title: Nanostring analysis of MC38 tumors in PBS and hetIL-15-treated mice

first: Maggie

last: Cam

address: Bldg 37, Rm 1136A, 37 Convent Drive

department: NCI

summary: Comparison of gene expression identified several significantly overexpressed genes in tumors recovered from hetIL-15-treated mice. These upregulated genes after hetIL-15 treatment represent an expression signature that corresponds to activated TILs with cytotoxic phenotype. Nanostring analysis also identified additional functional pathway signatures, including signal transducer and activator of transcription (STAT) intracellular signaling, TCR recognition of cognate antigen, interferons signaling, increased metabolic rate and immune cell chemotaxis

overall_design: nCounter PanCancer Immune Profiling Panel (NanoString Technologies) was used to monitor the expression of a panel of 770 genes related to immune-oncology in MC38 tumors of PBS- and hetIL-15-treated mice. Tumors wereanalyzed 3 hours after the 4th administration

first: Cristina

last: Bergamaschi

first: George

last: Pavlakis


title: Single-cell RNA-Seq analysis of WT and Bach2-deficient Foxp3+ Treg cells

status: Public on May 12 2020

city: Cambridge

first: Mohammed-Firas

last: Sadiyah

address: The Old Schools, Trinity Ln

country: United Kingdom

institute: University of Cambridge

type: Expression profiling by high throughput sequencing

summary: These are the FastQ files used for scRNA-Seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells

overall_design: RNA-seq profile from single EGFP+ Treg cells isolated from the spleens of tamoxifen-treated Bach2+/+ Foxp3EGFP-Cre-ERT2 (WT) mice and Bach2fl/fl Foxp3EGFP-Cre-ERT2 (CKO) mice , were generated by deep sequencing using Illumina HiSeq4000


title: Antigen-stimulated PBMC transcriptional signatures of protection upon malaria sporozoite and RTS,S/AS01E immunizations

status: Public on May 13 2020

city: Barcelona

first: Gemma

last: Moncunill

state: Please Select

address: Carrer Rosselló 153 (CEK building)

country: Spain

institute: ISGlobal

summary: Identifying immune correlates of protection and mechanisms of immunity accelerates and streamlines the development of vaccines. RTS,S/AS01E, the most advanced malaria vaccine, has moderate efficacy in African children. In contrast, immunization with sporozoites under antimalarial chemoprophylaxis (CPS immunization) can provide 100% sterile protection in naïve adults. We used systems biology approaches to identify correlates of vaccine-induced immunity based on transcriptomes of peripheral blood mononuclear cells from subjects immunized with RTS,S/AS01E or chemo-attenuated sporozoites stimulated with parasite antigens in vitro. Specifically, we used samples of subjects from two age cohorts and 3 African countries participating in an RTS,S/AS01E pediatric phase 3 trial and malaria-naïve subjects participating in a CPS trial. We identified both pre-immunization and post-immunization transcriptomic signatures correlating with protection. Signatures were validated in independent children and infants from the RTS,S/AS01E phase 3 trial and subjects from an independent CPS trial with high accuracies (>70%). Transcription modules revealed interferon, NF-B, TLR, and monocyte-related signatures associated with protection. Pre-immunization signatures suggest the potential for strategies to prime the immune system before vaccination towards improving vaccine immunogenicity and efficacy. Finally, signatures of protection could be useful to determine efficacy in clinical trials, accelerating vaccine candidate testing. Nevertheless, signatures should be tested more extensively across multiple cohorts and trials to demonstrate their universal predictive capacity.

overall_design: PBMC stimulated with CSP, DMSO, PfRBC and uRBC from 24 CPS-immunized individuals pre-immunization and post-immunization (total of 192 samples) and from RTS,S or comparator vaccinees pre- and post-vaccination (total of 686 samples).

first: Anja

last: Scholzen

first: Maximillian

last: Mpina

first: Augusto

last: Nhabomba

first: Aurore

middle: B

last: Hounkpatin

first: Lourdes

last: Osaba

first: Raquel

last: Valls

first: Joseph

middle: J

last: Campo

first: Hèctor

last: Sanz

first: Chenjerai

last: Jairoce

first: Nana

middle: A

last: Williams

first: Erica

middle: M

last: Pasini

first: David

last: Arteta

first: Joan

last: Maynou

last: Palacios

first: Miquel

last: Duran-Frigola

first: John

last: Aponte

first: Clemens

middle: H

last: Kocken

first: Selidji

middle: T

last: Agnandji

first: José

last: Mas

first: Benjamin

last: Mordmüller

first: Claudia

last: Daubenberger

first: Robert

last: Sauerwein

first: Carlota

last: Dobaño


title: Bulk RNA-Seq analysis of WT and Bach2-deficient Foxp3+ Treg cells

first: Mohammed-Firas

last: Sadiyah

summary: These are the FastQ files used for the RNA-seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells.

overall_design: RNA-seq profiles from Bach2high and Bach2low EGFP+ Treg, purified by FACS from Foxp3EGFP-DTR Bach2tdRFP/+ mice, were generated by deep sequencing using Illumina HiSeq2500.


title: Heterogeneous Bach2 expression distinguishes rTreg cells and aTreg cells

summary: These are the FastQ files used for RNA-Seq analysis of splenic Foxp3+ Treg cells that express either high or low levels of Bach2

overall_design: RNA-seq profile from single EGFP+ Treg cells isolated from the spleens of tamoxifen-treated Bach2+/+ Foxp3EGFP-Cre-ERT2 (WT) mice and Bach2fl/fl Foxp3EGFP-Cre-ERT2 (CKO) mice , were generated by deep sequencing using Illumina HiSeq2500


title: Distribution of genome-wide BACH2 or JunD binding sites identified by ChIP-Seq in iTreg cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In various tissues, cellular homeostasis is achieved by functionally quiescent stem cells which selfrenew while giving rise to differentiated progeny. Regulatory T (Treg) cells are composed of functionally quiescent resting Treg (rTreg) cells which differentiate into activated Treg (aTreg) cells upon antigen stimulation. How rTreg cells remain quiescent despite chronic exposure to cognate self- and foreign antigens is unclear. The transcription factor BACH2 is critical for early Treg lineage specification but its function following lineage commitment is unresolved. Here, we show Bach2 is highly expressed in lineage-committed rTreg cells but is downregulated in aTreg cells, and upon inflammation. BACH2 binds to AP-1 sites within Treg genomes and its high expression within rTreg cells functions to restrain their TCR-driven activation and differentiation into aTreg cells. As a consequence, cell-autonomous BACH2 expression is required following Treg lineagecommitment for the functional quiescence and long-term maintenance of Treg cell populations and for immune homeostasis.

overall_design: ChIP-seq profiles from iTreg cells, purified by FACS from WT mice, were generated by deep sequencing using Illumina HiSeq2000.


title: Epigenetic landscape of four exhausted CD8 T cell subsets

status: Public on May 11 2020

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

summary: Open chromatin accessibility analysis of four defiined CD8 Tcell subsets to understand the mechanism of exhaustion hierarchy

overall_design: 2-3 Biological replicates were analyzed for each of the four defined Tcell subsets of CD8 exhaustion

first: Jean-Christophe

last: Beltra

last: Wherry


title: BACH2 is repurposed following Treg lineage commitment to drive the functional quiescence and maintenance of resting Treg cells

summary:
In various tissues, cellular homeostasis is achieved by functionally quiescent stem cells which self renew while giving rise to differentiated progeny. Regulatory T (Treg) cells are composed of functionally quiescent resting Treg (rTreg) cells which differentiate into activated Treg (aTreg) cells upon antigen stimulation. How rTreg cells remain quiescent despite chronic exposure to cognate self- and foreign antigens is unclear. The transcription factor BACH2 is critical for early Treg lineage specification but its function following lineage commitment is unresolved. Here, we show Bach2 is highly expressed in lineage-committed rTreg cells but is downregulated in aTreg cells, and upon inflammation. BACH2 binds to AP-1 sites within Treg genomes and its high expression within rTreg cells functions to restrain their TCR-driven activation and differentiation into aTreg cells. As a consequence, cell-autonomous BACH2 expression is required following Treg lineage commitment for the functional quiescence and long-term maintenance of Treg cell populations and for immune homeostasis.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptional landscape of four exhausted CD8 T cell subsets

summary: Transcriptional study of four defiined CD8 Tcell subset to understand the mechanism of exhaustion hierarchy

overall_design: Three biological replicates were analyzed for each of thefour defined Tcell subsets of CD8 exhaustion


title: Chromatin accessibility in response to knockdown of GLI1 and SMARCA2 in GLI1-mediated gene expression.

