title: Essential and non-overlapping IL-2Rα-dependent signaling for thymic development and peripheral homeostasis of regulatory T cells

city: Miami

first: Thomas

last: Malek

state: FL

address: 1600 NW 10th Ave

institute: University of Miami

summary: IL-2R signaling is essential for regulatory T cell (Treg) function. However, the precise contribution for IL-2 during Treg thymic development, peripheral homeostasis, and lineage stability remains unclear. Here we show that IL-2R signaling is essential for thymic Tregs at an early step for expansion/survival and a later step for functional maturation. Using selective deletion of CD25 in peripheral Tregs, we also find that IL-2R signaling was absolutely essential for their persistence whereas Treg lineage stability was IL-2-independent. CD25 knockout peripheral Tregs showed increased apoptosis, oxidative stress, signs of mitochondrial dysfunction, and reduced transcription of key enzymes of lipid and cholesterol biosynthetic pathways. A divergent IL-2 transcriptional signature was noted for thymic Tregs versus peripheral Tregs. These data indicate that IL-2R signaling in the thymus and the periphery leads to distinctive effects on Treg function, where peripheral Treg survival depends on a non-conventional mechanism of metabolic regulation.

overall_design: To evaluate IL-2Rα-dependent transcriptional activity in thymic Tregs, CD25 KO Tregs were isolated from thymuses of Treg-targeted CD25 conditional KO animals, as well as CD25 WT controls. Groups of 5 biological replicates (mice) were compared. To evaluate IL-2Rα-dependent transcriptional activity in splenic Tregs, CD25 KO Tregs were isolated from tamoxifen-inducible, Treg-targeted CD25 conditional KO mice as well as CD25 WT reporter controls following tamoxifen induction. Groups of 4 biological replicates (mice) were compared. Libraries were prepared using KAPA’s RNA Hyperprep protocol and sequenced on a 75 bp paired-end run using the Illumina NextSeq 500 High Output Kit (150-cycle; 400 M flow cell). Reads from RNA-seq were mapped to the Mus musculus genome GRCm38 using STAR (ver.2.5.0) aligner. Raw counts were generated based on Ensembl genes (GENCODE M13) with featureCounts (ver.1.5.0). Differentially expressed genes between CD25 KO and WT Tregs were identified using DESeq2, and determined by a threshold of false discovery rate (FDR) <0.01.

first: Kevin

last: Toomer

first: Jen

last: Lui

first: Norman

last: Altman

first: Yuguang

last: Ban

first: Xi

last: Chen


title: Gene expression data from DEN-induced hepatocellular carcinoma mice

status: Public on Feb 01 2019

city: Shang Hai

first: Daiming

last: Xiang

address: 225 Changhai Road, 200438 Shanghai, China

country: China

institute: Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University

summary:
We used microarrays to detail the molecular mechanism underlying the HLF (hepatic leukemia factor)-triggered HCC (hepatocellular carcinoma) initiation
We conducted transcriptome microarray analysis of DEN (diethylnitrosamine)-induced HCCs from HLF-deficient mice or WT (wild type) mice.

overall_design: HCC in HLF-deficient  mice and WT mice was induced with DEN. Total RNA was extracted from HCC samples collected from HLF-deficient and WT mice and reverse-transcripted to cDNA, and microarray analysis of transcriptome was performed to identify differentially expressed genes

first: Jin

last: Ding

first: Daimin


title: Transcriptomic analysis of the RPS3-regulated genes in HCC cell line

city: Beijing

first: Xiaodong

last: He

institute: Peking Union Medical College Hospital

type: Expression profiling by high throughput sequencing

summary: The human ribosomal protein S3 (RPS3), a component of the small 40S ribosomal subunit, is mainly involved in ribosomal maturation and initiation of translation through association with initiation factors. In this study, we firstly identified that RPS3 played an important role in HCC progression. We performed RNA sequencing to profile gene expression patterns before and after RPS3 knockdown.

overall_design: SMMC-7721 cells were transfected with RPS3 siRNA or negative control, and overall transcriptomic changes were then examined by RNA sequencing, in duplicate, using Illumina Hiseq 2500 platform.

first: L

middle: J

last: Zhao

first: J

middle: Z

last: Cao

middle: M

last: Han


title: A code of mono-phosphorylation modulates the function of RB.

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

country: USA

institute: Mass. General Hospital Cancer Center

summary: Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB’s interactions and confer functional specificity. All 14 mP-RBs interact with E2F/DP proteins but they provide different shades of E2F regulation. RB mono-phosphorylation at S811, for example, alters RB transcriptional activity by promoting its association with NuRD complexes. The greatest functional differences between mP-RBs are evident beyond the cell cycle machinery. RB mono-phosphorylation at S811 or T826 stimulates the expression of oxidative phosphorylation genes, increasing cellular oxygen consumption. These results indicate that RB activation signals are integrated in a phosphorylation code that determines the diversity of RB activity.

overall_design: Transcriptional changes caused by replacing endogenous RB with exogenous wild-type RB, constitutive active RBΔcdk or any of the 14 mono-phosphorylation RB isoforms in human RPE1 cells.

first: Ioannis

last: Sanidas

first: Katerina

middle: A

last: Fella

first: Myriam

last: Boukhali

first: Eric

middle: C

last: Tai

first: David

middle: T

last: Ting

first: Michael

middle: S

last: Lawrence

first: Wilhelm

last: Haas

first: Nicholas

last: Dyson


title: Methylome landscape of epithelial and immune fractions of celiac disease

status: Public on Feb 04 2019

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

type: Methylation profiling by genome tiling array

summary: These samples were analyzed to gain insight into the mechanisms behind celiac disease, analyzing their methylome.

overall_design: 20 samples from duodenum of controls and celiac disease were sorted in epithelial and immune fractions. These fractions and 8 complete biopsies were analyzed using Infinium 450k methylation array.


title: Cellular and Molecular Changes in Psoriasis Lesions Inducedby Ustekinumab: Distinct Differences in Responders vs. Non responders

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: Ustekinumab provides clinical benefit to psoriasis patients, but precise cellular and molecular changes underlying its therapeutic utility are not yet fully understood. To assess differences between ustekinumab responders vs. non responders in modulating specific inflammatory pathways and provide reference data for exploring molecular effects  of next-generation interleukin(IL)-17 and IL-23-antagonists in psoriasis.

overall_design: Comparisson Ustekinumab vs. Etanercept, Lesional vs. Non-lesional tissue,Timepoint vs. Baseline, Responders vs. Non Responders.

first: Sandra

last: Garcet

first: Kim

last: Campbell


title: Functional separation of IL7Rα/KLRG1-defined CD8+ T cell populations in humans

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

summary: During acute viral infections in mice, IL-7Rα and KLRG1 together are used to distinguish the short-lived effector cells (SLEC; IL-7RαloKLRGhi) from the precursors of persisting memory cells (MPEC; IL-7RαhiKLRG1lo). We here show that these markers can be used to define distinct subsets in the circulation and lymph nodes during the acute phase and in ‘steady state’ in humans. In contrast to the T cells in the circulation, T cells derived from lymph nodes hardly contain any KLRG1-expressing cells. The four populations defined by IL-7Rα and KLRG1 differ markedly in transcription factor, granzyme and chemokine receptor expression. When studying renal transplant recipients experiencing a primary hCMV and EBV infection, we also found that after viral control, during latency, Ki-67-negative SLEC can be found in the peripheral blood in considerable numbers. Thus, combined analyses of IL-7Rα and KLRG1 expression on human herpes virus-specific CD8+ T cells can be used to separate functionally distinct subsets in humans. As a non-cycling IL-7RαloKLRG1hi population is abundant in healthy humans, we conclude that this combination of markers not only defines short-lived effector cells during the acute response but also stable effector cells that are formed and remain present during latent herpes infections.

overall_design: RNA was isolated from 4 different populations (IL-7RαloKLRG1lo, IL-7RαloKLRG1hi, IL-7RαhiKLRG1hi, IL-7RαhiKLRG1lo) of CD8+ T cells isolated from 6 donors.

first: E

middle: B

last: Remmerswaal

first: P

last: Hombrink

first: B

first: M

last: van Aalderen


title: Effects of culture conditions on epigenomic profiles of brain tumor cells

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed epigenomic analysis of brain tumor cells that were collected from micro-engineered three-dimensional tumor models. We used a low-input epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze genome-wide histone modification (H3K4me3). We compared H3K4me3 patterns in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. Our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modification.

overall_design: We obtained genome-wide H3K4me3 profiles in U251 cells cultured under different conditions (3D vs. 2D, Hypoxia vs. Normoxia). The MOWChIP-seq experiments were performed using 1000 cells per assay as described in our previous publication (Cao et al. Nature Methods 12 (2015) 959-962). We generated two replicates (R1 and R2) for each sample.

first: Chengyu

last: Deng


title: Comparison of the differentially expressed genes in normal vs ovarian cancer cells

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Identification of the differentially expressed genes in the cancer cells (mainly focusing on the growth factor receptors)

overall_design: High coverage deep sequencing of the transcriptome was performed using the Illumina HiSeq NGS platform to identify the diffentially expressed genes.

first: Sib

last: Roy

first: Rahul

last: Bhattacharya


title: Transcriptional responses of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture wine fermentation

city: Stellenbosch

first: Kirti

last: Shekhawat

address: Alexander Street

country: South Africa

institute: IWBT

summary: In wine fermentation, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact on yeast physiology and on genetic and metabolic regulation remain limited. Here we describe a transcriptomic analysis of single species and mixed species fermentations.

sample_organism:
Saccharomyces cerevisiae
Lachancea thermotolerans

overall_design: The fermentations were carried out in carefully controlled environmental conditions in a bioreactor to eliminate or reduce any transcriptomic responses that would be due to factors other than the presence of the second species.

first: Mathabatha

middle: E

last: Setati

first: Florian

middle: F

last: Bauer


title: Transcriptome analysis of lung epithelial cells from various developmental stages (E13.5, E15.5, E18.5, P14, and P56)

city: Tokyo

first: Kazushige

last: Shiraishi

address: 7-3-1, Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary: We investigated whether cell transplantation potential differs between the different developmental stages of the lungs. We found that epithelial cells derived from different developmental stages show different engraftment potential. To identify transcriptional signatures of epithelial cells that are associated with the phenomenon, we performed a time series transcriptome analysis of epithelial cells of the developing lungs.

