sorting and subjected to single cell RNA-seq. RNA-seq of bulk CRX+ and CRX- from the same experiment was carried out in parallel.

first: Joseph

last: Collin


title: Single cell gene expression profiling in normal HSCs and CML stem cells

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: CML stem cells (CMLSCs) and normal hematopoietic stem cells (HSCs) display the same set of surface markers (CD34+CD38-CD90+CD45RA-), making it infeasible to separate these two populations within the same sample. To overcome this challenge, and to minimize variations in gene expression due to individual variation, here we perform single-cell RNA-seq to compare expression profiles of CMLSCs and HSCs isolated from the same patient. We captured ~600 HSCs (CD34+CD38-CD90+CD45RA-) (~200 from each of three CML patient samples), separated them into CMLSCs (BCR-ABL+) or normal HSCs (BCR-ABL-) based on the presence of the BCR-ABL transcript, and performed paired-end deep sequencing. Typically, we obtained ~2.5 million mapped reads (>70% average mapping efficiency) and detected ~5,000 genes (transcript per million [TPM]>1) per cell. Despite the heterogeneity of the gene expression pattern, we were able to identify genes that were significantly more highly expressed in CMLSCs than in normal HSCs. Notably, among these genes are two cell surface markers, CD33 and CD47, that could potentially be used to distinguish CMLSCs from normal HSCs. We also found genes, such as PIM2, that could be targeted for CML therapy using available small molecule inhibitors.

overall_design: Hematopoietic stem cell population from three chronic phase CML patients with no detectable BCR-ABL mutation.

first: Leyuan

last: Ma


title: A small molecule promotes cartilage extracellular matrix generation and inhibits osteoarthritis development

city: Beijing

first: shi

last: yuanyuan

state: Bejing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

summary: These observations identify SOD3 as a relevant drug target, and BNTA as a potential therapeutic agent in osteoarthritis.

overall_design:
Examination a disease-modifying OA drugs and its molecular target.
Case: Cartilage tissues were collected from medial and lateral femoral condyles of anterior cruciate ligament transection-operated rat knee joints treated with BNTA (1.5 mg kg-1) twice a week for 4 w.
Control: Cartilage tissues were collected from medial and lateral femoral condyles of anterior cruciate ligament transection-operated rat knee joints treated with normal saline (vehicle) twice a week for 4 w.

first: Yingfang

last: Ao

first: Yuanyuan

last: Shi


title: Characterization of sperm lncRNA and its differently expression in the sperm of asthenozoospermic patients

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

summary: Growing evidences have shown that many transcripts have been discovered in sperm and small noncoding RNAs, such as miRNA and tsRNA, of sperm paly an important role in the transgenerational transmission of paternal lifetime experiences. However, the expression profile of long noncoding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Furthermore, Abnormal expression of lncRNA whether or not related with the asthenozoospermic is completely unknown. In the present study, highly purified RNA was served to investigate lncRNA expression profiles in human mature sperm by stranded-specific RNA-seq. We identified 38,307 known and 27,472 novel lncRNA genes, and the existence of intact LncRNA transcripts was confirmed by RT-PCR and fluorescence in situ hybridization (FISH) on two representative LncRNAs. Many lncRNAs exclusive were expressed in testis and sperm. 880 lncRNA sequences were conserved between human and mouse with > 80% overlap. Compared with normal population, the lncRNA profiles in asthenozoospermic patients’ sperm showed significant difference with 2437 up-regulation and 306 down-regulation of lncRNA. This study will provide a preliminary database valuable for identifying lncRNAs critical on sperm function regulation or important for screening the lncRNA markers of asthenozoospermia.

overall_design: LncRNA profiles of sperm and testis were generated by stranded-specific RNA-seq, using Illumina HiSeqTM 4000 with PE100.

first: Jianbo

last: Fu


title: Force expression LNK suppresses interferon Gamma signaling

status: Public on Mar 31 2019

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: LNK (SH2B3) is a key negative regulator of JAK-STAT signaling which has been extensively studied in malignant hematopoietic diseases. We found that LNK is significantly elevated in cutaneous melanoma; this elevation is correlated with hyperactive signaling of the RAS-RAF-MEK pathway. Elevated LNK enhances cell growth and survival in adverse conditions. Forced expression of LNK inhibits signaling by interferon-STAT1 and suppresses interferon (IFN) induced cell cycle arrest and cell apoptosis. In contrast, silencing LNK expression by either shRNA or CRISPR-Cas9 potentiates the killing effect of IFN. The IFN-LNK signaling is tightly regulated by a negative feedback mechanism; melanoma cells exposed to IFN upregulate expression of LNK to prevent overactivation of this signaling pathway. Our study reveals an unappreciated function of LNK in melanoma and highlights the critical role of the IFN-STAT1-LNK signaling axis in this potentially devastating disease. LNK may be further explored as a potential therapeutic target for melanoma immunotherapy.

overall_design: mRNA profiles of Control and LNK overexpressing cells were generated by deep sequencing using BGISEQ-500.

first: Ling-Wen

last: Ding

first: Qiao-Yang

last: Sun

first: Jarem

middle: J

last: Edwards

first: Lucia

middle: T

last: Fernández

first: Xue-Bin

last: Ran

first: Si-Qin

last: Zhou

first: Richard

last: Scolyer

first: James

last: Wilmott

first: John

middle: F

last: Thompson

first: Ngan

last: Doan

first: Jonathan

last: Said

first: Nachiyappan

last: Venkatachalam

first: Jin-Fen

last: Xiao

first: Xin-Yi

last: Loh

first: Maren

last: Pein

first: Liang

last: Xu

first: David

last: Mullins

first: Henry

last: Yang

first: De-Chen

last: Lin

first: H

last: Koeffler


title: Expression data from fibroblasts expressing p65 variants and depletion of Zbtb7a

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

summary: We used microarrays to assess gene expression in p65-knockout 3T3 fibroblasts, after stable reconstitution with normal and engineered forms of NFkB p65, and knock-down of Zbtb7a using stable shRNA interference. Cells were treated with 5ng/ml mouse TNF-alpha to stimulate NFkB pathway activation.

