title: Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. SEC is required for induction of heat-shock genes and treating cells with KL-1 and KL-2 attenuates the heat-shock response from Drosophila to human. SEC inhibition downregulates MYC and MYC-dependent transcriptional programs in mammalian cells and delays tumor progression in a mouse xenograft model of MYC-driven cancer, indicating that small-molecule disruptors of SEC could be used for targeted therapy of MYC-induced cancer.

overall_design: Determination of SEC inhitiors affecting transcription elongation. Examination of Pol II and Super Elongation complex in multiple cells with and without SEC knockdown, or SEC inhibitors inhibition.

first: Kaiwei

last: Liang

first: Ashley

last: Woodfin


title: Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

status: Public on Oct 26 2018

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

country: USA

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary:
Measuring multiple omics profiles from the same single cell opens up the opportunity to decode molecular regulation that underlies intercellular heterogeneity in development and disease. Here, we present co-sequencing of microRNAs and mRNAs in the same single cells using a half-cell genomics approach. This method demonstrates good robustness (~95% success rate) and reproducibility (R2=0.93 for both microRNAs and mRNAs), yielding paired half-cell microRNA and mRNA profiles that we can independently validate. By linking the level of microRNAs to the expression of predicted target mRNAs across 19 single cells that are phenotypically identical, we observe that the predicted targets are significantly anti-correlated with the variation of abundantly expressed microRNAs. This suggests that microRNA expression variability alone may lead to non-genetic cell-to-cell heterogeneity. Genome-scale analysis of paired microRNA-mRNA co-profiles further allows us to derive and validate regulatory
relationships of cellular pathways controlling microRNA expression and intercellular variability.

overall_design: This dataset contains single cell small RNA sequencing and RNA-seq analysis of K562 cells. Single K562 cells were subjected to small RNA sequencing and/or RNAseq analyses using a half-cell approach. Included in this dataset are twenty K562 cells with paired small RNA and RNAseq data.

first: Nayi

last: Wang

first: Zhuo

last: Chen

first: Rong

last: Fan


title: ATAC-seq of YB5 cells treated with HH1

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq was performed after YB5 cells were treated with DMSO or HH1

overall_design: Biological triplicates were performed for a total of 6 samples.

first: Hanghang

last: Zhang

first: Somnath

last: Pandey

first: Meghan

last: Travers

first: Hongxing

last: Sun

first: Yasuyuki

last: Okamoto

first: Takahiro

last: Sato

first: Judit

last: Garriga

first: Bela

last: Patel

first: Noël

last: J.-M. Raynal

first: Yi

first: Wayne

last: Childers

first: Magid

last: Abou-Gharbia

first: Stephen

last: B. Baylin

first: Cynthia

last: Zahnow

first: Jaroslav

last: Jelinek

first: Xavier

last: Graña

first: Jean-Pierre

last: J. Issa


title: ONECUT2 inhibition by chemical compound treatment in 22Rv1

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: To evaluate the specificity for inhibition of expression of OC2 target genes we generated microarray data of 22Rv1 cells treated for 4, 6 and 16 hours with the small molecule inhibitor.

overall_design: 22Rv1 cells treated for 4, 6 and 16 hours with the small compound

first: Micheal

middle: R

last: Freman

first: Mirja

last: Rotinen


title: HIV Stimulation Induces a Unique Innate Immune Response in Kupffer Cells

city: Miami

first: Emmanuel

last: Thomas

state: FL

address: 1550 NW 12th Ave, Papanicolaou Bldg., RM. PAP 514

department: Schiff Center for LIver Diseases

institute: University Of Miami School of Medicine

summary:
BACKGROUND: Patients with HIV that are coinfected with HCV are at increased risk for rapidly progressive liver disease and subsequently the development of Hepatocellular Carcinoma (HCC).  Specifically, HCC develops earlier in coinfected patients and these patients are more symptomatic than those with only HCV infection at diagnosis suggesting that both viruses increase the propensity for malignant transformation. Consequently, HCV coinfection and the associated liver disease is a major health burden for HIV infected persons in the U.S.  However, the genetic and cellular based mechanisms underpinning how HCV initiates and subsequently induces liver pathology and why coinfection with HIV results in significantly worse hepatic disease remains to be clarified.  In addition, the specific cell types that contribute to these clinical outcomes are unknown. METHODS: The goal of this project is focused on understanding the molecular mechanisms underlying the hepatic sequela in coinfected patients specifically focusing on the innate inflammatory responses activated by HIV in liver cells.  To this end, we have developed novel in-vitro models that utilize HIV stimulated primary kupffer cells (PKCs). RESULTS: HIV stimulation of primary kupffer cells resulted in rapid and robust upregulation of an inflammatory gene signature.
The goal of this study is to characterize the changes in gene expression triggered by HIV in primary human kupffer cells.

overall_design: PKCs were stimulated with HIV (MO.I = 2) for 24 hours. Three replicates were performed for each condition.

first: J

last: Hyun

first: E


title: Global microarray analysis of ONECUT2 transcription factor overexpression in human prostate cancer cells

summary: Treatment of prostate cancer by hormone suppression leads to the appearance of aggressive variants with variable or no dependence on the androgen receptor. Here we show that the developmental transcription factor, ONECUT2, is a master regulator of the AR network that is highly active in castration-resistant prostate cancer (CRPC).

overall_design: We performed gene expression profiling in 22Rv1 and LNCaP cell lines. OC2 was overexpressed in LNCaP and 22Rv1 or silenced in 22Rv1.

first: Michael

last: Freeman


title: LINE-1 elements are derepressed in senescent cells and elicit a chronic Type-I Interferon response

city: Providence

first: John

last: Sedivy

state: RI

address: 70 Ship Street

institute: Brown University

summary: It is not known to what extent retrotransposable elements contribute to the development of age-associated diseases. Here we show that during cellular senescence L1s become transcriptionally derepressed and trigger a type-I interferon (IFN-1) response. We propose that RTE activation is an important component of the sterile inflammation that is a hallmark of aging, and that L1 reverse transcriptase is a relevant target for the development of drugs to treat associated disorders.

overall_design: Human normal diploid lung fibroblast cells from proliferative, early senescent and late senescent stages were used to observe relative changes in gene expression and type-I interferon induction

first: Marco

last: DeCecco


title: Selective export into extracellular vesicles and function of tRNA fragments during T cell activation

status: Public on Oct 25 2018

city: San Francisco

first: Ni-Ting

last: Chiou

address: 513 Parnassus Ave

institute: University of San Francisco

summary: In order to identify small RNAs that are enriched in T-cell extracellular vesicles (EVs) upon T cell activation in a nSMase-dependent manner, we used a two-step ultracentrifugation procedure to isolate EVs released by T cells followed by small RNA profiling of EVs and T cells under resting, stimulated conditions and stimulated conditions in the presence of the vehicle control, DMSO, or nSMase inhibitor, GM4869.

overall_design: Primary T cells were isolated from wild-type B6 mice. Small RNA profiles of EVs and T cells under resting (R), stimulated (S), stimulated in the presence of DMSO (DM) and stimulated in the presence of GW4869 (GW) conditions, in triplicate.

first: K

middle: M

last: Ansel


title: CRISPR screen for interferon-alpha inducible inhibitors of yellow fever virus replication

city: Dallas

last: Schoggins

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). A genome-wide CRISPR screen using IFN alpha-treated Huh7.5 cells was performed to determine which ISGs were required in order for host cells to suppress yellow fever virus (YFV) infection.

overall_design: Human Huh7.5 cells were transduced with a human CRISPR library in a single replicate at 900X library coverage, treated with IFN alpha, infected with YFV-17D-venus, and GFP-positive cells that escaped IFN-alpha suppression of YFV-17D-venus infection were collected by FACS.

first: R

middle: B

last: Richardson

first: Maikke

last: Ohlson

first: Jennifer

middle: L

last: Eitson

first: Ashwani

last: Kumar

first: Matthew

last: McDougal

first: Ian

middle: N

last: Boys

first: Katrina

last: Mar

first: Pamela

middle: C

last: De La Cruz-Rivera

first: Connor

last: Douglas

first: Genevieve

last: Konopka

first: Chao

last: Xing

middle: W


title: Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation

city: Philadelphia

first: Caroline

last: Bartman

state: PA

address: 34th st.

department: Department of Bioengineering

institute: University of Pennsylvania

summary: We performed Pol II ChIP-seq to measure transcriptional changes upon different biological perturbations

overall_design:
Pol II ChIP-seq data upon 60 min JQ1, triptolide, or flavopiridol treatment in differentiated G1E-ER4 cells

Pol II ChIP-seq data upon 0 or 4h differentiation of G1E-ER4 cells

first: Arjun

last: Raj


title: Hemogenic Endothelium transcriptome along the timeline of hESC differentiation

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary:
The differentiation of human embryonic stem cells to hematopoietic lineages initiates with the specification of hemogenic endothelium, a transient specialized endothelial precursor of all blood cells.Unfortunately, absence of hemogenic endothelium-specific markers as well as lack of consensus in the timing of hemogenic potential analysis and methodologies used to study the hematopoietic potential of this precursor prevents reaching clear and definite conclusions. Here, we demonstrate that the hemogenic potential of the endothelium precursor population sharply decline over the course of the differentiation process.
Poly(A) RNA-sequencing on CD31+CD144+ population at day 6, day 8 and day 10 of EB diffferentiation with or without the addition of cytokines. Comparasion with hematopoietic committed population CD31+CD144- from day 10 of EB differentiation.

overall_design: CD31+CD144+ signature along the EB differentiation

first: Eva

last: Garcia-Alegria

first: Sara

last: Menegatti

first: Muhammad

middle: Z

last: Fadlullah

first: Pablo

last: Menendez

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Gene expression of macrophages treated with hY3

status: Public on Oct 24 2018

city: Manhattan

first: Tenzin

last: Lhakhang

state: NY

address: 550 First Avenue

institute: NYU School of Medicine

summary:
Based on the consistent demonstration of fibrosis of the atrioventricular node surrounded by macrophages and multinucleated giant cells in anti-Ro antibody exposed fetuses dying with heart block, this study focuses on macrophage signaling stimulated by ssRNA associated with the Ro60 protein and the impact of antagonizing innate cell drivers such as TLR7/8. Transcriptome and epigenetic modifications which affect transcription factors, NF-κB and STAT1, were selected to evaluate the phenotype of macrophages in which TLR7/8 was ligated following treatment with either anti-Ro60/Ro60/hY3 RNA immune complexes or transfection with hY3.
Based on microarray, TNF and IL6 were among the most highly upregulated genes in both stimulated conditions, each of which was significantly inhibited by preincubation with hydroxychloroquine (HCQ). In contrast, following stimulation of macrophages with either TNF-α or IFN-α, which do not signal through TLR, the resultant gene expression was refractory to HCQ. Ligation of TLR7/8 resulted in increased histone methylation as measured by increased H3K4me2, a requirement for binding of NF-κB at certain promoters, specifically the kB1 region in the TNF promoter (ChIP-qPCR), which was significantly decreased by HCQ. In summary, these results support that the HCQ-sensitive phenotype of hY3 stimulated macrophages reflects the bifurcation of TLR downstream signals involving NF-κB and STAT 1 pathways and for the former dimethylation of H3K4. Accordingly, HCQ may act more as a preventive measure in downregulating the initial production of IFN-α or TNF-α and not affect the resultant autocoid stimulation reflected in TNF-α and IFN-α responsive genes. The beneficial scope of antimalarials in the prevention of organ damage, inclusive of heart block in an anti-Ro offspring or more broadly SLE, may include in part, a mechanism targeting TLR-dependent epigenetic modification.