overall_design: Lung epithelial cells from various developmental stages (E13.5, E15.5, E18.5, P14, and P56) were purified by cell sorting. The time series transcriptome of the epithelial cells was generated by 3'SAGE-seq using Ion Proton sequencer.

first: Shigeyuki

last: Shichino


title: Cellular systems biology identifies dynamic trophoblast populations in early human placentas

city: Toronto

first: Frances

last: Wong

state: ON

address: 1 King's College Circle, MSB3360

country: Canada

institute: University of Toronto

summary: To address early human placenta development, we aimed to characterize the cell surface proteomic profile of early trophoblast cells in an effort to understand trophoblast heterogeneity and population dynamics. We quantify cell surface protein expression in early first trimester human placentas using a high throughput flow cytometry screen of 370 Cluster of Differentiation (CD) antigens and confidently identified 23 increasing and 13 decreasing markers of dynamic populations between weeks 6 and 10 of human placenta development. We were particularly interested in transient trophoblast populations expressing either EpCAM (CD326) or CDCP1 (CD318) populations of trophoblasts. Immunohistochemistry analysis revealed these CD antigens are expressed by discrete cells with EpCAM localized to trophoblast in the proximal villi columns while CDCP1 is expressed by cells in the distal columns. Multi-color flow analysis confirmed independence of CDCP1 and EPCAM expressing cell populations and identified EpCAM cells as positive for EGFR. Microarray analysis of gene expression indicated EpCAM+/EGFR+ and EGFR+ cells showed high degree of gene expression similarities to villus cytotrophbolast but that loss of EpCAM expression was concomitant with exit from the cell cycle as EpCAM/EGFR cell were mitotically active while CDCP1 positive trophoblast are enriched in gene sets related to immune regulation functions and cell cycle/cell division and have significant similar gene expression to extravillous cytotrophoblast. Our study indicates at least two distinct subpopulations of cytotrophoblasts exit in the early first trimester and that the column likely maintains pools of actively dividing progenitor cells giving rise to the developing placenta villus tree.

overall_design: Two placentas (week 5.5 and 6.6) were pooled and flow sorted based on EpCAM and CDCP1 or EpCAM and EGFR expression.

first: Brian

last: Cox


title: Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors

first: Kat

last: Moore

institute: Sanquin Research

summary: The aim of this study is to investigate how eIF2 phosphorylation affects mRNA translation in erythroblasts. Ribosome profiling combined with RNA sequencing was used to determine translation initiation sites and ribosome density on individual transcripts.

overall_design: Ribosome profiling samples with translation halted by harringtonine (ribosome stalls at start site) or cyclohexamide (ribosome is frozen at current location) were treated with tunicamycin to induce eIF2 phosphorylation vs untreated. Total RNAseq sample with and without tunicamcyin were also generated. Total RNAseq and cycolhexamide were used to calculate ribosome occupancy as a measure of translation efficiency. Harringtonin peaks were used to identify alternative sites of translation initiation under stress.

first: Nahuel

last: Paolini

first: Franca

last: di Summa

first: Ivo

last: Fokkema

first: Peter

last: 't Hoen

first: Marieke

last: von Lindern


title: Refining the set of ETV6-RUNX1-specific genes by employing gene expression profiles of patients in remission

city: Taipei

first: Hsi-Che

last: Liu

address: No. 92, Sec. 2, Chung-San North Rd.

country: Taiwan

institute: Mackay Memorial Hospital

summary: The chromosomal translocation t(12;21) resulting in the ETV6-RUNX1 fusion gene is the most common genetic abnormality in childhood acute lymphoblastic leukemia (ALL). As the emergence of microarray technology, finding subtype-specific genes becomes one of the main objectives in most ALL studies. However, the list of differentiated genes derived by comparing patients in the subtype versus the others contains many false positives, which are not really subtype-specific. In order to refine the list of subtype-specific genes for ALL with ETV6-RUNX1, this study conducted microarray experiments on patients in both diagnosis and remission status.

overall_design:
36 bone marrow samples (26 diagnosis/9 remission) of acute lymphoblastic leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips.

Please note that the median of the expression value of 'ETV6-RUNX1_D01' sample (around 90) is much smaller than the other samples (around 800-1,070). However, it didn't affect the analysis quality after rank-normalization was applied.

first: Chia-Lun

last: Wu

first: Ting-Chi

last: Yeh

first: You-Yu

last: Lin

first: Chien-Yu

last: Chen

first: Chao-Ping

last: Yang

first: Jen-Yin

last: Hou

first: Iou-Jih

last: Hung

first: Tang-Her

last: Jaing

first: Ming-Syan

first: Lee-Yung

last: Shih

first: Der-Cherng

last: Liang


title: Expression data from Periostin isoform 3 and 6 overexpressing oral cancer cells

status: Public on Jan 31 2019

city: Tokushima

first: Yasusei

last: Kudo

address: 3-18-15 Kuramoto

department: Institute of Biomedical Sciences

institute: Tokushima University Graduate School

summary: The aim to the study was to elucidate the character of Periostin isoform 3 and 6 by carrying out a geome-wide expression analysis.

overall_design: Total RNA from empty vector, Periostin isoform 3, and isoform 6 transfected human oral cancer cell line, HOC621 was hybridized on Affymetrix® GeneChip Human Gene 2.0 ST arrays. The key findings were verified by quantitative real-time PCR (QPCR).

first: Akiko

last: Watanabe


title: Expression data from human bone marrow hematopoietic stem and progenitor populations from elderly anemic patients

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: Expression data from FACS-purified hematopoietic stem cells, common myeloid progenitors, granulocyte-macrophage progenitors, and megakaryocyte-erythroid progenitors from human bone marrow samples of elderly anemic patients

overall_design: Human bone marrow samples from human elderly patients with anemia of unexplained etiology were sorted by FACS for immunophenotypic HSCs, CMPs, GMPs, and MEPs. RNA was extracted from sorted populations and hybridized to Affymetrix microarrays.

first: Wendy

last: Pang

first: Irving

last: Weissman


title: RNA sequencing profiles of B progenitor cells derived from mouse ES cell, Yolk sac, fetal liver, and adult bone marrow.

city: Kalamazoo

first: Momoko

last: Yoshimoto

state: MI

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

summary:
We induced mouse embryonic stem cells (ESCs) into B progenitors in in vitro culture.
We previously reported that B cells derived from extra-embryonic yolks sac (YS) belong to innate-like B-1 cells, not conventional B-2 cells.
Since ES cell differentiation into Blood lineage, it recapitulates YS hematopoiesis, we hypothesized that B cells produced by mouse ESCs belong to B-1 cells as well.
We transplanted ESC-derived B-progenitor cells into immunodeficient mice and confirmed that ES-derived B cells differentiate into only B-1 and marginal zone B cells, not B-2 cells in vivo. We preformed gene expression profiles by RNA sequencing comparing ESC-derived, YS-derived, fetal liver derived, and adult bone marrow derived B progenitor cells to see their characteristics.

overall_design:
We compared gene expression profllings among B-1 progeniotors derived from ES, Yolk sac, and fetal liver, and B-2 progenitors from adult bone marrow.
We isolated CD19+B220+ B-progenitor cells obtained from in vitro culture of mouse ES cells, yolk sac, and fetal liver (all B-1 biased) and bone marrow (B-2 biased) and performed RNA sequencing
Please note that Flk1 is a marker of mesoderm that differentiate into endothelial cells and blood cells and VEcad (VE-cadherin) is a marker of endothelial cells. It is known that all hematopoietic cells are derived from lateral mesoderm (Flk1+) cells via endothelial phenotype (VE-cad+). Therefore, we differentiated ESCs into Flk1+ mesoderm or VEcad+ endothelial cells and isolated them by sorting (as indicated in the sample source name field), and replated them onto OP9-stromal cells that support B cell development.

first: Yunlong

first: Houngyu

last: Gao


title: Expression analysis of cancer of unknown primary (CUP)

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

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

overall_design: Refer to individual Series


title: Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming III

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: We collected triplicate samples at day 15 under serum condition, generated single cell suspensions and performed scRNA-Seq (10X Genomics). We also collected samples from a bulk population and performed bulk RNA-seq (Quantseq, Lexogen).

overall_design: To determine the effect of GDF9 on reprogramming, we plated secondary MEFs at a concentration of 5,000 cells per well of a 24-well plate and added either recombinant mouse GDF9 daily from day 8 onward, or control. We tested different doses: 0.1 µg/ml, 0.5 µg/ml, and 1 µg/ml. We collected scRNA-seq profiles of ~50,000 cells at day 15 of iPSC induction under serum condition (10X Genomics). In addition, we collected bulk RNA-seq profiles (Quantseq, Lexogen).

first: Jian

last: Shu


title: Expression analysis of cancer of unknown primary (CUP) 2

summary:
Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed.
Results provide insight into the molecular pathogenesis of CUP.

overall_design: 74 samples; 1 array per sample

first: Kazunari

last: Kurahashi

first: Kazuto

last: Nishio


title: RNA seq analysis of the mouse pNC and Cornea transcriptome

city: Houston

first: Peter

middle: Y

last: Lwigale

state: Texas

address: 6100 Main street

department: BioSciences

institute: Rice University

summary:
Purpose: The goal of this study is to provide a detailed transcriptome expression profile of the mouse cornea  and evaluate changes in gene expression during mouse corneal development.
Methods: RNA-sequencing is used to profile the mouse transcriptome in the pNC isolated at E10.5 and corneas isolated at E14.5 and E16.5. Samples generated in triplicate for sequencing by Illumina Hiseq 4000. Clean reads are mapped to reference gene and GRCm38 by Bowtie2 and HISAT. Spatiotemporal expression patterns of select genes were validaed by in situ hybrdization.
Results: Analysis of the whole transcriptome profile between pNC and embryonic corneas identified 3815 unique differentially expressed genes. Pathway analysis revealed enrichment of differentially expressed genes involved in signal transduction (RA, TGFβ, and Wnt pathways) and transcriptional regulation.
Conclusions: Our study for the first time, identifies differential gene expression across progressive stages of mouse corneal development and provides a comprehensive transcriptomic profile of the developing cornea. This serves as a valuable resource for the identification of novel regulatory networks crucial for the advancement of studies in congential defects, stem cell therapy, bioengineering, and adult corneal diseases.