city: Rochester

first: Stephanie

middle: Lynn

last: Safgren

state: Minnesota

address: 200 1st Street SW, Gonda 19 366C

department: Oncology Research

institute: Mayo Clinic

summary: GLI1 is a transcription factor correlated to decreased survival in several cancers. We have identified SMARCA2 as a co-regulator that enhances GLI1-mediated transcriptional activity and functions through the C-terminal transcriptional activation domain of GLI1. Central domains including the ATPase motif of SMARCA2 physically interact with GLI1.  Evaluation of DNA density indicates GLI1, like SMARCA2, can increase the DNA accessibility with a preference for sites distal to gene transcription start sites and outside the promoter regions (i.e. enhancers).  The putative enhancers where accessibility is decreased by the knock down of GLI1 and SMARCA2 are located cis to genes, such as HHIP, that are regulated by GLI1 and implicated in cancer functions.  At the putative enhancer for HHIP, the localization of SMARCA2 is at least partially dependent on GLI1’s presence.  Understanding this transcriptional regulation by GLI1 and SMARCA2 through altering chromatin accessibility at enhances can provide additional therapeutic targets for cancers dependent on GLI1.

overall_design: Chromatin accessibilty was accessed using ATAC-seq on RMS13 cells following the siRNA knockdown of GLI1 and SMARCA2.

middle: L

first: Alexandre

last: Gaspar-Maia

first: Martin

middle: E

last: Fernandez-Zapico


title: Heterogeneity and chimerism of endothelial cells revealed by single cell transcriptome in orthotopic liver tumors

city: Tarrytown

first: Alexandra

last: Eichten

state: NY

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals Inc.

summary: To understand endothelial cell heterogeneity in naïve liver as well as in adjacent normal and liver tumor tissue. The single cells were profiled by single cell RNAseq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Tumors and normal tissue were dissociated, sorted into single cells, and profiled by 10x Genomics Chromium. Single cell 3' library, Gelbeads and multiplex kit were made by using 10x Genomics platform.

first: Gavin

last: Thurston


title: Selective Mediator-dependence of cell type-specifying transcription [ChIP-seq]

city: Wien

first: Georg

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

summary: The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.

overall_design: ChIP-seq for H3K27ac and H3K4me3 histone marks in wild-type KBM7 cells.

middle: G

last: Jaeger

first: Hana

last: Imrichova


title: Selective Mediator-dependence of cell type-specifying transcription [TT-seq]

overall_design: TT-seq in (1) KBM7 MED14-dTAG cells after 1-2h 500nM dTAG7 and/or 30min 500nM NVP2 and in (2) HCT-116 MED14-dTAG cells after 1-2h 500nM dTAGV-1.

first: Taras

last: Velychko

first: Björn

last: Schwalb

first: Patrick

last: Cramer


title: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

first: Orr

last: Ashenberg

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary: Single cell genomics is essential to chart tumor ecosystems. While single cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 212,498 cells and nuclei from 39 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate, and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.

overall_design:
We developed a systematic toolbox for fresh and frozen tumor processing using single cell (sc) and single nucleus (sn) RNA-Seq, respectively (Fig. 1a). The toolbox contains our experimental workflow and methods, computational pipelines, and evaluation metrics. To generalize across tumor and sample types, we tested eight tumor types with different tissue characteristics (Fig. 1b), including comparisons of matched fresh and frozen preparations from the same tumor specimen. We tested varying tissue and sample characteristics including resection, biopsy, ascites, and orthotopic patient-derived xenograft. We included samples from non-small cell lung carcinoma (NSCLC), metastatic breast cancer (MBC), ovarian cancer, neuroblastoma, glioblastoma (GBM), pediatric high-grade glioma, chronic lymphocytic leukemia (CLL), pediatric sarcoma, and melanoma (Fig. 1b). In total, we analyzed 212,498 cells and nuclei across 23 tumors, from 22 patients spanning 39 sample preparations. Our work provides direct recommended protocols for multiple tumor types, decisions trees that allow researchers to choose the most suitable protocol for their research goals, and guidelines on how to customize protocols for new tumor and specimen types.
-------------------
*Raw sequencing data is is available in the controlled access repository DUOS (https://duos.broadinstitute.org/), under DUOS Dataset IDs DUOS-000111, DUOS-000112, DUOS-000113 and DUOS-000114*
**Submitter declares reads will be made available through dbGaP.**

first: Michal

last: Slyper

first: Caroline

last: Porter

first: Julia

last: Waldman

first: Eugene

last: Drokhlyansky

first: Isaac

last: Wakiro

first: Christopher

last: Smillie

first: Gabriela

last: Smith-Rosario

first: Jingyi

last: Wu

first: Danielle

last: Dionne

first: Sébastien

last: Vigneau

first: Judit

last: Jané-Valbuena

first: Sara

last: Napolitano

first: Mei-Ju

last: Su

first: Anand

last: Patel

first: Asa

last: Karlstrom

first: Simon

last: Gritsch

first: Masashi

last: Nomura

first: Avinash

last: Waghray

first: Satyen

last: Gohil

first: Alexander

last: Tsankov

first: Livnat

last: Jerby-Arnon

first: Ofir

last: Cohen

first: Johanna

last: Klughammer

first: Yanay

last: Rosen

first: Joshua

last: Gould

first: Lan

last: Nguyen

first: Matan

last: Hofree

first: Bo

last: Li

first: Catherine

first: Benjamin

last: Izar

first: Rizwan

last: Haq

first: F

middle: S

last: Hodi

first: Charles

last: Yoon

first: Aaron

middle: N

last: Hata

first: Suzanne

last: Baker

first: Mario

last: Suvà

first: Raphael

last: Bueno

first: Elizabeth

last: Stover

first: Michael

middle: R


title: Selective Mediator-dependence of cell type-specifying transcription [PRO-seq]

first: Georg

last: Winter

overall_design: PRO-seq in KBM7 MED14-dTAG cells after 1-2h 500nM dTAG7 and/or 30min 500nM NVP2.

first: Martin

last: Jaeger


title: Selective Mediator-dependence of cell type-specifying transcription [Quant-Seq]

overall_design: Quant-seq (3' mRNA-seq) in engineered and wild-type KBM7 cells after 6h treatments with DMSO, 500nM dTAG7, 250nM THAL-SNS-032 (dCDK9), or 100nM dBET6.

first: Matthias

last: Brand


title: Selective Mediator-dependence of cell type-specifying transcription [HiChIP]

overall_design: H3K27ac HiChIP after 2h MED14-dTAG degradation by 500nM dTAG7 in KBM7 cells.

first: Sebastian

middle: D

last: Mackowiak

first: Denes

last: Hnisz


title: Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci [array]

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: To better understand the fundamental molecular mechanisms that contribute to complex human diseases such as coronary artery disease (CAD), we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells. To this end, we used a pooling approach to map quantitative trait locus associations (QTLs) for TCF21 binding (ChIPseq), chromatin accessibility (ATACseq), and chromosomal looping (HiC). We find significant overlap of these QTLs, and several analyses indicate their relationship to smooth muscle specific genes, the binding of smooth muscle transcription factors, and enrichment in CAD-associated loci. These QTLs are extensively validated and allele-specific chromatin looping at the FN1 disease locus is shown to be mediated by activation of the CAD-associated TGFb1 pathway. In sum, these results uncover thousands of loci affecting cis-regulation in a key cell type for CAD, including many that may contribute to CAD risk.