overall_design: Total 8 samples were subjected to microarray and data analysis. 4 samples were hY3 treated macrophages and 4 untreated macrophages were used as controls.

first: Robert

last: Clancy

first: Androo

middle: J

last: Markham


title: Invasive non-typhoidal Salmonella dysregulates the repertoire of dendritic cell responses to intracellular and extracellular stimuli [scRNA-seq]

city: Oxford

first: Anna

last: Aulicino

state: Oxfordshire

address: Headley Way, Headington

department: Human Immunology Unit, WIMM

institute: University of Oxford

summary: Non-typhoidal Salmonella (NTS) are among of the most important food-borne pathogens. Recently, a highly invasive multi-drug resistant S. Typhimurium of a distinct multilocus sequence type (MLST), ST313, has emerged across sub-Saharan Africa as a major cause of lethal bacteraemia in children and immunosuppressed adults. Encounters between dendritic cells (DCs) and invading bacteria determine the course of infection but whether or how ST313 might usurp DC mediated defence has not been reported. Here we utilised fluorescently labelled invasive and non-invasive strains of Salmonella combined with single-cell RNA sequencing to study the transcriptomes of individual infected and bystander DCs. The transcriptomes displayed a repertoire of cell instrinsic and extrinsic innate response states that differed between invasive and non-invasive strains. Gene expression heterogeneity was increased in DCs challenged with invasive Salmonella. DCs exposed but not harbouring invasive Salmonella exhibited a hyper-activated profile that likely facilitates trafficking of infected cells and dissemination of internalised intact bacteria. In contrast, invasive Salmonella containing DCs demonstrate reprogramming of trafficking genes required to avoid autophagic destruction.  Furthermore, these cells displayed differential expression of tolerogenic IL10 and MARCH1 enabling CD83 mediated adaptive immune evasion. Altogether our data illustrate pathogen cell-to cell variability directed by a Salmonella invasive strain highlighting potential mechanisms of host adaption with implications for dissemination in vivo.

overall_design: Single-cell RNA sequencing (SMARTSeq2) of 373 human monocyte derived dendritic cells infected with S. Typhimurium strain LT2 or D23580 or left uninfected

first: Kevin

last: Rue-Albrecht

first: Lorena

last: Preciado-llanes

first: Giorgio

last: Napolitani

first: Tim

last: Ambrose

first: Neil

last: Ashley

first: Adam

last: Cribbs

first: Melita

last: Gordon

first: David

last: Sims

first: Alison

last: Simmons


title: Invasive non-typhoidal Salmonella dysregulates the repertoire of dendritic cell responses to intracellular and extracellular stimuli

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

overall_design: Refer to individual Series


title: Invasive non-typhoidal Salmonella dysregulates the repertoire of dendritic cell responses to intracellular and extracellular stimuli [bulk RNA-seq]

overall_design: RNA-seq of mini-bulks (5000 cells) of human monocyte derived dendritic cells infected with S. Typhimurium strain LT2 or D23580 or left uninfected


title: H3.3K4M targets MLL3/MLL4 to prevent enhancer activation in adipogenesis

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Enhancers play a key role in regulating cell type-specific gene expression and are marked by histone modifications such as methylation and acetylation. Mono-methylation of lysine 4 on histone H3 (H3K4me1) initially primes enhancers, preceding enhancer activation via acetylation of lysine 27 on histone H3 (H3K27ac). MLL4 is a major enhancer H3K4 mono-methyltransferase with partial functional redundancy with MLL3. However, how H3K4me1 affects enhancer regulation in cell differentiation has remained unclear. By screening several lysine-to-methionine mutants of H3.3, we first found that depletion of H3K4 methylation by H3.3K4M mutation severely impairs adipogenesis in culture. Using tissue-specific expression of H3.3K4M in mice, we further demonstrate that H3.3K4M inhibits adipose tissue and muscle development in vivo. Mechanistically, H3.3K4M destabilizes MLL3/4 proteins but not other members of the mammalian Set1-like H3K4 methyltransferase family and prevents MLL3/4-mediated enhancer activation in adipogenesis. Using tissue-specific deletion of the enzymatic SET domain of MLL3/4 in mice, we also show that deletion of the SET domain prevents adipose tissue and muscle development in vivo and inhibits adipogenesis by destabilizing MLL3/4 in vitro. Notably, H3.3K4M expression mimics MLL3/4 SET domain deletion in preventing adipogenesis. Interestingly, H3.3K4M does not affect adipose tissue maintenance and function, suggesting that MLL3/4-mediated H3K4 methylation is dispensable for the maintenance and function of differentiated adipocytes. Together, our findings suggest that H3.3K4M targets MLL3/4 to prevent enhancer activation in adipogenesis.

overall_design: Expression profiling by RNA-seq at D7 of adipogenesis in brown preadipocytes in culture, and histone modifications (H3K4me1 and H3K27ac) by ChIP-seq, at D4 of adipogenesis of brown preadipocytes in culture.

first: Jang

last: Younghoon

first: Wang

last: Chaochen

first: Park

last: Young-Kwon

first: Zhuang

last: Lenan

first: Lee

last: Ji-Eun

first: Ge

last: Kai


title: Transcriptomes in healthy and CHB fetal hearts

first: Tenzin

last: Lhakhang

summary: Given that diseases associated with anti-SSA/Ro autoantibodies such as systemic lupus erythematosus and Sjögren’s syndrome are linked with an upregulation of IFN and type I IFN-stimulated genes, including Sialic Acid-Binding Ig-Like Lectin 1 (Siglec-1), a receptor on monocytes/macrophages, recent attention has focused on a potential role for IFN and IFN-stimulated genes in the pathogenesis of congenital heart block (CHB). Accordingly, three approaches were leveraged to address the association of IFN, IFN-stimulated genes, and the phenotype of macrophages in affected fetal cardiac tissue: a) cultured healthy human macrophages transfected with hY3, an anti-SSA/Ro-associated single-stranded RNA, b) RNA isolated from freshly sorted human leukocytes/macrophages after Langendorff perfusion of three fetal hearts dying with CHB and three healthy gestational age-matched hearts, and c) autopsy tissue from three additional human CHB hearts and one healthy heart. TLR ligation of macrophages with hY3 led to the upregulation of a panel of IFN transcripts, including SIGLEC1, a result corroborated using qPCR.  Utilizing independent and agnostic bioinformatics approaches, CD45+CD11c+ and CD45+CD11c- human leukocytes flow sorted from the CHB hearts highly expressed type I IFN response genes inclusive of SIGLEC1.  Furthermore, Siglec-1 expression was identified in the septal region of several affected fetal hearts. These data now provide a link between IFN, IFN-stimulated genes, and the inflammatory and possibly fibrosing components of CHB, positioning Siglec-1-positive macrophages as integral to the process.

overall_design: three CHB hearts of gestational ages 19, 20 and 23 and three healthy hearts of gestational ages 18, 22, and 23 weeks were utilized.

first: Robert

last: Clancy

first: Miao

last: Chang


title: Clonal deletion of tumor-specific T cells by IFN-g confers therapeutic resistance to combination immune checkpoint blockade

first: Anthony

state: California

address: 513 Parnassus Ave.

institute: University of California, San Francisco

summary: Combination immunotherapy is being developed with the goal of enhancing anti-tumor immunity. Despite remarkable clinical responses, most patients do not experience complete responses from combination checkpoint blockade treatments. Therefore, a need exists to further explore the mechanisms of resistance to these therapies. Here, we investigate whether tumor burden could be an important factor in determining the treatment outcomes of combination checkpoint blockade. We found that while combined anti-CTLA-4 and anti-PD-1 improves control of established tumors, this combination can paradoxically compromise anti-tumor immunity in the low tumor burden (LTB) state in pre-clinical models as well as in melanoma patients. This paradoxical outcome results from treatment-induced deletion of tumor-specific T cells that is mediated through IFN-γ. Activated tumor-specific T cells express higher levels of IFN-γ receptor and are more susceptible to apoptosis. As a result, combination treatment alters the T cell repertoire landscape, skewing the distribution of T cells toward lower frequency clonotypes. Deficiency of the IFN-γ receptor on immune cells restores anti-tumor activity. Additionally, tumor-specific T cells lacking the IFN-γ receptor demonstrate a significant survival advantage compared to their wild-type counterparts in tumor-bearing mice receiving combination therapy. Finally, we show that combination therapy induces significantly higher levels of IFN-γ in the low versus high tumor burden state on a per cell basis, reflecting their less exhausted immune status. This elevated IFN-γ secretion in the LTB state therefore contributes to the development of an immune-intrinsic mechanism of resistance to combination checkpoint blockade. Our report underscores the importance of achieving the optimal magnitude of immune stimulation for successful immunotherapy strategies.

overall_design: Spas-1+ CD8 cell RNA profiles from the draining lymph nodes of Tramp-C2 injected B57BL/6 wild type (WT) Mice were examined. There were four groups of mice with five mice per group and were treated with their respective checkpoint inhibitor on day 3 6, and 8 after tumor injection. Draining lymph nodes were harvested 28 days after tumor injection and for reach group, the cells were pooled and split into triplicates to be analyzed.

first: Chien-Chun

middle: S

last: Pai

first: Lawrence

last: Fong


title: A peninsular structure coordinates asynchronous differentiation with morphogenesis to generate pancreatic islets [bulk vs buds]

city: Seattle

first: Raghav

last: Chawla

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: This RNA-seq data is an integral part of a manuscript with the above title. To better characterize the buds appearing on the surface of the spheroidal clusters during the directed differentiation of HUES8 human embryonic stem cells to pancreatic endocrine cells, we performed bulk RNA-sequencing of the buds versus the bulks. Our results indicate that the buds indeed consist of pancreatic endocrine cells, illustrating our ability to recapitulate in vitro our in vivo observations of pancreatic islets forming via peninsular intermediates. See manuscript for more information.