overall_design: RNA sequencing of ocular tissues from a selection of three developmental stages: periocular neural crest (E10.5) and cornea (E14.5 and E16.5). Three biological replicates for each stage for a total of 9 samples. The E10.5 samples are considered the baseline but all samples are compared.

first: Justin

last: Ma


title: Mucin 1 knockdown in EMM myeloma cells

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

summary: The sialic glycoprotein, Mucin1, is known to be involved in the pathogenesis of various types of cancers. In a fraction of patients with multiple myeloma, their myeloma cells have high Mucin1 expression. We established a myeloma cell line designated EMM1 from a myeloma patient whose myeloma cells have high Mucin1 expression. Then we performed knockdown of Mucin1 to elucidate the role of the high Mucin1 expression.

overall_design: we performed knockdown of Mucin1 to elucidate the role of the high Mucin1 expression. Knockdown of MUC1 in EMM1 cells induced cell cycle arrest during S phase and apoptosis in EMM1 cells. To elucidate the role of Mucin1 in EMM1 cells, we generated EMM1 cells lines expressing shMucin1 or control shRNA and performed RNA-seq analysis of the two cell lines and compared the differences in gene expressions.

first: Shinya

last: Endo

first: Nao

last: Nishimura

first: Matsuoka

last: Masao


title: Genomic binding profile of Junctophilin 2 N-terminal truncate (JP2NT) and the effect of JP2NT overexpreesion on cardiac transcriptional reprogramming in response to Transverse Aortic Banding

city: Iowa City

first: Long-Sheng

last: Song

state: Iowa

address: 285 Newton Road

department: Department of Internal Medicine

institute: University of Iowa

summary: Calpain-mediated cleavage transfroms the full-length JP2 from a structural protein into a transcriptional regulator (JP2NT). We used RNA-seq to reveal the effect of JP2NT overexpression on cardiac transcriptional reprogramming induced by left ventricular pressure overload using transverse aortic banding in mice. We used ChIP-seq to reveal the genomic binding pattern of JP2NT. Additional ChIP-seq analyses against TBP and MEF2C were performed to reveal whether JP2NT overexpression affects endogeneous binding of TBP and MEF2C.

overall_design: Cardiac specific overexpression of HA-tagged JP2NT transgene was achieved by an a-MHC-promoter driven transgenic system. The JP2NT-OE and littermate controls were subjected to transverse aortic banding (TAB) for 3 weeks. Left ventricle RNA was subjected to RNA-seq. Baseline JP2NT-OE or control hearts were subjected to ChIP-seq using antibodies against HA tag, MEF2C or TBP.

first: Ang

last: Guo

first: Yunhao

last: Wang


title: E-C coupling structural protein junctophilin-2 encodes a stress-adaptive transcription regulator


title: Learning the cis sequence elements that determine AP-1 monomer specificity (RNA-seq data sets)

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

summary: Regulation of gene expression is mediated by combinations of DNA binding transcription factors that work in concert to recruit transcriptional machinery. Each cell type expresses hundreds of sequence-specific transcription factors, many of which recognize identical or similar DNA sequences. Such factors can play both redundant and non-redundant roles, but mechanisms determining overlapping or distinct biological outcomes are largely unknown. Here, we implement a machine learning approach to investigate how local combinations of sequence motifs influence the genome wide binding patterns of different members of the AP-1 transcription factor family in macrophages.  Significant motifs associated with family member specific binding patterns were validated by assessing effects of motif mutations in different strains of mice. We further confirmed the prediction of PPARg to be preferentially associated with the specific binding pattern of cJun using PPARg knockout macrophages.  Together, our results provide evidence that unique binding patterns of AP-1 family members result in part from the corresponding unique ensembles of nearby regulatory elements embedded within enhancers and promoters, and that these elements can be identified by machine learning models trained using genomic sequence.

overall_design: RNA-seqs were performed in mouse thioglycollate elicited macrophage cells in two strains of mice (C57BL6/EIJ and BALB/cJ) in either vehicle treatment and/or KLA treatments. RNA-seqs following CRISPR knockdown of Atf3, Jun and JunD (zsGreen indicates scramble CRISPR control) were performed on vehicle treated immortalized bone marrow derived macrophage cells derived from C57BL6/EIJ mice (with biological replicates). Nascent transcription was captured via GRO-seq in C57BL6/EIJ thioglycollate elicited macrophage cells (with biological replicates).

first: Gregory

last: Fonseca

first: Emma

last: Westin

first: Sascha

middle: H

last: Duttke

first: Nathanael

last: Spann

first: Tobias

last: Strid

first: Zeyang

last: Shen

first: Joshua

middle: D

last: Stender

first: Verena

last: Link

first: Christopher

last: Benner

middle: K

last: Glass


title: Chronic Chlamydia trachomatis infection of fallopian tube organoids

city: Berlin

first: Thomas

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

summary: Chronic infections of the Fallopian tubes with Chlamydia trachomatis (Ctr) can cause scarring and inflammation and can lead to infertility. Here we describe a model of human fallopian tube organoids for chronic Ctr infection. Interestingly, the normal human cells respond to infection with an active expulsion of the bacteria from the apical side of the epithelium and compensatory cellular proliferation clearly demonstrating a role of epithelial homeostasis in the defense against this infectious agent. Upon progression of the infected culture for over 9 months, the population of epithelial cells underwent a permanent shift towards a less differentiated state. LIF signaling is an essential feature, regulating stemness in the tube and organoid formation, and is activated in response to Ctr. Hallmarks of an organoid infection include a relative increase of secretory cells, expansion of the CD24+ positive population, upregulation of SPP1 factor, as well as downregulation of HOXA4 and HOXA5 homeobox genes. Moreover, Ctr increases hypermethylation of DNA in polycomb repressed genomic regions, an indicator of accelerated molecular aging. This infection model reveals an intriguing link between Ctr and regulation of the host epigenome and suggests that this pathogen has a long-term impact on the interaction of the epithelium with the microenviroment. These permanent changes in the epithelium may be a contributing factor in the development of tubal pathologies, including the development of high grade serous ovarian cancer (HGSOC).

overall_design: Genomic methylation profiling of long term CtrD infected and not infected fallopian tube organoids

first: Mirjana

last: Kessler

first: Kristin

last: Fritsche

first: Hilmar

last: Berger


title: Learning the cis sequence elements that determine AP-1 monomer specificity (ChIP-seq data sets)

overall_design: ChIP-seq targeting transcription factors from the AP-1 family (Atf3, cJun, Fos, Fra2, JunB, and JunD) and PPARg were performed in mouse thioglycollate elicited macrophage cells derived from two strains of mice (C57BL6/EIJ and BALB/cJ) in vehicle treatment and/or KLA treatment with corresponding input experiments and biological replicates. Additional ChIP-seq experiments targeting the transcription factors PU.1 and CEBPa were performed to validate previous studies using mouse thioglycollate elicited macrophage cells in vehicle treatment and KLA treatment. ChIP-seqs for Atf3, cJun, and JunD were also performed in immortalized bone marrow derived macrophage cells derived from C57BL6/EIJ mice (also with biological replicates).


title: Chronic Chlamydia infection in fallopian tube organoids alters epithelial differentiation and accelerate methylation changes

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Chlamydia trachomatis (Ctr) is able to colonize the human fallopian tube, causing scarring and inflammation, which can lead to infertility. Here we describe a chronic Ctr infection model using human fallopian tube organoids. The defense response of the organoids to infection includes active expulsion of the bacteria from the apical side of the epithelium and compensatory cellular proliferation, clearly demonstrating a role for core mechanisms of epithelial homeostasis in defense against this invading pathogen. During progression in culture for over 9 months, the population of epithelial cells underwent a permanent shift towards a more dedifferentiated state. We identify LIF signaling an essential for regulation of the stemness in the tube and formation of organoids, and report its activation triggered by Ctr . In the long term, chronic Ctr infection leads to changes in the composition of the epithelium, marked by an increase in the proportion of secretory cells, expansion of the CD24+ positive population, upregulation of SPP1 factor, as well as downregulation of inflammatory mediators CD90, CD83, and CCR7. Ctr increases hypermethylation of DNA in polycomb repressed genomic regions - indicator of accelerated molecular aging. This infection model reveals an important link between Ctr and regulation of the host epigenome and suggests that Ctr has a long-term impact on the epithelial interaction with the immune system. These permanent changes in the epithelium may be a contributing factor in the development of tubal pathologies, particularly development of high grade serous ovarian cancer (HGSOC).

overall_design:
Microarray experiments were performed as dual-color hybridizations on Agilent  4x44K and 8x60K Whole Mouse Genome Microarrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.
Microarray experiments were performed as single-color hybridizations on Agilent 4x44K and 8x60K Whole Mouse Genome Microarrays.

first: Karen

last: Hoffman


title: 24-hour transcriptome profile in the murine VTA

status: Public on Jan 30 2019

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

summary: This study aimed at identifying rhythmically regulated transcripts in the ventral tegmental area (VTA) of mice. Punch biopsies of the VTA from C57BL/6 brain slices were prepared at 6 different timepoints across the day and analyzed for transcriptome regulation

overall_design: n = 4 per time point; 4-hour intervals starting at ZT0 (= "lights on") in a 12-hour light: 12-hour dark (LD) cycle; male C57BL/6N mice of 10-12 weeks of age were used; brains were sliced at 0.5 mm thickness and micropunches (diameter 0.5 mm) isolated for total RNA isolation, cRNA conversion and microarray habridization

first: Chriistiane

last: Koch

first: Jana

last: Kiehn

first: Kimberly

last: Begemann

first: Jan

last: Mauer

first: Martin

last: Hess

first: Andreas

last: Moser

first: Sebastian

last: Schmid

first: Jens

last: Brüning


title: Inhibition of EHMT1/2 rescues synaptic and cognitive functions for Alzheimer's disease

city: Buffalo

first: Zhen

last: Yan

address: 124 Sherman Hall

department: Physiology and Biophysics

institute: University at Buffalo

summary: Epigenetic dysregulation, which leads to the alteration of gene expression in the brain, is suggested as one of the key pathophysiological bases of aging and neurodegeneration. Here we found that, in the late-stage familial Alzheimer’s disease (FAD) mouse model, repressive histone H3 dimethylation at lysine 9 (H3K9Me2) and euchromatic histone methyltransferases, EHMT1 and EHMT2 (H3K9Me2 catalyzer), were significantly elevated in the prefrontal cortex (PFC) region of post-mortem tissues from human patients with Alzheimer's disease. Concomitantly, H3K9Me2 at the promoter region of glutamate receptors was increased in PFC of aged FAD mice, which was linked to the diminished transcription, expression and function of AMPA and NMDA receptors. Treatment of FAD mice with specific EHMT1/2 inhibitors reversed histone hyper-methylation and led to the recovery of glutamate receptor expression and excitatory synaptic function in PFC and hippocampus. Chromatin immunoprecipitation-sequencing (ChIP-seq) data indicated that FAD mice exhibited genome-wide increase of H3K9Me2 enrichment at genes involved in neuronal signaling (including glutamate receptors), which was reversed by EHMT1/2 inhibition. Moreover, the impaired recognition memory, working memory, and spatial memory in aged FAD mice were rescued by the treatment with EHMT1/2 inhibitors. These results suggest that disrupted epigenetic regulation of glutamate receptor transcription underlies the synaptic and cognitive deficits in Alzheimer's disease, and targeting histone methylation enzymes may represent a novel therapeutic strategy for this prevalent neurodegenerative disorder.

