title: Tamoxifen-induced apoptosis of MCF-7 cells via GPR30/PI3K/MAPKs interactions: Verification by ODE modeling and RNA sequencing

city: Tehran

first: Milad

last: Rouhimoghadam

address: 3rd Floor., NO.3., 12th Alley., Shahid Ghandi St., Sohrevardi Shomali St., Tehran., Iran

country: Iran

institute: University of Tehran

summary: Tamoxifen (Nolvadex) is one of the most widely used and effective therapeutic agent for breast cancer. It benefits nearly 75% of patients with ER-positive breast cancer that receive this drug. Its effectiveness is mainly attributed to its capacity to function as an estrogen receptor (ER) antagonist, blocking estrogen binding sites on the receptor, and inhibiting the proliferative action of the receptor-hormone complex. Although, tamoxifen can induce apoptosis in breast cancer cells via upregulation of pro-apoptotic factors, it can also promote uterine hyperplasia in some women. Thus, tamoxifen as a multi-functional drug could have different effects on cells based on the utilization of effective concentrations or availability of specific co-factors. Evidence that tamoxifen functions as a GPR30 (G-Protein Coupled Receptor 30) agonist activating adenylyl cyclase and EGFR (Epidermal Growth Factor Receptor) intracellular signaling networks, provides yet another means of explaining the multi-functionality of tamoxifen. Here ordinary differential equation (ODE) modeling, RNA sequencing and real time qPCR analysis were utilized to establish the necessary data for gene network mapping of tamoxifen-stimulated MCF-7 cells, which express the endogenous ER and GPR30. The gene set enrichment analysis and pathway analysis approaches were used to categorize transcriptionally upregulated genes in biological processes. Of the 2,713 genes that were significantly upregulated following a 48 h incubation with 250 μM tamoxifen, most were categorized as either growth-related or pro-apoptotic intermediates that fit into the Tp53 and/or MAPK signaling pathways.  Collectively, our results display that the effects of tamoxifen on the breast cancer MCF-7 cell line are mediated by the activation of important signaling pathways including Tp53 and MAPKs to induce apoptosis.

overall_design: Gene expression analysis between tamoxifen-treated MCF-7 cells and untreated MCF-7 cells.

first: Shahrokh

last: Safarian

first: Jason

middle: S

last: Carroll

first: Nader

last: Sheibani

first: Gholamreza

last: Bidkhori


title: GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion

status: Public on Jun 14 2018

city: Ann Arbor

first: Tomonori

last: Hosoya

state: MI

address: 109 Zina Pitcher Place

department: CDB

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ChIP-seq data for H3K27 acetylation from 7-month-old mdx mouse hearts wild-type and deficient for cardiomyocyte-specific IKKβ

city: Toledo

first: Jennifer

middle: M

last: Peterson

state: OH

address: 2801 W Bancroft St

department: SERS

institute: The University of Toledo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found genetic deletion of IKKβ in mdx cardiomyocytes improved cardiac function and normalized calcium transients, and that differential gene expression favored a repressive function for NF-[kappa]B in these mice. We suspected that NF-[kappa]B was conferring a more restrictive chromatin conformation in a subset of genes. ChIP-seq was performed for H3K27 acetylation to show this repressive function for NF-[kappa]B was a global effect and to identify specific genes with more permissive chromatin conformation in hearts of mdx mice with IKKβ-deficient cardiomyocytes compared to mdx mice with intact IKKβ signaling.

overall_design: mdx mice conditionally deleted for IKKβ specifically in cardiomyocytes were created crossing IKKβ floxed mdx mice with mdx mice positive for the alpha myosin heavy chain (Myh6) promoter driving cre recombinase. Myh6 cre positive was our experimental condition and denoted “mdx heart Myh6-cre;IKKβ[delta]. An age matched littermate without the cardiac-specific Myh6 cre was our control and denoted “mdx heart IKKβf/f”. ChIP was performed on whole hearts using an H3K27 acetylation antibody.

first: Denis

middle: C

last: Guttridge


title: Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model (small RNA-seq)

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

type: Non-coding RNA profiling by high throughput sequencing

summary: We found that LP daughters have lower birthweight, alterations in mammary gland morphology and higher rates of mammary cancer. Further, we found that mammary glands and tumors of LP daughters are metabolic rewired, with alterations in the AMPK and amino-acid metabolism pathways. These changes were associated with differential expression of miRNAs 451a, miR-200c and miR-92a.  Importantly, some of the same miRNAs and target genes alterations were detected in breast tumors of women from populations with high rates of low birthweight.

overall_design: Male mice were fed AIN93G-based diets containing either 17.7% (control) or 8.9% (LP) energy from protein from 3 to 10 weeks of age.  Males on either group were mated to females raised on a control diet. Female offspring from control and LP fathers were treated with 7,12-dimethylbenz[a]anthracene (DMBA) to initiate mammary carcinogenesis and used for mammary tissue collection. Mature sperm from fathers and normal mammary tissue from female offspring were used for RNA-seq analyses.

first: Raquel

last: Santana

first: Elissa

middle: J

last: Carney

first: Johan

last: Clarke

first: Hong

last: Cao

first: M

middle: I

last: Cruz

first: Carlos

last: Benitez

first: Yi

last: Fu

first: Zuolin

last: Cheng

first: Yue

last: Wang

first: Sonia

last: de Assis


title: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 5

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

summary: Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated co-inhibitory receptor expression on CD4+ T cells promotes autoimmunity while sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and cancer.  Here, we used RNA and protein expression profiling at single-cell resolution to identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, Tim-3, Lag-3, and TIGIT), but also a number of novel surface receptors. We functionally validated two novel co-inhibitory receptors, Activated protein C receptor (Procr) and Podoplanin (Pdpn). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in multiple physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors Prdm1 and c-Maf as cooperative regulators of the co-inhibitory module, which we validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies novel regulators of T cell function with the potential to regulate autoimmunity and tumor immunity.

overall_design: Single cell RNAseq analysis of IL-27 induced T cell gene signature in the tumor


title: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 3


title: The comparison of high-throughput single-cell RNA-seq methods

city: BEIJING

first: Xiannian

last: Zhang

state: BEIJING

address: YIHEYUAN ROAD NO.5

country: China

institute: Peking University

summary: Here we compare the performance of these three approaches (inDrop, Drop-seq and 10x) using the same kind of sample with a unified data processing pipeline. We generated 2-3 replicates for each method using lymphoblastoid cell line GM12891. The average sequencing depth was around 50-60k reads per cell barcode. We also developed a versatile and rapid data processing workflow and applied it for all datasets. Cell capture efficiency, effective read ratio, barcode detection error and transcript detection sensitivity were analyzed as well.

overall_design: We used a human lymphoblastoid cell line GM12891 assuming homogeneous within the cell population throughout the experiments. Biological replicates were setup for all three methods, inDrop, Drop-seq and 10X Genomics Chromium (10X), with various cell inputs in different days and batches

first: Tianqi

last: Li

first: Zeyao

first: Feng

last: Liu

first: Jianbin

first: Yanyi

last: Huang


title: KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation

city: Detroit

first: Benjamin

middle: L

last: Kidder

address: 4100 John R St

institute: Wayne State University


title: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 1


title: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 4


title: KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [RNA-seq]

summary: Trophoblast stem (TS) cells derived from the trophectoderm (TE) of mammalian embryos have the ability to self-renew indefinitely or differentiate into fetal lineages of the placenta. Epigenetic control of gene expression plays an instrumental role in dictating the fate of TS cell self-renewal and differentiation. However, the roles of histone demethylases and activating histone modifications such as methylation of histone 3 lysine 4 (H3K4me3/me2) in regulating TS cell expression programs, and in priming the epigenetic landscape for trophoblast differentiation, are largely unknown. Here, we demonstrate that the H3K4 demethylase, KDM5B, regulates the H3K4 methylome and expression landscapes of TS cells. Depletion of KDM5B resulted in downregulation of TS cell self-renewal genes and upregulation of trophoblast-lineage genes, which was accompanied by altered H3K4 methylation. Moreover, we found that KDM5B resets the H3K4 methylation landscape during differentiation in the absence of the external self-renewal signal, FGF4, by removing H3K4 methylation from promoters of self-renewal genes, and of genes whose expression is enriched in TS cells. Altogether, our data indicate an epigenetic role for KDM5B in regulating H3K4 methylation in TS cells and during trophoblast differentiation.

overall_design: RNA-Seq of undifferentiated and differentiated murine shLuc and Kdm5b TS cells


title: GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion [GATA3 overexpression]

first: Tomonori

last: Hosoya

summary: RNA-seq in DN3a stage thymocytes isolated from wild type and GATA3 overexpression Tg mouse

overall_design: DN3a stage thymocytes were isolated from adult mouse, and then analyzed by RNA-seq.

first: Chia-Jui

last: Ku

first: Tomonoti

first: James

middle: D

last: Engel


title: RNA-Seq gene expression regulated by Drosophila insulin-like peptides DILP2 and DILP5 in S2 cells

city: Providence

first: Stephanie

last: Post

state: Rhode Island

address: 84 Olive St room 502

department: EEB

institute: Brown University

summary: Mammalian insulin and IGF induce similar but not identical changes in gene expression downstream of their respective receptors. Signaling bias at the receptor differentiates the two similar ligands, though the precise mechanism is not entirely understood. We used Drosophila insulin-like peptides DILP2 and DILP5 to determine how similar insulin-like ligands regulate similar and distinct patterns of gene expression in S2 cells by RNA-Seq. Overall, DILP2 and DILP5 stimulate many of the same changes in gene expression. However, some genes are uniquely regulated by DILP2 or by DILP5. Shared and distinct gene targets were validated by q-RT-PCR with indepedent replicates. Some unique gene targets of DILP2 are involved in sugar metabolism, which is functionally related in vivo to DILP2 and not DILP5. We find that gene expression is largely regulated in parallel by DILP2 and DILP5 but some key unique targets may lead to differential physiological functions for the two insulin-like genes.