overall_design: Buds were detached and separated from the spheroids at stage 5 of the differentiation protocol by mechanical agitation and filtering. RNA-sequencing of buds versus bulks was performed on samples from 5 separate differentiation flasks, whereby bulks could be collected from all and buds from 3 of the differentiation flasks. Sequencing libraries were prepared using the PrepX RNA-Seq for Illumina Library Kit (Takara Bio USA) and sequenced on an Illumina NextSeq 500. Paired-end sequencing reads were aligned to the human genome version GRCh38 and quantified with RSEM using the STAR alignment algorithm with default settings.

first: R

first: N

last: Sharon

first: J

last: Straubhaar

first: D

last: Melton


title: Essential role of Arid1a in intestinal stem cell maintenance and homeostasis through Sox9 regulation (ChIP-Seq)

city: Kyoto

first: Yukiko

last: Hiramatsu

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, have been reported in multiple human cancers, however, its functional role in intestinal homeostasis remains unclear. To investigate the role of Arid1a in murine intestine, we have employed ChIP experiments in intestinal spheroid cells generated from crypt cells of wild type mice. ChIP assay revealed that Arid1a binds directly to the Sox9 promoter to support its expression.

overall_design: We used intestinal spheroid cells generated from crypt cells of wild type mice.

first: Akihisa

last: Fukuda


title: Complex cell-state changes revealed by single cell RNA sequencing of 76,149 microglia throughout the mouse lifespan and in the injured brain

city: Framingham

first: Timothy

last: Hammond

state: MA

address: 49 New York Avenu

institute: Sanofi

summary: Single cell RNA sequencing of FACS purified mouse microglia from embryogenesis to old age, and following injury using a demyelinating mouse model.

overall_design: 41 total animals, 3-4 replicates per timepoint and condition. E14.5, P4/P5, P30, P100, P540, and Injury

first: Beth

last: Stevens


title: Histone demethylase KDM4B promotes DNA damage by activating long interspersed nuclear element-1

city: Wuhan

first: Xiang

last: Ying

address: Donghu road 185

department: medical genetics

country: China

institute: Wuhan University

summary: We assess whole-genome H3K9me3 distribution in cancer cells and find that H3K9me3 is largely enriched in long interspersed nuclear element-1 (LINE-1). A significant proportion of KDM4B-dependent H3K9me3 was located in evolutionarily young LINE-1 elements, which likely retain retrotransposition activity. Ectopic expression of KDM4B promoted LINE-1 expression, while depletion of KDM4B reduced it. Furthermore, KDM4B overexpression enhanced LINE-1 retrotransposition efficacy, copy number, and associated DNA damage, presumably via the histone demethylase activity of KDM4B. Breast cancer cell lines expressing high levels of KDM4B also exhibited increased LINE-1 expression and copy number compared with other cell lines. Pharmacological inhibition of KDM4B significantly reduced LINE-1 expression and DNA damage in breast cancer cells with excessive KDM4B. Our study not only identifies KDM4B as a novel regulator of LINE-1, but it also suggests an unexpected oncogenic role for KDM4B overexpression in tumorigenesis, providing clues for the development of new cancer prevention strategies and therapies.

overall_design: We performed H3K9me3 ChIP-seq with wild-type (WT), shKDM4B and  KDM4B in MCF7 cell lines

first: F

last: Li

first: Y

last: Xiang


title: The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

type: Methylation profiling by high throughput sequencing


title: Sox9-Meis1 inactivation is required for adipogenesis, advancing Pref-1+ to PDGFRa+ cells [PDGFRa+ RNA-Seq]

city: Berkeley

first: Hei Sook

last: Sul

address: Morgan Hall

department: NST

institute: UC Berkeley

summary: Adipocytes arise from commitment and differentiation of adipose precursors in white adipose tissue (WAT). In studying adipogenesis, precursor markers, including Pref-1 and PDGFRα, are used to isolate precursors from stromal vascular fraction of WAT, but the relationship among the markers is not known. Here, we used Pref-1 promoter-rtTA system in mice for labeling Pref-1+ cells and for inducible inactivation of Pref-1 target, Sox9. We show requirement of Sox9 for maintenance of Pref-1+ proliferative, early precursors. Upon Sox9 inactivation, these Pref-1+ cells become PDGFRa+ cells that express early adipogenic markers. Thus, we show for the first time that Pref-1+ cells precede PDGFRa+ cells in the adipogenic pathway and that Sox9 inactivation is required for WAT growth and expansion. Furthermore, we show that, in maintaining early adipose precursors, Sox9 activates Meis1 which prevents adipogenic differentiation. Our study also demonstrates the Pref-1 promoter-rtTA system for inducible gene inactivation in early adipose precursor population.

overall_design: RNA-Sequencing for differentially  expressed genes (more than 2-fold) between PDGFRa+ ingWAT SVF cells from floxed and Sox9 PreASKO mice (n=3 pooled).

first: Olga

last: Gulyaeva

first: Hei


title: Sox9-Meis1 inactivation is required for adipogenesis, advancing Pref-1+ to PDGFRa+ cells [microrarray]

summary:
Adipocytes arise from commitment and differentiation of adipose precursors in white adipose tissue (WAT). In studying adipogenesis, precursor markers, including Pref-1 and PDGFRα, are used to isolate precursors from stromal vascular fraction of WAT, but the relationship among the markers is not known. Here, we used Pref-1 promoter-rtTA system in mice for labeling Pref-1+ cells and for inducible inactivation of Pref-1 target, Sox9. We show requirement of Sox9 for maintenance of Pref-1+ proliferative, early precursors. Upon Sox9 inactivation, these Pref-1+ cells become PDGFRa+ cells that express early adipogenic markers. Thus, we show for the first time that Pref-1+ cells precede PDGFRa+ cells in the adipogenic pathway and that Sox9 inactivation is required for WAT growth and expansion. Furthermore, we show that, in maintaining early adipose precursors, Sox9 activates Meis1 which prevents adipogenic differentiation. Our study also demonstrates the Pref-1 promoter-rtTA system for inducible gene inactivation in early adipose precursor population.
Sox9 ablation increases PDGFRα+ cells, inhibiting cell cycle, muscle  and osteoblast/osteoclast differentiation, while inducing genes of hematopoietic cell lineage and inflammatory response.

overall_design: Microarray heatmap of differentially expressed genes (more than 1.5-fold) between floxed and PreASKO PDGFRα+  ingWAT SVF of 6 wk-old female mice fed dox at P1 (n=3 pooled).


title: Sox9-Meis1 inactivation is required for adipogenesis, advancing Pref-1+ to PDGFRa+ cells [Sox9 ChIP-Seq]

overall_design: ChIP-Sequencing for genes bound by Sox9 in 3T3-L1 cells


title: Sox9-Meis1 inactivation is required for adipogenesis, advancing Pref-1+ to PDGFRa+ cells


title: SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states [SUMO-ChIP-seq]

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Mouse embryonic fibroblasts (MEFs) were generated from Ubc9fl/- and Ubc9+/+ embryos (E13.5). MEFs were treated with tamoxifen for six days to cause CreERT2 activation, and induce Ubc9 floxed allele deletion. We determined the ChIP-seq profiles of SUMO-1 and SUMO-2 using chromatin of wild-type MEFs Ubc9+/+ and of the corresponding Ubc9 KO MEFs which are entirely depleted for sumoylation. The analysis revealed the nearly complete absence of genome-wide binding of SUMO-1 and SUMO-2 in Ubc9-/- MEFs, attesting for antibody specificities.

overall_design: One replicate per condiition and mark

first: Jack-Christophe

last: Cossec

first: Ilan

last: Theurillat

first: Anne

last: Dejean


title: Comparison of whole transcript and 3’ RNA Sequencing methods

city: Los Angeles

first: Feiyang

last: Ma

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

department: Molecular Biology Institute

institute: UCLA

summary: We used two RNA-Seq methods to measure the the global transcription levels in mouse liver cells. The data here provide insight into the pros and cons of whole transcript method and 3' RNA-Seq method.

overall_design: KAPA (whole transcript method) and Lexogen (3' RNA-Seq method) were used to compare global expression in 6 mice of two conditions: 1) 3 normal diet mice 2) 3 iron-loaded diet mice.

first: Brie

middle: K

last: Fuqua

first: Matteo

last: Pellegrini


title: Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1-dependent gene expression by Epstein-Barr virus latent membrane protein 1

first: Italo

last: Tempera

address: 3307 N. Broad Street, PAHB, Room 206

department: Fels Institute

institute: Temple University

summary: Latent membrane protein 1 (LMP1) is the major transforming protein of Epstein-Barr virus (EBV) and is critical for EBV-induced B-cell transformation in vitro. Poly(ADP-ribose) polymerase 1 (PARP1) regulates accessibility of chromatin, alters functions of transcriptional activators and repressors, and has been directly implicated in transcriptional activation. Previously we showed that LMP1 activates PARP1 and increases Poly(ADP-ribos)ylation (PARylation) through PARP1. Therefore, to identify targets of LMP1 that are regulated through PARP1, LMP1 was ectopically expressed in an EBV-negative Burkitt’s lymphoma cell line. These LMP1-expressing cells were then treated with the PARP inhibitor olaparib and prepared for RNA sequencing. The LMP1/PARP targets identified through this RNA-seq experiment are largely involved in metabolism and signaling. Interestingly, Ingenuity Pathway Analysis of RNA-seq data suggests that hypoxia-inducible factor 1-alpha (HIF-1α) is an LMP1 target mediated through PARP1. PARP1 is acting as a coactivator of HIF-1α-dependent gene expression in B cells, and this co-activation is enhanced by LMP1-mediated activation of PARP1. HIF-1α forms a PARylated complex with PARP1 and both HIF-1α and PARP1 are present at promoter regions of HIF-1α downstream targets, leading to accumulation of positive histone marks at these regions. Complex formation, PARylation and binding of PARP1 and HIF-1α at promoter regions of HIF-1α downstream targets can all be attenuated by PARP1 inhibition, subsequently leading to a buildup of repressive histone marks and loss of positive histone marks. In addition, LMP1 switches cells to a glycolytic ‘Warburg’ metabolism, preferentially using aerobic glycolysis over mitochondrial respiration.  Finally, LMP1+ cells are more sensitive to PARP1 inhibition and, therefore, targeting PARP1 activity may be an effective treatment for LMP1+ EBV-associated malignancies.