overall_design: Examination of histone H3 dimethylation at lysine 9 in wild type mice, familial AD mice and familial AD mice treated with EHMT1/2 inhibitor

first: Yan

last: Zheng

first: Aiyi

last: Liu

first: Zijun

last: Wang

first: Qing

last: Cao

first: Wei

first: Lin

last: Lin

first: Kaijie

last: Ma

first: Freddy

last: Zhang

first: Jing

last: Wei

first: Emmanuel

last: Matas

first: Jia

last: Cheng

first: Guojun

last: Chen

first: Xiaomin


title: Epigenome analysis of pre- and post-neoadjuvant chemotherapy breast tumor samples

city: Guangzhou

first: Yumei

last: Luo

state: Guangdong

address: 63 Duobao Road

institute: The Third Affiliated Hospital of Guangzhou Medical University

summary: Methylome-wide DNA methylation profiling of spatially separated breast tumor samples pre- and post-neoadjuvant chemotherapy (NAC) to characterize methylation heterogeneity alteration by NAC. The Illumina Infinium HumanMethylation450K Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs in the 47 samples derived from 8 breast cancer patients.

overall_design: Bisulphite converted DNA from the 47 samples were hybridised to the Illumina HumanMethylation450K BeadChip v1.2

first: Detu

last: Zhu


title: Nephron progenitor commitment is a stochastic process influenced by cell migration.

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

summary: Kidney development depends on a balance of nephron progenitor self-renewal and commitment. Here we examine how cells shift from a motile progenitor state to a static committed state during nephrogenesis. Cells that express Wnt4, an early marker of commitment, give rise to both the nephron lineage and a migrating sub-population that may re-enter the progenitor pool. Single cell transcriptional profiling reveals Wnt4-lineage cells across a range of transcriptional states, including cells that return to an uninduced progenitor state.

overall_design: Single cell RNA-seq from Wnt4 expressing cells of E15.5 embryonic kidneys

first: Kynan

last: Lawlor

first: Alexander

middle: N

last: Combes

first: Melissa

last: Little


title: Expression data from cytokine producing human CD4+ T cells

city: London

first: Esperanza

last: Perucha

address: Great Maze Pond

department: Inflammation Biology

country: United Kingdom

institute: King's College London

summary:
Immune system homeostasis depends on signals that drive effector (like secretion of pro-inflammatory cytokines like IFNg) and regulatory (like secretion of the anti-inflammatory cytokine IL-10) functions.
In this study we aimed at understand the signals that drive the switching from IFNg+ to IL-10+ state in CD4+ human T cells

overall_design: Peripheral blood CD4+ T cells were isolated from 9 individuals and stimulated for 36h in the presence of anti-CD3 and anti-CD46 antibodies and IL-10. After incubation, cells were harvested, double IFNg/IL-10 cytokine secretion assay run and IFNg+IL10-; IFNg+IL10+; IFNg-IL10+ and IFNg-IL10- cytokine-producing populations sorted by FACS. Finally, gene expression arrays were performed in the sorted populations

first: Rossella

last: Melchiotti


title: NextGen microRNA sequencing of mouse plasma collected from myocardial infarction mice and sham mice

city: Birmingham

first: Junjie

last: Yang

state: AL

address: 1670 University Blvd

department: BME

institute: UAB

type: Non-coding RNA profiling by high throughput sequencing

summary: Many microRNA expression levels in plasma are greatly changed after mouse myocardial infarction. We aim to find out the steadily-expressed microRNAs in plasma under hypoxia and normoxia, so as to be further utilized for normalization of microRNA expression detection.

overall_design: Plasma microRNA profiles of myocardial infarcted mice and normal mice were generated by deep sequencing, in duplicate, using Illumina GAIIx. This method calculates a normalization factor based on multiple reference miRNAs for more accurate and reliable normalization of miRNA expression data. It is based on the principle that the expression ratio of two reference miRNAs (using standard deviation of log-transformed reference miRNA ratios) should be identical in all samples. Stability measures will be returned which are the average pairwise variation between a particular reference miRNA and all other reference miRNAs using stepwise exclusion of the worst scoring miRNAs. The ten miRNAs with the best miRNA stability measures are listed as long as their value is less than 1.5.

first: Gangjian

last: Qin


title: Learning the cis sequence elements that determine AP-1 monomer specificity

first: Jenhan

last: Tao


title: The commensal-derived metabolite butyrate imprints an antimicrobial program in macrophages

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

institute: University of Oxford

summary: The balance between tolerogenic and inflammatory responses determines immune homeostasis in the gut. Dysbiosis and a defective host defense against invading intestinal bacteria can shift this balance via bacterial-derived metabolites and trigger chronic inflammation. We show that the short chain fatty acid butyrate modulates monocyte to macrophage differentiation by promoting antimicrobial effector functions. The presence of butyrate modulates antimicrobial activity via a shift in macrophage metabolism and reduction in mTOR activity. This mechanism is furthermore dependent on the inhibitory function of butyrate on histone deacetylase 3 (HDAC3) driving transcription of a set of antimicrobial peptides including calprotectin. The increased antimicrobial activity against several bacterial species is not associated with increased production of conventional cytokines. Butyrate imprints antimicrobial activity of intestinal macrophages in vivo. Our data suggest that commensal bacteria derived butyrate stabilize gut homeostasis by promoting antimicrobial host defense pathways in monocytes that differentiate into intestinal macrophages.

overall_design: Paired samples of control and butyrate-treated macrophages prepared from two individuals.

first: Julie

last: Schulthess

first: Sumeet

last: Pandey

first: Melania

last: Capitani

first: Kevin

last: Rue-Albrecht

first: Isabelle

last: Arnold

first: Fanny

last: Franchini

first: Agnieszka

last: Chomka

first: Nicholas

last: Ilott

first: James

last: McCullagh

first: Stephen

last: Sansom

first: Carolina

middle: V

last: Arancibia

first: Holm

last: Uhlig


title: Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in larval carcasses

status: Public on Jan 29 2019

city: Cardiff

middle: van der

last: Graaf

address: Museum Avenue

department: Cardiff School of Biosciences

institute: Cardiff University

summary: We used larval carcasses of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 21M to 32M reads across all samples. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. A python script extracting intron data of genes from the FlyMine database identified a trend where down-regulated genes had a higher total intron length and had more introns. Up-regulated genes had a lower total intron length and less introns when compared to the non-differentially expressed genes. Furthermore, down-regulated genes showed that the majority of genes are involved in the production of circular RNAs

overall_design: Examination of gene expression in 2 different genotypes, WT and Nxt1 trans-heterozygotes.

last: van der Graaf

first: Helen

last: White-Cooper


title: CRAC channel-mediated gene expression in Treg cells

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

institute: New York University School of Medicine

summary: T regulatory (Treg) cells maintain immunological tolerance and their depletion in humans and mice results in autoimmune disease. The development of Treg cells in the thymus, their differentiation into effector T cells and their activation depends on Ca2+ release-activated Ca2+ (CRAC) channels formed by STIM and ORAI proteins. Gene expression analysis of murine Treg cells with genetic deletion of Stim1 and Stim2 genes after their development in the thymus shows an important role of CRAC channel-mediated Ca2+ influx in the regulation of transcription factors and signaling pathways that control the identity and differentiation of Treg cells.

overall_design: Comparing transcriptome of WT and Stim1/2-deficient (DKO) Treg cells

first: Martin

last: Vaeth


title: Bi-directional interaction between mesenchymal stem cells and transit amplifying cells in mesenchymal tissue homeostasis [Axin2beta]

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

summary: We sequenced mouse incisor mRNA from 6 mice (3 WT and 3 mutant) to compare their gene expression profile

overall_design: Incisor mRNA of one-month-old Axin2-CreER;β-cateninfl/fl and β-cateninfl/fl mice were generated for RNA sequencing

first: Junjun

last: Jing

first: Jifan

last: Feng


title: Histone arginine methylation by Prmt controls lung branching morphogenesis through transcriptional repression of Bmp

city: Beijing

first: jie

last: jiao

address: No. 1 West Beichen Road, Chaoyang District

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

summary: We report that a protein arginine methyltransferase Prmt and symmetric dimethylation at histone H arginine  (HRsme) directly associates with chromatin of Bmp to suppress its transcription. Inactivation of Prmt in the lung epithelium results in halted branching morphogenesis, altered P-D airway patterning and neonatal lethality.

overall_design: The sample are E14.5 mouse lung ,for each sample, seven lungs were collected and pooled.The Control sample is E14.5 wildtype lung. Total RNA was extracted from these two samples and performed RNA-sequencing.

first: Qiuling

last: Li

first: Jie

last: Jiao


title: Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in whole larvae

first: Kevin

summary: We used whole larvae of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 6.4M to 11.1M reads across all samples. In wandering larvae, stationary larvae and white prepupae, a total of 435, 855, and 611 genes were differentially expressed. A high percentage of down-regulated genes were highly expressed/testis-specific in the Drosophila testis.


title: Comprehensive Analysis of TCR-β Repertoire in Patients with Neurological Immune-mediated Disorders