overall_design: 3T3 fibroblasts were transduced with retroviral vectors expressing p65 variants, and sorted for expression levels comparable to those of p65 in normal cells. shRNAs targeting Zbtb7a were expressed from a retroviral vector carrying histidinol resistance. Subconfluent cultures of cells were treated for 1hr with TNF-alpha before RNA extraction.

first: Simona

last: Saccani


title: Differential expression of Hdc-GFPhi HSPC VS Hdc-GFPlo HSPC hematopoetic stem and progenitor cells from mouse bone marrow

city: New York

first: Timothy

last: Wang

address: 1130 St. Nicholas Ave

institute: Columbia University Medical Center

overall_design:
Bone marrow Hdc-GFPhi and  Hdc-GFPlo HSPC (LSK, Lin-c-kit+Sca-1+) hematopoetic stem and progenitor cells were isolated from  femur, tibia, illium, and vertebra bones of histidine decarboxylase (Hdc) green fluorescent protein (Hdc-GFP) mice Hdc-GFPhi HSPC and Hdc-GFPlo HSPC cells were sorted by combinations of GFP and the cell surface markers of LSK, total RNA was isolated from sorted 2,000 HSPCs using ARCTURUS PicoPure RNA isolation kit (Life Technologies). cDNA was amplified and libraries were constructed by using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories) and the Nextera XT DNA Library Preparation kit (Illumina) according to the respective manufacturer’s instructions. Sequencing was performed on the Illumina HiSeq 2500 platform.
a. Hdc-GFPhi bone marrow HSPC cells (n=4)
b. Hdc-GFPlo bone marrow HSPC cells (n=4)

first: Xiaowei

last: Chen

first: Alexander

middle: A

last: Friedman

first: Siddhartha

last: Mukherjee


title: MicroRNA profiling in Asthma

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

institute: University of Leicester

summary: Small RNA sequencing in peripheral blood mononuclear cells from patients with asthma and healthy individual with no respiratory disease

first: Catherine

last: Vial


title: Transcriptional response of Acinetobacter baumannii AB1 to bacteriophage Abp1 infection

city: Chongqing

first: zichen

last: yang

address: Gaotanyan

institute: Army Medical University (Third Military Medical University)

summary: Explore the genome-scale phage–host interactions across different developmental infection stages

sample_organism:
Acinetobacter phage AB1
Acinetobacter phage Abp1

overall_design: Samples were taken from the AB1 Lysates infected with phage Abp1 at six internal time (5,10,20 min). Three independent experiments were performed

first: Zichen


title: Gene expression profiling of LNCaP cells following shRNA-mediated knockdown of TMEFF2 and growth in presence and absence of dihydrotestosterone

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: TMEFF2 is an androgen regulated transmembrane protein mainly restricted to brain and prostate, that functions as a tumor suppressor in prostate cancer (PCa). Studies using publically available prostate cancer (PCa) datasets, reveal changes in the expression of TMEFF2 with disease stage, supporting an important role of TMEFF2 in this disease. However, the role of TMEFF2 in the biology and pathogenesis of PCa is still unknown.  Using a transgenic TMEFF2 mouse, we have demonstrated that TMEFF2 overexpression modulates prostate branching morphogenesis, and androgen regulated process, during prostate regeneration. We hypothesized that TMEFF2 may have a regulatory function within androgen signaling that could explain its role in PCa. To better understand its function in androgen signaling and PCa, we compared the transcriptome of LNCaP prostate cancer cells transduced with control shRNA and shRNA targeting TMEFF2 in the presence and absence of dihydrotestosterone (DHT). The results indicated that globally, there is a significant interaction between the effects of DHT and shTMEFF2. Of the 519 genes with significant gene expression changes after DHT treatment of Scramble control cells, 208 (40%) had significant differential expression when the shTMEFF2 +DHT group was compared to Scramble +DHT group, including numerous androgen activated and androgen repressed genes.

overall_design: Transcriptome profiles of LNCaP tissue under 4 conditions investigating effects of long term (17 days) shRNA targeting TMEFF2 or scrambled sequence in the presence or absence of dihydrotestosterone (DHT). Each sample was run in triplicate.

first: Maria

last: Ruiz-Echevarria

first: Joshua

middle: M

last: Corbin


title: Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

city: Cambridge

first: Paul

last: Blainey

state: Massachusetts

address: 415 Main St

institute: Broad Institute

summary: The human immune system consists of many specialized cell subsets that simultaneously carry out a diverse range of functions using overlapping pathways and signals. Subset-specific immune profiling can resolve immune activity in autoimmune disease, cancer immunity, and infectious disease that may not be discoverable or detectable in analyses of crude blood samples. Here, we present a low-input microfluidic system for sorting immune cells into subsets and profiling their cellular states by gene expression analysis using full-length RNA-seq. We validate the device’s technical performance by benchmarking its subset enrichment and genomic profiling performance against gold standard benchtop protocols and make the added value of subset-resolved profiling over crude sample analysis clear through in vitro experiments that show subset-specific stimulated responses. Our results show that even the canonical cytokine, IFN-α, can elicit opposing responses across different subsets. Finally, we show the scalability of our device by profiling four immune cell subsets in blood from systemic lupus erythematosus (SLE) patients and matched controls enrolled in a clinical study.

overall_design:
Subset-specific expression profiling of PBMCs from healthy and SLE individuals.

Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Nir

last: Hacohen

first: Miguel

last: Reyes


title: A network of core promoter factors in developing Drosophila brains

first: Alexandre

last: Neves

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

overall_design: Refer to individual Series


title: Genome-wide replication timing in the mutants deleted for telomere-binding proteins in S. pombe

city: Suita

first: Junko

last: Kanoh

state: Osaka

address: 3-1 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

summary: We report the regions of newly replicated DNA in the presnece of HU in mutants deleted for telomere-binding proteins. Cells were grown at permissive temperature (25°C) in EMM medium for more than 14 hours to induce the expression of TK (thymidine kinase) and then shifeted to 35.5°C for 4 hours to arrest cell cycle. Cells were released from the cell-cycle arrest at 25°C in the presence of 10 mM HU and 200µM BrdU. for 90 min. and then were  fixed with NaN3 on ice. Genomic DNA was purified from the cells by vortexing with phenol/chloroform and ethanol extraction, and then sonicated with BIORUPTOR UCD-250. The fragmented DNA was mixed with anti-BrdU antibodies, and BrdU-positive DNA was purified and analyzed.

overall_design: Analyses of early replicated chromosomal regions in wild-type, rap1-deleted, rif1-deleted, and taz1-deleted strains.

first: Yudai

last: Hasegawa


title: A Preclinical Model of Human Acute Myeloid Leukemia with an Autologous Immune System for Studying Mechanisms of Tumorigenesis and Immunotherapy

city: CAMBRIDGE

first: Mandeep

last: Kaur

address: 500 MAIN STREET

institute: MIT

summary: Next generation sequencing of bulk leukemic and leukemic stem cells in  de novo human AML driven by NPM1c. Data revelas co-operating pathways in NPM1c tumorigenesis.

overall_design:
Three AML humanized mice generated from 3 independent human hematopoietic stem cell transductions with NPM1c were used for this analysis.
Bone marrow cells from moribund mice were harvested and labeled with anti-CD123 and anti-CD33 antibodies followed by cell sorting with the ARIA sorter.
GFP expression, a surrogate for NPM1c expression, was also used as a parameter for sorting. 2 populations of cells were sorted from each bone marrow samples:
i) Bulk leukemic cells which were GFP+ and CD33+, and ii) Leukemic stem cells which were GFP+, CD33+ and CD123+

first: Guangan

last: Hu

first: Jianzhu


title: Engram-specific transcriptome profiling of contextual memory consolidation

status: Public on Mar 30 2019

city: Rotterdam

first: Steven

last: Kushner

state: Zuid Holland

address: Dr. Molewaterplein 40

department: Psychiatry

institute: Erasmus MC

summary: Sparse populations of neurons in the dentate gyrus (DG) of the hippocampus are causally implicated in the encoding of contextual fear memories. However, engram-specific molecular mechanisms underlying memory consolidation remain largely unknown. Here we perform unbiased RNA sequencing of DG engram neurons 24h after contextual fear conditioning to identify transcriptome changes specific to memory consolidation. DG engram neurons exhibit a highly distinct pattern of gene expression, in which CREB-dependent transcription features prominently (P=6.2x10-13), including Atf3 (P=2.4x10-41), Penk (P=1.3x10-15), and Kcnq3 (P=3.1x10-12). Moreover, we validate the functional relevance of the RNAseq findings by establishing the causal requirement of intact CREB function specifically within the DG engram during memory consolidation, and identify a novel group of CREB target genes involved in the encoding of long-term memory.

overall_design: Biological replicates: Fear conditioned: n=14, No shock controls: n=4, Home cage controls:n=3. The contents 10 dVenus+ and 10 dVenus- cells were aspirated from each animal (biological replicate)

first: Priyanka

last: Rao-Ruiz

first: Jonathan

last: Couey

first: Ivo

last: Marcelo

first: Christian

last: Bouwkamp

first: Denise

last: Slump

first: Mariana

middle: R

last: Matos

first: Rolinka

last: van der Loo

first: Gabriela

last: Martins

first: Mirjam

last: van den Hout

first: Wilfred

last: van IJcken

first: Rui

last: Costa

first: Michel

middle: C

last: van den Oever


title: Dual RNA-seq of Xanthomonas oryzae pv. oryzicola infecting rice

status: Public on Mar 29 2019

city: Nanning

first: Sheng

last: Huang

state: Guangxi

address: 100 Daxue Road

department: College of Life Science and Technology

institute: Guangxi University

summary: In this study, using a novel dual RNA-seq approach we monitored the global transcriptional changes in real time of Xanthomonas oryzae pv. oryzicola and rice during infection. Our transcriptome maps of Xoc strains infecting rice provide mechanistic insights into the bacterias adaptive responses to the host niche, with modulation of central metabolism being an important signature. The study also uncovers that infected rice responds by substantial alteration of the cell wall, stress and structural proteins.

sample_organism:
Oryza sativa
Xanthomonas oryzae pv. oryzicola

overall_design: mRNA and ncRNA profiles of both Xanthomonas oryzae pv. oryzicola and rice from infected rice leaves, in duplicate. A Xanthomonas oryzae pv. oryzicola mRNA profile from liquid cultures.

first: Zhouxiang

last: Liao

first: Zhe

last: Ni

first: Xinli

last: Wei

first: Long

last: Chen

first: Jianyuan

last: Li

first: Yanhua

last: Yu

first: Wei

last: Jiang

first: Bole

first: Yongqiang

last: He


title: miR-155 harnesses Phf19 to potentiate cancer immunotherapy through epigentic reprogramming T cell fate

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: T cell senescence and exhaustion are major barriers to successful cancer immunotherapy. Here, we show that miR-155 increased CD8+ T cell antitumor function by restraining T cell senescence and functional exhaustion through epigenetic silencing of drivers of terminal differentiation. miR-155 enhanced Polycomb Repressor Complex 2 (PRC2) activity indirectly by promoting the expression of the PRC2 associated factor Phf19 through downregulation of the Akt inhibitor, Ship1. Phf19 orchestrated a transcriptional program extensively shared with miR-155 to restrain T cell senescence and sustain CD8+ T cell antitumor responses. These effects relied on Phf19 histone-binding capacity, which is critical for PRC2 recruitment to chromatin. These findings establish the miR-155–Phf19–PRC2 as a pivotal axis regulating CD8+ T cell differentiation, paving new ways for potentiating cancer immunotherapy through epigenetic reprogramming of CD8+ T cell fate.

overall_design: Cells were sorted ex vivo and total RNA was isolated with a miRNeasy Mini kit (Qiagen). 10 ng total RNA was used for Nanostring analysis following the NanoString® nCounter®Expression CodeSet Design Manual. Background levels were calculated and subtracted from the samples, which were then normalized against the positive control and housekeeping gene probes.