overall_design: mRNA profiles from S2 cells treated with DILP2, DILP5 or solvent were sequenced on an Illumina HiSeq2500

first: S

first: M

last: Tatar


title: Opposing roles of miR-290 family and muscleblind-like proteins in the regulation of embryonic stem cell-specific alternative splicing and gene expression program

city: Beijing

first: Yangming

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

summary: RNA profiling of WT,Dgcr8-/- mESCs and miR-294 or siMbnl1/2 transfected Dgcr8-/- ESCs showed that miRNAs, especially miR-294 regulate a large number of alternative splicing events, among which  muscleblind-like proteins are responsible for a significant portion. Besides, upon depletion of miRNAs, RBPs and SFs are globally downregulated in mESCs.

overall_design: Total RNA was analyzed from WT, Dgcr8-/- mESCs and Dgcr8 deficient mESCs transfected with miR-294 or siRNAs against Mbnl1/2.

first: Da-Ren

last: Wu

first: Wen-Ting

last: Guo

first: Kai-Li

last: Gu


title: KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [ChIP-seq]

overall_design: ChIP-Seq of undifferentiated and differentiated murine shLuc and Kdm5b TS cells


title: The fate of CD8+ T cells during infection is linked to their developmental origin [VirtualMemory_and_TrueNaïve_timestamp]

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: During immune ontogeny the thymus is colonized by distinct waves of hematopoietic stem cells that give rise to unique lineages of immune cells. In this report, we asked whether the developmental origin of CD8+ T cells influences their response to infection later in adulthood. To answer this question, we developed a system to ‘timestamp’ CD8+ T cells in situ at various stages of development (1d and 28d) and examined their behavior after post-thymic differentiation. We found that neonatal-derived CD8+ T cells have an intrinsic propensity to become virtual memory cells prior to infection and are the first cells to proliferate and become effectors after microbial challenge. These data indicate that there are developmental layers in the adult CD8+ T cell response to infection and that the heterogeneity in the effector pool is linked to the variation in the developmental origins of the responding cells. This dataset profiles gene expression in 1day- and 28day-timestamped virtual memory (CD44hi) and "true naive" (CD44 lo) CD8+ T cells in cells that had undergone the same amount of post-thymic maturation (4 weeks, transgenic mice, different sorts).

overall_design: Gene expression profiling of virtual memory (CD44hi) and "true naïve" (CD44lo) CD8+ T cells (gBT-I TCR transgenic) after 4 weeks of post-thymic maturation, comparing three types of samples: virtual memory cells made at 1 day or 28 days of life, and true naïve cells made at 28 days of life (each in duplicate).

first: Norah

last: Smith

first: Brian

last: Rudd


title: Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model

first: Lu

last: Jin

type: Methylation profiling by high throughput sequencing


title: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 2

first: Asaf

last: Madi


title: The fate of CD8+ T cells during infection is linked to their developmental origin [VirtualMemory_and_TrueNaïve_timestamp_ATACseq]

summary: During immune ontogeny the thymus is colonized by distinct waves of hematopoietic stem cells that give rise to unique lineages of immune cells.  In this report, we asked whether the developmental origin of CD8+ T cells influences their response to infection later in adulthood.  To answer this question, we developed a system to ‘timestamp’ CD8+ T cells in situ at various stages of development (1d and 28d) and examined their behavior after post-thymic differentiation.  We found that neonatal-derived CD8+ T cells have an intrinsic propensity to become virtual memory cells prior to infection and are the first cells to proliferate and become effectors after microbial challenge. These data indicate that there are developmental layers in the adult CD8+ T cell response to infection and that the heterogeneity in the effector pool is linked to the variation in the developmental origins of the responding cells. This dataset profiles chromatin accessibility in 1day- and 28day-timestamped virtual memory (CD44hi) and "true naive" (CD44 lo) CD8+ T cells in cells that had undergone the same amount of post-thymic maturation (4 weeks, transgenic mice, different sorts).

overall_design: Profiling chromatin landscape of virtual memory (CD44hi) and "true naïve" (CD44lo) CD8+ T cells (gBT-I TCR transgenic) after 4 weeks of post-thymic maturation, comparing three types of samples: virtual memory cells made at 1 day or 28 days of life, and true naïve cells made at 28 days of life (each in duplicate).


title: RNAseq of Wild Type and IL27ra KO CD8+ Tumor infiltrating lymphocytes isolated from B16F10 melanoma.

overall_design: RNAseq analysis of IL-27 dependent CD8 T cell gene signature in the tumor.


title: The fate of CD8+ T cells during infection is linked to their developmental origin [Virtual_Memory_following_infection_timestamp]

summary: During immune ontogeny the thymus is colonized by distinct waves of hematopoietic stem cells that give rise to unique lineages of immune cells. In this report, we asked whether the developmental origin of CD8+ T cells influences their response to infection later in adulthood. To answer this question, we developed a system to ‘timestamp’ CD8+ T cells in situ at various stages of development (1d and 28d) and examined their behavior after thymic differentiation. We found that neonatal-derived CD8+ T cells have an intrinsic propensity to become virtual memory cells prior to infection and are the first cells to proliferate and become effectors after microbial challenge. These data indicate that there are developmental layers in the adult CD8+ T cell response to infection and that the heterogeneity in the effector pool is linked to the variation in the developmental origins of the responding cells. This dataset profiles gene expression in 1day- and 28day-timestamped virtual memory (CD44hi) CD8+ T cells aged for 4 weeks of post-thymic differentiation and then transferred into congenically marked recipients. Timestamped cells were recovered 5 days following infection with Listeria monocytogenes.

overall_design: Gene expression profiling of virtual memory (CD44hi) transgenic CD8+ T cells, 5 days following infection with Listeria, comparing cells made at 1 day or 28 days of life (in duplicate).


title: Transcriptional plasticity, priming and commitment in hematopoietic lineages [CRISP-seq]

status: Public on Jun 19 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Differentiation of adult hematopoietic stem cells (HSC) constantly produces the cell types of the blood and immune system. The dynamics of this process and the hierarchy of downstream oligopotent stem cell differentiation remain controversial. Here we dissect hematopoietic progenitor populations in a minimally biased fashion using extensive single cell sampling from murine bone marrow. We characterize the HSC population, define its quiescent transcriptional program and validate it with label retaining assays and cytokine mediated stimulations. Analysis of initial HSC commitment defines marked bifurcation of erythroid/megakaryocytic cells from myeloid/lymphoid lineages. Unexpectedly, we find states that mix transcription of pre-myeloid and pre-lymphoid genes. This suggests a model in which more than one differentiation trajectory can link HSC to several cell types. Dendritic cells are thus linked with both monocyte and lymphocyte precursors. Our data support a model of hematopoiesis balancing relaxation of an HSC quiescent state, gradual bifurcations and trans-differentiation.

overall_design: Cas9-GFP LSK cells were infected with BFP+ lentiviral guide RNAs and transplanted into irradiated mice. Both mRNA content and matched lentiviral transcribed barcodes were extracted and sequenced in different batches on an Illumina NextSeq

first: Amos

last: Tanay

first: Amir

last: Giladi

first: Franziska

last: Paul


title: Proteogenomic Analysis of Medulloblastoma [gene expression microarray]

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

institute: Children’s National Health System

summary: These gene expression microarrays were performed as part of a project aiming to integrate quantitative proteomic, gene expression and epigenetic data from the childhood brain tumor medulloblastoma.

overall_design: A total of 19 pediatric medulloblastoma and 5 normal cerebellum samples were analized

first: Rivero-Hinojosa

last: Samuel

first: Stampar

last: Mojca

first: Rood

middle: R

last: Brian


title: Proteogenomic Analysis of Medulloblastoma

type: Methylation profiling by genome tiling array


title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells [BiSulfite-seq]

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

summary: Long noncoding RNAs are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment is largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole genome bisulfite sequencing. Selected candidate lncRNAs were further characterized by PCR, Gene-Ontology analysis and targeted bisulfite sequencing. Differential expression in response to therapy was observed more frequently in cis-acting compared to overlapping lncRNAs (78% vs 22%, fold change ≥1.5), while significantly altered methylation profiles were more commonly associated with overlapping lncRNAs (29% vs. 8%; p<0.001). Moreover, overlapping lncRNAs contain more CpG islands (CGIs) (25% vs. 17%) and the majority of CGI-containing overlapping lncRNAs share these CGIs with their associated coding genes (84%). The differences in expression between sensitive and resistant cell lines were replicated in 87% of the selected candidates (p<0.05), while our bioinformatics approach identifying differential methylation was confirmed in all of the selected lncRNAs (100%). Five lncRNAs under epigenetic regulation appear to be involved in cisplatin resistance (AC091814.2, AC141928.1, RP11-65J3.1-002, BX641110 and AF198444). These novel findings provide new insights into epigenetic mechanisms and acquired resistance to cisplatin that highlight specific lncRNAs, some with unknown function that may signal strategies in epigenetic therapies.

overall_design: A total of four cell lines were purchased from ATCC and ECACC (Sigma-Aldrich) and cultured as recommended. To analyze the changes in the transcriptome as a result of CDDP treatment, we established the CDDP-resistant variants of H23-R, H460-R, A2780-R and OVCAR3-R from the parental-sensitive variants H23, H460, A2780 and OVCAR3, after exposure to increasing doses of CDDP treatment in a time period of 6–18 months.