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown in serum. Approximately 97.5M HCASMC, 1.5M from 65 different cell lines were pooled and fixed with 1 % formaldehyde and quenched by glycine.

first: Quanyi

last: Zhao

last: Dacre

first: Trieu

last: Nguyen

first: Milos

last: Pjanic

first: Boxiang

last: Liu

first: Dharini

last: Iyer

first: PoSheng

middle: P

last: Cheng

first: Robert

last: Wirka

first: Juyong

last: Kim

first: Hunter

last: Fraser


title: YAP and/or TAZ inhibition in HepG2 cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: The Hippo pathway effectors yes-associated protein (YAP) and WW domain containing transcription regulator 1 (TAZ/WWTR1) support tumor initiation and progression in various cancer entities including hepatocellular carcinoma (HCC). However, to which extent YAP and TAZ contribute to liver tumorigenesis via common and exclusive molecular mechanisms is poorly understood.   RNAinterference (RNAi) experiments illustrate that YAP and TAZ individually support HCC cell viability and migration, while for invasion additive effects were observed. Comprehensive expression profiling revealed partly overlapping YAP/TAZ target genes as well as exclusively regulated genes.

overall_design:
Gene-specific siRNAs (YAP1, YAP2: two independent siRNAs both targeting the gene YAP1, and TAZ2, TAZ3: independent siRNAs both targeting the gene TAZ) were transiently transfected in HepG2 cells (20 nM each). Nonsense/Scrambled siRNA-transfected and combined YAP/TAZ-specific siRNAs were transiently transfected in HepG2 cells (in total 40 nM). Total mRNA was extracted 24 hours after transfection.

Control and YAP1/2 samples are also available in GSE121732 and are included here so that all samples can be downloaded together.

first: Kai

last: Breuhahn


title: Selective Mediator dependence of cell-type-specifying transcription

first: Georg

last: Winter

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


title: Genome-wide stabilization of mRNA during E. coli growth from "feast to famine" (transcriptiome)

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

summary: Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. It results from both mRNA transcription and degradation controls. However, the contribution of transcript stability regulation in gene expression is poorly characterized. Using combined transcriptome and mRNA decay analyses, we investigated (i) how transcript stability changes in E. coli during the glucose-acetate-starvation transition and (ii) if these changes contribute to gene expression changes. Our work highlights that transcript stability increases along carbon depletion. Most of the stabilization occurs at glucose-acetate transition when glucose is exhausted, then stabilized mRNAs remain stable during acetate consumption and carbon starvation. Meanwhile, expression of most genes is downregulated and we observed three time less gene expression upregulation. Using control analysis theory on 375 genes, we show that most of gene expression regulation is driven by changes in transcription. Although mRNA stabilization is not the controlling phenomenon, it contributes to the emphasis or attenuation of transcription regulation. However, upregulation of 18 genes (33% of our studied upregulated set) is mainly governed by transcript stabilization. Because these genes are associated with response to nutrient changes and stress, this illustrates the importance of post-transcriptional regulations in bacterial response to nutrient starvation.

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

overall_design: A microarray study was performed to estimate genome wide mRNA half-lives in E. coli K12 MG1655 cultured in M9+glucose (3g/l). In three growth phases, at glucose exhaustion (P2),  during acetate consumption (P3) and during carbon starvation (P4), sampling was performed before addition of rifampicin. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in replicates. Three independent kinetics were performed for each growth condition.

first: Manon

last: Morin

first: Brice

last: Enjalbert

first: Delphine

last: Ropers

first: Muriel

last: Cocaign-Bousquet


title: EZH2 mutations reprogram the immune response to yield a pre-malignant lymphoma niche

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College


title: Genome-wide stabilization of mRNA during E. coli growth from "feast to famine" (stabilome)

overall_design: A microarray study was performed to estimate genome wide mRNA half-lives in E. coli K12 MG1655 cultured in M9+glucose (3g/l). In three growth phases, at glucose exhaustion (P2),  during acetate consumption (P3) and during carbon starvation (P4), sampling was performed before the addition of rifampicin (500 µg/l) for transcription arrest and over the time after rifampicin addition. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in replicates. Three independent kinetics were performed for each growth condition.


title: Transcriptional responses in newly-hatched Oryzias latipes associated with developmental malformations following diluted bitumen exposure

city: Quebec

first: Valerie

last: Langlois

state: QC

address: 490 rue de la Courrone

department: Centre Eau Terre Environnement

country: Canada

institute: Intitut national de la recherche scientifique (INRS)

summary: Japanese medaka (Oryzias latipes) embryos were exposed to two concentrations of the water accommodated fractions and chemically-enhanced water accommodated fractions of two types of diluted bitumen (dilbit). Chemical-dispersion did not significantly alter transcriptional responses to dilbit toxicity but may have acted through alternative mechanisms to give similar phenotypic responses, such as normal swim bladder development. This study identified novel biomarkers in fish with or without visual malformations exposed to dilbit that can be used to assess aquatic ecosystem health. Microarray analyses identified novel biomarkers and gene networks in dilbit-exposed malformed embryos that were not evident in unaffected dilbit-exposed fish or in controls.

overall_design: Newly-hatched medaka from both dilbit types (AWB, CLB) and treatments (WAF, CEWAF) were pooled for further transcriptomic analysis following the chronic exposure. This included Lo fish (n = 12; 4 pools of 3 fish each) that showed no visible signs of BSD (e.g., normal fish, or norm) and Hi treatment fish (n = 12) that all showed signs of BSD (i.e., malformed fish, or malf) with 40% no SB. For fish grouped for additional analyses, no malformations (i.e., normal, or norm) were reported for water control fish (normal control, or NC, n = 6 pools), and all dispersant control fish (DC, n = 3 pools) had BSD and no SB (6 to 9 pools of three fish each per treatment, Table SB1).

first: Barry

last: Madison

first: Sarah

last: Wallace

first: Jing

last: Zhang

first: Peter

middle: V

last: Hodson


title: EZH2 mutations reprogram the immune response to yield a pre-malignant lymphoma niche [RNA-Seq]

summary: The mechanism through which lymphoma-associated EZH2 gain-of-function mutations disrupt the immune system to initiate malignant transformation is poorly understood. Conditional expression of mutant Ezh2 in germinal center (GC) B-cells provides a competitive advantage to activated B-cells in expanding the GC light zone (LZ) that is not caused by failure to differentiate and exit the GC. Instead, the LZ enlargement is explained by reduced apoptosis of Ezh2 mutant centrocytes, aberrant LZ proliferation, and failure of these centrocytes to re-enter the dark zone (DZ). Ezh2 mutant GCs fail to engage T-cells and to undergo clonal diversification, exhibiting a reduced IgV mutation frequency. Hence the dominant competitive advantage effect of Ezh2 mutation during early stages of transformation is to uncouple GC B-cells from T-cell help checkpoint, which allows GC B-cells entering the LZ to persist and expand regardless of their immunoglobulin status, reflecting the biology of low-grade follicular lymphomas.

overall_design: Twenty-four samples total: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre (four biological replicates), centroblast Cγ1-cre (four biological replicates), centrocytes Ezh2(Y641F)fl/wt;Cγ1-cre (four biological replicates), centrocytes Cγ1-cre (four biological replicates), naïve B-cells Ezh2(Y641F)fl/wt;Cγ1-cre (four biological replicates), naïve B-cells Cγ1-cre (four biological replicates) of 3 months-old mice immunized with SRBC and euthanized 8 days post-immunization

first: Wendy

last: Béguelin

first: Matt

last: Teater

first: Kenneth

middle: B

last: Hoehn

first: Alexey

last: Soshnev

first: Jude

last: Phillip

first: Leandro

last: Venturutti

first: María

last: Calvo-Fernández

first: Hao

last: Shen

first: Jeannie

last: Camarillo

first: Neil

last: Kelleher

first: Christopher

last: Mason

first: Olivier

last: Elemento

first: C

last: Allis

first: Steven

last: Kleinstein

first: Ari

last: Melnick


title: EZH2 mutations reprogram the immune response to yield a pre-malignant lymphoma niche [ChIP-Seq]

first: Cem

last: Meydan

overall_design: Twelve samples total: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre (three biological replicates), centroblast Cγ1-cre (three biological replicates), centrocytes Ezh2(Y641F)fl/wt;Cγ1-cre (three biological replicates), centrocytes Cγ1-cre (three biological replicates), of 3-4 months-old mice immunized with SRBC and euthanized 8 days post-immunization. Drosophila cells were added as spike-in for ChIP.