first: Yun

last: Ji

first: Jessica

last: Fioravanti

last: Zhu

first: Hongjun

last: Wang

first: Tuoqi

last: Wu

first: Jinhui

last: Hu

first: Neal

last: Lacey

first: Sanjivan

last: Gautam

first: John

last: Le Gall

first: Xia

last: Yang

first: James

middle: D

last: Hocker

first: Thelma

last: Escobar

first: Shan

first: Stefania

last: Dell'Orso

first: Nga

last: Hawk

first: Veena

last: Kapoor

first: William

last: Telford

first: Luciano

last: Di Croce

first: Stefan

last: Muljo

first: Yi

last: Zhang

first: Vittorio

last: Sartorelli


title: AMPK signaling for naïve pluripotency [Mm]

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: We show activation of AMP kinase (AMPK) with single chemical compounds can endow naïve pluripotency. AMPK activators reverted early-stage differentiating cells or epi-stem cells to naïve state. Moreover, AMPK activators reverted human ESCs to naïve state with pluripotent gene expression profiles and X-chromosome reactivation.

overall_design: We analyzed gene expression profiles of mESCs with AICAR during differentiation and reversion

first: Jun

middle: K

last: Yamashita

first: Yajing

last: Liu

first: Yasuhiro

last: Takashima

first: Zhennan

first: Yasutaka

last: Mizoro

first: Chihiro

last: Okada

first: Masahiro

last: Nakamura


title: AMPK signaling for naïve pluripotency [Hs]

overall_design: We analyzed gene expression profiles of human ESCs with AICAR during differentiation and reversion

last: Yang


title: Clever-1 controls site-specific interactions between vasculature and lymphocytes in mouse and human spleen

city: Turku

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: The goal of this study is to compare gene expression differences between  WT and Stab1-/- spleen endothelial cells for the identification of biological processes regulated by Stab1 expression.

overall_design: Transcriptome profiles of spleen endothelial cells of wild type (WT) and stab1-/-  mice were generated by NGS, in triplicate, using Illumina Hiseq3000

first: Maija

last: Hollmén

first: Sirpa

last: Jalkanen


title: AMPK signaling for naïve pluripotency

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Distinct and collaborative functions of Yb and Armitage in  transposon-targeting piRNA biogenesis

status: Public on Mar 28 2019

city: Tokyo

first: Hirotsugu

last: Ishizu

address: 35 Shinanomachi

institute: Keio University

summary: PIWI-interacting RNAs (piRNAs) repress transposons to maintain germline genome integrity. Previous studies showed that artificial tethering of Armitage (Armi) to reporter RNAs induced piRNA biogenesis. However, lack of female sterile (1) Yb (Yb) in Drosophila ovarian somatic cells (OSCs) impaired production of transposon-targeting piRNAs even in the presence of Armi. Here, we show that specific interaction of Armi with RNA transcripts of flamenco piRNA cluster, the primary source of transposon-targeting piRNAs in OSCs, is strictly regulated by Yb. Lack of Yb allowed Armi to bind RNAs promiscuously, leading to the production of piRNAs unrelated to transposon silencing. The ATP hydrolysis-defective mutants of Armi failed to unwind RNAs and were retained on them, abolishing piRNA production. These findings shed light on distinct and collaborative requirements of Yb and Armi in transposon-targeting piRNA biogenesis. We also provide evidence supporting the direct involvement of Armi but not Yb in Zucchini-dependent piRNA phasing.

overall_design: Armi-associated RNAs characterized by FAST-iCLIP and CLIPPARE, and Piwi-associated small RNA levels in OSCs (Ovarian Somatic Cells)

first: Mikiko

last: Siomi


title: Experimentally-evolved male effects on female gene expression in the head and abdomen

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

summary: We measured gene expression of D. melanogaster female heads and abdomens after mating with males from six populations evolved under either enforced monogamy (no male-male competition, 3 populations) or sustained polygamy (intense male-male competition, 3 populations).

overall_design: Three samples of virgin female heads and six samples of mated female heads (one each per male evolved population, of which there are three monogamous and three polygamous), for nine libraries. Also, three samples of virgin female abdomens and six samples of mated female abdomens (one each per male evolved population, of which there are three monogamous and three polygamous), for nine libraries. In total, eighteen libraries sequenced in 8 lanes.

first: B


title: Male reproductive tract gene expression and male effects on female gene expression in populations of Drosophila melanogaster evolving in manipulated mating systems


title: Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

city: Edinburgh

first: Jeffrey

last: Pollard

state: Scotland

address: 47 Little France Cres

department: MRC Centre for Reproductive Health,

institute: Queen's Medical Research Institute, The University of Edinburgh

summary: The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorly understood. Here, we show that monocyte subpopulation distribution and transcriptomes are significantly altered by the presence of endometrial and breast cancer. Furthermore, TAMs from endometrial and breast cancers are transcriptionally distinct from monocytes and their respective tissue-resident macrophages. We identified a breast TAM signature that is highly enriched in aggressive breast cancer subtypes and associated with shorter disease-specific survival. We also identified an auto-regulatory loop between TAMs and cancer cells driven by tumor necrosis factor alpha involving SIGLEC1 and CCL8, which is self- reinforcing through the production of CSF1. Together these data provide direct evidence that monocyte and macrophage transcriptional landscapes are perturbed by cancer, reflecting patient outcomes.

overall_design: RNA-seq of purified human circulating monocytes and tumor-associated macrophages (TAMs) in breast and endometrial cancers.

first: Luca

last: Cassetta

first: Stamatina

last: Fragkogianni


title: Sexual selection on the dynamics of accessory gland gene expression in maturing Drosophila males

summary: We measured size gene expression of the accessory glands (the main production site of SFPs) at 2 and 4 days after eclosion in D. melanogaster males from six populations subjected to >160 generations of experimental evolution under either enforced monogamy (no male-male competition, 3 populations) or sustained polygamy (intense male-male competition, 3 populations).

overall_design: 6 populations (three monogamous -- M1, M2, M3, three polygamous -- P1, P2, P3) x 2 timepoints (48h and 96h) for 12 total libraries, all multiplexed on 2 lanes.