first: Olga

last: Vera

last: Rodriguez-Antolin

first: Javier

last: de Castro

first: Florian

middle: A

last: Karreth

first: Thomas

last: Sellers

first: Inmaculada

last: Ibañez de Caceres


title: Males undergo a transient X-chromosome inactivation-like state at the onset of naïve cell differentiation

status: Public on Jun 13 2018

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: A hallmark of naïve cell identity is the presence of two active X-chromosomes in females. However, little is known if the naïve gene network prevents the initiation of X-chromosome-inactivation (XCI). Here, we demonstrate that robust naïve pluripotent stem cell (nPSC) self-renewal abolishes expression of Xist, the master regulator of XCI. Intriguingly, at the onset of differentiation when nPSCs become Nanog-negative they accumulate Xist on the male X-chromosome and on both female X-chromosomes. In fact, XCI occurs in males as characterised by appearance of a repressive chromatin signature and partial X-linked gene silencing, albeit transiently and rapidly. Likewise, in the embryo Xist is transiently expressed in males and in females from both X-chromosomes at the onset of epiblast differentiation. In conclusion, we propose that XCI initiation is gender independent and triggered by the destabilization of the naïve identity, which suggests that gender-specific mechanisms follow rather than precede XCI initiation.

overall_design: RNA seq analysis of differentiating embryonic stem cells using different methods.

first: Elsa

last: Sousa

first: Jose

last: Silva


title: The induction and transcriptional regulation of the co-inhibitory gene module in T cells by IL-27

first: Asaf

last: Madi

overall_design: Refer to individual Series


title: Characterization of human CD30+ B cells and their relationship to Hodgkin and Reed-Sternberg cells of Hodgkin lymphoma

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary: Small subsets of B cells in the germinal center (GC) and in extrafollicular regions of lymph nodes express the activation marker CD30. Very little is known about the specific features of these cells and their relationship to the CD30-expressing Hodgkin and Reed/Sternberg (HRS) cells of Hodgkin lymphoma. Phenotypic and immunoglobulin V gene analyses revealed that CD30+ GC B lymphocytes represent typical GC B cells, and that CD30+ non-GC B cells are mostly post-GC B cells. However, despite these seemingly distinct identities, both CD30+ subsets share an unexpectedly large overlap in specific transcriptome patterns, and are strikingly different from bulk GC B cells and classical memory and plasma cells, respectively. A main common feature of these CD30+ B cells is a strong MYC signature. CD30+ GC B cells appear to represent the recently described MYC+ GC B cell subset of recirculating centrocytes at the stage of centroblast transition. CD30+ non-GC B cells rather represent highly activated and proliferating memory B cells, differentiating into plasma cells. Notably, CD30+ B cells were more similar in their transcriptome patterns to HRS cells than any other B cell subset investigated, suggesting that HRS cells may either derive from CD30+ B cells or acquired a similar activation signature. In comparison to CD30+ B cells and other lymphomas, HRS cells show a remarkable downregulation of genes regulating cell cycle, genomic stability and polyploidity, providing a potential explanation for the genomic instability and multinuclearity of HRS cells.

overall_design: The present GSE record complements GSE records GSE12453, GSE14879 and GSE40160 by adding the following 10 samples:

first: Ralf

last: Küppers


title: EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association

status: Public on Jun 12 2018

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

summary: The transcriptional regulator EVI1 has an essential role in early hematopoiesis and development. However, aberrantly high expression of EVI1 has potent oncogenic properties and confers poor prognosis and chemo-resistance in leukemia and solid tumors. To investigate to what extent EVI1 function might be regulated by posttranslational modifications, we carried out mass spectrometry- and antibody-based analyses and uncovered an ATM-mediated double phosphorylation of EVI1 at the carboxy-terminal S858/S860 SQS motif. In the presence of genotoxic stress, EVI1-WT (SQS), but not site mutated EVI1-AQA was able to maintain transcriptional patterns and transformation potency, while under standard conditions carboxy-terminal mutation had no effect. Maintenance of hematopoietic progenitor cell clonogenic potential was profoundly impaired with EVI1-AQA compared with EVI1-WT, in particular in the presence of genotoxic stress. Exploring mechanistic events underlying these observations, we showed that after genotoxic stress EVI1-WT, but not EVI1-AQA increased its level of association with its functionally essential interaction partner CtBP1, implying a role for ATM in regulating EVI1 protein interactions via phosphorylation. This aspect of EVI1 regulation is therapeutically relevant, as chemotherapy-induced genotoxicity might detrimentally sustain EVI1 function via stress response mediated phosphorylation, and ATM-inhibition might be of specific targeted benefit in EVI1-overexpressing malignancies.

overall_design: Poly-A RNA sequencing (RNAseq) analysis of EVI1-mediated modulation of gene expression RNA was extracted from HEK293 cells, which were subjected to transient transfection using half confluent cultures with pCMV-flag, pCMV-EVI1-WT-flag or pCMV-EVI1-AQA-flag, exposed to 150 μM H2O2 or left untreated for 8 h.

first: Stefan

last: Meyer


title: Acute effects of active breaks during prolonged sitting on subcutaneous adipose tissue gene expression

city: Melbourne

first: Marta

last: Brozynska

state: VIC

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: Breaking up prolonged periods of time spent sitting has a range of beneficial impacts on cardiometabolic risk biomarkers. The molecular mechanisms include regulation of skeletal muscle gene and protein expression controlling metabolic, inflammatory and cell development pathways. An active communication network exists between adipose and muscle tissue, but the effect of active breaks in prolonged sitting on adipose tissue have yet to be investigated. This study characterised the acute transcriptional events induced in adipose tissue by regular active breaks during prolonged sitting. In a subset of 8 overweight/obese adults participating in an acute randomised three-intervention crossover trial, subcutaneous adipose tissue biopsies were obtained after each condition. The three experimental conditions were conducted in the postprandial state and included: i) prolonged uninterrupted sitting; or prolonged sitting interrupted with 2-minute bouts of ii) light- or iii) moderate-intensity treadmill walking every 20 minutes. Microarrays identified 36 differentially expressed genes between the three conditions (fold change≥0.5 in either direction; p<0.05). Pathway analysis indicated that breaking up of prolonged sitting led to differential regulation of adipose tissue metabolic networks and inflammatory pathways, increased insulin signalling, increased adipocyte turnover, and facilitated cross-talk between adipose tissue and other organs. This study provides insight into the adipose tissue regulatory systems and transcriptional processes that contribute to the physiological benefits of interrupting prolonged sitting.

overall_design: Total RNA was extracted from abdominal subcutaneous adipose tissue at the 3 different experimental condition from 8 participants.

first: Megan

last: Grace

first: Melissa

middle: F

last: Formosa

first: Kiymet

last: Bozaoglu

first: Audrey

last: Bergouignan

first: Andrew

last: Carey

first: Camilla

last: Bertuzzo Veiga

first: Parneet

last: Sethi

first: Francis

last: Dillon

first: David

last: Bertovic

first: Michael

last: Inouye

first: Neville

last: Owen

middle: W

last: Dunstan

first: Bronwyn

last: Kingwell


title: 7-month-old mdx mouse hearts wild-type and deficient for cardiomyocyte-specific IKKβ

first: Jennifer

last: Peterson

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


title: RNAseq of Wild Type and Prdm1/c-Maf cDKO CD8+ Tumor infiltrating lymphocytes isolated from B16F10 melanoma

first: Asaf

last: Madi

summary: Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated co-inhibitory receptor expression on CD4+ T cells promotes autoimmunity while sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and cancer.  Here, we used RNA and protein expression profiling at single-cell resolution to identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, Tim-3, Lag-3, and TIGIT), but also a number of novel surface receptors. We functionally validated two novel co-inhibitory receptors, Activated protein C receptor (Procr) and Podoplanin (Pdpn). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in multiple physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors Prdm1 and c-Maf as cooperative regulators of the co-inhibitory module, which we validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies novel regulators of T cell function with the potential to regulate autoimmunity and tumor immunity.

overall_design: RNAseq analysis of Prdm1 and/or c-Maf deficient CD8 T cell gene signature in the tumor.


title: E14.5-born neurons at P3 repress L4 neuron-type and induce L2/3 neuron-type genes upon Kir2.1 in utero electroporation

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Experimental in vivo hyperpolarization of E14.5 apical progenitors shifted their transcriptional programs with precocious generation of intermediate progenitors, and a forward shift in the laminar, molecular, morphological and circuit features of their neuronal progeny. In particular, we reported an overall repression of  L4-type neuronal genes and a premature induction of L2/3-type neuronal genes following Kir2.1 overexpression.

overall_design: We performed bulk RNA sequencing of P3 neurons electroporated at E14.5 with mCherry-reporter plasmid or Kir2.1-GFP plasmid, and at E15.5 with mCherry-reporter plasmid.

first: V

last: Ilaria

first: T

last: Ludovic


title: Single Cell sequencing of E14.5, E15.5 and E14.5 Kir electroporated cortical neurons.

overall_design: Mice were electroporated with pCAG-Kir2.1-  IRES-GFP at E14.5 or with pCAG-IRES-GFP at E15.5.FlashTag was injected in these pups after 12h to compare isochronic  cohorts of labeled cells within single animals (see Telley et al.,DOI: 10.1126/science.aad8361).


title: ML29755 RNA-seq data

city: South San Francisco

first: Craig

last: Cummings

state: CA

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech/Roche

summary: Programmed death-ligand 1 (PD-L1) expression has been associated with response to PD-1/PD-L1 inhibition, but responses are also seen in patients with PD-L1 negative tumors when assessed immunohistochemically (IHC) with various antibodies. To help elucidate these findings, we performed a positron emission tomography (PET) imaging study in human with the anti-PD-L1 antibody atezolizumab labeled with Zirconium-89 (89Zr) prior to treatment with atezolizumab to assess normal tissue distribution and evaluate tumor tracer uptake. Additionally, to help explain why some patients respond to checkpoint inhibitors despite low or absent PD-L1 expression, we compared PD-L1 expression and immune phenotypes based on both CD8 IHC and RNA sequencing of post-tracer biopsies to tumor tracer uptake (SUVmax).

overall_design: In this trial, 22 patients completed the full imaging series of up to 4 PET scans and were subsequently treated with atezolizumab monotherapy until progressive disease (PD) from which 11 post-tracer tumor biopsies were available for RNA sequencing, which are available here.