overall_design: Examination of the effect of LMP1 and PARP inhibition on global gene expression in EBV-negative Burkitt's lymphoma DG75 cell line. mRNA profiles of LMP1+ or LMP1- (pBABE empty vector) DG75 cell lines treated with 1 uM olaparib for 72 hrs were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Michael

last: Hulse

first: Lisa

last: Caruso

first: Jozef

last: Madzo

first: Yinfei

last: Tan

first: Sarah

last: Johnson


title: Sox9-Meis1 inactivation is required for adipogenesis, advancing Pref-1+ to PDGFRa+ cells [GFP+ RNA-Seq]

overall_design: RNA-Sequencing for differentially expressed genes (more than 2-fold) between GFP+ (Pref-1+)  ingWAT SVF cells from floxed and Sox9 PreASKO mice (n=6 pooled).


title: mRNA sequencing of Aniridia limbal epithelial cells.

city: Saarbrücken

first: Karl

last: Nordström

address: Gebäude A2 4

department: FR 8.3 Biowissenschaften

country: Germany

institute: Universität des Saarlandes

summary: PAX6-related Aniridia is a sight-threatening disease due to progression of secondary glaucoma and aniridia associated keratopathy (AAK). Changes or loss of limbal epithelial progenitors causes the epithelial surfaces defects. We analyzed how PAX6 contribute to this with a two-step approach. 1) mRNA Sequencing of limbal epithelial cells isolated from controls and aniridia patients. 2) confirming the bioinformatical and literature-based result list on a siRNA based primary aniridia cell model (PAX6- knockdown). With this approach genes which are directly influenced by PAX6 should be distinguishable from genes secondary affected by AAK disease state. Therefore epithelial cells were isolated from the limbus region of two patients with aniridia and cultured in KSFM medium. Normal cells were obtained from limbus region of cadaveric control patients. For the siRNA based anridia cell model cells were transfected with lipofectamine and 5 nM siRNA against PAX6 or scrambled control. All cells were lysed to obtain DNA, RNA and protein. Reduction of PAX6 protein was controlled by Western Blot. Aniridia and Control Poly-A enriched RNA-librarys were subjected to Next Generation Sequencing. The differential analysis was a combination of quantification with RSEM and differential tests with edgeR. Gene lists were filtered by comparing to NCBI GEO Datasets, annotation with DAVID and manually annotation using literature search. For the resulting filtered gene list qPCR primer were ordered and postulated changes were verified with qPCR on siRNA based aniridia- cell model (Namely: TP63, ABCG2, ADH7, ALDH1A1, PITX1, DKK1, DSG1, K12, K3, K13, SPINK6, SPINK7, CTSV, SPERPINB1). We could identify genes which might be regulated by PAX6. We could show that SPINK7 mRNA coding for a protease inhibitor is downregulated in patients as well as in our primary aniridia cell model. ALDH1A1 and AHD7 mRNAs were reduced in limbal epithelial cells of aniridia patients (AN-LEC). Both transcripts were downregulated upon PAX6 knockdown in our cell model.Our siRNA-based aniridia cell model is a tool to proof identified PAX6 affected genes which might drive AAK pathogenesis. We could demonstrate, that this is the fact for transcripts coding for retinol converting enzymes. This provides evidence that PAX6 might drive corneal epithelial differentiation process by direct or indirect controlling retinoic acid signaling processes.

overall_design: two Ctrls and two Anirdia samples were included

first: Jasmin

last: Kirch


title: GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Background: Amyotrophic lateral sclerosis (ALS) is currently an incurable disease without highly effective pharmacological treatments. The peptide drug GM604 (GM6) was developed as a candidate ALS therapy, which has demonstrated safety and encouraging outcomes in a phase II clinical trial. GM6 is hypothesized to bolster neuron survival through regulation of developmental pathways, but mechanisms of action are not fully understood. Methods: This study used RNA-seq to evaluate transcriptome responses in SH-SY5Y neuroblastoma cells following GM6 treatment (6, 24 and 48 hours).  Results: We identified 2867 protein-coding genes with expression significantly altered by GM6 (FDR < 0.10). Early (6 hour) responses included up-regulation of Notch and hedgehog signaling components, with increased expression of developmental genes mediating neurogenesis and axon growth. Prolonged GM6 treatment (24 and 48 hours) altered the expression of genes contributing to cell adhesion and the extracellular matrix. GM6 further down-regulated the expression of genes associated with mitochondria, inflammatory responses, mRNA processing and chromatin organization. GM6-increased genes were located near GC-rich motifs interacting with C2H2 zinc finger transcription factors, whereas GM6-decreased genes were located near AT-rich motifs associated with helix-turn-helix homeodomain factors. Such motifs interacted with a diverse network of transcription factors encoded by GM6-regulated genes (STAT3, HOXD11, HES7, GLI1). We identified 77 ALS-associated genes with expression significantly altered by GM6 treatment (FDR < 0.10), which were known to function in neurogenesis, axon guidance and the intrinsic apoptosis pathway. Discussion: Our findings support the hypothesis that GM6 acts through developmental-stage pathways to influence neuron survival. Gene expression responses were consistent with neurotrophic effects, ECM modulation, and activation of the Notch and hedgehog neurodevelopmental pathways. This multifaceted mechanism of action is unique among existing ALS drug candidates and may be applicable to multiple neurodegenerative diseases.

overall_design: SH-SY5Y neuroblastoma cells were treated with GM6 or water (CTL) with independent replicates at 6 hours (n = 5 GM6, n = 3 CTL), 24 hours (n = 5 GM6, n = 5 CTL) and 48 hours (n = 5 GM6, n = 5 CTL). The test material (GM6 peptide) was dissolved in cell culture medium and tested at a final concentration of 1mg/ml for incubation times of 6, 24 or 48 hours.


title: Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders

status: Public on Oct 23 2018

first: Xia

last: Yang

address: 610 Charles E Young Dr East

overall_design: Refer to individual Series


title: RNA-seq analysis of cells (siglecF+CD11C+, MHCII-high or MHC-low) from bleomycin-treated and control mouse lungs

city: San Francisco

first: Leqian

last: Liu

address: 1700 4th street

department: BTS

institute: UCSF

summary: Cell suspensions were prepared from lungs dissociated at baseline, at 14 days, and at 28 days after injury. Cells (siglecF+CD11C+ and MHCII-high or -low) were isolated with FACS. RNA-seq was performed with sorted cells.

overall_design: RNAseq was performed on siglecF+, CD11c+ and MHCII high or low cells isolated from bleomycine-treated and control mouse lungs.

first: Mallar

last: Bhattacharya

first: Agnieszka

middle: P

last: Lonney

first: Dvir

last: Aran


title: Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (ChIP-Seq)

status: Public on Oct 31 2018

first: dario

last: nicetto

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Domains of transcriptionally repressed heterochromatin, decorated by histone 3 lysine 9 trimethylation (H3K9me3), are reduced in embryonic stem cells compared to fully differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein coding genes, in natural embryologic development, has not been described. We developed a novel, antibody-independent method to isolate and map compacted heterochromatin from low cell number samples. Unexpectedly, we uncovered extensive high levels of H3K9me3-decorated, compacted heterochromatin at protein coding genes in early, uncommitted cells in the three germ layers, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed that H3K9me3 heterochromatin is required to maintain cell lineage fidelity. We propose a key role for chromatin-based restriction of gene activity via H3K9me3 during embryologic development

overall_design: Study is an analysis by ChIP-seq (H3K9me3 and H3K27me3) of pancreatic and hepatic development, with a trajectory including definitive endoderm (e8.25 ENDM1+), hepatic precursor (e10.5 Liv2+), and adult hepatocytes as well as pancreatic precursor (e10.5 PDX1+), immature beta cells (e18.5 INS-RFP+) and mature beta cells (8 week INS-RFP+); mesoderm precursor cells (e8.25, FLK1+) and neuroectoderm cells (e8.25, dissected); 1month old CTRL and TKO sampels from liver; each stage has two replicates; ENDM1+ is treated for some analyses as a baseline condition

first: Dario

last: Nicetto

first: Greg

last: Donahue

first: Tanya

last: Jain

first: Tao

last: Peng

first: Simone

last: Sidoli

first: Lihong

last: Sheng

first: Thomas

last: Montavon

first: Justin

last: Becker

first: Jessica

last: Grindheim

first: Kimberly

last: Blahnik

first: Benjamin

middle: A

last: Garcia

first: Kai

first: Roberto

last: Bonasio

last: Jenuwein

first: Kenneth

last: Zaret


title: Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders (RNA-Seq)

first: Xia

last: Yang

summary: The health impacts of endocrine disrupting chemicals (EDCs) remain debated and their tissue and molecular targets are poorly understood. Here, we leveraged systems biology approaches to assess the target tissues, molecular pathways, and gene regulatory networks associated with prenatal exposure to the model EDC Bisphenol A (BPA). Prenatal BPA exposure led to scores of transcriptomic and methylomic alterations in the adipose, hypothalamus, and liver tissues in mouse offspring, with cross-tissue perturbations in lipid metabolism as well as tissue-specific alterations in histone subunits, glucose metabolism and extracellular matrix. Network modeling prioritized main molecular targets of BPA, including Pparg, Hnf4a, Esr1, Srebf1, and Fasn. Lastly, integrative analyses identified the association of BPA molecular signatures with cardiometabolic phenotypes in mouse and human. Our multi-tissue, multi-omics investigation provides strong evidence that BPA perturbs diverse molecular networks in central and peripheral tissues, and offers insights into the molecular targets that link BPA to human cardiometabolic disorders.

overall_design: We utilized next-generation sequencing technologies to characterize perturbations in both the transcriptome (RNA-seq) and the epigenome (RRBS) across three tissues (white adipose tissue, hypothalamus, liver) in mouse offspring who had experienced in utero exposure to BPA

first: Le

last: Shu

first: Qingying

last: Meng


title: Determination of the Forkhead box A2 (FOXA2) Cistrome in the Human Endometrium [ChIP-seq]

city: Columbia

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: FOXA2  chromatin immunoprecipitation sequencing (ChIP-Seq) was performed on proliferative (P) and mid-secretory (MS) phase human endometrium.

overall_design: Illumina sequencing of FOXA2  chromatin immunoprecipitation DNA by  ChIP-Seq method.