first: M

last: Koppik


title: RNAseq analysis on E14.5 midbrain material from mouse, Lmx1b fl/fl; Pitx3-Cre vs Lmx1v wt/wt;Pitx3-Cre littermates

status: Public on Mar 27 2019

city: Amsterdam

first: Marten

middle: Piet

last: Smidt

state: NH

address: Sciencepark 904

department: SILS

institute: UVA

summary: Lmx1b influences the subsets specification in midrbain DA neurons

overall_design: Examination of 2 groups from 2 genotypes as stated above, N=3 from both; RNA samples from E14.5 midbrain dissected material.

middle: P

first: I

last: Wever


title: A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. [bulk RNA-Seq]

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: While the roles of parenchymal microglia in brain homeostasis and disease are fairly clear, other brain-resident myeloid cells remain less understood. By dissecting border regions and combining single-cell RNA sequencing with high-dimensional cytometry, bulk RNA-sequencing, fate-mapping and microscopy, we reveal the diversity of non-parenchymal brain macrophages. Border-associated macrophages (BAMs) residing in the dura mater, subdural meninges and choroid plexus consisted of distinct subsets with tissue-specific transcriptional signatures, and their cellular composition changed during postnatal development. BAMs exhibited a mixed ontogeny and subsets displayed distinct self-renewal capacities upon depletion and repopulation. Single-cell and fate-mapping analysis both suggested there is a unique microglial subset residing on the apical surface of the choroid plexus epithelium. Finally, gene network analysis and conditional deletion revealed IRF8 as a master regulator that drives the maturation and diversity of brain macrophages. Our results provide a framework for understanding host-macrophage interactions in the healthy and diseased brain.

overall_design: 4 replicates of ME-MHCII-high, 4 replicates of ME-MHCII-int, 4 replicates of PM, 4 replicates of NCPM and 4 replicates of NMG. We compared these samples with the AMF Cre- and KC Cre- samples of GSE117081

first: Hannah

last: Van Hove

first: Isabelle

last: Scheyltjens

first: Karen

last: De Vlaminck

first: Ana

last: Pombo Antunes

first: Sofie

last: De Prijck

first: Niels

last: Vandamme

first: Sebastiaan

last: De Schepper

first: Gert

last: Van Isterdael

first: Charlotte

middle: L

last: Scott

first: Jeroen

last: Aerts

first: Geert

last: Berx

first: Guy

middle: E

last: Boeckxstaens

first: Roosmarijn

last: Vandenbroucke

first: Lars

last: Vereecke

first: Diederik

last: Moechars

first: Martin

last: Guilliams

first: Jo

last: Van Ginderachter

first: Yvan

last: Saeys

first: Kiavash

last: Movahedi

last: Vanginderachter


title: A549 cells and MSR-A549 cells

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai


title: mRNA expression profile of A549 cells and MSR-A549 cells with or without JQ1 treatment

summary: To establish effective multitargeted KRAS pathway therapy, we analyzed mediators of acquired resistance to chronic momelotinib and MEK inhibitor exposure in A549 cells. Since inhibitor resistance was completely reversible after drug withdrawal for several passages, suggesting epigenetic reprogramming, we investigated whole mRNA expression profiles in A549, momelotinib and selumetinib resistant (MSR)-A549 cells and MSR-A549 cells following drug withdrawal for 10 days. In parallel, we also examined mRNA expression profiles of MSR-A549 cells treated with the BET inhibitor JQ1, to identify specific targets regulated by H3K27 acetylation.

overall_design: mRNA profile of MSR-A549 cells with or without JQ1 treatment.

first: Shunsuke

last: Kitajima

first: David

last: Barbie


title: Circular RNAs associated with pork quality traits

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

summary: We firstly compared the expression file of circRNAs in longissimus muscle (LM) between the Chinese indigenous Huainan (HN, the fat type line ) and the Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type line) to identify the key circRNAs involved in the genetic basis of pork quality traits.

overall_design: The longissimus muscle from three Huainan pigs and three Duroc×(Landrace×Yorkshire) pigs (reference group)

first: Qiaoling

last: Ren

first: Liushuai

last: Hua


title: IL-1beta, IL-23, and TGF-beta drive plasticity of human ILC2s towards IL-17-producing ILCs in nasal inflammation

status: Public on Mar 26 2019

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

institute: Utrecht University

summary: Innate lymphoid cells (ILCs) are crucial for the immune surveillance at mucosal sites.  ILCs coordinate early eradication of pathogens and contribute to tissue healing and remodelling, features that are dysfunctional in patients with cystic fibrosis (CF). The mechanisms by which ILCs contribute to CF-immunopathology are ill-defined. Here, we report that group 2 ILCs (ILC2s) transdifferentiated into IL-17-secreting cells in the presence of the epithelial derived-cytokines IL-1β, IL-23 and TGF-β. This conversion was abrogated by IL-4 or vitamin D3. IL-17 producing ILC2s induced IL-8 secretion by epithelial cells and their presence in nasal polyps of CF patients is associated with neutrophilia. Our data suggest that ILC2s undergo transdifferentiation in CF nasal polyps in response to local cytokines, which are induced by infectious agents.

overall_design: 9 samples of 1 cell type, 3 conditions with 3 replicates

first: Korneliusz

last: Golebski

first: Xavier

last: Ros

first: Maho

last: Nagasawa

first: Sophie

last: van Tol

first: Hajar

last: Aglmous

first: Chantal

last: Kradolfer

first: Mara

last: Shikhagaie

first: Sven

last: Seys

first: P

last: Hellings

first: Cornelis

last: van Drunen

first: Wytske

last: Fokkens

first: Hergen

last: Spits

first: Suzanne

last: Bal


title: Genome-wide maps of histone H3K27 acetylation in A549 and MSR-A549 cells.

first: Hideo

last: Watanabe

summary: To establish effective multitargeted KRAS pathway therapy, we analyzed mediators of acquired resistance to chronic momelotinib and MEK inhibitor exposure in A549 cells. Since inhibitor resistance was completely reversible after drug withdrawal for several passages, suggesting epigenetic reprogramming, we examined genome-wide H3K27 histone acetylation in parental A549 and momelotinib and selumetinib resistant (MSR)-A549 cells.