first: Frederike

last: Bensch

first: Elly

last: van der Veen

first: Marjolijn

middle: N

last: Lub-de Hooge

first: Annelies

last: Jorritsma-Smit

first: Ronald

last: Boellaard

first: Iris

last: Kok

first: Sjoukje

last: Oosting

first: Carolina

middle: P

last: Schröder

last: Hiltermann

first: Anthonie

last: van der Wekken

first: Harry

last: Groen

first: Thomas

last: Kwee

first: Sjoerd

middle: G

last: Elias

first: Jourik

last: Gietema

first: Sandra

last: Sanabria Bohorquez

first: Alex

last: de Crespigny

first: Simon-Peter

last: Williams

first: Christoph

last: Mancao

first: Adrienne

middle: H

last: Brouwers

first: Bernard

last: Fine

first: Elisabeth

middle: E

last: de Vries


title: Transcriptional profiling of MCF7 cells treated with H3B05942, E2, or standard of care compounds

city: Cambridge

first: Zhenhua

last: Wu

address: 300 Technology Square floor 5

institute: H3 Biomedicine

summary: The objective of this experiment was to compare the affect of H3B-5942 treatment on global  gene expression and to compare to treatment with standard of care agents tamoxifen and fulvestrant.

overall_design: 4 conditions were assessed (H3B-5042, tamoxifen, fulvestrant, and DMSO as control). Three samples of each condition were collected.

first: Craig

last: Furman


title: ChIP-Seq analysis of estrogen deprived MCF7 cells treated with H3B-5942 and standards of care compounds

summary: The goal of this experiment was to interrogate the potential transcriptional impact of H3B-5942 by investigating its influence on genome-wide DNA-binding modes of ERa in MCF7 cells using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-Seq).  Affects of H3B-5942 on chromatin recruitment were compared to results from treatment with E2, 4-OHT, and fulvestrant.

overall_design: A total of 5 treatments were analyzed.  These included H3B-5942, E2, reference compounds 4-OHT and fulvestrant, and DMSO as control. Material from two plates per treatment were pooled and then analyzed.


title: ESR1 mutations maintain higher ER pathway activity relative to vehicle and ERa-WT controls following treatment with Raloxifene or fulvestrant.

summary: The goal of the study was to understand whether mutations in ERa can promote resistance to various ERa antagonists of the SERD and SERM class. We found that ESR1 mutations can maintain higher ER pathway activity relative to control lines following short-term treatment with ERa antagonists raloxifene or fulvestrant.

overall_design: MCF7 lines were grown in media supplemented with 10% FBS. Cells were treated with raloxifene/fulvestrant for 16 hours prior to RNA collection and microarray analysis.

first: Manav

last: Korpal

first: Jeremy


title: Transcriptional profiling of Ishikawa cells treated with H3B-5942, E2, or standard of care compounds

summary: The objective of this experiment was to determine the affect of H3B-5942 treatment on global  gene expression in an estrogen-deprived setting (agonist mode) and to compare to treatment with a saturated analog of H3B-5942, GDC-0810, and standard of care agents tamoxifen and fulvestrant.

overall_design: 7 conditions were assessed  (H3B-5924, H3B-9224, E2, fulvestrant, tamoxifen,  GDC-810, and DMSO as negative control). Compounds were added at 2 concentrations (3nM and 30nM). Two samples of each condition were collected.

first: Xiaoling

last: Puyang


title: Discovery of Selective Estrogen Receptor Covalent Antagonists (SERCAs) for the treatment of ERa(WT) and ERa(MUT) breast cancer.


title: Nitric oxide engages an anti-inflammatory feedback loop mediated by peroxiredoxin 5 in phagocytes

first: Daniel

middle: Bartholomew

last: Graham

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

summary: Transcriptional profiling of murine dendritic cells stimulated with LPS and IFNg after shRNA knockdown of redox regulators.

overall_design: shRNA targeting redox regulators were delivered to bone marrow derived dendritic cells. Cells were stimulated with LPS and IFNg prior to transcriptional profiling by RNAseq over a time course. Each sample sequenced on two Illumina lanes.

middle: B

first: Ramnik

last: Xavier


title: High-resolution comparative analysis of great ape genomes

city: San Francisco

middle: Aaron

last: Pollen

state: California

address: 35 Medical Center Way

institute: UCSF

summary: We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Single cell mRNA sequencing of iPS-derived neural progenitor cells using the Fluidigm C1 system

first: Evan

last: Eichler


title: Comparing transcriptomes of wild-type, hyperfilamentous, and hypofilamentous biofilms in S. cerevisiae

city: Buffalo

first: Paul

middle: J

last: Cullen

address: 341 Cooke Hall

department: Biology

institute: SUNY-Buffalo

summary: Purpose was to identify common and unique genes regulated by the following filamentous growth regulators: Dig1, Ste12, Ras2, Rtg3, Spt8. By harvesting cells from various biofilms we attempted to identify major regulatory targets that underpin biofilm/mat formation in fungi.

overall_design: Biofilms made by various strains were harvested and compared

first: Jacky

last: Chow


title: Chromatin associated RNA sequencing during the IFN response induced by poly(I:C)

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: Type-I Interferons (IFNs) are central components of the antiviral response in vertebrates. Most cell types have the ability to respond to viral infection by secreting IFNs, however, the mechanisms that regulate correct expression of these cytokines are still not completely understood. Here, we show that activation of the IFN response regulates the expression of miRNAs in a post-transcriptional manner. Specifically, IFN impairs the binding of the nuclear Microprocessor complex to pri-miRNAs, which leads to a transient accumulation of unprocessed pri-miRNAs and consequently, decreased levels of specific miRNAs. We propose a model by which the inhibition of Microprocessor activity is an essential step to induce a robust type-I IFN response in mammalian cells.

overall_design: Comparison between RNA samples from mock and poly(I:C) transfected HeLa cells

first: Sara

last: Macias

first: Al

first: Jeoren

last: Witteveldt


title: Targeting CREBBP/EP300 bromodomains in cancer

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

summary: Changes in gene expression caused by CREBBP/EP300 bromodomain inhibitors in a CML cell line

overall_design: K562 cells were treated with CBP30 and I-CBP112 and changes in gene expression were evaluated by RNA-seq

first: Veronica

last: Garcia-Carpizo

first: Osvaldo

last: Graña


title: A non-canonical-PPARg/RXRa-binding sequence regulates leptin expression in response to changes in adipose tissue mass

status: Public on Jun 11 2018

city: New York

first: Yinxin

last: Zhang

state: New York

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University/HHMI

summary: Leptin expression decreases after fat loss and is increased when obesity develops and its proper quantitative regulation is essential for the homeostatic control of fat mass. We previously reported that a distant leptin enhancer (LE1), 16kb upstream from the transcription start site (TSS), confers fat-specific expression in a BAC transgenic reporter mouse (BACTG). However this and the other elements that we identified do not account for the quantitative changes in leptin expression that accompany alterations of adipose mass. In this report, we used ATAC-seq to identify a 17bp non-canonical-PPARγ/RXRα-binding site leptin regulatory element 1 (LepRE1) within LE1, and show that it is necessary for the fat-regulated quantitative control of reporter (luciferase) expression. While BACTG reporter mice with mutations in this sequence still show fat-specific expression, luciferase is no longer decreased after food restriction and weight loss. Similarly the increased expression of leptin reporter associated with obesity in ob/ob mice is impaired. A functionally analogous LepRE1 site is also found in a second, redundant DNA regulatory element 13kb downstream of the TSS. These data uncouple the mechanisms conferring qualitative and quantitative expression of the leptin gene and further suggest that factor(s) that bind to LepRE1 quantitatively control leptin expression and might be components of a lipid sensing system in adipocytes.

overall_design: 6 ATAC-seq experiments conducted in isolated iWAT nuclei from mice. Library from each mouse was sequenced in one lane using 50bp x2 paired-end reads on an Illumina HiSeq 2500.

first: Jeffrey

last: Friedman


title: Transcriptional analysis of murine norovirus infection of primary bone marrow-derived macrophages

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Murine norovirus is genetically similar to human norovirus, and offers both an efficient in vitro cell culture system and animal model by which to investigate the molecular basis of replication.  Here, we present a detailed global view of host alterations to cellular pathways that occur during the progression of a norovirus infection. This was accomplished for both RAW264.7 (RAW) cells, an immortalized cell line widely used in in vitro replication studies, and primary bone marrow-derived macrophages (BMDM), representing a permissive in vivo target cell in the host. Murine norovirus replicated in both cell types, although detected genome copies were approximately one log lower in BMDM compared to RAW cells. RAW and BMDM cells shared an IRF3/7-based IFN response that occurred early in infection. In RAW264.7 cells, transcriptional upregulation and INF-ß expression were not coupled, in that a significant delay in the detection of secreted INF-ß was observed.  In contrast, primary BMDM showed an early upregulation of transcripts and immediate release of INF-ß that might account for lower virus yield. Differences in the transcriptional pathway responses included a marked decrease in expression of key genes in the cell cycle and lipid synthesis pathways in RAW264.7 cells compared to that of BMDM.  Our comparative analysis indicates the existence of varying host responses to virus infection in populations of permissive cells. Awareness of these differences at the gene level will be important in the application of a given permissive cell culture system to the study of norovirus immunity, pathogenesis, and drug development.

overall_design: Time course study of murine primary bone marrow derived macrophages gene expression infected with Murine nororvirus.

first: Eric

last: Levenson

first: Kishore

last: Kanakabandi

first: Charles

last: Turner

first: Kimmo

last: Virtaneva

first: Monica

last: Paneru

first: Stanislav

middle: V

last: Sosnovtsev

first: Stacy

last: Ricklefs

first: Jordan

last: Johnson

first: Stephan

last: Porcella

first: Kim

middle: Y

last: Green


title: Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR7 deficiency in Neurons

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: The goal of this study is to compare gene expression of mouse cultured cortical and hippocampal neurons in response of TLR7 defiency at mature stage

overall_design: At 18 day in vitro, wild-type mouse cortical and hippocampal neurons and Tlr7-/- neurons were collected. The total RNAs were extracted for deep sequencing, in triplicate, using the NextSeq500 High-output v2 (75 cycle) sequencing kit on the Illumina NextSeq500 instrument.