title: Landscape of four exhausted CD8 T cell subsets

first: E

last: WHERRY

overall_design: Refer to individual Series


title: scRNAseq of CD45+ cells within PDAC tumors treateted with CD40/ICB

status: Public on May 10 2020

first: Austin

last: Huffman

address: 3400 Civic Center Blvd

summary: Goal: determine how transcriptome of immune cells within the tumor microenvironment changes as a function of CD40 agonist and/or immune checkpoint blockade (anti-PD-1 AND anti-CTLA-4; "ICB") therapy

overall_design: Mice were injected with KPC-derived pancreatic ductal adenocarcinoma (PDAC) cell line; mice were treated +/- CD40 agonist and +/- ICB; mice were sacrificed and CD45+ immune cells were FACS-isolated from the tumor microenvironment and sequenced

first: A

first: J

last: Lin

first: R

last: Vonderheide


title: miRNA Expression from Cerebrospinal Fluid (CSF) from Prodromal Huntington Disease Patients

city: Medford

first: Eric

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of microRNA (miRNA) expression in CSF from prodromal Huntington disease patients.

overall_design: miRNA levels were measured in CSF from 60 PREDICT-HD study participants using the HTG protocol. Using a CAG–Age Product score, 30 prodromal HD participants were selected based on estimated probability of imminent clinical diagnosis of HD (i.e., low, medium, high; n = 10/group). For comparison, participants already diagnosed (n = 15) and healthy controls (n = 15) were also selected.

first: Richard

last: Myers

first: Jeanne

middle: C

last: Latourelle

first: Jeremy

last: Bockholt

first: Joli

last: Bregu

first: Justin

last: Smock

first: Jane

last: Paulsen


title: Plakophilin 1 enhances MYC expression to promote squamous cell lung cancer

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

institute: University of Granada

summary: Plakophilin 1 (PKP1) is a component of desmosomes. Although desmosome function loss has been associated with increased cell migration and pro-oncogenic activity, we previously observed PKP1 overexpression in squamous cell lung cancer (SqCLC). We developed in vitro and in vivo functional models of PKP1 gain/loss in SqCLC to explore this paradox. Greater cell dissemination but reduced cell proliferation was observed in CRISPR-Cas9 PKP1-knockout clones. PKP1 expression promoted cell proliferation, cell survival, and in vivo xenograft engraftment, and these pro-oncogenic activities were mediated by the functional relationship of PKP1 with MYC. PKP1 bound to the 5’UTR of MYC mRNA, enhancing MYC translation, and MYC bound directly to the PKP1 promoter, enhancing PKP1 transcription. We propose PKP1 as a novel oncogene in SqCLC and a post-transcriptional regulator of MYC. PKP1 may be a valuable diagnostic biomarker and potential therapeutic target for SqCLC. Importantly, PKP1 inhibition may indirectly target MYC, a primary anti-cancer target.

overall_design: 4 non-paired samples were analyzed (2 controls and 2 treated)

first: Laura

last: Boyero-Corral

first: Joel

last: Martín-Padrón

first: María

middle: I

last: Rodríguez

first: Álvaro

last: Andrades

first: Isabel

middle: F

last: Coira

first: Esther

last: Fárez-Vidal

last: Medina


title: RNA-sequencing of bronchial epithelial cells from an adult cohort including asthmatics, COPD and healthy controls, cultured with Rhinovirus 1A

city: Perth

first: Niamh

last: Troy

address: Northern Entrance, 15 Hospital Ave, Nedlands

country: Australia

institute: Telethon Kids Institute

summary: Rhinovirus infections exacerbate chronic respiratory inflammatory diseases such as asthma and chronic obstructive pulmonary disease (COPD). Airway epithelial cells are the primary site of rhinovirus replication and responsible for initiating the host immune response to infection. Numerous studies have reported that the anti-viral innate immune response in asthma is deficient leading to the conclusion that epithelial innate immunity is a key determinant of disease severity during a rhinovirus induced exacerbation. However, deficient rhinovirus-induced epithelial interferon production in asthma has not always been observed. We hypothesised that disparate in vitro airway epithelial infection models lacking genome-wide, time-course analyses have obscured the role of epithelial innate anti-viral immunity in asthma and COPD. To address this, we developed a low multiplicity of infection (MOI) rhinovirus model of differentiated primary epithelial cells obtained from healthy, asthma and COPD donors. Using genome-wide gene expression following infection, we demonstrated that gene expression patterns are similar across patient groups, but that the kinetics of induction are delayed in cells obtained from asthma and COPD donors. Rhinovirus-induced innate immune responses were defined by interferons (type-I, II and III), interferon response factors (IRF1, IRF3 and IRF7), TLR signalling and NF‐kB and STAT1 activation. Induced gene expression was evident at 24 hours and peaked at 48 hours post‐infection in cells from healthy subjects. In contrast, in cells from donors with asthma or COPD induction was maximal at or beyond 72-96 hours post infection. Thus, we propose that propensity for viral exacerbations of asthma and COPD relate to delayed (rather than deficient) expression of epithelial cell innate anti-viral immune genes which in turns leads to a delayed and ultimately more inflammatory host immune response.

overall_design: Three participant groups: asthmatics, COPD and healthy controls. Cultured with/without virus over a timecourse with four timepoints (24, 48,72 and 96). Paired virus-infected and mock infected samples at each timepoint for each subject.

first: Punnam

last: Veerati

middle: M

first: Andrew

last: Reid

first: Ngan

last: Li

first: Kristy

last: Nichol

first: Parwinder

last: Kaur

first: Stephen

last: Maltby

first: Peter

middle: A

last: Wark

first: Darryl

last: Knight

first: Anthony

last: Bosco

first: Chris

last: Grainge

first: Nathan

middle: W

last: Bartlett


title: RNA Seq profiling of transcriptional response in IFNg-primed C57BL6 mouse primary bone marrow derived macrophages exposed to vehicle, compound 2062 and an inactive control analog at 0, 1, 2 and 6 hours post treatment

first: Ruslana

last: Bryk

address: 413 East 69 Street

department: Microbiology and Immunology

institute: Weill Cornell Medicine

summary:
The goals of this study were to probe cellular networks that became engaged upon small molecule 2062 exposure in primary mouse bone marrow macrophages and compare them with the control inactive compound. Compound 2062 activated BMDM to enhance the production of nitric oxide and TNFa and potentiated rifampin activity in a mouse model of  tuberculosis.
We used biochemical, pharmacologic, transcriptomic and genetic approaches to identify the targets of 2062. RNASeq demonstrated that early changes in the BMDM transcriptome in response to 2062 exposure were consistent with an extensive stress response.
INFg-primed BMDM were exposed to vehicle, compound 2062, a TFEB activator, or a close structural analog for 1, 2 or 6 hours. Cells were collected, mRNA isolated and subjected to NGS. Transcriptional response was compared between the timepoints for the vehicle vs active 2062 compound and vehicle vs inactive compound.

overall_design: mRNA profiles were generated for the timecourse of exposure to compound 2062 or its inactive analog and compared to vehicle control. BMDM from three individual mice were plated and treated separately to represent three replica experiments.


title: Genome-wide single nucleotide resolution of oxaliplatin-DNA adduct repair in drug sensitive and resistant colorectal cancer cell lines

city: Chapel Hill

first: Courtney

middle: Michelle

last: Vaughn

state: NC

address: 120 Mason Farm Rd CB#7260

institute: The University of North Carolina at Chapel Hill

summary: Platinum-based chemotherapies, including oxaliplatin, are a mainstay in solid tumor treatment and induce cell death by forming intrastrand dinucleotide DNA adducts. Despite their common use, they are highly toxic and approximately half of patients have tumors that are either intrinsically resistant, or that develop resistance. Studies suggest that this resistance is mediated by variations in DNA repair levels or net drug influx. We aimed to better define the roles of nucleotide excision repair and DNA damage formation in platinum resistance by profiling DNA damage levels and repair efficiency in a panel of seven oxaliplatin-sensitive and three oxaliplatin-resistant colorectal cancer cell lines. We assayed repair indirectly as toxicity, and directly measured bulky adduct formation and removal from the genome by slot blot, repair capacity by excision assay, and mapped repair events genome-wide at single nucleotide resolution using XR-Seq. Using this comprehensive approach of combining novel methods and in some cases using proxies for oxaliplatin-DNA damage, we found no significant difference in repair efficiency that could explain the relative sensitivity and resistance of our cell lines. In contrast, the overall levels of oxaliplatin-DNA damage were significantly lower in resistant cells, indicating that decreased formation of damage, rather than increased repair of that damage, is a major determinant of oxaliplatin resistance. Analysis of gene expression using our XR-seq data showed upregulation of membrane transport pathways in resistant cells, and these pathways may contribute to resistance. Additional research is needed to characterize factors mitigating cellular DNA damage formation by platinum compounds.