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Infiltrating T-lymphocytes from the peripheral blood into the central nervous system (CNS) play a dynamic role in the development of a neurological immune-mediated diseases. HAM/TSP is a chronic progressive inflammatory neurological disorder associated with human T-cell lymphotropic virus type I (HTLV-I) infection. In this chronic myelopathy, virus-infected circulating T-cells infiltrate the CNS and an immune response is initiated against the components of CNS. As the HTLV-I proviral load (PVL) has been used as the best clinical marker for patient diagnostic with HAM/TSP, we hypothesized there might be a signature on T-cell receptor (TCR) clonal repertoire in these patients, which could distinguish HAM/TSP patients from the healthy population, as well as from patients with a more heterogeneous CNS-reactive inflammatory disease as multiple sclerosis (MS). With this in mind, we applied an innovative unbiased molecular technique – unique molecular identifier (UMI) library-strategy to investigate with high accuracy the TCR clonal repertoire by high throughput sequencing (HTS) technology. cDNA-TCR β-chain libraries were sequenced from 2 million peripheral mononuclear cells (PBMCs) in 14 HAM/TSP patients, 34 MS patients and 20 healthy controls (HC). To address whether the clonal expansion correlates with the patient’s PVL level, analysis of longitudinal TCR repertoire was performed in 2 HAM/TSP patients. Over 5.6 million TCR sequences were generated per sample on HiSeq 2500 Illumina system and analyzed through the molecular identifier groups-based error correction pipeline (MiGEC). Bioinformatic analysis showed that clones with more than 8 reads had a lower coefficient of variation (CV) and then could be used with confidence to evaluate the TCR clonal expansion. While HAM/TSP patients showed the higher clonal T-cell expansion compared to MS and HC, increase of the TCR clonal expansion was inversely correlated with the diversity of TCR repertoire in all subject’s group. In addition, correlation of the PVL with TCR clonal expansion was observed in HAM/TSP patients at longitudinal time-points. Surprisingly, MS patients showed a higher diversity of TCR repertoire along with a very slight clonal T-cell expansion in comparison to either HAM/TSP patients or HC. Despite of the higher TCR clonal expansion in HAM/TSP patients, a non-shared or “private” TCR repertoire was observed in these patients. No clones that shared the same CDR3 amino acid sequences were seen in HC and MS patients. However, a cluster of related CDR3 amino acid sequences were observed for 18 out of 34 MS patients when evaluated by phylogenetic tree analysis. It suggestes that a TCR-repertoire signature might characterize patients with MS. Our findings suggest that even though a unique TCR-b repertoire shapes the immune response in patients with neurological immune-mediated disease, a relatedness on clonal T-cell repertoire exist in MS.

overall_design: TCR-β profiles for 68 human samples were generated via deep sequencing using the Illumina HiSeq 2500 system and reagents. Of those profiled, 20 were not diagnosed as having HAM/TSP or MS (i.e., Healthy Control, "HC"), 14 were diagnosied as having HAM/TSP, and 34 were diagnosed as having MS.

first: Alessandra

last: de Paula Alves Sousa

first: Joan

last: Ohayon

first: Jun

last: Zhu

first: Paolo

last: Muraro

first: Steven

last: Jacobson


title: REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease (Affymetrix NPC data set)

city: Boston

first: Derek

last: Drake

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Alzheimer’s disease (AD) is preceded by a long prodromal period of decades during which pathology accumulates in the brain prior to the onset of dementia.  The molecular basis of these changes as well as how and when they start are unclear. Here we have analyzed neural progenitor (NP) cells and neurons generated from induced pluripotent stem cells (iPSCs) from individuals with sporadic AD (AD) and age-matched controls.  Transcriptome analysis does not distinguish between iPSCs from individuals with SAD and age-matched controls, but shows major differences in iPSC-derived NP cells and neurons in gene networks related to neuronal differentiation, neurogenesis and synaptic transmission.  SAD NP cells exhibit accelerated neuronal differentiation, leading to the generation of neurons with increased synapse formation and electrical excitability. Network analysis of the transcriptome implicates the transcriptional repressor REST/NRSF and two components of the polycomb repressive complex 2, SUZ12 and EZH2.  Accelerated differentiation of SAD NP cells was reversed by exogenous REST expression and mimicked in normal NP cells by REST knockdown.  The phenotype of accelerated neural differentiation was recapitulated in NP cells and cerebral organoids derived from gene-edited iPSC lines that express apolipoprotein E4 (APOE4), the major genetic risk factor for AD.  Network analysis of the APOE4-related transcriptome again showed reduced function of REST, EZH2 and SUZ12 to be the major predicted regulatory changes. Reduced function of the REST repressor was due to reduced nuclear translocation and chromatin binding, and was associated with disruption of the nuclear membrane and lamina in SAD and APOE4 NP cells.  Thus, impaired function of specific transcription factors and changes in nuclear architecture may be among the earliest events in the pathogenesis of AD.

overall_design: Comparison of SAD (n=5) and NL (n=5) NPCs.

first: Heather

last: Feldman

first: Tao

last: Lu

first: Nicholas

last: Bishop

first: Bruce

last: Yankner


title: REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease (Affymetrix neurons data set)

overall_design: Comparison of SAD (n=5) and NL (n=6) neurons.


title: REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease (RNA-seq data set)

overall_design: Explore the effects of isogenic editing of APOE E4 to E3 in cerebral organoids. Comparison of APOE E4 vs E3 isogenic organoids with 3 biological replicates per group.

first: Katharina

last: Meyer

first: Elaine

last: Lim

first: George

last: Church


title: REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease

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

overall_design: Refer to individual Series


title: miR-140 mutation and skeletal dysplasia [seCLIP]

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA–target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs.

overall_design: seCLIP analysis for Ago2 and Ybx1 in chondrocytes with miR-140 G mutation

first: Giedre

last: Grigelioniene

first: Tatsuya

last: Kobayashi


title: Transcriptome profiling of caspase-2 deficient lymphomas from EμMyc and neuroblastomas from Th-MycN mice

status: Public on Jan 28 2019

city: Adelaide

first: Loretta

last: Dorstyn

state: South Australia

address: UniSA CRI Building, Corner North Terrace and Morphett Street Bridge, GPO Box 2471

department: Centre for Cancer Biology

institute: University of South Australia and SA Pathology

summary: The project used next generation sequencing for RNA-seq analysis, to identify transcriptome changes associated with tumorigenesis in two different caspase-2 knockout mice models. We describe key changes in both lymphoma and neuroblastoma associated genes in the two tumor types that may contribute to tumor outcome following loss of Casp2. We identified a panel of genes with altered expression in Th-MYCN/Casp2-/- tumors, that are strongly associated with neuroblastoma outcome, and which have roles in melanogenesis, Wnt and Hippo pathway signaling, that also contribute to neuronal differentiation. In addition, we found that key changes in gene expression in the EμMyc/Casp2-/- tumors, are associated with increased immune signaling and suggest that Casp2 deficiency augments immune signaling pathways that may be in turn, enhance lymphomagenesis. Overall, our study has identified new genes and pathways that contribute to the caspase-2 tumor suppressor function and highlight distinct roles for caspase-2 in different tissues.

overall_design: We used tumors from EμMyc/Casp2-/- mice (which are more aggressive compared to their EμMyc counterarts) as well as tumors from Th-MycN/Casp2-/- mice (which show delayed tumour onset compared to Th-MycN mice) and compared the transcriptomes to their Casp2 wild type counterpart tumors. Sequencing was carried out with  Illumina HiSeq 2000 and used short, single-end reads (1x 50bp flow cells) with 4 samples per lane. This yielded approximately 20-30 million raw reads per sample.

first: Emily

last: Hackett-Jones

first: Sharad

last: Kumar


title: Differential gene expression patterns of Yersinia pestis and Yersinia pseudotuberculosis during infection and biofilm formation in the flea digestive tract

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Yersinia pestis, the etiologic agent of plague, emerged as a flea-borne pathogen only within the last 6,000 years.  Just five simple genetic changes in the Yersinia pseudotuberculosis progenitor, which served to eliminate toxicity to fleas and to enhance survival and biofilm formation in the flea digestive tract, were key to the transition to the arthropod-borne transmission route.  To gain a deeper understanding of the genetic basis for the development of a transmissible biofilm infection in the flea foregut, we evaluated additional gene differences and performed in vivo transcriptional profiling of Y. pestis, Y. pseudotuberculosis wild-type (unable to form biofilm in the flea foregut), and a Y. pseudotuberculosis mutant strain (able to produce foregut-blocking biofilm in fleas) recovered from fleas 1 day and 14 days after an infectious bloodmeal.  Surprisingly, the Y. pseudotuberculosis mutations that increased c-di-GMP levels and enabled biofilm development in the flea did not change expression levels of the hms genes responsible for the synthesis and export of the extracellular polysaccharide matrix required for mature biofilm formation.  The Y. pseudotuberculosis mutant uniquely expressed much higher levels of one of the Yersinia Type VI secretion systems (T6SS-4) in the flea, and this locus was required for flea blockage by Y. pseudotuberculosis, but not by Y. pestis.  Significant differences between the two species in expression of several metabolism genes, the Psa fimbrial genes, quorum sensing related genes, transcriptional regulators, and stress response genes were evident during flea infection.  The results provide insights into how Y. pestis has adapted to life in its flea vector and point to evolutionary changes in the regulation of biofilm development pathways in these two closely related species

sample_organism:
Yersinia pestis
Yersinia pseudotuberculosis

platform_organism:
Yersinia pseudotuberculosis
Yersinia pestis KIM10+
Yersinia pestis CO92

overall_design: Yersinia strain comparisons

first: Iman

last: Chouikha

first: Daniel

first: Clayton

last: Jarrett

first: Yi-cheng

last: Sun

first: B

middle: J

last: Hinnebusch


title: Role of Sko1 sumoylation in regulating target site binding

city: Toronto

first: Emanuel

last: Rosonina

address: 4700 Keele Street

department: Biology

institute: York University

summary: We examine how SUMO post-translational modification of the yeast transcription factor Sko1 affects its binding site selection and affinity. Chromatin immunoprecipitation followed by next-generation sequencing was performed in strains expressing wild-type Sko1 (Sko1-WT) or Sko1 that harbors an Arg-to-Lys mutation at Lys 567 (Sko1-MT), that impairs its sumoylation. We find that, compared with Sko1-WT, SUMO-deficient Sko1 binds numerous additional sites that are near promoters of non-Sko1 target genes. Furthermore, Sko1-MT shows higher occupancy levels than Sko1-WT on most genes that are occupied by both forms. Osmotic stress causes a general rearrangement of Sko1 positions across the genome, but increased numbers of binding sites and occupancy levels are still observed for Sko1-MT after treatment with NaCl. This study indicates that sumoylation attenuates Sko1 association with chromatin and increases its binding specificity.