first: Yun-Fen

last: Hung

first: Chiung-Ya

last: Chen


title: Transcriptional dysregulation in a primary cortical neuron model of Huntington's disease

status: Public on Jun 09 2018

city: St. Louis

first: Hiroko

last: Yano

address: 660 South Euclid Avenue

department: Neurological Surgery

overall_design: RNA-seq of primary cortical neurons transduced with control vector, wildtype Htt or Mutant Htt.


title: Effect of BRD4 deletion on the Transcriptome of Different Thymocyte Subpopulations

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

summary: By conditionally deleting BRD4 at various stages of thymic differentiation, we have established that BRD4 deficiency selectively affects a unique developmental subpopulation of thymocytes.

overall_design:
We examined by RNA-seq the effect on gene expression of BRD4 deletion in ex vivo DN, ISP, DP, CD4 and CD8 thymocyte subpopulations.
The analysis was also performed on WT or BRD4 deleted ISP and DP thymocytes cultured for 16 hours at 37oC
In this analysis, the conditional deletion of BRD4 (cKO) is achieved using the LCK-cre Transgene.

first: Anne

last: Gegonne

first: Qing-Rong

first: Daoud

last: Meerzaman


title: Epigenetic optical mapping of 5-hydroxymethylcytosine in nanochannel arrays

status: Public on Jun 08 2018

city: Tel Aviv

first: Yuval

last: Ebenstein

address: Haim Levanon

department: Physical Chemistry

institute: Tel Aviv University

summary: We present a long-read, single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5-hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long single-molecule read-length of 100 kbp-1 Mbp produces 5-hmC profiles across variable genomic regions that failed to show up in the sequencing data. In addition, optical 5-hmC mapping shows a strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression.

overall_design:
Optical mapping of 5-hmC and 5-hmC DNA immunoprecipitation of human PBMCs. This series contains only the hMeDIP samples.

Optical mapping data (.cmap and .xmap files) are available at ftp://ftp.ncbi.nlm.nih.gov/pub/supplementary_data/bionanomaps.csv in files: SUPPF_0000002688 and SUPPF_0000002687


title: RNAseq data of brain cortex from mice at d10 post-microglia depletion and non-depleted controls

city: Boston

first: Stephen

last: Rubino

address: 60 Fenwood Road, 10032

institute: Brigham and Women's Hospital

summary: Previous studies have reported that microglia depletion leads to impairment of synapse formation and these cells rapidly repopulate from CNS progenitors. However, the impact of microglia depletion and repopulation on the long-term state of the CNS environment has not been characterized. Here, we found by RNA-seq analysis that acute and synchronous microglia depletion results in a type 1-interferon inflammatory signature in degenerating somatosensory cortex in microglia-depleted mice.  Transcriptomic and mass cytometry analysis of repopulated microglia demonstrates an interferon regulatory factor 7-driven activation state. Minocycline and anti-IFNAR1 antibody treatment attenuate the CNS type-1 interferon-driven inflammation and restore microglia homeostasis. Together, we found that acute microglia ablation induces a type-1 interferon activation state of grey matter microglia associated with acute neurodegeneration.

overall_design: RNAseq analysis of brain cortical tissue from control and microglia-depleted mice.


title: Tracking adipose-tissue Treg provenance, dependencies, and activities via T cell receptor transgenic mice

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Regulatory T (Treg) cells located within parenchymal tissues safeguard tissue homeostasis. A paradigmatic "tissue-Treg" population is that found in visceral-adipose tissue (VAT) of male mice. VAT-Treg cells have a unique transcriptome, are clonally expanded, and promote metabolic health through effects on local immunocytes and adipocytes. Because of their rarity and inaccessibility, cardinal questions such as what factors control their accumulation in fat and when/where/how do they adopt their distinctive phenotype remained unanswered. We addressed these issues using VAT- Treg T-cell-receptor (TCR) transgenic mice. Accumulation of VAT-Tregs was driven by combined effects of TCR specificity, Foxp3 expression, and a cell-intrinsic response to interleukin-33. Their characteristic phenotype emerged in two stages: a minority of splenic Treg cells weakly up-regulated a slice of the VAT-Treg transcriptional signature, reflecting cell activation, but the definitive phenotype, arming cells for fat survival, was manifest only in VAT. This deeper understanding of tissue-Treg generation should facilitate precision-targeting strategies.

overall_design: CD4+FOXP3+ Tregs were FACS-purified from thymus, spleen and visceral-adipose tissue and ATAC-seq (Assay for Transposase-Accessible Chromatin) was performed. The mouse strain is a novel VAT TCR transgenic (Tg) mouse line published in Li et al., (pending), called vTreg53. It was crossed with a FOXP3-reporter line containing an ires-GFP construct inserted into the FOXP3 locus, allowing FOXP3+ cells to be FACS-purified. In addition to standard T cell markers and FOXP3, Tregs from transgene-carrying mice were also purified as Valpha2-hi and Vbeta4-hi cells. Sample titles derived from mice carrying the TCR transgene are prepended with "TgP", for "Transgene-Positive", while samples derived from control, transgene-negative littermates are prepended with "TgN". Additionally, TCR transgene-carrying mice were crossed with a novel PPARg-reporter strain published in Li et al (pending). Two CD4+FOXP3+ Treg populations were purified from the spleens of these mice, as indicated by the sample titles: "SpPparNeg" are Pparg-negative Tregs and "SpPparLo" are Pparg-positive Tregs. "WO" in sample titles refers to "weeks-old", "Thy/Sp/VAT" refer to the Thymus, Spleen, or Visceral Adipose Tissue source and Rep* refers to biological replicate number.

first: Joanna

last: DiSpirito

first: Chaoran

last: Li

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5

city: Berkeley

first: Yeon

last: Lee

address: 1 Barker Hall

institute: UC Berkeley

summary: Alternative pre-messenger RNA (pre-mRNA) splicing is a post-transcriptional mechanism for controlling gene expression. Splicing patterns are determined by both RNA binding proteins and nuclear pre-mRNA structure. Here, we analyze pre-mRNA splicing patterns, RNA binding sites and RNA structures near these binding sites coordinately controlled by two splicing factors, the heterogeneous nuclear ribonucleoprotein hnRNPA1 and the RNA helicase DDX5. We identified thousands of alternative pre-mRNA splicing events controlled by these factors by RNA-seq following RNA interference. Enhanced CLIP (eCLIP) on nuclear extracts was used to identify protein-RNA binding sites for both proteins in the nuclear transcriptome. We found a significant overlap between hnRNPA1 and DDX5 splicing targets and that they share many closely linked binding sites as determined by eCLIP analysis. In vivo SHAPE chemical RNA structure probing data was used to model RNA structures near several exons controlled and bound by both proteins. Both sequence motifs and in vivo UV crosslinking sites for hnRNPA1 and DDX5 were used to map binding sites in their RNA targets and often these sites flanked regions of higher chemical reactivity suggesting an organized nature to nuclear pre-mRNPs. This work provides a first glimpse into the possible RNA structures surrounding pre-mRNA splicing factor binding sites.

overall_design: A human myeloid leukemia cell line, K562 cells, were treated with hnRNPA1 and DDX5 siRNA. Two replicate samples of hnRNPA1 knockdown and DDX5 knockdown were prepared for RNA-seq for differential pre-mRNA splicing analysis, along with control scramble siRNA samples. Triplicate eCLIP samples were prepared for hnRNPA1 and DDX5 using nuclear extracts in K562 cells, with input control and no UV treatment control samples.

first: Donald

last: Rio


title: Transcriptional profiling of Regulatory T (Treg) cells and CD4+ conventional T (Tconv) cells from vTreg53 TCR transgenic and PPARg reporter mice

summary: We reported transcriptional characterization of Treg and Tconv cells from thymic, splenic, and visceral adipose tissue (VAT) of vTreg53 TCR transgenic mice and control littermates. We examined the effect of Foxp3 on splenic and VAT CD4+ T cell transcriptome. We profiled gene expression in a novel PPARg+ splenic Treg population. We uncovered that the characteristic phenotype of VAT Treg cells was acquired in two stages.

overall_design: Gene expression profiles of thymic, splenic, VAT Treg, Tconv, and Foxp3-transduced Tconv cells from vTreg53 TCR transgenic and PPARg reporter mice.


title: mRNA expression of murine hematopoietic stem cells and ex vivo murine MLL-AF9 cells deficient for total PRDM16 or f-PRDM16, and AF9 cells overexpressing individual PRDM16 isoforms

first: Hans-Willem

last: Snoeck

address: 650 W. 168th Street, BB816

institute: Columbia University Medical Center

summary: Group 1 -- WT or PRDM16-KO ex vivo murine MLL-AF9 cells, and PRDM16-KO AF9 cells overexpressing either f-PRDM16 or s-PRDM16. Group 2 -- WT or total PRDM16-KO murine HSCs isolated from adult BM. Group 3 -- WT or total PRDM16-KO murine HSCs isolated from fetal liver. Group 4 -- WT or f-PRDM16-KO murine HSCs (expressing s-PRDM16 only) isolated from fetal liver.

overall_design: Sorted ex vivo MLL-AF9 cell (group 1) or sorted murine HSC (groups 2-4) mRNA profiles were generated by deep sequencing, in 3 or 4 independent replicates, using Illumina HiSeq2500/NS500

first: David

last: Corrigan

first: Alexandros

last: Strikoudis


title: Lysine benzoylation is a novel histone mark

city: Chicago

first: He

last: Huang

institute: The University of Chicago

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

overall_design: Refer to individual Series


title: Lysine benzoylation is a novel histone mark [ChIP-seq]

summary: We identified and characterized a previously undescribed histone mark, lysine benzoylation. This histone mark could be modulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone lysine benzoylation marks are involved in regulation of gene expression and associated with diverse biological processes. This study therefore reveals a new type of physiological relevant histone mark and identifies non-conical functions of a widely used chemical food preservative.