first: Andrew

last: Kelleher

first: Susanta

last: Behura

first: Gregory

last: Burns

first: Steven

last: Young

first: Franco

last: DeMayo

middle: E


title: RNA-Seq of human induced pluripotent stem cell-derived cardiomyocytes from a cardiomyopathy patient and familial control

city: La Jolla

first: Neil

last: Chi

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

overall_design: Three biologic replicates of human induced pluripotent stem cell-derived cardiomyocytes from a cardiomyopathy patient and familial control were independently sequenced and relative differences in gene expression levels were analyzed


title: Single cell transcriptomics of hiPSC-derived forward programmed megakaryocytes

city: Cambridge

first: Thomas

middle: Pierre

last: Moreau

address: Long Road

department: Haematology

institute: Univeristy of Cambridge

summary: We have published a novel method for the large-scale in vitro generation of megakaryocytes (MKs), the blood platelet precursors, by applying a transcription factor (TF) driven forward programming strategy to human pluripotent stem cells (hPSCs). We have demonstrated that the concurrent expression of GATA1, FLI1 and TAL1 in hPSCs and chemically defined culture conditions with minimal supportive cytokines produce highly pure MK cultures with long-term growth and release of functional platelets. Unravelling the molecular mechanisms underlying MK forward programming will bring biological insights that shall lead to improvements of the MK programming technology. Particularly, we have been focusing on the characterisation of the MK progenitor that allows long-term expansion of pure MK cultures, which is a key asset of the method. Using single cell RNA sequencing of long-term cultures, we have started to identify and functionally confirmed surface markers of the MK progenitor.

overall_design: Whole genome single cell transcriptome analysis of long-term MK culture (one hiPSC line), balanced for the eight transgenic patterns (upstream FACS using transgene expression reporters)

first: Amanda

last: Dalby

first: Winnie

last: Lau

first: James

last: Baye

first: Lila

last: Diamanti

first: Berthold

last: Gottgens

first: Cedric

middle: G

last: Ghevaert


title: p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: We have discovered that loss of wild-type p53 correlates with elevated expression of mevalonate pathway genes in murine liver cancer and in human tumors. Mechanistically p53 blocks activation of SREBP-2, the master transcriptional regulator of this pathway, by transcriptionally inducing the ABCA1 cholesterol transporter gene, which inhibits SREBP-2 maturation. In mice the increase in mevalonate gene expression occurs in premalignant p53-null hepatocytes at a stage when p53 is needed to actively suppress tumorigenesis. Either RNAi mediated suppression of key genes in the mevalonate pathway or pharmacological inhibition of its rate-limiting enzyme restricts the development of mouse hepatocellular carcinomas driven by p53 loss. Conversely, like p53 loss, ablation of ABCA1 promotes tumorigenesis in a murine model and is associated with increased SREBP-2 maturation. Our findings thereby demonstrate that repression of the mevalonate pathway is a crucial component of p53-mediated tumor suppression and outline the mechanism by which this occurs.

overall_design: 4 samples were analyzed in replicates of 2 conditions.  1. Control, p53 WT hepatocytes transduced with MYC transposons delivered by hydrodynamic tail vein injection and isolated 6 days after injection. 2. Experimental, p53 null hepatocytes transduced with MYC transposons delivered by hydrodynamic tail vein injection and isolated 6 days after injection.

first: Carol

last: Prives

first: Scott

last: Lowe

first: Sung-Hwan

last: Moon

first: Chun-Hao

last: Huang

first: Shauna

last: Houlihan


title: Transcriptomic analysis of T84 colon carcinoma cell line treated with trametinib, JQ1 or their combination

city: Sutton

last: Whittaker

address: 15 Cotswold Road

institute: The Institute of Cancer Research

summary: T84 cells were treated with DMSO, 30nM trametinib (MEKi), 1µM JQ1 (BRD4i) or the combination of trametinib and JQ1 (combo) for 24h.

overall_design: 3 replicates per condition were analyzed by RNA-seq.

middle: R


title: Whole-genome gene expression profiles of peripheral blood cells in an individual with Long QT syndrome and Beckwith-Wiedemann syndrome

city: Caserta

first: Andrea

last: Riccio

address: Via Vivaldi

country: Italy

institute: Università degli Studi della Campania

summary: We report RNAseq profiles of an individual carrying a maternally inherited splice variant in the first intron of the KCNQ1 gene and displaying complete loss of methylation at KCNQ1OT1:TSS DMR, the Imprinting Control Region of the centromeric domain of the Beckwith-Wiedemann locus. The half-sister was used as control. We show that the most 5’ 10 kb of  KCNQ1 is about 2-3-fold more abundant than the rest of the gene in the proband, while RNA level was homogeneously distributed along the entire gene in the control. These results are consistent with data obtained from locus-specific analyses and overall suggest that premature termination of the KCNQ1 gene is occurring in cis with the splice variant and is associated with lack of methylation of the KCNQ1OT1:TSS DMR on the maternal chromosome.

overall_design: Examination of RNA level (RNAseq) in perypheral blood leukocytes of two individuals

first: Cerrato

last: Flavia

first: Franzese

last: Monica


title: Next Generation Sequencing Facilitates Putative Target Identification for the Small RNA RydC

city: Urbana

first: Alisa

middle: Margaret

last: King

state: IL

address: 601 S Goodwin Ave Room C211

department: Microbiology

institute: University of Illinois at Urbana-Champaign

summary: We report the transcriptomic profile of Escherichia coli when the small RNA RydC is overexpressedand how this can be used to identify putative mRNA targets. This technique allowed us to identify potential mRNA targets to further validate in vivo.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We had two conditions: 1) No expression of the small RNA RydC and 2) Overexpression of the small RNA RydC

middle: M

first: Carin

last: Vanderpool


title: E14.5 pancreatic islet single-cell RNA-seq

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

institute: Vanderbilt University

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


title: E14.5 pancreatic islet single-cell RNA-seq [wt]

summary: pancreas islet single-cell RNA-seq

overall_design: isolated from 2 wt

first: Guoqiang

last: Gu

first: Alan

last: Simmons


title: RNA-seq transcriptome analyses in T47D cells treated with ActA and Palbociclib.

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

institute: University of Tokyo

summary: We performed SMAD2 ChIP-seq analysis in T47D cells with/without Palbociclib treatment. To validate whether the changes in SMAD2 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analyses in T47D with/without ActA stimulation and Palbo treatment.

overall_design: RNA-seq transcriptome analyses performed in estrogen receptor positive breast cancer T47D with/without ActA stimulation and Palbo treatment.

first: Mayumi

last: Harada

first: Masato

last: Morikawa

first: Takayuki

last: Ozawa

first: Yusuke

last: Tamura

first: Kohei

last: Miyazono


title: Transcriptomic analysis of trametinib-resistant HCT116 colorectal carcinoma cells compared to the parental control cells

first: Steven

summary: HCT116 cells were treated with with increasing concentrations of trametinib over 2 months. Drug-resistant clones emerged and were cultured in the presence of 30 nmol/L trametinib. These cells exhibited a greater than 10-fold increase in the GI50 for trametinib compared to the parental cell line. RNA-seq of the resistant clone HCT116_R4 versus the parental cells identified differentially expressed genes potentially involved in resistance.

overall_design: For the parental and resistant clone, 3 replicates each were analysed by RNA-seq.


title: SMAD2 binding regions in triple negative breast cancer cell line, Hs578T

summary: Inhibitors for cyclin-dependent kinase (CDK) 4 and CDK6 have been established as effective therapeutic options for hormone receptor (HR)-positive, HER2-negative advanced breast cancer. Although the CDK4/6 inhibitors mainly target the cyclin D-CDK4/6-retinoblastoma tumor suppressor protein (RB) axis, little is known about clinical impact of inhibiting phosphorylation of other CDK4/6 target proteins. Here, we have focused on other CDK4/6 targets, SMAD proteins. We showed that a CDK4/6 inhibitor Palbociclib and Activin-SMAD2 signaling cooperatively inhibited cell cycle progression of a luminal-type breast cancer cell line T47D. Mechanistically, Palbociclib enhanced SMAD2 binding to the genome through inhibiting linker phosphorylation of the SMAD2 protein by CDK4/6. Comparison of the SMAD2 ChIP-seq data of T47D with those of a triple-negative breast cancer cell line Hs578T indicated that Palbociclib augments different SMAD2-mediated program defined based on types of cells, and enhances SMAD2 binding to the target regions on the genome without affecting its binding pattern. Collectively, the CDK4/6 inhibitor facilitates the cytostatic effects of Activin-SMAD2, while it also enhances its tumor promoting effects depending on types of breast cancer.

overall_design: SMAD2 ChIP-seq analysis was performed in triple negative breast cancer after Activin A with/without Palbociclib treatment


title: SMAD2 binding regions in breast cancer cell line and RNA-seq transcriptome analyses in T47D


title: Colonic adenoma and adjacent normal single-cell RNA-seq

summary: colonic adenoma and adjacent normal from Lrig1-creERT2;Apc-fl/+ mouse

overall_design: tumor and adjacent normal


title: Human Organ-Specific Endothelial Cell Heterogeneity

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: The endothelium first forms in the blood islands in the extra-embryonic yolk sac and then throughout the embryo to establish circulatory networks that further acquire organ-specific properties during development to support diverse organ functions. Here, we investigated the properties of endothelial cells (ECs), isolated from four human major organsthe heart, lung, liver, and kidneys in individual fetal tissues at three months' gestation, at gene expression, and at cellular function levels. We showed that organ-specific ECs have distinct expression patterns of gene clusters, which support their specific organ development and functions. These ECs displayed distinct barrier properties, angiogenic potential, and metabolic rate and support specific organ functions. Our findings showed the link between human EC heterogeneity and organ development and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.

overall_design: We examined the human fetal organ sets from three donors, constituting three biological replicates at 3 months' gestation (100-125 days). At this stage, all four major organs of interest - the heart, kidney, lung, and liver - have an established microvascular supply and exhibit organ-specific function. The heart beats at 120-160 bpm and is approximately 2 cm, the lungs have developed the entire air-conducting bronchial tree up to 20 generations with respiratory ducts and start to form barriers between alveoli and blood vessels, the liver is the major site of blood cell production and has also started to produce bile, and the kidneys have established nephrons and start to produce urine.

first: Raluca

last: Marcu

first: Yoon

last: Choi

first: Jun

last: Xue

first: Chelsea

middle: L

last: Fortin

first: Yuliang

last: Wang

first: Ryan

last: Nagao

first: Jin

last: Xu

first: Theo

last: Bammler

first: Charles

last: Murry

first: Kimberly

last: Muczynski

first: Kelly

last: Stevens

first: Jonathan

last: Himmelfarb

first: Stephen

last: Schwartz

first: Ying

last: Zheng


title: SMAD2 binding regions in estrogen receptor-positive breast cancer cell line, T47D

first: Daizo

last: Koinuma

overall_design: SMAD2 ChIP-seq analysis was performed in estrogen receptor-positive breast cancer after Activin A with/without Palbociclib treatment

first: Mayumi

last: Harada

first: Masato

last: Morikawa

first: Takayuki

last: Ozawa

first: Yusuke

last: Tamura

first: Kohei


title: MEF2C interaction profiles (4C-seq) in SH-SY5Y and HEK cell lines

status: Public on Oct 22 2018

city: Gent

first: Sarah

last: Vergult

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

summary: To characterize enhancer elements regulating the MEF2C gene during neurodevelopment, we performed among others Circularized Chromosome Conformation Capture (4C) sequencing  in a neuronal cell line, SH-SY5Y, and a non-neuronal control, HEK. We found that, in a neuronal cell line, the MEF2C promoter interacts with several putative enhancer elements in its upstream region, forming a complex interaction network. Moreover, these interactions are completely absent in HEK cells.