overall_design: Examination of histone H3K27 acetylation in A549 and MSR-A549 cells.

first: Shunsuke

last: Kitajima

first: David

last: Barbie


title: TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression [ChIP-Seq]

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: The majority of genetic variation associated with coronary artery disease (CAD) resides in non- coding regions that are expected to involve transcriptional and epigenetic mechanisms of gene expression. We have identified a transcriptional network downstream of the CAD associated transcription factor (TF) TCF21 and provide evidence for TCF21 colocalization and co- regulation with the activator protein-1 (AP-1) complex in disease loci. We show that TCF21 and AP-1 regulate expression of two causal CAD genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone acetyltransferases and deacetylases. Genome-wide, TCF21 and AP-1 are jointly localized, regulate chromatin accessibility, and are enriched in CAD loci. These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription and thus risk in CAD associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features contributes to the genetic risk in loci where they colocalize.

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with an antibody to H3K27ac, or input control with siRNA of JUN, shRNA of TCF21 or control knockdown.

first: Quanyi

last: Zhao

first: Robert

last: Wirka

first: Trieu

last: Nguyen

first: Manabu

last: Nagao

first: Paul

last: Cheng

first: Clint

last: Miller

first: Juyong

middle: B

last: Kim

first: Milos

last: Pjanic


title: TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression [ATAC-Seq]

overall_design: The chromatin accessibility of human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with shRNA of JUN, TCF21 or control knockdown.


title: Aberrant expression profile of lncRNA and mRNA in dilated cardiomyopathy by RNA-sequence

city: Ji'nan

first: Huang

last: Guangyong

address: Cultural West Road,No.44

institute: Shandong University

summary: We aimed to identify aberrantly expressed lncRNA and mRNA expression profiles of dilated cardiomyopathy (DCM) and explore their potential functions. 8 DCM blood samples and paired healthy control blood samples underwent RNA-sequence.

overall_design: A prospective case-control study was designed to identify the changes in expression of lncRNA and mRNA. 8 DCM blood samples and paired healthy control blood samples underwent RNA-sequencing, using Illumina HiSeq 4000.

first: Guangyong

last: Huang


title: Dual RNAseq of human leprosy lesions identifies bacterial determinants linked to host immune response

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type I IFNs and antibody production.  We performed dual RNAseq on patient lesions, identifying a continuum of distinct bacterial states that are linked to the host immune response.  The bacterial burden, represented by the fraction of bacterial transcripts, correlates with a host type I IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial transcriptional activity, defined by the bacterial mRNA/rRNA ratio, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease

sample_organism:
Mycobacterium leprae
Homo sapiens

platform_organism:
Mycobacterium leprae
Homo sapiens

overall_design: RNA sequencing was performed on the total RNA from 24 leprosy skin biopsy specimens (9 L-lep, 6 T-lep, 9 RR).  Microbeads with consensus sequences to human and bacterial ribosomal RNA (rRNA) were utilized for depletion.  The enriched mRNA was then converted into sequencing libraries by random hexamer priming, sequenced via standard Illumina protocol, and mapped to both the human and M. leprae genomes

first: Matteo

last: Pellegrini

last: Modlin


title: Role of TERRA lncRNA during epithelial-to-mesenchymal transition

city: Barcelona

first: Rocco

last: Mazzolini

address: Carrer Dr. Aiguader, 88

country: Spain

institute: PRBB-IMIM

summary: We analyzed the contribution of TERRA lncRNA in an invitro model of epithelial-to-mesenchymal transition induced by TGFβ.

overall_design: We overexpressed TERRA-like long-non-coding RNA in murine NMuMG cells by stably overexpressing Vp16-TRF1ΔN protein. Then, we induced epithelial-to-mesenchymal transition (EMT) by 24hr TGFβ exposure. The aim to is analyze changes in the EMT signature induced by TERRA overexpression.

first: Mazzolini

last: Rocco

first: Canudas

last: Silvia

first: García

last: de Herreros Antonio


title: TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression

first: Thomas

last: Quertermous

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

overall_design: Refer to individual Series


title: TRIM59 promotes gliomagenesis by inhibiting TC45 dephosphorylation of STAT3

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: Although the oncogenic signalings driven by amplification and mutations of EGF receptor (EGFR) gene play a major role in glioblastoma pathogenesis, the responsible downstream mechanisms remain less clear. Here we demonstrate that tripartite motif-containing protein 59 (TRIM59), acting as a new downstream effector of EGFR signaling, regulates STAT3 activation in glioblastoma. EGFR signaling leads to TRIM59 upregulation through SOX9 that results in enhancing TRIM59 interaction with STAT3 in nucleus, and inhibiting STAT3 association with TC45 (the nuclear form of T cell protein tyrosine phosphatase TC-PTP), thereby maintaining STAT3 phosphorylation and activation and promoting tumorigenesis. Silencing TRIM59 suppresses cell proliferation, migration, and orthotopic xenograft brain tumorigenesis of GBM cells. Moreover, evaluation of GBM patient samples reveals an association among EGFR activation, TRIM59 expression, STAT3 phosphorylation, and poor prognoses. Our study identifies TRIM59 as a new regulator of oncogenic EGFR-STAT3 signaling and a potential therapeutic target for GBM patients with EGFR activation.

overall_design: Examination of effects of TRIM59 knockdown on differential gene expression in glioma cells with EGFRvIII overexpression.