overall_design: We have a control group and a SB-treated group. For RNA-seq, each group contains 4 bilogical replicates. For ChIP-seq, each group contains an input, a lysine acetylation, and a lysine benzoylation samples.

first: Yingming

last: Zhao


title: Lysine benzoylation is a novel histone mark [RNA-seq]


title: Gene expression changes in Ing1- and Gadd45a- single- or double-knockout mouse embryonic fibroblasts

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is required to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the impact of ING1-GADD45a on gene expression, we compared the  expression profile of wildtype mouse embryonic fibroblasts (MEFs) with Ing1- and Gadd45a- single- or double-knockout (DKO) MEFs.

overall_design: Gene expression profiling in all 4 genotypes of undifferentiated MEFs in triplicates.

first: Andrea

last: Schäfer

first: Bernadette

last: Mekker

first: Medhavi

last: Mallick

first: Viviana

last: Vastolo

first: Dominik

last: Sebastian

first: Carina

last: von der Lippen

first: Bernd

last: Epe

first: Damien

last: Downes

first: Carola

last: Scholz

first: Christof

last: Niehrs


title: Gene expression after 24h Cocoa Extract incubation in HT29 cells

city: Barcelona

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary: Cocoa consumption is associated with beneficial effects on human health. This has been attributed to its polyphenol components and their oligomers, which have been shown to decrease the risk of cardiovascular and inflammatory diseases, metabolic disorders, and to play a role in cancer prevention. We tested cocoa modulation on the gene expression profile of colon cancer HT-29 cells using Affymetrix microarrays.  Among the genes differentially expressed in HT-29 cells upon incubation with cocoa extract, 48 were identified as Interferon regulated genes using the INTERFEROME database. Furthermore, a BAN constructed using the Pathway Architect software revealed that STAT1, IF44 and AGT were all highly interconnected nodes.

overall_design: HT29 cells (300,000) were plated and the following day they were treated in triplicate with either saline (control) or 500  µg PCE for 24 hours. After the incubation Total RNA was extracted using Qiagen RNAeasy minikit. Gene expression was analyzed by hybridization to the GeneChip® Human Genome U133 PLUS 2.0 microarrays from Affymettrix containing over 54,700 transcripts and variants. Microarray results were analyzed using the GeneSpring GX software.

first: Carlota

last: Oleaga

first: Veronica

last: Noe


title: Gene expression profiling of adult human hepatocytes

status: Public on Jun 07 2018

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

summary:
Understanding gene expression profile and transcriptional regulation of healthy adult human hepatocytes
Gene expression was analyzed

overall_design: Gene expression profile was obtained from freshly isolated adult human hepatocytes


title: Tissue-restricted adaptive type-2 immunity is orchestrated by OX40L expression on group 2 innate lymphoid cells

city: Cambridge

first: Andrew

last: McKenzie

address: Francis Crick Ave

department: PNAC

institute: MRC LMB

summary: We investigated the transcriptional profiles of lung ILC2, Th2 and Treg (Gata3+ and -) cells from naïve and IL-33-treated mice. This experiment accompanies our manuscript, where we showed that IL-33-dependent accumulation of adaptive type-2 immune cells (Th2 and Treg) was dependent on OX40L expression by ILC2.

overall_design: Analysis of gene-expression in FACS purified populations from naïve (2 samples per cell-type) and IL-33-treated mice (2 samples per cell-type).

first: Batika

middle: M

last: Rana

first: Timotheus

last: Halim

first: Jennifer

last: Walker

first: Bernhard

last: Kerscher

first: Martin

middle: D

last: Knolle

first: Helen

last: Jolin

first: Eva

last: Serrao

first: Liora

last: Haim-Vilmovsky

first: Sarah

last: Teichmann

first: Hans-Reimer

last: Rodewald

first: Marina

last: Botto

first: Timothy

last: Vyse

first: Padraic

last: Fallon

first: Zhi

last: Li

first: David

last: Withers


title: Histone Variant H2A.Z Defines Cell Identity in Vascular Smooth Muscle Cells as Revealed by Single-Cell Transcriptomics

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: We applied single-cell RNA-Seq to analyze human diseased arteries, and identified histone variant H2A.Z as a key histone signature to maintain vascular smooth muscle cell (VSMC) identity. We show that H2A.Z occupies genomic regions near VSMC marker genes and its occupancy is decreased in VSMC undergoing dedifferentiation. Mechanistically, H2A.Z occupancy preferentially promotes nucleosome turnover, facilitates the recruitment of Smad3 and Med1 to VSMC marker genes, thereby activating gene expression. In human diseased vascular tissue, H2A.Z expression dramatically decreased. Notably, in vivo overexpression of H2A.Z rescued injury-induced loss of VSMC identity and neointima formation. Together, our data introduce dynamic occupancy of histone variant as a novel regulatory basis contributing to cell fate decisions, and imply H2A.Z as a potential intervention node for vascular diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Single-cell RNA-seq of human diseased arteries; ChIP-seq of H2A.Z, SMAD3, SRF and MED1 in wild-type cultured vscular smooth muscle cells;VSMC nucleosome occupancy by Mnase.

Please note that, given the number of raw files associated with each sample, two sample records have been created for each scRNA-seq sample (e.g. SC_92467_1 & _2, SC_92558_1 & _2).

first: Peng

last: Yu

first: Fang

last: Yao

first: Xinli

last: Yuan


title: A network of noncoding regulatory RNAs acts in the mammalian brain II

last: Bartel

address: 9 Cambridge Center

institute: Whitehead Institute / MIT

summary: Noncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs—a long ncRNA, a circular RNA, and two microRNAs—using gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more efficient than previously described examples of target-directed microRNA degradation, which come from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7–targeted mRNAs and enables the accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network.

overall_design: mRNA expression profiling by RNA-seq of cerebellum and cortex from wild-type (WT), Cyrano miR-7 site mutant (CyrMut), Cyrano–/– (CyrKO), and Mir7a1–/–; Mir7b–/– (Mir7DKO) mice. This study consists of 33 polyA-selected stranded NEXTflex libraries prepared from 3-4 biological replicates for each tissue and each genotype. To minimize batch effects, libraries for wild-type tissues were prepared and sequenced for each experiment and only intra-experiment comparisons were made.

first: Benjamin

last: Kleaveland


title: RNA- and ATAC-seq data of Wt, Ebf1-KO and Pax5-KO FL-ProB-cells.

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: EBF1 and PAX5 are crucial factors for B-cell development. Knock down of either factor leads to an arrest in differentiation. RNA-seq data of WT, Ebf1-/- and Pax5-/- FL-ProB cells allowed for identification of activated and repressed target genes. ATAC-seq data of corresponding cell populations could connect gene activity and chromatin accessibility. This finding provided an explanation to the lineage instability observed in early B-cell progenitors. Taken together, the reported data provide an increased insight into mechanisms governing regulation of stage- and lineage specific transcription in early B-lymphocyte development.

overall_design:
ATAC-seq was performed on 80k cultured Fetal Liver ProB cells from Wt, Ebf1-/- or Pax5-/- mice to study changes in chromatin accessibility due to the loss of these proteins important for B-cell development. RNA seq was performed on cultured Fetal Liver ProB cells from Wt, Ebf1-/- or Pax5-/- mice to study changes in genes expression due to these genetic alterations. Data was aligned to mouse reference genome (mm10 /GRCm38)analysis and analyzed using the HOMER platform.

ATAC and RNA-seq data was analyzed in relation to ChIP binding positions for Ebf1 and Pax5 on re-analyzed data retrieved from previously published ChIP-seq data deposited on GEO under: EBF1 (GSE69227) (Ungerback et al., 2015), PAX5 (GSE38046) (Revilla et al., 2012), or in relation to RNA seq data from CLP sub-fractions deposited under GSE92540

Please note that each processed data file was generated from multiple samples, as indicated in the corresponding sample description field.

first: Kazuki

last: Okuyama

first: Tobias

last: Strid

first: Rajesh

last: Somasundaram

first: Mahadesh

last: Prasad

first: Josefine

last: Åhsberg


title: A network of noncoding regulatory RNAs acts in the mammalian brain I

summary: Noncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs—a long ncRNA, a circular RNA, and two microRNAs—using gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more efficient than previously described examples of target-directed microRNA degradation, which come primarily from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7–targeted mRNAs and enables the accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network.

overall_design: mRNA expression profiling by RNA-seq of 10 tissues from wild-type (WT) and Cyrano–/– (CyrKO) mice. This study consists of 96 polyA-selected unstranded Tru-seq libraries prepared from 4–6 biological replicates per genotype for each tissue.


title: Optimization of interneuron function by direct coupling of cell migration and axonal targeting

city: Leuven

first: Lynette

last: Lim

address: Herestraat 49, ON5

department: Centre for Brain and Disease

country: Belgium

institute: VIB-KUL

summary: We compared transcripts from somatostatinpositive inteneruons in the migrating marginal zone and subventricle zone at embryonic stage E17.5

overall_design: E17.5 cortex from SST-cre;Ai9 mice were dissected and the migratory streams were separated by horizontal section. Cells in sections representing marginal zone or subventricle zone were purified by FACS. Reporter positive cells were collected and RNA were extracted for RNAseq.

first: Lim

last: Lynette

first: Marin

last: Oscar


title: A network of noncoding regulatory RNAs acts in the mammalian brain


title: Positional specificity of different transcription factor classes within enhancers

first: Sharon

middle: R

last: Grossman

address: 415 Main Street

institute: Broad Institute

summary: Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within NDRs fall into six distinct classes. These patterns are highly consistent across cell types, and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence.

overall_design:
ATAC-seq in two immune cell lines, Jurkat and U937.