overall_design: 4C-seq interaction profiles for the MEF2C promoter and seven putatively interacting regions (called reciprocal viewpoints) in SH-SY5Y and HEK cells (all except one in duplicate).

first: Eva

last: D'haene


title: RNA-seq of Treg and Tconv subsets from murine spleen

first: Alexander

middle: Y

last: Rudensky

state: New York (NY)

department: Immunology

summary: While unique subsets of Treg cells have been described in some non-lymphoid tissues, their relationship to Treg cells in secondary lymphoid organs and circulation remains unclear. We have identified a recirculating and highly suppressive effector Treg cell subset that expresses the α2 integrin, CD49b, and exhibits a unique tissue distribution. To identify genes and pathways enriched in CD49b+ Treg cells, we performed RNA-seq of splenic CD49b+ and CD49b− Treg cells that were of otherwise similar activation status based on expression of CD44 and CD62L. This revealed that splenic CD49b+ Treg cells express genes related to migration and activation, but are relatively depleted of genes whose expression is TCR-dependent in Treg cells. These results shed light on the identity and development of a functionally potent subset of mature effector Treg cells that recirculates through and surveys peripheral tissues.

overall_design: RNA was extracted from FACS-purified splenic Tconv and Treg cells of different activation states from Foxp3GFP mice. 2 CD4+ T-cell lineages x 3 activation states x 4 replicates. There is no sample 3 (RNA was degraded); there are 23 samples in total.

first: Xiying

last: Fan


title: SHQ1 regulation of RNA splicing is required for T-lymphoblastic leukemia cell survival

city: Wuhan

first: Hudan

last: Liu

address: No.185, Donghu Road

institute: Wuhan University

summary: T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with complicated heterogeneity. Although expression profiling reveals common elevated genes in distinct T-ALL subtypes, little is known about their functional role(s) and regulatory mechanism(s). We here show the expression of SHQ1, an H/ACA snoRNPs assembly factor involved in snRNA pseudouridylation, is specifically and highly expressed in T-ALL. Mechanistically, oncogenic NOTCH1 directly binds to the SHQ1 promoter and activates its transcription. SHQ1 depletion induces massive leukemia cell death in vitro and in vivo, and prolongs animal survival in murine T-ALL models. RNA-Seq reveals that SHQ1 depletion impairs widespread RNA splicing, and MYC is one of the most prominently downregulated genes due to inefficient splicing. Ectopically expressed MYC significantly rescues T-ALL cell death resulted from SHQ1 inactivation. We herein report a previously unsuspected mechanism of NOTCH1-SHQ1-MYC axis in T cell leukemogenesis. Our findings not only shed light on the role of SHQ1 in promoting RNA splicing and tumorigenesis, but also provide a new mechanism of MYC regulation.

overall_design: Examination of intron rentention in SHQ1-depleted KOPTK1 and HPB-ALL cells

first: Hexiu

last: Su

first: Juncheng

last: Hu

first: Yang

last: Yang

first: Yu

last: Zhou

first: Guoliang

last: Qing

first: Zhichao

last: Chen


title: RNA-seq of bulk Treg and Tconv cells from murine liver and lymphoid tissues

summary: With the aim of understanding how Treg cells in highly vascularized tissues are related to Treg cells in other organs, we performed RNA-seq analysis of bulk Treg and Tconv cells isolated from liver, blood, spleen, and the liver-draining portal lymph node. This revealed a clear separation of cell transcriptomes by both tissue and Treg/Tconv identity, with cells from the liver falling between blood- and spleen-derived cells. Compared to splenic Treg cells, hepatic Treg cells were enriched for genes related to proliferation and activation, and genes encoding chemokine and cytokine receptors.

overall_design: RNA was extracted from FACS-purified Tconv and Treg cells from various tissues of Foxp3Thy1.1 mice. Each sample contains cells pooled from 3 mice. 2 cell types from each of 4 tissues x 3 replicates = 24 samples.


title: Identifying Ipr1 binding sites in RAW264.7 cells using ChIP-seq

city: xianyang

first: Fayang

state: shannxi

address: taicheng street

institute: Northwest A&F University

summary: It has been demonstrated that Ipr1 participate in gene expression regulation during Mycobatrium infection. To better understand whether Ipr1 can regulate gene expression by interacting with gene promoter directly or not, we performed ChIP-seq to identify interaction between Ipr1 and DNA fragments.

overall_design: Raw-Bap-Ipr1-P2A-BirA and Raw-Bap-P2A-BirA (negative control) cells were used for ChIP-seq, Flag (FlagChIP bond) and biotin (BioChIP bond) tags were used to isolate Ipr1-DNA complexes.

first: Yongyan

last: Wu

first: Kezhen

last: Yao


title: Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders (RRBS)

city: Los Angeles

first: Xia

state: CA

institute: UCLA

summary: The health impacts of endocrine disrupting chemicals (EDCs) remain debated and their tissue and molecular targets are poorly understood. Here, we leveraged systems biology approaches to assess the target tissues, molecular pathways, and gene regulatory networks associated with prenatal exposure to the model EDC Bisphenol A (BPA). Prenatal BPA exposure led to scores of transcriptomic and methylomic alterations in the adipose, hypothalamus, and liver tissues in mouse offspring, with cross-tissue perturbations in lipid metabolism as well as tissue-specific alterations in histone subunits, glucose metabolism and extracellular matrix. Network modeling prioritized main molecular targets of BPA, including Pparg, Hnf4a, Esr1, Srebf1, and Fasn. Lastly, integrative analyses identified the association of BPA molecular signatures with cardiometabolic phenotypes in mouse and human. Our multi-tissue, multi-omics investigation provides strong evidence that BPA perturbs diverse molecular networks in central and peripheral tissues, and offers insights into the molecular targets that link BPA to human cardiometabolic disorders.

overall_design: We utilized next-generation sequencing technologies to characterize perturbations in both the transcriptome (RNA-seq) and the epigenome (RRBS) across three tissues (white adipose tissue, hypothalamus, liver) in mouse offspring who had experienced in utero exposure to BPA

first: Le

last: Shu

first: Qingying

last: Meng


title: Single-cell RNA-seq of splenic Treg and Tconv cells

summary: While unique subsets of Treg cells have been described in some non-lymphoid tissues, their relationship to Treg cells in secondary lymphoid organs and circulation remains unclear. We have identified a short-lived effector Treg cell subset that expresses the α2 integrin, CD49b, and exhibits a unique tissue distribution. Projection of the CD49b+ Treg signature onto the Treg phenotypic landscape as inferred by single-cell RNA-seq analysis, placed these cells at the apex of the Treg developmental trajectory. These results shed light on the identity and development of a functionally potent subset of mature effector Treg cells that recirculate through and survey peripheral tissues.

overall_design: Single-cell RNA-seq libraries (10x Genomics) were prepared from FACS-purified Tconv and Treg cells from pooled spleens of Foxp3GFP mice.

first: Roshan

last: Sharma

first: Linas

last: Mazutis

first: Dana

last: Pe'er


title: RNA-Seq analysis of Yeast following temporal knockdown of core spliceosome components

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

institute: University of Manchester

summary: To investigate the consequences of reduced expression of core spliceosome factors (Dib1 and Snu114)

overall_design: Yeast strains were produced whereby expression of the genes Dib1 or Snu114 was subject to a Galactose inducable promoter. Expression of Dib1 and Snu114 was then temporaly reduced by culturing strains in the absence of galactose for up to 8h. RNA was extracted at 4h and 8h time points and the expression of both gene regions and intron regions of all genes was quantified by RNA-Seq. Control samples were cultured in Galactose-containing media for 6h and processed identically.

middle: B

first: Katherine

last: Wood

first: Moses

last: Tandiono

first: Kathryn

last: Hentges

first: William

last: Newman

first: Raymond

middle: T

last: O'Keefe


title: Transcriptomic and T-cell receptor profiling of Treg cells from lymphoid and vascular tissues

first: Alexander

last: Rudensky

overall_design: Refer to individual Series


title: Chromatin Profiling of Micro-dissected Mouse Embryonic Heart and CPP regions

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: Co-development of the lungs and heart underlies key evolutionary innovations in the transition to terrestrial life. Cardiac specializations that support pulmonary circulation, including the atrial septum, are generated by second heart field (SHF) cardiopulmonary progenitors (CPPs). It has been presumed that transcription factors required in the SHF for cardiac septation, e.g. Tbx5, directly drive a cardiac morphogenesis gene regulatory network. Here, we report instead that TBX5 directly drove Wnt ligands to initiate a bi-directional signaling loop between cardiopulmonary mesoderm and the foregut endoderm for endodermal pulmonary specification, and subsequently, atrial septation. TBX5 ChIP-seq identified cis-regulatory elements at Wnt2 sufficient for endogenous Wnt2 expression domains in vivo and required for Wnt2 expression in pre-cardiac mesoderm in vitro. Thus, Tbx5 initiated a mesoderm-endoderm-mesoderm signaling loop in lunged vertebrates that provides a molecular basis for the co-evolution of pulmonary and cardiac structures required for terrestrial life.

overall_design: For ATAC-seq, 4 biological replicates were generated for each the micro-dissected hearts and CPP regions from 5 E9.5 CD-1 mouse embryos per replicate. For ChIP-seq, 2 biological replicates were generated for each the micro-dissected hearts and CPP regions from 50 E9.5 CD-1 mouse embryos per replicate. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516), 1μg of anti-H3K4me3 (Wako Chemicals #305-34819; Lot #14004), or 1μg of anti-H3K4me1 (Abcam ab8895; Lot #GR257926-1) at 4°C for >12 hours in a total volume of 200 μL.