overall_design: We applied XR-seq on 10 colorectal cancer cell lines obtained from ATCC (Rko, Ls1034, Dld1, Ls180, Colo205) and from the UNC Tissue Culture Facility (Colo320, Hct116, Ht29, Sw480, Ls174t). For oxaliplatin treatments, cells were plated into R-150 plates and grown to about 90 percent confluence.  200μM oxaliplatin was added to each plate and cells were incubated at 32 degrees celcius for 2 hours.  Plates were then placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, and resuspended in 2mL of lysis buffer.  Samples were immunoprecipitated with anti-XPG antibody, and then ligated to adapters and processed for sequencing (XR-seq).

first: Christopher

last: Selby

first: Yanyan

last: Yang

first: David

last: Hsu

first: Aziz

last: Sancar


title: Quantitative Analysis of Wild Type and CISH-/- induced pluripotent stem cell derived NK cells (iPSC-NK) Transcriptomes

status: Public on May 09 2020

city: La Jolla

first: Huang

last: Zhu

address: 2880 Torrey Pines Scenic Dr.

department: Medicine

institute: University of California-San Diego

summary: We developed human CISH-knockout (CISH-/-) NK cells using an induced pluripotent stem cell-derived NK cell (iPSC-NK cell) platform. And compare transcriptomes of CISH-/- iPSC NK cells with wild type iPSC NK cells using RNA seq. RNA seq data suggested that genes involved in the JAK-STAT signaling pathway and lymphocyte activations were significantly activated in CISH-/- iPSC NK cells.

overall_design: mRNA profiles of wild type and CISH knockout iPSC NK cells were generated by deep sequencing, in dulpicate, using Illumina HiSeq 2000.

first: Dan

last: Kaufman


city: Boston

first: Vanessa

last: Mitsialis

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: This scRNA-seq dataset of five human subjects with ulcerative colitis (derived from colonic lamina propria samples), was analyzed and published as part of a larger manuscript (Mitsialis, V et al, "“Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease” in Gastroenterology), which reported immune signatures of blood and intestinal tissue differentiating ulcerative colitis from Crohn's disease from non-IBD human subjects using mass cytometry as well as scRNA-seq.

overall_design:
scRNA-seq was performed on the lamina propria fraction of colonic intestinal tissue (obtained from diagnostic colonoscopy) of five human subjects with active ulcerative colitis. These samples were obtained during colonoscopy, cryopreserved according to the methods outlined in the aforementioned manuscript, thawed and processed for scRNA-seq. Detailed information regarding clinical metadata for each subject can be found in the supplementary files of the manuscript.

Please note that raw data are not provided as they are derived from human subjects.

first: Sarah

last: Wall

first: Peng

last: Liu

first: Jose

last: Ordovas-Montanes

first: Tamar

last: Parmet

first: Marko

last: Vukovic

first: Dennis

last: Spencer

first: Michael

last: Field

first: Collin

last: McCourt

first: Jessica

last: Toothaker

first: Athos

last: Bousvaros

first: Alex

middle: K

last: Shalek

first: Leslie

last: Kean

first: Scott

last: Snapper

first: Liza

last: Konnikova


title: Selective Mediator-dependence of cell type-specifying transcription [4C-seq]

first: Georg

middle: E

last: Winter

overall_design: 4C-seq after 2h MED14-dTAG degradation by 500nM dTAG7 in KBM7 cells.

first: Martin

last: Jaeger

first: Sebastian

last: Mackowiak

first: Denes

last: Hnisz


title: Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma (RNA-Seq Neutrophils)

status: Public on May 08 2020

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

summary:
Purpose: we aimed at providing the phenotypic profile of G-MDSCs based on their prognostic significance in MM, immunosuppressive potential, and molecular program.
Methods and results: The pre-established phenotype of G-MDSCs was evaluated in bone marrow samples from controls and MM patients using multidimensional flow cytometry and, surprisingly, we found that CD11b+CD14-CD15+CD33+HLADR- cells overlapped with common eosinophils and neutrophils, which were not expanded in MM patients. Thus, we relied on automated clustering to unbiasedly identify all granulocytic subsets in the tumor microenvironment: basophils, eosinophils, immature, intermediate and mature neutrophils. In a series of 267 newly-diagnosed MM patients (GEM2012MENOS65 trial), only the frequency of mature neutrophils at diagnosis was significantly associated with patients’ outcome, and a high mature-neutrophils/T-cell ratio resulted in inferior progression-free survival (P<.001). Upon FACSorting of each neutrophil subset, T cell proliferation decreased in presence of mature neutrophils (0.5-fold; P=.016) and the cytotoxic potential of T cells engaged by a BCMAxCD3 bispecific antibody increased notably with the depletion of mature neutrophils (4-fold; P=.0007). Most interestingly, RNAseq of the three subsets revealed that G-MDSCs-related genes were specifically upregulated in mature neutrophils from MM patients vs controls due to differential chromatin accessibility.
Conclusion: Taken together, we established a correlation between the clinical significance, immunosuppressive potential and transcriptional network of well-defined neutrophil subsets, providing for the first time, a set of optimal markers (CD11b/CD13/CD16) for accurate monitoring of G-MDCSs in MM.

overall_design: Various neutrophil subsets were isolated from total BM samples of HA (N = 8) and MM patients (N = 8) and bulk RNAseq was obtained using a protocol adapted from single-cell massively parallel single-cell RNA-sequencing

first: Cristina

last: Perez

first: Aintzane

last: Zabaleta

first: Noemi

last: Puig

first: Maria-Teresa

last: Cedena

first: Ibai

last: Goicoechea

first: Daniel

last: Alameda

first: Edurne

last: San José-Eneriz

first: Juana

last: Merino

first: Paula

last: Rodríguez-Otero

first: Catarina

last: Maia

first: Diego

last: Alignani

first: Patricia

last: Maiso

first: Irene

last: Manrique

first: David

last: Lara-Astiaso

first: Amaia

last: Vilas-Zornoza

first: Sarai

last: Sarvide

first: Caterina

last: Riillo

first: Marco

last: Rossi

first: Laura

last: Rosiñol

first: Albert

last: Oriol

first: María-Jesús

last: Blanchard

first: Rafael

last: Rios

first: Anna

last: Sureda

first: Jesus

last: Martin

last: Martinez

first: Joan

last: Bargay

first: Javier

last: de la Rubia

first: Miguel-Teodoro

last: Hernandez

first: Joaquin

last: Martinez-Lopez

first: Alberto

last: Orfao

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Maria-Victoria

last: Mateos

first: Juan-José

last: Lahuerta

last: Blade

first: Jesús

last: San-Miguel

first: Bruno

last: Paiva


title: ZBED2 is an antagonist of Interferon Regulatory Factor 1 and modifies cell identity in pancreatic cancer (ChIP-seq)

city: Cold Spring Harbor

first: Tim

middle: D D

last: Somerville

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory

summary: Lineage plasticity is a prominent feature of pancreatic ductal adenocarcinoma (PDA) cells, which can occur via deregulation of lineage-specifying transcription factors. Here, we show that the zinc finger protein ZBED2 is aberrantly expressed in PDA and regulates tumor cell identity in this disease. Unexpectedly, our epigenomic experiments reveal that ZBED2 is a sequence-specific transcriptional repressor of interferon-stimulated genes, which occurs through antagonism of Interferon Regulatory Factor 1 (IRF1)-mediated transcriptional activation at co-occupied promoter elements. Consequently, ZBED2 attenuates the transcriptional output and growth arrest phenotypes downstream of interferon signaling in multiple PDA cell line models. We also found that ZBED2 is preferentially expressed in the squamous molecular subtype of human PDA, in association with inferior patient survival outcomes. Consistent with this observation, we show that ZBED2 can repress the pancreatic progenitor transcriptional program, enhance motility, and promote invasion in PDA cells. Collectively, our findings suggest that high ZBED2 expression is acquired during PDA progression to suppress the interferon response pathway and to promote lineage plasticity in this disease.