H3K27ac ChIP-seq in two immune cell lines, Jurkat and U937, representing a re-analysis of SRR1057274 from sample GSM1296384 (Jurkat) and ERR671846 from sample ERS420369 (U937).  We generated the following processed data files:
Jurkat-H3K27ac.gappedPeak.gz
U937-H3K27ac.gappedPeak.gz.


title: A network of noncoding regulatory RNAs acts in the mammalian brain IV

overall_design: miRNA expression profiling by small-RNA-seq of of K562 cells stably expressing both dead Cas9 (dCas9) fused to a KRAB domain and either a control guide or a guide targeting CYRANO. This study consists of 6 libraries generated from 3 biological replicates per guide RNA.


title: RNA-Seq profiling of iPSC-derived ventricular and atrial cardiomyocytes

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We profiled RNA expression in human iPSC-derived ventricular and atrial cardiomyocytes

overall_design: 4 biological replicates of human iPSC-derived ventricular cardiomyocytes and 4 biological replicates of iPSC-derived atrial cardiomyocytes (from 3 individual iPSC lines)

first: Lukas

last: Cyganek

first: Kaomei

last: Guan


title: Transcriptional responses of melanoma cells to BRAF inhibition

city: Los Angeles

first: Jennifer

last: Tsoi

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

summary: We performed a time-course experiment to determine the temporal transcriptional changes that occur in human melanoma cells when cultured with the BRAF inhibitor vemurafenib from 3 days to 73-90 days.

overall_design: mRNA profiles of M229 and M397 melanoma cell lines after treatment with DMSO control or vemurafenib for the indicated timepoints

first: Lidia

last: Robert

first: Thomas

last: Graeber

first: Antoni

last: Ribas


title: AmpliSeq Transcriptome Analysis of Human Alveolar and Monocyte-Derived Macrophages Over Time in Response to Mycobacterium tuberculosis infection

status: Public on Jun 06 2018

city: Columbus

first: Maciej

last: Pietrzak

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq’s reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways that differ in part between MDM and HAM. A similar number of expressed genes are detected at all time-points between uninfected MDM and HAM, in common pathways including inflammatory and immune functions, but canonical pathway differences also exist. In particular, at 2 h, multiple genes relevant to the immune response are preferentially expressed in either uninfected HAM or MDM, while the HAM RNA profiles approximate MDM profiles over time in culture, highlighting the unique RNA expression profile of freshly obtained HAM. MDM demonstrate a greater transcriptional response than HAM upon M.tb infection, with 2 to >10 times more genes up- or down-regulated. The results identify key genes involved in cellular responses to M.tb in two different human macrophage types. Follow-up bioinformatics analysis indicates that approximately 30% of response genes have expression quantitative trait loci (eQTLs in GTEx), common DNA variants that can influence host gene expression susceptibility or resistance to M.tb, illustrated with the TREM1 gene cluster and IL-10.

overall_design: Assessment of transcriptome profiles from cells infected with Mycobacterium tuberculosis using AmpliSeq.

first: Wolfgang

last: Sadee

first: Larry

middle: S

last: Schlesinger

first: Audrey

last: Papp

first: Abul

last: Azad


title: Gene expression changes in HEI-193 (NF2-deficient Schwannoma) cells by NF2-restoring or TEW7197 treatment.

city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary:
Neurofibromatosis type 2 (NF2) syndrome is a very rare human genetic disease and until now, it’s proper treatment has not been suggested. In our recent study, it has been reported that the loss of NF2 activates MAPK signaling through reduction of RKIP in a mesothelioma model. Here, we show that loss of NF2 induces reduction of the TGF-β receptor 2 (TβR2) expression and an overwhelming expression of TGF-β receptor 1 is activated by physical stimuli such as pressure or heavy materials. Activated TR1 induced the phosphorylation and degradation of RKIP. RKIP reduction consequently results in MAPK activation as well as Snail-mediated p53 suppression and occurrence of EMT in NF2-deficient cells by physical stimuli. Thus, TβR1 kinase inhibitors restore cell differentiation and induce growth suppression in NF2 deficient Schwannoma cell line and MEF. Moreover, TEW7197, a specific TβR1 kinase inhibitor, reduces tumor formation in the NF2-model mouse (Postn-Cre;NF2f/f). Gene expression profiling reveals that TEW7197-treatment induces the expression of lipid metabolism-related gene set such as NF2-restored cells in HEI-193 (NF2-deficient Schwannoma). Our results indicate that reduction or deletion of TβR2 or NF2 induces the TβR1-mediated oncogenic pathway, and therefore inhibition of the unbalanced TGF-β signaling is a putative strategy for NF2-related cancers (NF2 syndrome and mesothelioma) and TβR2 mutated advanced cancers.
To know the global effect of TEW7197, we performed the microarray with HEI-193.

overall_design: For differential gene expression analysis by NF2 transfection and TEW7197 treatment, microarray was performed using the Affymetrix GeneChip (Human Gene 2.0 ST Array; DNA Link, Inc, Korea). Total RNA obtained from HEI-193 transfected with NF2 (about 60% transfection yield) or treated with TEW7197 (10 M for 12 hr or 24 hr) was quantified and used for analysis. For differentially expressed gene (DEG) analysis, probes were selected if the difference in expressions were 1.5 fold compared to the HEI-193 control, and were statistically filtered by t-test (p<0.05). For the functional analysis, only DEG probes were used. Web tool DAVID (david.abcc.ncifcrf.gov/home.jsp), data base of which are Gene Ontology, KEGG, BIOCARTA and OMIM_DISEAE, was used for functional grouping of probes. All statistical and functional analysis were performed by DNA Link, Inc.

first: Jung-Hyun

last: Cho

first: Ah-Young

last: Oh

first: Soyoung

first: So-mi

last: Kang

first: Min-Ho

last: Yoon

first: Tae-Gyun

last: Woo


title: Comparative analysis of the cistromes of ERα and phosphorylated CREB1 in breast cancer cells

city: Genéve

first: Didier

last: Picard

address: Quai Ernest-Anserment, 30

department: Cell Biology- Science 3

institute: University of Genéve

summary: We report the genome-wide chromatin binding profiles of ERα and phosphorylated CREB1 (pCREB1) upon stimulation of human MDA-MB-134 breast cancer cells with estradiol or cAMP. We highlight the unique and the shared cistromes for each transcription factor.

overall_design: ChIP-seq of ERα and phosphorylated CREB1 with human MDA-MB-134 breast cancer cells; duplicate samples were treated with vehicle (DMSO), estradiol or cAMP

first: Melissa

last: Berto


title: Male Germ Cells Support Long-Term Propagation of Zika Virus

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Evidence of male-to-female sexual transmission of Zika virus (ZIKV) and viral RNA in semen and sperm months after infection support a potential role for testicular cells in ZIKV propagation. Here, we demonstrate that germ cells (GC) are most susceptible to ZIKV. We find that only GC infected by ZIKV, but not those infected by dengue fever (DENV) and yellow fever virus (YFV), produce high levels of infectious virus. This observation coincides with decreased expression of interferon-stimulated gene Ifi44l in ZIKV-infected GC and over-expression of Ifi44l results in reduced ZIKV production. Using primary human testicular tissue, we demonstrate that human GC are also permissive for ZIKV infection and production. Finally, we identify berberine chloride as a potent inhibitor of ZIKV infection in both murine and human testes. Together, these studies identify a potential cellular source for propagation of ZIKV in testes and a candidate drug for preventing sexual transmission of ZIKV.

overall_design: RNA-seq was used to compare the gene expression profiles in mock-infected GC with those infected with ZIKV, DENV, and YFV. Among the top 150 most-upregulated genes in DENV- (> 10-fold) or YFV-infected GC (> 4-fold), we selected genes that were upregulated in both DENV- and YFV-infected GC but not in ZIKV-infected GC.

first: C

last: Robinson

first: A

last: Chong

first: S


title: A network of noncoding regulatory RNAs acts in the mammalian brain III

first: David

last: Bartel

department: Biology

overall_design: miRNA expression profiling by small-RNA sequencing of cerebellum and hippocampus from wild-type (WT) and Cyrano–/– (CyrKO) mice, and of cerebellum from Cdr1as miR-671 site mutant (Cdr1as671), and double mutant (CyrKO;Cdr1as671) mice. This study consists of 18 libraries generated from 3 biological replicates per genotype for each tissue.

first: Benjamin

last: Kleaveland


title: Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

summary: We develop Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables genome-wide detection of higher-order interactions that occur simultaneously within the nucleus in a proximity-ligation independent manner. We generated SPRITE maps in two mammalian cell types – mouse embryonic stem cells (mES) and human lymphoblastoid cells (GM12878). We generated ~1.5 billion sequencing reads from each sample and recapitulate known genome structures identified by Hi-C, including chromosome territories, compartments, topologically associated domains, and loop structures, and identify that many of these occur within higher-order structures in the nucleus. Because SPRITE does not rely on proximity-ligation, we find that SPRITE identifies interactions that occur across larger spatial distances than can be observed by Hi-C. These long-range interactions include two major hubs of inter-chromosomal interactions. We extended SPRITE to enable simultaneous measurements of RNA and DNA interactions and observe ribosomal RNA interactions across specific regions on the genome that correspond to DNA organization around the nucleolus. We show that gene-dense regions that are highly transcribed by PolII organize around nuclear speckles and gene poor, and therefore transcriptionally inactive, regions that are centromere-proximal organize around the nucleolus. In addition to the regions that directly associate around these nuclear bodies, we find that a substantial fraction of the genome exhibits preferential spatial positioning in the nucleus relative to each of these nuclear bodies and that the spatial preferences identified by SPRITE are highly correlated with 3D distances measured by microscopy.

overall_design:
DNA SPRITE was used to study 3D genome organization in mouse ES cells and human lymphoblasts. RNA-DNA SPRITE was used to map RNA and DNA interactions simultaneously in mouse ES cells.