first: Kohta

last: Ikegami

first: Rangarajan

last: Nadadur

first: Ivan

last: Moskowitz


title: Genome-wide maps of apurinic sites (AP-sites) and 8-oxoG derived secondary AP-sites

city: London

first: Anna

last: Poetsch

address: 1 Midland Rd

institute: The Francis Crick Instutute

summary: We developed a novel method, AP-seq, capable of mapping apurinic sites and 8-oxo-7,8-dihydroguanine bases at approximately 250bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of apurinic sites varies widely across the genome, with hot spots acquiring many times more damage than cold spots. The experiment was performed in triplicates on HepG2 cells, 30 min after X-ray treatment (6Gy). AP-Seq is an approach that specifically enriches AP-sites via a biotin-labelled aldehyde-reactive probe under pH neutral conditions, which has been well established for the specific detection of AP-sites since its development by Kubo et al. in 1992. Under neutral conditions (pH7), 1h at 37ºC, the probe is highly specific for the aldehydes occurring at AP-sites. After biotin labelling of genomic DNA, DNA is sonicated into ~250 bp fragments, enriched, in vitro repaired (PreCR, NEB), and used for Illumina short read sequencing (125 bp, paired end, HiSeq2000). To assess oxidative damage as the sum of AP-sites and 8-oxoG, we applied recombinant OGG1 in vitro to the extracted DNA (OGG1-AP-seq). Under the conditions chosen, any remaining 8-oxoG is excised in a largely sequence-independent fashion after DNA extraction to result in a set of secondary AP-sites and to a lesser extent the associated beta-elimination product.

overall_design: 24 samples, 125bp paired-end illumina sequencing

first: Simon

middle: J

last: Boulton

first: Nicholas

last: Luscombe


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and SMAD4 Y95 Mutation Transcriptomes

city: Hangzhou

first: Mu

last: Xiao

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of Y95 phosphorylation on SMAD4-mediated transcription in response to TGF-b signals. The goals of this study are to compare transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: mRNA profiles of HaCaT parental and SMAD4 KO cells stably expressing wild-type SMAD4 (WT), Y95E or Y95F mutant, and GFP (as control) under with or without TGF-b were generated by deep sequencing, using Illumina HiSeq X Ten. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: hierarchical clustering of the global gene expression profiles of TGF-β treated cells revealed that wild-type-SMAD4- and Y95F-mutant-rescued SMAD4-null cells were highly similar to the parental HaCaT cells, whereas GFP- and Y95E-mutant-rescued cells formed a separate cluster

overall_design: Wild Type and SMAD4 Y95 Mutation

first: Qianting

last: Zhang

first: Shuchen

last: Gu

first: Yongxian

last: Xu

first: Lan

last: Qin

first: Ting

last: Liu

first: Hao

last: Li

first: Yi

last: Yu

first: Yezhang

last: Zhu

first: Yulong

last: Wang

first: Chen

last: Ding

first: Hongbin

last: Ji

first: Zhe

last: Chen

first: Youli

last: Zu

first: Stephen

last: Malkoski

first: Tingbo

last: Liang

first: Junfang

first: Jun

first: Pinglong

first: Bin

last: Zhao

first: Li

last: Shen

first: Xia

last: Lin

first: Xin-Hua

last: Feng


title: RNA sequencing of Asthmatic Human Airway Smooth Muscle Cells

city: Rochester

first: YS

last: Prakash

state: MN

address: 200 1st St

institute: Mayo Clinic

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


title: RNA sequencing of Asthmatic Human Airway Smooth Muscle Cells II

summary: The goal of the was to evaluate the mRNA expression profile of asthmatic and non-asthmatic airway smooth muscle using Next Generation Sequencing (RNA seq).

overall_design: RNA Seq was performed on nonasthmatic (n=7 individuals) and asthmatic (n=6  individuals) human airway smooth muscle cells

first: Y

middle: S

first: Sarah

last: Wicher

first: Rodney

last: Britt Jr


title: Expression profiling of TNBCs following atRA treatment [Affymetrix II]

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

country: Canada

institute: Dalhousie University

summary:
All-trans retinoic acid (atRA) regulates gene expression and is used to treat acute promyelocytic leukemia. Attempts to use atRA for breast cancer treatment without a stratification strategy have resulted in limited overall effectiveness. To identify biomarkers for the treatment of triple-negative breast cancer (TNBC) with atRA, we characterized the effects of atRA on the tumor growth of 13 TNBC cell lines. This resulted in a range of tumor growth effects that was not predictable based on the levels of retinoid signaling molecules and transcriptional responses that were mostly independent of retinoic acid response elements. Given the importance of DNA methylation in regulating gene expression, we hypothesized that differential DNA methylation could predict the response of TNBCs to atRA. We identified over 1400 CpG sites that were differentially methylated between atRA resistant and sensitive cell lines. These CpG sites predicted the response of four TNBC patient-derived xenografts to atRA treatment and we utilized these xenografts to refine the profile to 6 CpGs. We identify as many as 17% of TNBC patients who could benefit from atRA treatment. These data illustrate that differential DNA methylation of specific sites may predict the response of patient tumors to atRA treatment.
This study characterizes the gene expression of 2 triple-negative patient-derived breast cancer xenografts

overall_design: Total RNA from 2 PDXs were processed with the Affymetrix HuGene 2.0ST array. Three biological replicates were performed for each sample.

first: Krysta

last: Coyle

first: Cheryl

last: Dean

first: Margaret

last: Thomas

first: Dejan

last: Vidovic

first: Carman

last: Giacomantonio

first: Lucy

last: Helyer


title: RNA sequencing of Asthmatic Human Airway Smooth Muscle Cells I

summary: The goal of the was to evaluate the mRNA expression profile of non-asthmatic and asthmatic airway smooth muscle.

overall_design: RNA Seq was performed on nonasthmatic (n=5 individuals) and asthmatic (n=5  individuals) human airway smooth muscle cells.


title: Expression profiling of TNBCs following atRA treatment [Affymetrix I]

summary: All-trans retinoic acid (atRA) regulates gene expression and is used to treat acute promyelocytic leukemia. Attempts to use atRA for breast cancer treatment without a stratification strategy have resulted in limited overall effectiveness. To identify biomarkers for the treatment of triple-negative breast cancer (TNBC) with atRA, we characterized the effects of atRA on the tumor growth of 13 TNBC cell lines. This resulted in a range of tumor growth effects that was not predictable based on the levels of retinoid signaling molecules and transcriptional responses that were mostly independent of retinoic acid response elements. Given the importance of DNA methylation in regulating gene expression, we hypothesized that differential DNA methylation could predict the response of TNBCs to atRA. We identified over 1400 CpG sites that were differentially methylated between atRA resistant and sensitive cell lines. These CpG sites predicted the response of four TNBC patient-derived xenografts to atRA treatment and we utilized these xenografts to refine the profile to 6 CpGs. We identify as many as 17% of TNBC patients who could benefit from atRA treatment. These data illustrate that differential DNA methylation of specific sites may predict the response of patient tumors to atRA treatment.

overall_design:
This study characterizes the transcriptional response of 11 triple-negative breast cancer cell lines to all-trans retinoic acid.
Total RNA from 11 cell lines and 2 PDXs were processed with the Affymetrix HuGene 2.0ST array. Three biological replicates were performed for each sample.


title: Expression profiling and DNA methylation of TNBCs

type: Methylation profiling by genome tiling array


title: A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus [DamID]

city: Durham

first: Michael

last: Krangel

state: NC

address: 207 Research Drive, Jones Building, Room 316

institute: Duke University

summary: Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here we used DamID to profile Tcrb locus interactions with the nuclear lamina at high-resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border caused an enhancer-dependent spread of H3K27ac from the active recombination center into recombination center-proximal LAD chromatin. This was associated with a disruption to LAD organization, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a Tcrb locus LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.

overall_design:
DamID in VL3-3M2-cell lines (one wild-type and one modified)
Please note that the 'WT_DamID_LAD.bed' contains LAD calls based on DamID tracks in .bed (Bioinformatic calling based on DamID).

first: Shiwei

last: Chen

first: Teresa

last: Luperchio

first: Xianrong

last: Wong

first: Europe

last: Doan

first: Aaron

last: Byrd

first: Kingshuk

last: Choudhury

first: Karen

last: Reddy


title: Chemical Modulation of Glycolysis Regulates the KEAP1-NRF2 Pathway Through a Metabolite-Induced Posttranslational Modification

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: Glycolysis is a master regulator of cellular energy, synthesis and redox regulation, however the mechanisms that underlie the responses to and regulation of changing glucose metabolism are incompletely understood. The NRF2-antioxidant response element (ARE) pathway serves as a central regulator of cellular stress by sensing and eliminating 2 chemically reactive species in the cell. A phenotypic high-throughput chemical screen for novel activators of NRF2 signaling identified an inhibitor of the glycolytic enzyme PGK1. Metabolomic and proteomic profiling experiments revealed that inhibition of PGK1 results in the accumulation of central glycolytic intermediates, as well as the reactive dicarbonyl metabolite methylglyoxal (MGx). MGx selectively modifies reactive residues on KEAP1, resulting in the formation of a covalent KEAP1 homodimer, accumulation of NRF2 and activation of the NRF2 transcriptional program. Proteomic and NMR experiments verified that KEAP1 homodimerization is mediated by a novel post-translational modification, termed MICA, formed by the reaction of methylglyoxal with proximal cysteine and arginine residues. The identified PGK1 inhibitor series was found to be efficacious in a NRF2-dependent mouse model of UV-damage, demonstrating that activation of KEAP1- NRF2 signaling through this mechanism is physiologically relevant. Together, these results demonstrate the existence of direct inter-pathway communication between glycolysis and the KEAP1-NRF2 transcriptional program, which is mediated by a reactive metaboliteinduced post-translational modification (rmPTM). In addition, they provide new insight into metabolic regulation of cell stress response, and a potential therapeutic axis for controlling the cytoprotective antioxidant response in numerous human diseases.

overall_design: IMR32 cells were treated with 5 µM CBR-470-1 or an equivalent volume of DMSO vehicle control for 24 hours. 3 independent biological replicates per treatment condition were performed for a total of 6 samples.

last: Bollong

first: Gihoon

last: Lee

first: John

last: Coukos

first: Hwayoung

last: Yun

first: Claudio

last: Zambaldo

first: Jae-Won

last: Chang

first: Insha

last: Ahmad

first: Luke

last: Lairson

first: Peter

last: Schultz

first: Raymond

last: Moellering


title: A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus.

first: Michael

last: Krangel


title: A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus [ChIP-seq]

overall_design: H3K9me2 and H3K27ac ChIP-seq in primary Rag2-/- DN and DP thymocytes and VL3-3M2-cell lines (one wild-type and two modified)

first: Shiwei

last: Chen

first: Teresa

last: Luperchio

last: Wong


title: Reduced Representation Bisulphite Sequencing on FACS purified cell subpopulations of human prostate cancers and normal tissues.