overall_design: FLAG-ZBED2 ChIP-seq in AsPC1 and SUIT2 cells was performed in FLAG-ZBED2 expressing cells with input genomic DNA as control. IRF1 ChIP-seq was performed using antibody recognizing endogenous protein with input genomic DNA following 12 hours stimulation with IFN-gamma or control and following transduction of empty vector or ZBED2 cDNA.

first: Christopher

last: Vakoc


title: Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma (RNA-Seq Epigenetic treatments)

first: Cirino

last: Botta

overall_design: Various neutrophil subsets were isolated from total BM saples from MM patients (N = 3) and bulk RNAseq was obtained using a protocol adapted from single-cell massively parallel single-cell RNA-sequencing

first: Cristina

last: Perez

first: Aintzane

last: Zabaleta

first: Noemi

last: Puig

first: Maria-Teresa

last: Cedena

first: Ibai

last: Goicoechea

first: Daniel

last: Alameda

first: Edurne

last: San José-Eneriz

first: Juana

last: Merino

first: Paula

last: Rodríguez-Otero

first: Catarina

last: Maia

first: Diego

last: Alignani

first: Patricia

last: Maiso

first: Irene

last: Manrique

first: David

last: Lara-Astiaso

first: Amaia

last: Vilas-Zornoza

first: Sarai

last: Sarvide

first: Caterina

last: Riillo

first: Marco

last: Rossi

first: Laura

last: Rosiñol

first: Albert

last: Oriol

first: María-Jesús

last: Blanchard

last: Rios

last: Sureda


title: Basal gene expression in Daxx deficient murine pancreas

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: We conducted basal gene expression analysis from total pancreas isolated from six week old mice

overall_design: RNA sequencing analysis was conducted in 4 (2 female and 2 male) mice per genotype

first: Amanda

last: Wasylishen

first: Guillermina

last: Lozano


title: EZH2 mutations reprogram the immune response to yield a pre-malignant lymphoma niche [Single cell RNA-Seq (10X Genomics)]

first: Cem

last: Meydan

overall_design: Six samples total: germinal center and post-germinal center B-cells R26-stop-YFPfl/wt;Ezh2(Y641F)fl/wt;Cγ1-cre (three biological replicates); germinal center and post-germinal center B-cells R26-stop-YFPfl/wt;Cγ1-cre (three biological replicates) of 10 weeks-old female mice immunized with SRBC and euthanized 8 days post-immunization

first: Wendy

last: Béguelin

first: Matt

last: Teater

first: Kenneth

last: Hoehn

first: Alexey

last: Soshnev

first: Jude

last: Phillip

first: Leandro

last: Venturutti

first: María

middle: T

last: Calvo-Fernández

first: Hao

last: Shen

first: Jeannie

last: Camarillo

first: Neil

middle: L

last: Kelleher

first: Christopher

last: Mason

first: Olivier

last: Elemento

first: C

last: Allis

first: Steven

middle: H

last: Kleinstein

first: Ari

last: Melnick


title: Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma (ATAC-Seq Neutrophils)

first: Cirino

last: Botta

overall_design: Approximately 20,000 cells of various neutrophils subsets were FACSorted from total BM samples of HA (N = 3) or MM patients (N = 3) for ATACseq analysis

first: Cristina

last: Perez

first: Aintzane

last: Zabaleta

first: Noemi

last: Puig

first: Maria-Teresa

last: Cedena

first: Ibai

last: Goicoechea

first: Daniel

last: Alameda

first: Edurne

last: San José-Eneriz

first: Juana

last: Merino

first: Paula

last: Rodríguez-Otero

first: Catarina

last: Maia

first: Diego

last: Alignani

first: Patricia

last: Maiso

first: Irene

last: Manrique

first: David

last: Lara-Astiaso

first: Amaia

last: Vilas-Zornoza

first: Sarai

last: Sarvide

first: Caterina

last: Riillo

first: Marco

last: Rossi

first: Laura

last: Rosiñol

first: Albert

last: Oriol

first: María-Jesús

last: Blanchard

first: Rafael

last: Rios

first: Anna

last: Sureda

first: Jesus

last: Martin

last: Martinez

first: Joan

last: Bargay

first: Javier

last: de la Rubia

first: Miguel-Teodoro

last: Hernandez

first: Joaquin

last: Martinez-Lopez

first: Alberto

last: Orfao

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Maria-Victoria

last: Mateos

first: Juan-José

last: Lahuerta

last: Blade

first: Jesús

last: San-Miguel

first: Bruno

last: Paiva


title: Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection (microarray)

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: The phenotypic and functional dichotomy between IRF8+ type 1 and IRF4+ type 2 conventional dendritic cells (cDC1-cDC2) is well accepted; it is unknown how robust this dichotomy is under inflammatory conditions, when additionally monocyte-derived cells (MCs) become competent antigen presenting cells (APC). Using single-cell technologies in models of respiratory viral infection, we found that lung cDC2s acquired expression of Fc receptor CD64 shared with MCs, and of IRF8 shared with cDC1s. These inflammatory (Inf-)cDC2s were superior in inducing CD4+ T helper (Th) cell polarization while simultaneously presenting antigen to CD8+ T cells. When carefully separated from inf-cDC2s, MCs lacked APC function. Inf-cDC2 matured in response to cell-intrinsic toll-like receptor and type 1 interferon receptor signaling, upregulated an IRF8-dependent maturation module and acquired antigens via convalescent serum and Fc receptors. Since hybrid inf-cDC2s are easily confused with monocyte-derived cells, their existence could explain why APC functions have been attributed to MCs.

overall_design:
Microarray = Lung cDC1, cDC2, monocyte-derived cells and inf-cDC2 in mock and virus (flu) condition.
Single cell RNA Seq = Lung CD45+MHCII+CD11c+ cells derived from PVM infected WT:Irf8 fl/fl Itgax-cre chimeric mice.

first: Cedric

last: Bosteels

first: Katrijn

last: Neyt

first: Manon

last: Vanheerswynghels

first: Mary

middle: J

last: van Helden

first: Dorine

last: Sichien

first: Nincy

last: Debeuf

first: Sofie

last: De Prijck

first: Victor

first: Niels

last: Vandamme

first: Yvan

last: Saeys

first: Els

last: Louagie

last: Lesage

first: David

last: Williams

first: Shiau-Choot

last: Tang

first: Johannes

middle: U

last: Mayer

first: Franca

last: Ronchese

first: Charlotte

last: Scott

first: Hamida

last: Hammad

first: Martin

last: Guilliams

first: Bart

middle: N

last: Lambrecht


title: Nuclear Poly(A)-binding Protein 1-like (PABPN1L) Mediates Cytoplasmic mRNA Decay As a Placeholder during Maternal-to-zygotic Transition

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

summary: Maternal mRNA degradation is a critical event of maternal-to-zygotic transition (MZT) that determines the developmental potential of early embryos. Nuclear Poly(A)-binding proteins (PABPNs) are extensively involved in mRNA post-transcriptional regulations, but their functions in mammalian MZT has not been investigated. In this study, we identified a novel maternal-effect factor PABPN1-like (PABPN1L), rather than its ubiquitously expressed homolog PABPN1, as an RNA-binding adapter of the mammalian MZT licensing factor BTG4 which mediates maternal mRNAs clearance. Female Pabpn1l null mice produced morphologically normal oocytes but were infertile owing to early developmental arrest of the resultant embryos at the 1-to-2-cell stages without undergoing ZGA. Deletion of Pabpn1l impairs the deadenylation and degradation of a subset of BTG4-targeted maternal mRNAs during MZT. In addition to recruiting BTG4 to the mRNA 3ʹ-poly(A) tails, PABPN1L is also required for BTG4 protein accumulation in maturing oocytes by protecting BTG4 from SCF-βTrCP1 E3 ubiquitin ligase-mediated polyubiquitination and degradation. This study highlights a noncanonical cytoplasmic function of nuclear poly(A)-binding proteins mRNA turnover as well as its physiological importance during MZT.