Heatmaps are included in tar archives at the foot of this record in addition to the cluster data. Please see the file SPRITE_readme_heatmaps.rtf for information on heatmap generation.

first: Mitchell

last: Guttman


title: CRISPR/Cas9-mediated Gene Knockout Reveals a Guardian Role of NF-kB/RelA in Maintaining the Homeostasis of Human Vascular Cells

status: Public on Jun 05 2018

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: Dysfunction of blood vessels leads to severe vasculature pathogenesis. Previous studies have demonstrated that constitutive NFkB activation results in chronic vascular inflammation, leading to various cardiovascular diseases. However, how NFkB regulates blood vessel homeostasis remains largely elusive. Here, using CRISPR/Cas9-mediated gene editing, we generated RelA knockout human embryonic stem cells (hESCs) and differentiated them into human vascular derivatives to study how NFkB modulates vascular cells under basal and inflammatory conditions. Multi-dimensional phenotypic assessments and transcriptomic analyses revealed that RelA deficiency affected vascular cells via modulating vascular inflammation, survival, vasculogenesis, differentiation and extracellular matrix organization in a cell type-specific manner under basal condition, and that RelA protected vascular cells against apoptosis and modulated vascular inflammatory response upon TNFa stimuli. Lastly, further evaluation of gene expression patterns in IkBa knockout vascular cells demonstrated that IkBa acted largely independent of NFkB signaling pathway. Taken together, our data reveals a protective role of NFkB/RelA in modulating human blood vessel homeostasis and maps the human vascular transcriptomic landscapes for the discovery of novel therapeutic targets.

overall_design: Transcriptomic analyses of WT, RelA and IkBa deficiency vascular cells under basal and inflammatory condition.

first: Guanghui


title: Radiation-induced GEPs in immortalized and primary breast cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Today, Radiation therapy (RT) regimens are often used for many types of cancer including breast cancer (BC) disease. BC is an heterogeneous disease, at both clinical and molecular levels, presenting distinct subtypes associated with different clinical outcomes. This variability response may be caused by some factors linked to radiation or dependent to BC specific features such as tumor stage and hormone receptor (HR) status. We analyze and compare molecular responses, in term of gene expression profile (GEP) changes, induced by 9 and 23Gy of ionizing radiation (IR) in immortalized and primary cell cultures grouped according their Estrogen (ER) and Progesteron (PR) receptors positive or negative expression. Our explorative study gives some comprehensive hallmarks of the effects of the irradiation in BC cells. We trust that this study could have a role in driving RT towards personalised treatments, based also on the molecular characterization in BC.

overall_design: Radiation-induced gene expression changes in non- tumorigenic (MCF10A) and in tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines; and in healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures obtained from surgical biopsies, were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. New Samples were named as follow: MCF10A_9Gy; MCF7_9Gy; MDA-MB-231_9Gy; HMEC_9Gy; BCpc7_9Gy; BCpcEMT_9Gy; MDA-MB-231_23Gy. In addition, we have used the our existing samples following listed:  GSM1611676-81;GSM1554983-88; GSM3019056-61;GSM3019068-73;GSM3019080-85.


title: Hepatic pyruvate kinase muscle isoform 2 (Pkm2) induction in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-elicited oxidative stress is independent of NRF2  (ChIP-Seq)

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induces hepatic oxidative stress following activation of the aryl hydrocarbon receptor (AhR). Our recent studies revealed induction of pyruvate kinase muscle isoform 2 (Pkm2) as a novel antioxidant response in normal differentiated hepatocytes. To investigate cooperative regulation between nuclear factor, erythroid derived 2, like 2 (Nrf2) and the AhR, hepatic ChIP-seq analyses were integrated with RNA-seq time course data from mice treated with TCDD for 2 - 168h. ChIP-seq analysis 2h following TCDD treatment revealed genome-wide changes in NRF2 binding. 842 NRF2 enriched regions were in the regulatory region of differentially expressed genes (DEGs) while 579 DEGs showed both NRF2 and AhR enrichment. Sequence analysis showed over-representation of AhR and NRF2 binding motifs in these regions, though presence of motifs were largely independent. NRF2 was negligibly enriched within the Pkm gene loci in a closed chromatin region despite its role in antioxidant defenses. Furthermore, TCDD induced Pkm2 in primary hepatocytes from wild-type and Nrf2 null mice, indicating NRF2 is not required. Although NRF2 and AhR cooperate in the regulation of gene expression associated with antioxidant responses, the induction of Pkm2 by TCDD is not dependent on ROS-mediated activation of NRF2.

overall_design: Five biological replicates, pooled

first: Claire

last: Doskey

first: Kelly

middle: A

last: Fader

first: Timothy

last: Zacharewski


title: Effect of TDNC1 ectopic expression on global gene expression pattern

city: Montreal

first: Naghmeh

last: Nikpoor

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary:
Type 2 Diabetes (T2D) is a complex metabolic disorder due to a progressive insulin secretory defect on the background of insulin resistance. We found a muscle specific lncRNA we named TDNC1(T2D down-regulated non-coding RNA 1) whose expression is reduced in T2D patients as well as young individuals with family history of T2D.
We used Microarray to assess for global gene expression pattern following ectopic expression of this lncRNA.

overall_design: Inducible flp in HEK293cells stably expressed TDNC1 along with random control RNA were created using Flp-In T-Rex Core kit according to manufacture protocol (Invitrogen).  Stable clonies were pooled and RNA was extracted using Trizol and Qiagen Rneasy columns. Total RNA was hybridyzed to Affymetrix Human Gene ST 2.0 array

first: Nikpoor

last: Naghmeh

first: Sladek

last: Robert


title: Differential expression profiling of the TamR cells following AR knockdown

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

institute: Garvan Institute of Medical Research

summary: The androgen receptor (AR) has emerged as a candidate target for the treatment of breast cancer. In this study, we sought to characterize the functional consequences of AR knockdown using a siRNA-mediated approach in a tamoxifen-resistant (TamR) derivative of MCF7 breast cancer cell line.

overall_design: We evaluated the role of AR in endocrine-resistance using tamoxifen resistant (TamR) cells derived from the MCF7 breast cancer cell line. The TamR line was continuously cultured in RPMI 1640 media (Thermo Fisher) supplemented with 10% fetal bovine serum (GE Healthcare), 20 mM HEPES (Thermo Fisher) and 0.28 IU/ml insulin (Novo Nordisk). Base media for TamR cells was also supplemented with 5 µM 4-hydroxytamoxifen (Sigma). Gene expression profiling was performed on the TamR cells 48 hours post transfection with nonsense (NS) control or AR siRNA (5'-GGAACUCGAUCGUAUCAUU-3' , Thermo Fisher Silencer® Select Pre-Designed siRNA #4390824) using 3 biological replicates. Microarray hybridization was performed on the Affymetrix PrimeView™ Human Gene Expression Array following the manufacturer's protocol. CEL files were further processed in the R software (v 3.4.3) environment using affy (Gautier et al., 2004) and limma (Ritchie et al., 2015) packages from Bioconductor.

first: KeeMing

last: Chia

first: Niantao

last: Deng

first: Elgene

last: Lim


title: Genome-wide mapping of Yap1 in the normal and hypertrophied hearts

city: Newark

first: Maha

last: Abdellatif

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

summary: anti-Yap1 ChIP-high throughput sequencing (Seq) was performed on normal and 7 day post-transverse aortic constriction mouse heart tissue

overall_design: Mice were subjected to a sham or transverse aortic constriction operation (TAC, n=3, each). After one week the hearts were isolated and analyzed by anti-Yap1 ChIP-Seq


title: DHX15 regulates CMTR1-dependent gene expression and cell proliferation

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

summary: We discovered that the RNA helicase DHX15 is a regulator of the methyltransferase CMTR1.  To determine the biological consequences of this interaction we overexpressed CMTR1 or a mutated CMTR1 (2LA)that does not bind DHX15, in the human breast cancer cell line HCC1806.  To assess the effects of the DHX15-CMTR1 interaction on translation, polysomes were separated on a sucrose gradient and sequencing libraries generated from the polysomal and input RNA.  We found that the DHX15-CMTR1 interaction controls ribosome loading of a subset of mRNAs and impacts on cell proliferation.

overall_design: Polysome and input RNA samples were sequenced from two replicate experiments.  In each experiment  HCC1806 cells were transfected with either pcDNA5 (vector control), pcDNA 5 HA-CMTR1 WT (wildtype CMTR1) or pcDNA 5 HA-CMTR1 2L/A mutant (mutant CMTR1 that does not interact with DHX15).

first: Francisco

last: Inesta-Vaquera

first: Victoria

last: Cowling


title: Notch signaling facilitates in vitro generation of cross-presenting classical dendritic cells

first: Margaret

last: Kirkling

institute: Columbia University

summary: The IRF8-dependent subset of classical dendritic cells (cDC), termed cDC1, is important for cross-priming cytotoxic T cell responses against pathogens and tumors. Culture of hematopoietic progenitors with DC growth factor Flt3 ligand (Flt3L) yields very few cDC1 (in humans) or only immature "cDC1-like" cells (in the mouse). We report that OP9 stromal cells expressing Notch ligand Delta-like 1 (OP9-DL1) optimize Flt3L-driven development of cDC1 from murine immortalized progenitors and primary bone marrow cells. Co-culture with OP9-DL1 induced IRF8-dependent cDC1 with the phenotype (CD103+ Dec205+ CD8α+) and expression profile resembling ex vivo cDC1. OP9-DL1-induced cDC1 showed preferential migration towards Ccr7 ligands in vitro and superior T cell cross-priming and antitumor vaccination in vivo. Co-culture with OP9-DL1 also greatly increased the yield of IRF8-dependent CD141+ cDC1 from human bone marrow progenitors cultured with Flt3L. Thus, Notch signaling optimizes cDC generation in vitro and yields authentic cDC1 for functional studies and therapeutic applications.

overall_design: Samples 1-8 are RNA-seq data to determine expression changes from in vitro-generated dendritic cell subsets between Flt3L- and Flt3L plus OP9 DL1- driven cultures.

first: Colleen

last: Lau

first: Alireza

last: Khodadadi-Jamayran

first: Christian

last: Siebel

first: Boris

last: Reizis