city: Vancouver

first: Davide

last: Pellacani

state: British Columbia

address: Terry Fox Laboratory BC Cancer research centre

department: Terry Fox Laboratory

institute: BC Cancer Agency

summary: Prostate adenocarcinomas contain a predominance of cells with luminal features that display aberrant DNA methylation patterns with useful diagnostic and prognostic potential.  However, the DNA methylation features of basal and luminal cells in both normal and cancer tissues remain largely unknown. We have generated genome-wide DNA methylation profiles for FACS purified basal and luminal prostate tumour cells, obtained from radical prostatectomy samples and their paired normal counterparts isolated from unaffected regions in the same patient’s gland.

overall_design:
Matched tumour-directed (cancer) and contralateral (normal) core needle biopsies, obtained from 4 treatment-naïve prostate cancer patients undergoing radical prostatectomies, were enzymatically dissociated and FACS sorted into EpCAM+CD49f-CD24+ (luminal) and EpCAM+CD49f+CD24- (basal) cell populations at >95% purity. For convenience, we named these supbopulations as follows. CL: EpCAM+CD49f-CD24+ cells purified from tumor-directed biopsies; CB: EpCAM+CD49f+CD24- cells purified from tumour-directed biopsies; NL: EpCAM+CD49f-CD24+ cells from contralateral biopsies; NB: EpCAM+CD49f+CD24- cells purified from contralateral biopsies. This yielded 4 CL and CB populations, and 3 matched NL and NB populations (in one prostate the palpable tumour was extended to most of the prostate and it was not possible to obtain a contralateral biopsy). DNA obtained from each of these isolates was then subjected to Reduced Representation Bisulphite Sequencing (RRBS).
---------------------
*Raw data is not available due to privacy concerns.  Thus, this dataset is incomplete.*


title: Expression data from PDGF-B induced murine gliomas at different progression stages

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

summary: The different phases of tumor immunoediting in vivo were dissected thanks to a murine model of glioma induced by PDGF-B overexpression. We show that low-grade gliomas are highly immunostimulatory and that the adaptive immune system prevents the development of secondary tumor in syngeneic mice. During tumor progression, glioma cells downregulate immunostimulatory genes and the immune infiltrate becomes pro-tumorigenic.

overall_design: Cells from early-onset / low grade and late-onset / high grade were explanted, dissociated and sorted by FACS, basing on the expression of the EGFP transgene expressed together with PDGF-B as a bicistronic transcript. RNA extraction, sample labeling, array hybridization and scanning were carried out by Genopolis Consortium for Functional Genomics - (University of Milano-Bicocca, Italy , Dept. of Biotechnology and Bioscience)

first: Irene

last: Appolloni


title: Expression data from PDGF-B induced murine gliomas at different stages and after transplantation


title: ChIP-seq profiling of PU.1 binding sites in plasmacytoid and conventional mouse dendritic cells

status: Public on Oct 21 2018

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Dendritic cells (DCs) are can be broadly divided into conventional (cDC) and plasmacytoid (pDC) subsets. Despite the importance of this lineage diversity, its genetic basis is not fully understood. ChIP-seq profiling of PU.1 binding sites in cDCs and pDCs revealed a key role for PU.1 in maintaining cDC identity.

overall_design: ChIP-seq was conducted for two biological replicates of cDCs and pDCs with a PU.1 antibody. Sequencing was undertaken at the Beijing Genomic Institute (BGI) on an Illumina HiSeq 2000 to generate 49 base-pair single-end reads.


title: Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks

city: Solna

first: Franziska

last: Bonath

state: Stockholm

address: Tomtebodavägen 23A

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

country: Sweden

institute: Stockholm University

summary: Recent studies suggest that the repair of DNA double-strand breaks (DSBs) is supported by damage-induced small RNAs (diRNAs) that are generated by Drosha and Dicer from transcripts that originate from the regions flanking the break. However, transcription and diRNA production at naturally occurring DSBs in mammalian genomes remain controversial. We have used the homing endonuclease I-PpoI to produce DSBs in human and mouse cells, and we have analyzed the biogenesis of diRNAs at I-PpoI induced breaks in the 28S rDNA and the Ryr2 gene. We provide direct evidence that RNA polymerase II transcribes the sequences that flank the DSBs. Our results also reveal that the resulting transcripts are processed into two types of diRNAs with characteristic length and terminal nucleotide signatures. Furthermore, diRNA production is independent of Drosha and DGCR8, and only a subset of diRNAs depends on Dicer, as shown by small RNA analyses of knock-out cells that lack specific RNA processing enzymes. Our findings are compatible with previous observations of a general transcription inhibition at DSBs and provide novel insights into the mechanisms of RNA synthesis and processing at DSBs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells (either mESCs or HeLa) were transfected with a plasmid coding for the homing endonuclease I-PpoI that induces a double strand break in the 28S rDNA. After transfection the small RNA fraction was sequenced using standard Illumina sequencing and analyzed for reads mapping to the 28S rDNA.

first: Judit

last: Domingo-Prim

first: Marcel

last: Tarbier

first: Marc

last: Friedländer

first: Neus

last: Visa


title: The integrated stress response regulates cell health of cardiac progenitors

city: Indianapolis

first: Keith

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

summary: The discovery of mammalian cardiac progenitor cells has suggested that the heart consists of not only terminally differentiated beating cardiomyocytes, but also a population of self-renewing stem cells with the potential to generate new cardiomyocytes (Anderson, Self et al. 2007; Bearzi, Rota et al. 2007; Wu, Chien et al. 2008).  A consequence of longevity is continual exposure to environmental and xenobiotic stresses, and recent literature suggests that hematopoietic stem cell pools tightly control cell health through upregulation of the integrated stress response and consequent cellular mechanisms such as apoptosis.  However, whether or not this biological response is conserved in progenitor cells for later lineages of tissue specific stem cells is not well understood.  Using human induced pluripotent stem cells (iPSC) of both cardiac progenitor and mature cardiomyocyte lineages, we found that the integrated stress response was upregulated in the iPSC cardiac progenitors leading to an increased sensitivity for apoptosis relative to the mature cardiomyocytes.  Of interest, C/EBP homologous protein (CHOP) signaling plays a mechanistic role in the cell death phenotype observed in iPSC progenitors, by which depletion of CHOP prevents cell death following cellular stress by thapsigargin exposure.  Our studies suggest that the integrated stress response plays a unique role in maintaining iPSC cardiac progenitor cellular integrity by removing unhealthy cells via apoptosis following environmental and xenobiotic stresses, thus preventing differentiation and self-renewal of damaged cells.

overall_design: IPSC cardiomyocytes (Cellular Dynamics) were cultured for 24hrs (progenitors) or 2 weeks (mature), followed by compound treatment for 24hrs. All treatments were performed in triplicate. Compound treatments were 1uM thapsigargin, 2uM tunicamycin, or 0.1uM halifuginone. RNA was hybridized to Affymetrix Human Genome U133_Plus_2.0 arrays. Data was analyzed using the MAS 5.0 algorithm, with global scaling to 1500.

first: George

middle: H

last: Searfoss

first: Brianna

last: Paisley

first: Thomas

last: Baker

first: Jeffrey

middle: A

last: Willy


title: WNT signaling memory is required for ACTIVIN to function as a morphogen

city: New York

first: Albert

last: Ruzo

state: NY

address: 1230 York Avenue

department: Laboratory of Stem Cell Biology and Molecular Embryology

institute: The Rockefeller University

summary: It has now become clear that the process of fate specification during early embryogenesis is mediated by a handful of key signaling pathways. However, how the temporal and spatial integration of these signals plays out to give rise to self-organization of tissues remains obscure. Here we use artificial human gastruloids and quantitative single-cell analysis to dissect the temporal integration of two key pathways WNT and ACTIVIN that along with BMP control gastrulation and primitive streak patterning in model systems. We showed that ACTIVIN elicits a transient signaling response, as well as a transient induction of differentiation. However, unlike BMP and WNT, ACTIVIN cannot induce stable primitive streak formation and mesodermal patterning. Pre-exposure to WNT switches the response of cells to ACTIVIN whereby it becomes a concentration dependent morphogen. This provides evidence for WNT signaling memory that occurs at the transcriptional level and not as a modifier of ACTIVIN signaling dynamics.

overall_design: Time series RNAseq analysis of the effect of the addition of activin to a hESC culture. The study consists of 3 control samples (0, 6, 12h) and 5 activin-treated samples (collected at 1, 2.5, 4, 8, 12h). There are no replicates per timepoint/condition.

first: Ali

last: Brivanlou

first: Anna

last: Yoney


title: DNA methylation Profiling in Kawasaki disease (KD): DNA methylation profile in healthy control subjects, acute-phase KD subjects and convalescent-phase KD subjects

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary:
DNA methylation analysis of DNA samples from total WBC collection
The DNA samples from each subject was first subject to bisulfite conversion, followed by sample preparation and microarray experiment.

overall_design:
We analyzed 12 pooled healthy control DNA samples, 12 pooled acute-phase KD DNA samples and 12 convalescent-phase KD DNA samples.
[contributor] Kaohsiung Chang Gung memorial Hospital, Taiwan

first: Ho-Chang

last: Kuo


title: Global transcriptional profiling changes upon knockdown of G9a in human non-small cell lung cancer cells

city: Duarte

first: keqiang

last: zhang

address: 1500 East Duarte Road

department: Molecular Pharmacology

institute: City of Hope National Medical Center

summary: The experiment was designed to display differential gene expression profiling changes in two human Non-small cell lung cancer cells upon knockdown of G9a/EHMT2, by using RNAseq technology.

overall_design: G9a/EHMT2 was first silenced in two non-small cell lung cancer: A549 and H1299 by siRNA-mediated knockdown. Total RNA was extracted from duplicated cancers cells transfected with control siRNA and G9a specific siRNA at 72h posttransfection for RNAseq analysis. Differentially expressed genes in G9a-attenuated cells were identified in comparison to that in non-small cell lung cancer transfected with control siRNA.

first: Keqiang

last: Zhang

first: Jinghan

last: Wang

first: Lu

last: Yang

first: Dan

last: Raz


title: Breast Milk-Associated Oxysterol Reverses Neonatal Brain Injury Through Gli2-Dependent Oligodendrogenesis

status: Public on Oct 20 2018

first: Yasuhito

last: Yahara

address: Duke Hospital South, 200 Trent Drive, Orange Zone 5th floor

institute: Duke Univ

summary: We identified an emerging oligodendrocyte committed subpopulation based on their gene expression that included Pdgfra, Cspg4 also known as Ng2, Olig1, Olig2.

overall_design: Postnatal neural stem cells were expanded and divided into DMSO (vehicle control) or 1μM 20HC-treated groups and sequenced 3 days after EGF and FGF withdrawal.

first: Agnes

last: Chao

first: Pavle

last: Matak

first: Jason

last: Gibson

first: Simon

last: Gregory

first: Ronald

middle: N

last: Goldberg

first: Eric

last: Benner