overall_design: GV oocytes, zygotes and 2-cell embryos of WT and Pabpn1l knockout for duplicates are performed RNA sequencing.

first: Yezhang

last: Zhu


title: ZBED2 is an antagonist of Interferon Regulatory Factor 1 and modifies cell identity in pancreatic cancer (RNA-seq)

first: Tim

last: Somerville

overall_design: For RNA-seq performed following ZBED2 or IRF1 knock out in PDA cells, two independent sgRNAs targeting the DNA binding domain of each factor were used a technical repeats. For RNA-seq performed following IRF1 cDNA expression in AsPC1 cells, two biological repeats were analyzed. For RNA-seq performed following ZBED2 cDNA expression in 15 human PDA cell lines, 1 technical repeat for each cell line was used. For RNA-seq performed following treatment of AsPC1-empty and AsPC1-ZBED2 cells with IFN-beta, IFN-gamma or control, two biological repeats were used for each condition.

middle: D

first: Christopher

middle: R

last: Vakoc


title: Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome

status: Public on May 07 2020

city: Heidelberg

first: Julian

last: Gutekunst

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center

type: Methylation profiling by genome tiling array

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. Using ATAC-see/-seq and Infinium MethylationEPIC BeadChip-mediated DNA methylation profiling, we demonstrate that dermal fibroblasts from HGPS patients exhibit both chromatin accessibility and DNA methylation changes that are enriched in LADs. Importantly, we further show that these epigenetic alterations are associated with HGPS-specific gene expression changes. Together, our results establish a central involvement of LADs in the epigenetic deregulation of HGPS and provide novel insight into the molecular changes associated with the disease.

overall_design: Bisulphite converted DNA from the 15 samples were hybridized to the Illumina Infinium Human MethylationEPIC BeadChip

first: Florian

last: Köhler

first: Felix

last: Bormann

first: Günter

last: Raddatz

first: Tanja

last: Musch

first: Frank

last: Lyko

first: Manuel

last: Rodriguez-Paredes


title: Temporal dissection of breast cancer brain metastases

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

summary: The goal of this study was to identify temporal changes to breast cancer cells as they adapt to the brain metastatic microenvironment. MDA-MB-231-tdTomato human breast cancer cells were injected into the carotid artery of Rag1-/- mice and dissected at 7 or 40 days post injection for RNA-sequencing.

overall_design: 3 samples were analyzed at 7 days post injection, and 9 samples were analyzed at 40 days post injection

first: Erin

last: Howe


title: Benchmarking of viruses detection from single-cell RNA sequencing data

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We developed a new computational pipeline called Viral-Track that can detect the viruses in a single-cell RNA sequencing sample. To validate this tool, we benchmarked it on several mouse models of infection, including lymph node infection by the Lymphocytic choriomeningitis virus (LCMV) and the Vesicular Stomatitis Virus (VSV). We also used a GFP expressing LCMV strain to infect a mouse and then sequenced the infected (GFP+) cells.

overall_design: Tissue from LCMV or VSV infected mouse are collected 24h (Lymph Node) or 72h (Spleen) after infection. For spleen samples, an LCMV-GFP virus is used and GFP+ cells are sorted sequenced. For Lymph Node samples, Cd45+ non B/T cells are sorted and sequenced

first: Pierre

last: Bost

first: Amir

last: Giladi

first: Yang

last: Liu

first: Yanis

last: Bendjelal

first: Gang

last: Xu

first: Eyal

last: David

first: Ronnie

last: Blecher-Gonen

first: Merav

last: Cohen

first: Aleksandra

last: Deczkowska

first: Chiara

last: Medaglia

first: Hanjie

last: Li

first: Shuye

first: Benno

last: Schwikowski

first: Zheng


title: Daxx-dependent chromatin accessibility changes in a mouse model of chronic pancreastitis

first: Yuan

last: Qi

summary: Chromatin accessibility was evaluated by ATAC-seq of mouse pancreas 5 days following chronic caerulein-induced pancreatitis. Four different genotypes were evaluated: i) wild-type, ii) Men1fl/flPdx1-CreTg, iii) Daxxfl/flPdx1-CreTg iv) Daxxfl/flMen1fl/flPdx1-CreTg.

overall_design: 4 independent biological replicates for each genotype were sequenced (8 samples total)

first: Amanda

last: Wasylishen

first: Guillermina

last: Lozano


title: Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection (scRNA-Seq)

first: Liesbet

last: Martens

first: Cedric

last: Bosteels

first: Katrijn

last: Neyt

first: Manon

last: Vanheerswynghels

first: Mary

last: van Helden

first: Dorine

last: Sichien

first: Nincy

last: Debeuf

first: Sofie

last: De Prijck

first: Victor

first: Niels

last: Vandamme

first: Yvan

last: Saeys

first: Els

last: Louagie

last: Lesage

first: David

last: Williams

first: Shiau-Choot

last: Tang

first: Johannes

last: Mayer

first: Franca

last: Ronchese

first: Charlotte

last: Scott

first: Hamida

last: Hammad

first: Martin

last: Guilliams

first: Bart

last: Lambrecht


title: PhosphoRiboTrap and Single nucleus sequecing data of MCH neurons

city: Cologne

first: Hong

last: Jiang

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

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

overall_design: Refer to individual Series


title: Single nucleus sequecing data of MCH neurons [scRNA-seq]

summary: In order to understand heterogeneity of MCH neurons, by using MCH-Cre dependent ZsGreen (fl/fl) reporter mice, we isolated nuclear from 16 hypothalami of 16 mice at the age of 16-18weeks. Through flow cytometry, we were able to distinguish ZsGreen positive nuclei, and collected puried MCH nuclei in suspension. Those nuclei suspension were subjected to single cell sequence by 10x™ GemCode™ Technology for further single nuleus mRNA analysis and unravel subclusters of MCH neurons

overall_design: 16 genotype with MCH-Cre;ZsGreen positive mice with mixed gender at the age of 16-18weeks mice were subjected to acute decapitation. Hypothalami from each mouse were dissected by using brain matrix with blades. Collected hypothalami from each brain were fast frozen in liquid nitrogen and subjected by homogenetization and single nucleus extration. Fresh single nuclei suspension were subjected to flow cytometry and isolated ZsGreen positive nuclei were collected and polled followed by single nucleus sequecing by 10x™ GemCode™ Technology. Further analysis allowed us to get subcluster of MCH neurons from 1266 cells in the end.

first: Jens

last: Brüning


title: ALS/FTD-associated protein FUS induces mitochondrial dysfunction by preferentially sequestering respiratory chain complex mRNAs

city: New York

first: Yueh-Lin

last: Tsai

address: 1212 Amsterdam Ave.

institute: Columbia University

summary: We report polyadenylated transcripts associated with R521C mutant FUS in the insoluble fraction.

overall_design: FLAG-tagged R521C mutant FUS was transiently expressed in U87-MG glioma cells for 36 hours followed by NP-40 lysis. The NP-40 insoluble fraction was extracted with 0.1M urea and the supernatant was used for RNA-IP using FLAG antibody. RNAs co-IPed with FLAG-tagged mutant FUS were subjected to 3' region extraction and deep sequencing (3'READS).

first: Tristan

last: Coady

first: Lei

last: Lu

first: Dinghai

last: Zheng

first: Isabel

last: Alland

first: Bin

last: Tian

first: Neil

last: Shneider

first: James

last: Manley


title: PhosphoRiboTrap sequencing data of chemogenetic MCH neuron activation

summary: We report phosphoRiboTrap experiments result which aim to explore the nature of the cell types in the Median Eminence (ME) regulated as a consequene of chemogenetic MCH neuron activation. Control and MCH-hM3Dq mice were 12 hrs-fasted and i.p. injected with CNO (3 mg/kg), Arcuate (ARC) and median eminence expat were extracted for preciptation of S6-marked ribosomes from both groups of mice. Extracted RNA from Immunoprecipitated ribosomes (IP) and total tissue (ARC+ME) from each mouse were subjected to deep mRNA sequencing. By analyzing the overlap of genes enriched in the IP/Input of MCH neuron activated mice with previously identified cell types using single cell mRNA sequencing of cells in the mediobasal hypothalamus (Campbell et al., 2017), we identified gene clusters which were activated upon MCH neuron activation.