title: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

summary: The interplay of DNA (de)methylation and the architectural chromatin protein CTCF is an important regulator of cellular differentiation, but molecular mechanisms determining differential CTCF binding are not well understood. Mouse embryonic stem cells (ESCs) contain up to 10% of CpG residues in 5-hydroxymethylated form (5hmC) and smaller amounts in 5-formylated or 5-carboxylated forms (5fC, 5caC). Here, we studied double knock out ESCs (DKO) deficient for TET1 and TET2 enzymes which are responsible for the conversion of 5mC to 5hmC, 5fC and 5caC. For both wild type (WT) and DKO cells, we measured changes in nucleosome positions, CTCF binding, DNA methylation and gene expression. Our integrative data analysis combined with biophysical modelling suggests that both differential (de)methylation and CTCF binding are to a large degree predictable from the DNA sequence. Common CTCF sites that remained bound in DKO cells were significantly enriched at unmethylated CpG islands, while CTCF loss was associated with differential DNA methylation. 5hmCs and 5fCs had the opposite effects in terms of CTCF priming: CTCF was preferentially lost from sites that were marked in WT cells by 5hmCs but not 5fCs. Interestingly, the losses of CTCF at TAD boundaries lead to aberrant spreading of DNA methylation, as well as downregulation of neighbouring genes. Overall, our study clarifies the fundamental mechanism of differential CTCF binding and provides evidence of DNA sequence-encoded temporal chromatin changes during cell differentiation.

overall_design:
Two samples are analyzed without replicates. The first sample is a control sample, the other one a treated sample.
Please note that the mouse embryonic stem cells used in this study were isolated from mice, that were maintained in a mixed C57BL/6 x 129 genetic background (B6;129; see also PMID: 23352810)

first: Frank

last: Lyko

first: Laura

last: Wiehle


title: Imprinted genes in Three Capsella Species

city: Sentul

first: Marcelinus

middle: Rocky

last: Hatorangan

state: Jawa Barat

address: Cijayanti, Babakan Madang

department: Biotechnology

country: Indonesia

institute: PT SMART, Tbk.

summary: Genome-wide identification of imprinted genes in Capsella grandiflora and Capsella orientalis

sample_organism:
Capsella grandiflora
Capsella orientalis

overall_design: Two replicates of Capsella grandiflora reciprocal hybrid seeds and two replicates of Capsella orientalis hybrid seeds

first: Kim

last: Steige

first: Tanja

last: Slotte

first: Claudia

last: Köhler


title: Intrinsic Apoptosis Shapes the Tumor Spectrum Linked to Inactivation of the Deubiquitinase BAP1

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

country: USA

institute: Genentech


title: Genome wide association study of bone size yields eleven loci that also affect height, bone density, osteoarthritis and fractures

status: Public on Mar 22 2019

city: Reykjavik

first: Olafur

middle: Andri

last: Stefansson

address: Sturlugata 8

department: Population Genomics

country: Iceland

institute: deCODE / Amgen Inc

summary: Bone area is one measure of bone size that is easily derived from dual-energy X-ray absorptiometry (DXA) scans, primarily performed to evaluate bone density and osteoporosis risk. Here, we report on a genome-wide association (GWA) study of DXA bone area of the hip and spine (N ≥ 28,954). We found associations of common variants at eleven loci that replicate in samples of European and East Asian descent (N = 13,608 – 21,277). We also examined association of these markers with osteoarthritis and fractures in European samples (Ncases = 3,293 – 27,321). The strongest DXA area association is with a variant in the microRNA MIR196A2 gene at the HOXC locus that associates with reduced lumbar spine area (rs11614913[T], P = 2.3 × 10-42, β = −0.090) and confers risk of hip fractures (P = 1.0 × 10-8, OR = 1.11). We demonstrate that the hip fracture risk allele [T] is less efficient in repressing miR-196a-5p target genes. We also show that the DXA area measure contributes to the risk of hip fracture independent of bone density.  Eight DXA area loci associate with osteoarthritis, including rs143384 in the 5’ UTR of the GDF5 gene and a missense variant in the COL11A1 gene (rs3753841[G], NP_001177638.1:p.Pro1284Leu). We also report a complex relationship between the variants associated with DXA area measures and height and bone mineral density (BMD).

overall_design:
Examination of mRNA expression in transfected HEK293T cells; MIR196A2 expression plasmids containing either the rs11614913[C] or rs11614913[T] alleles of MIR196A2, or empty vector plasmid
deCODE genetics/Amgen Inc.


title: Precise small molecule cleavage of a r(CUG) repeat expansion in a myotonic dystrophy mouse model

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: Myotonic dystrophy type 1 (DM1) is an incurable neuromuscular disorder caused by an expanded CTG repeat that is transcribed into r(CUG)exp.  The RNA repeat expansion sequesters regulatory proteins such as Muscleblind-like protein 1 (MBNL1), which causes pre-mRNA splicing defects.  The disease-causing r(CUG)exp has been targeted by antisense oligonucleotides, CRISPR-based approaches, and RNA-targeting small molecules.  Herein, we describe a designer small molecule, Cugamycin, that targets the structure of r(CUG)exp and cleaves it in cells and in vivo.  Cugamycin selectively cleaves r(CUG)exp while leaving short repeats of r(CUG) untouched.  In contrast, oligonucleotides that recognize r(CUG) sequence rather than structure cleave both long and short r(CUG)-containing transcripts.  In the HSALR mouse model of DM1, Cugamycin selectively ablates r(CUG)exp in disease-affected muscle.  Transcriptomic, histological, and phenotypic studies demonstrate that Cugamycin broadly and specifically relieves DM1-associated defects without detectable off-targets.  Thus, small molecules that bind and cleave RNA may have utility as lead chemical probes and medicines.

overall_design: RNA-Seq was perfomed on tibialis anterior muscle from HSALR and WT mice treated with PBS or small molecule drug.

first: Alicia

middle: J

last: Angelbello

first: Suzanne

middle: G

last: Rzuczek

first: Kendra

last: Mckee

first: Jonathan

last: Chen

first: Hailey

last: Olafson

first: Walter

middle: N

last: Moss

first: Matthew

last: Disney


title: RNA-seq of microalga Dunaliella tertiolecta determine growth-switch genes in response to higher light intensity

status: Public on Mar 23 2019

city: Singapore

first: Siti Radiah

last: Binte Safie

address: 5 Science Drive 2

department: Microbiology and Immunology

institute: National University Of Singapore

summary:
Purpose: Determine rate-limiting genes in response to higher light intensity
Method: Cell division was observed at 8 h but not 4 h post light shift. The transcriptome of 4 h and 8 h post light shift were compared using RNA-seq. The reference transcriptome used was Dt-v10 (GEO accession no. GSE70876)
Results and Conclusions: Genes belonging TCA cycle and amino acid syntheses increased later at 8 h, suggesting that they are the rate-limiting in the response to higher light intensity

overall_design: Gene expressions of sample at 8 h post light shift were expressed relative to the sample at 4 h post light shift.