overall_design: Comparison of binding sites and affinity between wild-type and sumoylation-deficient forms of Sko1.

first: Veroni

last: Sri Theivakadadcham

first: Benjamin

middle: G

last: Bergey


title: CEBPA-mutated leukemia is sensitive to genetic and pharmacological inhibition of the MLL complex

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: The gene encoding the transcription factor C/EBPα is mutated in 10-15% of all patients with de novo acute myeloid leukemia (AML). N-terminal CEBPA mutations cause selective ablation of full-length C/EBPα without affecting the expression of a shorter oncogenic isoform, termed p30. The mechanistic basis of p30-induced leukemogenesis is not well understood. Here, we show that the SET/MLL histone methyltransferase complex represents a critical actionable vulnerability in CEBPA-mutated AML. The oncogenic C/EBPα p30 isoform and MLL show global co-localization on chromatin and core SET/MLL complex components exhibit robust physical interaction with p30. We also show that C/EBPα p30-expressing cells require the expression of an intact MLL protein, as targeted CRISPR/Cas9-mediated mutagenesis results in proliferation arrest and myeloid differentiation. In line with this, CEBPA-mutated hematopoietic progenitor cells are hypersensitive to pharmacological inhibition of the SET/MLL complex. SET/MLL complex inhibition impairs proliferation, induces cell cycle arrest and causes apoptosis in mouse and human AML cells with CEBPA mutations. Global analysis of gene expression changes shows that inhibitor treatment restores myeloid differentiation potential in CEBPA-mutated cells. Finally, we identify the transcription factor GATA2 as a direct critical target of the cooperative gene regulation between p30 and MLL in CEBPA-mutated AML. Taken together, we show that C/EBPα p30 requires the SET/MLL complex to regulate oncogenic gene expression and that CEBPA-mutated AML is hypersensitive to perturbation of the SET/MLL complex. These findings expand our understanding of CEBPA-mutated AML and identify the SET/MLL complex as a potential therapeutic target in this disease.

overall_design: RNA-seq and ChIP-seq

first: Luisa

last: Schmidt

first: Florian

last: Grebien


title: FACS Sequencing Analysis of DCX+ cells in the DG of Wild Type and Fmr1-/y; Dcx-DsRed mice

city: Madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

summary:
Purpose: The goals of this study are to investigate the molecular mechanism underlying FMRP-regulated maturation of newborn neurons

Methods: DG tissue were isolated from 6-7 weeks old Fmr1-/y; Dcx-DsRed mice and their WT littermates. All cell populations were isolated into single cells using a Becton Dickinson FACS Aria II contained in a Biosafety Carbinet using 20 psi pressure and 100-μm nozzle aperture. 10,000 total alive or Dcx-DsRed+ alive Cells were collected directly in Trizol. Total RNA from the sorted cell was isolated using the Direct-zol™ RNA MiniPrep Kit. Strand-specific, poly(A) selected cDNA libraries were generated using Nugen  Ovation® Ultralow Library Systems  (Illumina) according to the manufacturer’s protocol.  Cluster generation and high-throughput sequencing were performed on a HiSeq 2500 (Illumina), using the paired-end 100 bp protocol. Reads were aligned to the mouse genome GRCm38 with annotation from Gencode.

Results: RNA isolated from DsRed+ cells were subjected to next generation sequencing and 519 differentially expressed (DE) genes were identified that showed significant changes (FDR-adjusted P < 0.05) between Fmr1 KO and WT cells.

overall_design: RNA-Seq of FACS-sorted DCX-DsRed cells from DG of 6-7 weeks old Fmr1-/y and wild type mice

first: Minjie

last: Shen

first: Feifei

last: Wang


title: ADAMTS-9 is an aggrecan-degrading enzyme in mouse cartilage

city: Melbourne

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

institute: MCRI

summary: Although ADAMTS-4 and ADAMTS-5 are the principal aggrecanases in mice and humans, mice lacking both these enzymes (ADAMTS-4/-5Dcat) are healthy, viable, with no overt skeletal phenotype, suggesting the presence of an alternative aggrecanase in these mice. We previously identified a novel aggrecanase activity that was regulated by retinoic acid, but not IL-1a. The upregulated activity cleaved aggrecan at E↓A bonds. This study aimed to identify the alternative aggrecanase. Femoral head cartilage from TS-4/5Dcat mice was stimulated with IL-1a or retinoic acid and total RNA was analysed by microarray. Candidate, upregulated genes identified by Quantile Normalisation included ADAMTS, MMPm cathepsin and calpain families as putative aggrecanases. Three criteria, including quantitative RT-PCR analyses, sensitivity to retinoic acid treatment and sensitivity to TIMP-3 inhibition, were then used as readouts to identify candidate extracellular proteinases whose mRNA expression levels were increased by retinoic acid, but not by IL-1a treatment. Thereafter, gene silencing was used to identify the most likely aggrecanase in chondrocytes from TS-4/5Dcat mice. Aggrecanase activity was monitored by Western blotting and immunohistochemistry with neoepitope antibodies. The microarray analyses identified ADAMTS-9, MMP-11 and calpain-5 as candidate aggrecanases that were upregulated by retinoic acid. While qPCR confirmed this finding, calpain 5 was excluded from the candidate list because it was not inhibited by TIMP-3. MMP-11 was also excluded because it was upregulated by IL-1a. ADAMTS-9 therefore emerged as a candidate for the novel aggrecanase. Gene silencing confirmed ADAMTS-9 as the putative aggrecanase. Immunohistochemistry revealed that ADAMTS-9 in mouse knee joints was expressed in the proliferative zone of both wildtype and TS-4/5Dcat growth plates, and also in the calcified cartilage of the wildtype hypertrophic zone. In conclusion, ADAMTS-9 is an aggrecanase that cleaves at FREEE1467↓1468GLGS in the chondroitin sulphate-rich region of aggrecan.

overall_design: The experiment compared three conditions (untreated, IL-1a-treated and retinoic acid treated) in two genotypes (Donut and Gertrude ADAMTS4/5Dcat mice), in duplicate.

first: Fraser

last: Rogerson

first: Karena

last: Last

first: Suzanne

last: Golub

first: Stephanie

last: Gauci

first: Heather

last: Stanton

first: Amanda

last: Fosang


title: Differential expression of genes in fibroblasts and epithelial cells infected with dsDNA viruses

status: Public on Jan 27 2019

city: Princeton

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

institute: Princeton University

summary: We studied changes in a whole transcriptome during dsDNA virus infection.

overall_design: Fibroblasts (MRC5 & HFF) and epithelial cells (ARPE19) were infected with HCMV, HSV1 or Ad5 and total RNA was isolated at 48, 9, or 24 hpi, respectively. Total 15 treatments were used. There were 2 biological replicates analyzed per each treatment.

first: M

middle: T

last: Nogalski

first: A

last: Solovyov

first: T

first: B

last: Greenbaum


title: Differential expression of genes in AD169-infected MRC5.

first: Thomas

summary: We studied changes in a whole transcriptome during HCMV infection.

overall_design: Fibroblasts (MRC5) were infected with HCMV and total RNA was isolated at 48. Total 2 individual samples were used. There were 3 replicates analyzed per individual sample.


title: RNA-seq transcriptome profiling of hybrid (hawaii mother and bristol father) C. elegans H3K27me3 M+P+ vs. M+P- hermaphrodite germlines

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

type: Genome variation profiling by high throughput sequencing

summary: Worms that inherited the sperm genome lacking the repressive mark H3K27me3 (K27me3 M+P-) misexpress genes in their germlines when compared to genetically identitical worms that inherited the sperm genome with H3K27me3 (K27me3 M+P+).

overall_design: Transcriptome profiles of hermaphrodite germlines  from hybrid worms that inherited the sperm genome with H3K27me3 (4 replicates of K27me3 M+P+) vs without H3K27me3 (4 replicates K27me3 M+P-) to compare to 4 replicates of 'wildtype'.

first: Kiyomi

last: Kaneshiro

first: Andreas

last: Rechtsteiner


title: RNAseq analysis of hematopoietic stem cells isolated from control and Regnase1 null mice

status: Public on Jan 25 2019

city: Suita

first: Hiroyasu

last: Kidoya

state: Osaka

address: 3-1 Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka university

summary: The balance between self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) maintains hematopoietic homeostasis, failure of which can lead to hematopoietic disorder. HSPC fate is controlled by signals from the bone marrow niche resulting in alteration of the stem cell transcription network. Regnase-1, a member of the CCCH zinc finger protein family possessing RNAse activity, mediates post-transcriptional regulatory activity through degradation of target mRNAs. The precise function of Regnase-1 has been explored in inflammation-related cytokine expression but its function in hematopoiesis has not been elucidated. To clarify the role of Regnase-1 for hematopoiesis, we performed gene expression analysis on sorted HSC from control and Regnase1 null mice.

overall_design: Bone marrow cells were obtained from femur of individual eight-week old Vav1-iCre; Reg1flox/flox mice (Reg1Δ/Δ, case) and control Reg1flox/flox mice (Reg1flox/flox ,control). RNAseq analyses were performed on HSCs (Lin- ScaI+ cKit+ CD34- Flt3- cells) purified by flow cytometry sorting.

first: Nobuyuki

last: Takakura


title: Transcriptional profiling of CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ,  cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains in the absence or presence of alpha pheromone in Candida albicans

status: Public on Jan 26 2019

city: Montréal

first: Raha

last: Parvizi Omran

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

institute: Concordia University

summary: Twenty-one pheromone-induced genes were selected from the literature (Zhao, Daniels et al. 2005 was the major source) as the reference set for assessing the pheromone response of  CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ,  cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains.Our aim was to check whether or not these 21 pheromone-induced genes are up-regulated in response to pheromone in each mutant strain.

overall_design: Total RNA was extracted from CAI4, cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains. Cultures were grown overnight in SC-   Glucose media at room temperature and were diluted to OD600 of 0.1 in 10 ml the next day. for each   strain 2 sets of samples were prepared, one set were treated with α-pheromone (1μg/ml)   and the other was untreated. After 3 hours of treatment cells were collected at an OD600   of between 0.8 and 1.