first: Siti

last: Radiah

first: Yi-Kai

last: Ng

first: Lina

last: Yao

first: Yuan

last: Lee


status: Public on Mar 25 2019

city: Colchester

first: Vladimir

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

summary: Coordinated changes of DNA (de)methylation, nucleosome positioning and chromatin binding of the architectural protein CTCF play an important role for establishing cell type specific chromatin states during differentiation. To elucidate molecular mechanisms that link these processes we studied the perturbed DNA modification landscape in mouse embryonic stem cells (ESCs) carrying a double knockout (DKO) of the Tet1 and Tet2 dioxygenases. These enzymes are responsible for the conversion of 5-methylcytosine (5mC) into its hydroxymethylated (5hmC), formylated (5fC) or carboxylated (5caC) forms. We determined changes in nucleosome positioning, CTCF binding, DNA methylation and gene expression in DKO ESCs, and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, while unmethylated and nucleosome-depleted CpG islands were enriched for CTCF sites that remained occupied. A number of CTCF sites also displayed direct correlations with the CpG modification state: CTCF was preferentially lost from sites that were marked with 5hmC in wild type cells but not from 5fC enriched sites. In addition, we found that some CTCF sites can act as bifurcation points defining the differential methylation landscape. CTCF loss from such sites, e.g. at promoters, boundaries of chromatin loops and topologically associated domains (TADs), was correlated with DNA methylation/demethylation spreading and can be linked to downregulation of neighbouring genes. Our results reveal a hierarchical interplay between cytosine modifications, nucleosome positions and DNA sequence that determines differential CTCF binding and regulates gene expression.

overall_design: Two WT and two Tet1/2-deficient (DKO) mouse ES cell lines were isolated from WT and Tet1/Tet2 double-mutant mice with a mixed 129 and C57BL/6 background as described (Daw+B1laty et al., 2013). ESCs were maintained in regular ESC medium (KnockOut DMEM supplemented with 15% fetal calf serum, 1x non-essential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin, 2 mM L-glutamine, 0.0008% β-mercaptoethanol and 1000 U/ml leukemia inhibiting factor) at 37 °C and 7% CO2 on inactivated MEF feeders seeded on gelatin (0.2%) coated dishes. For CTCF ChIP-seq experiments cells were trypsinized and pre-plated on gelatin coated dishes three times to remove feeders. ESCs were resuspended in medium, fixated for 10 min at room temperature and lysed as described (Wiehle and Breiling 2016). After nuclei lysis, samples were sonicated 4 × 5 min with 30 s on/off intervals (Bioruptor, Diagenode). SDS content was reduced by dilution as described (Wiehle and Breiling 2016). Chromatin from 6 x 10^6 cells was immunoprecipitated overnight at 4°C using 5 µg of antibody against CTCF (#61311, Active Motif). Further processing occurred according to instructions of the ChIP-IT High Sensitivity kit (Active Motif). Immunoprecipitated DNA was eluted from Protein A/G agarose beads and purified using the IPure kit (Diagenode). For ChIP-sequencing libraries were generated from 10 ng of DNA using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB) according to the manufacturer´s instructions. Final libraries were quality controlled and pooled to equimolar amounts and sequenced in 50 bp single-read mode on an Illumina HiSeq 2000 device. For MNase-assisted histone H3 ChIP-seq cells were cross-linked with 1% methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS. The cell pellet was treated with 40 U MNase for 5 min at 37°C, then stopped with 10x Covaris buffer (Covaris Ltd) and chromatin was sheared for 15 min with the Covaris S2 device (burst 200; cycle 20%; intensity 8).  Immunoprecipitation was performed for ~5 x 10^6 cells with anti-H3 antibody (Abcam #ab1791, Lot: GR103864-1). Then chromatin was treated with RNaseA and proteinase K. Purified DNA was cloned into Illumina libraries with the NEBNext Ultra library preparation kit (NEB).

first: Laura

last: Wiehle

first: Graeme

last: Thorn

first: Günter

last: Raddatz

first: Christopher

last: Clarkson

first: Karsten

last: Rippe

first: Frank

last: Lyko

first: Achim

last: Breiling


title: Peg10 eCLIP in pluripotent trophoblast stem cells

first: Rohit

last: Reja

summary:
The prevailing dogma that approximately 50% of our genome is “junk” DNA composed of transposable elements and retroviral insertions has recently been challenged. It has become evident that our genome has taken advantage of these transposable elements and uses them as a source of DNA to generate novel genes, which subsequently allow the organism to evolve. This process is termed “domestication of transposable elements” and the majority of these genes have been found to be essential for the existence of the organism.
One of these developmentally essential domesticated genes: Peg10 (paternally expressed gene 10), was derived from a Ty3/gyspy LTR retrotransposon, yet lost its ability to transpose due to mutational events during its domestication. Remarkably, Peg10 has successfully maintained its Gag and Pol-like domains for millions of years.
Peg10 orthologues are expressed in eutherian mammals and are essential for placentogenesis. To address the functional mechanisms of Peg10 we studied it in Trophoblast Stem Cells (TSCs). We find that the Gag of Peg10 is fully active: it promotes budding of vesicles, akin to the viral counterpart that catalyzes the budding of viruses. TSCs, deleted for Peg10, fail to differentiate into placental lineages, underscoring a critical role in lineage specification. This paper discusses our efforts to characterize the contents of Peg10 vesicles and whether such vesicles regulate lineage specification.

overall_design: eCLIP-seq was performed on Peg10 wildtype (WT) and knockout (KO) TSC cells at Day 0 and Day 5 during differentiation. Two replicates per samples were generated.

first: M

last: Abed

first: R