first: Debra

last: Fulton


title: Transcription Factors Dlx1/2 Are Required for Making All Interneurons in the Olfactory Bulb [Dlx1/2]

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
Purpose: To assess changes in gene expression profiles from the E16.5 wild type littermate controls LGE and Dlx1/2-/- mutant mice LGE (lateral ganglionic eminence).
Methods: Total RNA was isolated and sequenced using an Illumina Hi-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed which perform fold-change>=2 and P value <= 0.05.
Results: Compared to controls, 804 genes were significantly down regulated, and 673 genes were up regulated in the RNA expression level of the mutant LGE.

overall_design: LGE RNA profiles of E16.5 Wild type mouse brain and Dlx1/2-/- mutant mouse brain.

first: Teng

last: Guo

first: Heng

last: Du

first: Yan

last: Wen

first: Song

last: Wei

first: Meiyuzhen

last: Li

first: Guangxu

last: Tao

first: Zicong

last: Shang

first: Xiaolei

last: Song

first: Zhuangzhi

last: Zhang

first: Zhejun

last: Xu

last: You

first: Bin

last: Chen

first: Kazuaki

last: Yoshikawa

first: John

middle: L

last: Rubenstein

first: Zhengang

last: Yang


title: MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [ChIP, MNase]

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

summary: MeCP2 plays a multifaceted role in gene expression regulation and chromatin organization. Interaction between MeCP2 and methylated DNA to regulate gene expression is well established. However, the widespread MeCP2 distribution suggests its additional interactions with chromatin. Here we show, by both biochemical and ChIP-seq analyses, that MeCP2 directly binds to nucleosome subunit proteins and is recruited to distinct chromatin regions where H3K27me3 is enriched. We further observed that the impact of MeCP2 on transcriptional changes is correlated with histone post-translational modification patterns. Our findings indicate that MeCP2 can be recruited to genomic loci via indirect binding and that interaction between MeCP2 and histone proteins plays a significant role in gene expression regulation.

overall_design: Examination of two epigenetic markers from the olfactory epithelium in two biological samples. This dataset is created to supplement the MeCP2 ChIP-seq and MNase-seq datasets (GSE71126) generated by Rube HT. Nature Communications 2016.

first: Qizhi

last: Gong


title: REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease (Affymetrix iPSC data set)

first: Derek

last: Drake

overall_design: Comparison of SAD (n=4) and NL (n=6) iPSCs.

first: Heather

last: Feldman

first: Tao

last: Lu

first: Nicholas

last: Bishop

first: Bruce

middle: A

last: Yankner


title: The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: differential ChIP-seq of CP190 and CLAMP under CP190 knockdown

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Chromatin insulators are DNA-protein complexes that establish higher order independent DNA domains to influence transcriptional regulation. Insulators are defined by two different functions: they can block communication between an enhancer and a promoter and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy-insulator complex contains three core components: Su(Hw), CP190 and Mod(mdg4)67.2. Here we identify a novel role for Chromatin-linked adaptor for MSL proteins (CLAMP) in promoting gypsy chromatin insulator function. When Clamp is depleted by RNAi, gypsy-dependent enhancer blocking activity decreases and barrier activity is reduced in all tissues. Furthermore, Clamp RNAi knockdowns and mutation result in disorganized insulator complex localization in the nucleus. Co-immunoprecipitation experiments showed that CLAMP physically associates with core gypsy-insulator proteins. Co-localization of CLAMP with gypsy components on polytene chromosomes and ChIP-seq analysis demonstrates co-localization of CLAMP with a subset of insulator sites across the genome. Thus, our findings suggest a ubiquitous, genome-wide role for CLAMP in promoting gypsy-dependent chromatin insulator activity.

overall_design: ChIP-seq of CP190 in Drosophila melanogaster Kc167 cells in mock treatment and CLAMP knockdown. Two replicates per condition, with paired inputs.

first: Indira

last: Bag

first: Elissa

middle: P

last: Lei


title: Mitotic chromosome binding predicts transcription factor properties in interphase [ChIP-Seq]

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary: Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/ non-specific DNA binding affinity. How these properties affect the ability of TFs to occupy their specific binding sites in the genome and modify the epigenetic landscape is unclear. Here we combined live cell quantitative measurements of mitotic chromosome binding (MCB) of 502 TFs, measurements of TF mobility by fluorescence recovery after photobleaching, single molecule imaging of DNA binding in live cells, and genome-wide mapping of TF binding and chromatin accessibility. MCB scaled with interphase properties such as association with DNA-rich compartments, mobility, as well as large differences in genome-wide specific site occupancy that correlated with TF impact on chromatin accessibility. As MCB is largely mediated by electrostatic, non-specific TF-DNA interactions, our data suggests that non-specific DNA binding of TFs enhances their search for specific sites and thereby their impact on the accessible chromatin landscape.

overall_design: NIH-3T3 cells overexpressing different HA-tagged transcription factors were subjected to ChIP-seq

first: Elias

last: Friman


title: Engineered FGF19 promotes HDL biogenesis and transhepatic cholesterol efflux to prevent atherosclerosis

city: South San Francisco

first: Lei

last: Ling

address: 333 Oyster Point Blvd

institute: NGM Biopharmaceuticals

summary:
Cholesterol is an essential cell membrane component and precursor in metabolic pathways. Control of cholesterol levels is essential to human health. The endocrine hormone FGF19 potently inhibits CYP7A1, which controls a key step in cholesterol catabolism. However, the molecular mechanisms that integrate FGF19 with other cholesterol metabolic pathways are incompletely understood. Here we show that FGF19 and analogue promote HDL biogenesis and cholesterol efflux from the liver by selectively modulating liver X receptor signaling without inducing hepatic steatosis. We further identify ATP-binding cassette transporter A1 and FGFR4 as mediators of this effect. In dyslipidemic Apoe-/- mice fed a Western diet, treatment with FGF19 analogue dramatically reduced atherosclerotic lesion area in aortas. In healthy human volunteers, FGF19 analogue caused a placebo-adjusted increase in HDL cholesterol levels of 26% in seven days. These findings outline a regulatory role for FGF19 in cholesterol metabolism and advance our understanding of the mechanisms that coordinate sterol homeostasis.
We used microarrays to detail the global programme of gene expression affected by FGF19 treatment in mice.

overall_design: Mouse livers were selected for RNA extraction and hybridization on Affymetrix microarrays. RNA was isolated from the livers of db/db mice 2 weeks after administration of AAV-FGF19 or a control virus. RNA integrity and purity were confirmed by Bioanalyzer with RIN numbers > 8.0. Affymetrix mouse gene 1.0 ST whole-transcript arrays were used for hybridization.

first: Mei

last: Zhou

first: Marc

last: Learned

first: Stephen

last: Rossi

first: Hui

last: Tian

first: Alex

last: DePaoli


title: Transcription Factors Dlx1/2 Are Required for Making All Interneurons in the Olfactory Bulb [Pax6]

first: Guoping

last: Liu

summary:
Purpose: To assess changes in gene expression profiles from the E16.5 wild type littermate controls cortex and Pax6 sey/sey mutant mice cortex.
Methods: Total RNA was isolated and sequenced using an Illumina Hi-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed which perform P value <= 0.05.
Results: Compared to controls, 173 genes were significantly down regulated, and 245 genes were up regulated in the RNA expression level of the mutant cortex.

overall_design: Cortex RNA profiles of E16.5 Wild type mouse brain and Pax6 sey/sey mutant mice brain.

first: Teng

last: Guo

first: Heng

last: Du

first: Yan

last: Wen

first: Song

last: Wei

first: Meiyuzhen

last: Li

first: Guangxu

last: Tao

first: Zicong

last: Shang

first: Xiaolei

last: Song

first: Zhuangzhi

last: Zhang

first: Zhejun

last: Xu

last: You

first: Bin

last: Chen

first: Kazuaki

last: Yoshikawa

first: John

last: Rubenstein

first: Zhengang

last: Yang


title: Hedgehog signaling patterns the oral-aboral axis of the mandibular arch

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: E10.5 mouse mandibular arch cells were analyzed using 10X single-cell rna-seq

overall_design: single-cell RNA-Seq of E10.5 mouse mandibular arch cells

first: Rulang

last: Jiang


title: IL-6 trans-signaling induced gene expression in airway epithelial cells

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

summary:
Background: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) with asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthma is unclear.
Objective: To explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthma.
Methods: Primary human bronchial epithelial cell (HBEC) air-liquid interface (ALI) cultures were stimulated with IL-6 and sIL-6R to establish an IL-6TS gene signature. Two separate RNA sequencing (RNA-seq) studies were performed: The “IL-6 vs T2 study” compared gene expression after stimulation with control medium, IL-6, IL-6/sIL-6R and IL-4/IL-13, while the “JAK1-inhibition study” addressed the effect of JAK1 inhibition on IL-6TS induced gene expression.   The IL-6TS gene signature was used to stratify lung epithelial transcriptomic data obtained from asthmatics (n=103) in the U-BIOPRED cohorts by hierarchical clustering. Molecular phenotyping was based on the transcriptional profiling of epithelial brushings, pathway analysis and immunohistochemistry analysis of bronchial biopsies.
Results: Activation of IL-6TS in HBEC ALI cultures reduced epithelial barrier function and induced a specific epithelial gene signature enriched in airway remodeling genes. The IL-6TS signature identified a subset (n=17) of IL-6TS High asthma patients with increased epithelial expression of IL-6TS inducible genes in absence of increased systemic levels of IL-6 and sIL-6R. The IL-6TS High subset had an increased exacerbation frequency (p=0.028), blood (>300/μl; p=0.0028) and sputum (>20%; p=0.007) eosinophilia, and submucosal infiltration of CD4 T cells, CD8 T cells (p<0.001) and macrophages (p=0.001). In bronchial brushings, TLR pathway genes were up-regulated while the expression of epithelial tight junction genes was reduced (all with q<0.05). Sputum sIL-6R levels correlated with sputum markers of remodeling and innate immune activation, in particular YKL-40, MMP3, IL-8 and IL-1β (all with q<0.001).
Conclusions: Local lung epithelial IL-6TS activation in absence of type 2 airway inflammation defines a novel subset of asthmatics and may drive airway inflammation and epithelial dysfunction in these patients.

overall_design: Primary human bronchial epithelial cells grown and differentiated on air-liquid interface were stimulated basolaterally for 24h with cytokines corresponding to IL-6TS (IL-6 + sIL-6R), IL-6 alone, a Type 2 immune response (IL-4 + IL-13) or media alone as non-stimulated control. Each stimulation condition was done in triplicates. Cells were lysed, the RNA isolated and converted into libraries then used for next generation sequencing in order to identify genes that were up- or downregulated in response to the different stimulations.

first: Zala

last: Jevnikar Rojnik

last: Ax

first: Kristofer

last: Thörn

first: Lisa

last: Öberg

first: Henric

last: Olsson


title: Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq]

first: David

last: Suter

overall_design: NIH-3T3 cells overexpressing different transcription factors (or no overexpression control) were subjected to ATAC-seq by Tn5 transposition

first: Elias

last: Friman


title: En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements

city: Seoul

first: Hyeon

middle: Joo

last: Lee

state: - Please choose -

address: 222 Wangsimni-ro, Seongdong-gu

department: Department of Life Science

institute: Hanyang University

summary:
RNA-seqs followed by whole and segmental deletions of XIST genes in human K562 cells.
The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and the XCI-involving RNA elements remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, ten smaller XIST segments, including repeats A, D, and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and fluorescence in-situ hybridization experiments on XIST RNA.

overall_design: There are mock transfected cells as control and 24 clones containing whole and segmental deletion of XIST.

first: Ramu

last: Gopalappa

first: Hongjae

last: Sunwoo

first: Seo-Won

last: Choi

first: Suresh

last: Ramakrishna

first: Jeannie

first: Hyongbum

last: Kim

first: Jin-Wu

last: Nam


title: Gene expression for surgically treated pancreatic cancer after one neoadjuvant vaccine dose

status: Public on Jan 24 2019

city: Baltimore

first: Lei

last: Zheng

state: Maryland

address: 1650 Orleans St; CRB1

department: Oncology

institute: Johns Hopkins University School of Medicine

summary: RNA seq gene expression analysis of patients with resected pancreatic cancer following 1 dose of GM-CSF expressing whole cell pancreatic vaccine 2 weeks prior to resection. Samples were obtained for IHC analysis of protein expression, IHC analysis of immune cell infitration and RNA sequencing correlates

overall_design: Data were used to make conclusions regarding the relationship of stromal expressed IDO, immune cell infiltration by IHC and the gene expression of different interluekins to describe pathways modified by IDO inhibitor treatment. Pending publication. IHC slides of each tumor case was obtained. Dissecting microscope was used by pathologist to obtain stroma. RNA were obtained, RNA sequencing was performed.

first: Alex

middle: B

last: Blair


title: Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

summary: The generation of terminally differentiated cell lineages during organogenesis requires multiple, coordinated cell fate choice steps. However, this process has not been clearly delineated, especially in complex solid organs such as the pancreas. Here, we performed single-cell RNA-sequencing in pancreatic cells sorted from multiple genetically modified reporter mouse strains at embryonic stages E9.5–E17.5. We deciphered the developmental trajectories and regulatory strategies of the exocrine and endocrine pancreatic lineages as well as intermediate progenitor populations along the developmental pathways. Notably, we discovered previously undefined programs representing the earliest events in islet alpha- and beta cell lineage allocation as well as the developmental pathway of the “first wave” of alpha-cell generation. Furthermore, we demonstrated that repressing ERK pathway activity is essential for inducing both alpha- and beta-lineage differentiation. This study provides key insights into the regulatory mechanisms underlying cell fate choice and stepwise cell fate commitment and can be used as a resource to guide the induction of functional islet lineage cells from stem cells in vitro.

overall_design: The overall goal of this study was to comprehensively define a fate map of mouse pancreatic lineage differentiation using the Smart-seq2 single-cell RNA-seq method. We used a Pdx1-GFP transgenic mouse line to purify E9.5 – E11.5 pancreatic progenitor cells; Pdx1-Cre; ROSA-RFP to isolate all pancreatic lineages at each day from E10.5 to E15.5. Because the percentage of endocrine cells in the pancreas is relatively low, to enrich the pancreatic endocrine lineages, we used an Ngn3-GFP knock-in mouse strain to sort GFP lower (Ngn3-GFPlow) and higher (Ngn3-GFPhigh) expressing cells from E13.5 to E15.5. Because Ngn3-GFPlow and Ngn3-GFPhigh cells could not be effectively separated by FACS at an earlier developmental stage and later stages, we generally sorted Ngn3+ cells at E12.5, E16.5 and E17.5. To obtain the differentiated beta and alpha cells, we sorted RFP+ and GFP+ cells from E15.5 Ins1-RFP and Gcg-P2A-GFP embryos, respectively. We purified pancreatic ductal cells at E16.5 and E17.5 from Sox9-CreER; ROSA-RFP mouse. To investigate the characteristics of the earlier differentiated endocrine cells, also called “first wave” endocrine cells, we purified Ngn3-GFP+ cells at E10.5 and E12.5, and Ngn3-Cre; ROSA-RFP+ cells at E11.5. To study whether ERK pathway represses pancreatic endocrine differentiation, we performed single-cell RNA-seq in Ins1-RFP+ cells from pancreas explants treated with U0126 (a MEK1/2 inhibitor). We also analyzed the datasets of E14.5 pancreatic cells generated by the 10X Genomics platform to parallelly compare the datasets generated using Smart-seq2 method.

first: Xin-Xin

last: Yu

first: Wei-Lin

last: Qiu

first: Liu

last: Yang

first: Yu

last: Zhang

first: Mao-Yang

last: He

first: Lin-Chen

last: Li


title: Gene Expression Data of Adipose Stem Cells from Normal-Weight Polycystic Ovary Syndrome Women vs. Controls

city: Los Angeles

first: Greogorio

last: Chazenbalk

state: California

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

country: USA

institute: University of California, Los Angeles

summary:
In vitro studies of subcutaneous (SC) abdominal adipose stem cells (ASC) from women with polycystic ovary syndrome (PCOS) show altered ASC commitment to preadipocytes and differentiation to mature adipocytes related to hyperandrogenism.
The goal of the study is to use microarrays to examine whether SC abdominal ASC gene expression are altered in normal-weight PCOS women and correlated with hyperandrogenemia and/or insulin resistance, which are prevalent clinical pathologies of PCOS.

overall_design:
ASCs were isolated from SC adipose tissue following SC abdominal biopsy in 4 PCOS women and 4 age and BMI matched controls for gene expression comparison. First generation of stem cells were cultured until cells reached confluency and isolated for RNA extraction and hybridization on Affymetrix microarrays.

Grant#: P50 HD071836
Title: Androgen excess as a mechanism for adipogenic dysfunction in PCOS women
Period: 2018-2022

first: Julia

middle: D

last: Phan

first: Karen

last: Leung

first: Xiangming

last: Ding

first: Xinmin

first: Gregorio


title: Dlx1/2 Are Central and Essential Components in the Transcriptional Code for Generating Olfactory Bulb Interneurons

first: Guoping

last: Liu

summary:
Generation of olfactory bulb (OB) interneurons requires neural stem/progenitor cell specification, proliferation, differentiation, and young interneuron migration and maturation. Here, we show that the homeobox transcription factors Dlx1/2 are central and essential components in the transcriptional code for generating OB interneurons. In Dlx1/2 constitutive null mutants, the differentiation of GSX2+ and ASCL1+ neural stem/progenitor cells in the dorsal lateral ganglionic eminence is blocked, resulting in a failure of OB interneuron generation. In Dlx1/2 conditional mutants (hGFAP-Cre; Dlx1/2F/- mice), GSX2+ and ASCL1+ neural stem/progenitor cells in the postnatal subventricular zone also fail to differentiate into OB interneurons. In contrast, overexpression of Dlx1&2 in embryonic mouse cortex led to ectopic production of OB-like interneurons that expressed Gad1, Sp8, Sp9, Arx, Pbx3, Etv1, Tshz1 and Prokr2. Pax6 mutants generate cortical ectopia with OB-like interneurons, but do not do so in compound Pax6; Dlx1/2 mutants. We propose that DLX1/2 promote OB interneuron development mainly through activating the expression of Sp8/9, which further promote Tshz1 and Prokr2 expression. Based on this study, in combination with earlier ones, we propose a transcriptional network for the process of OB interneuron development.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Helios expression defines two distinct populations of Foxp3+ Treg cells

city: Hamilton

first: Craig

last: Martens

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: The transcription factor Helios is expressed in a large subset of Foxp3+ Tregs of both mouse and man. We previously demonstrated that Treg induced in peripheral sites (pTreg) from Foxp3- T conventional (Tconv) cells were Helios- and proposed that Helios is a marker of thymic derived Treg (tTreg). To compare the two Treg subpopulations, we generated Helios-GFP reporter mice and crossed them to Foxp3-RFP reporter mice. The Helios+ Treg population expressed a more activated phenotype and had a higher suppressive capacity in vitro. Both populations expressed a highly demethylated TSDR and both subsets were equivalent in their ability to suppress inflammatory bowel disease in vivo. However, Helios+ Treg more effectively inhibited the proliferation of activated, autoreactive splenocytes from scurfy mice. When Helios+ and Helios- Treg were transferred to lymphoreplete mice, both populations maintained comparable Foxp3 expression, but Foxp3 expression was less stable in Helios- Treg when transferred to lymphopenic mice. Gene expression profiling of the two populations demonstrated a large number of differentially expressed genes and that Helios- Treg subpopulation expressed certain genes normally expressed in CD4+Foxp3- T cells. TCR repertoire analysis indicated very little overlap between Helios+ and Helios- Treg. Thus, Helios+ and Helios- Treg subpopulations are phenotypically and functionally distinct, consistent with thymic and peripheral sites of origin, respectively. Because of their superior suppressive activity and enhanced stability Foxp3+Helios+ Treg represent the optimal Treg population for cellular immunotherapy.

overall_design: 5 replicates of wildtype vs knockout Helios gene in Treg cells.

first: Angela

last: Thornton

first: Jinghua

last: Lu

first: Patricia

middle: E

last: Korty

first: Yong

middle: C

first: Peter

last: Sun

first: Ethan

last: Shevach