overall_design: 7 control and 5 MCH-hM3Dq mice were subjected to 12 hrs and 1 hr CNO injection. Mice were acutely decapitated. ARC and ME from hypothalamus tissue were cut with brain matrix and collected on dry ice and frozen in liquid nitrogen and stored in -80 freezers. All the samples were subjected to PhosphoRiboTRAP protocol (see details in protocol part) and both IP and Input were harvested and concentration were measured by Qbid machine. Those samples were deep mRNA sequenced for further analysis.


title: OppZ target identification

city: Jena

first: Mona

last: Hoyos

address: Winzerlaer Straße 2

department: Institute for General Microbiology

institute: FSU Jena

summary: In this study we determined the target spectrum of the Vibrio cholerae OppZ sRNA via pulse-expression followed by RNA-sequencing.

overall_design: V. cholerae wild-type cells carrying pBAD1K-ctrl (empty control vector) or pBAD1K-oppZ (inducible sRNA expression vector) were grown to exponential phase (OD600=0.5). Expression of OppZ was induced by L-arabinose and total RNA samples were collected 15 minutes after induction. The experiment was performed with three independent biological replicates.

first: Michaela

last: Huber

first: Konrad

last: Förstner

first: Kai

last: Papenfort


title: Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma (RNA-Seq Neutrophils TGFbeta)

first: Cirino

last: Botta

overall_design: We exposed whole PB from HA (N = 3) to 1ng/mL TGF-β and performed RNAseq analysis

first: Cristina

last: Perez

first: Aintzane

last: Zabaleta

first: Noemi

last: Puig

first: Maria-Teresa

last: Cedena

first: Ibai

last: Goicoechea

first: Daniel

last: Alameda

first: Edurne

last: San José-Eneriz

first: Juana

last: Merino

first: Paula

last: Rodríguez-Otero

first: Catarina

last: Maia

first: Diego

last: Alignani

first: Patricia

last: Maiso

first: Irene

last: Manrique

first: David

last: Lara-Astiaso

first: Amaia

last: Vilas-Zornoza

first: Sarai

last: Sarvide

first: Caterina

last: Riillo

first: Marco

last: Rossi

first: Laura

last: Rosiñol

first: Albert

last: Oriol

first: María-Jesús

last: Blanchard

first: Rafael

last: Rios

first: Anna

last: Sureda

first: Jesus

last: Martin

last: Martinez

first: Joan

last: Bargay

first: Javier

last: de la Rubia

first: Miguel-Teodoro

last: Hernandez

first: Joaquin

last: Martinez-Lopez

first: Alberto

last: Orfao

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Maria-Victoria

last: Mateos

first: Juan-José

last: Lahuerta

last: Blade

first: Jesús

last: San-Miguel

first: Bruno

last: Paiva


title: Expression data from control-knockout (CTR-KO) and MIF-KO human multiple myeloma (MM) cells

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

summary:
Macophage migration inhibitor (MIF) is important for MM resistance to proteasome inhibitors. To determine what signalling pathways are affected by MIF in MM cells, we established MIF-KO MM.1S and ARP-1 MM cell lines. Total RNAs of 2 x 106 CTR-KO and MIF-KO MM cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for RNA-seq followed by data analysis.
We use microarray data to determine differential expression of genes in MIF-KO and CTR-KO MM cells.

overall_design: Examination of gene-profiling data in CTR-KO and MIF-KO MM cells.


title: Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (ATAC-Seq)

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

institute: Stanford University

summary: To better understand the fundamental molecular mechanisms that contribute to complex human diseases such as coronary artery disease (CAD), we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells. To this end, we used a pooling approach to map quantitative trait locus associations (QTLs) for TCF21 binding (ChIPseq), chromatin accessibility (ATACseq), and chromosomal looping (HiC). We find significant overlap of these QTLs, and several analyses indicate their relationship to smooth muscle specific genes, the binding of smooth muscle transcription factors, and enrichment in CAD-associated loci. These QTLs are extensively validated and allele-specific chromatin looping at the FN1 disease locus is shown to be mediated by activation of the CAD-associated TGFb1 pathway. In sum, these results uncover thousands of loci affecting cis-regulation in a key cell type for CAD, including many that may contribute to CAD risk.

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown in serum and 71 lines were pooled. Approximately 50k cells per sample were freshly prepared for nuclei extraction.

first: Quanyi

last: Zhao

first: Michael

last: Dacre

first: Trieu

last: Nguyen

first: Milos

last: Pjanic

first: Boxiang

last: Liu

first: Dharini

last: Iyer

first: PoSheng

middle: P

last: Cheng

first: Robert

last: Wirka

first: Juyong

middle: B

last: Kim

first: Hunter

last: Fraser


title: Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (Hi-C)

summary: To better understand the fundamental molecular mechanisms that contribute to complex human diseases such as coronary artery disease (CAD), we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells. To this end, we used a pooling approach to map quantitative trait locus associations (QTLs) for TCF21 binding (ChIPseq), chromatin accessibility (ATACseq), and chromosomal looping (HiC). We find significant overlap of these QTLs, and several analyses indicate their relationship to smooth muscle specific genes, the binding of smooth muscle transcription factors, and enrichment in CAD-associated loci. These QTLs are extensively validated and allele-specific chromatin  looping at the FN1 disease locus is shown to be mediated by activation of the CAD-associated TGFb1 pathway. In sum, these results uncover thousands of loci affecting cis-regulation in a key cell type for CAD, including many that may contribute to CAD risk.

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown in serum.Approximately 97.5M HCASMC, 1.5M from 65 different cell lines were pooled and fixed with 1 % formaldehyde and quenched by glycine.


title: Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci

overall_design: 72 Human coronary artery smooth muscle cells (HCASMC) grown in serum. Approximately 1M cells per sample were freshly prepared for nuclei extraction.


title: Aberrant phase separation of transcription factors in human developmental disorders

city: Berlin

first: Denes

last: Hnisz

state: Berlin

address: Ihnestraße 63-73

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary:
Components of the transcription machinery can undergo liquid-liquid phase separation, but the functional importance of phase-separated condensates in transcriptional control is not well understood. Here we report that disease-causing mutations in several transcription factors (TFs) alter the phase separation capacity of those TFs. We first demonstrate that the Hoxd13 TF, and its intrinsically disordered N-terminus form phase-separated condensates. Expansions of a polyalanine repeat, which cause hereditary synpolydactyly in humans, facilitate phase separation of Hoxd13, and alter the transcriptional program of several cell types in a cell-specific manner in vivo.  Disease-associated expansions of aminoacid repeats in intrinsically disordered regions of other TFs were similarly found to alter phase separation. These results suggest that aberrant phase separation of transcriptional regulators may underlie a spectrum of human pathologies.

The paper is available at https://doi.org/10.1016/j.cell.2020.04.018

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design:
Single-cell RNAseq data was performed on mouse limb buds from embyros at developmental stage E12.5 from a WT and a SPDH mutant condition. Samples from each condition were sequenced with the 10X Genomics singlecell RNA sequencing system. Further, we use H3K27ac and H3K27me3 ChIPseq to see if transcriptional changes are reflected in chromosome structure.
Reanalysis of Samples GSM3568504 and GSM3568505 (processed data file:  H3K27Ac-L-E125-Wt-Mm_merged_8_peaks.bed ).
Third-party reanalysis of Samples GSM2151014 and GSM2151018 (processed data file:  hoxd13_peaks_pv1e10_e11_5.bed).  Data processing steps same as those for the other ChIP-seq samples in GSE128818.

first: Sebastian

last: Mackowiak

first: Shaon

last: Basu

first: Vahid

last: Asimi

first: Stefanie

last: Grosswendt

first: Abhishek

last: Sampath Kumar

first: Dora

last: Knezevic

first: Daniel

middle: M

last: Ibrahim

first: Henri

last: Niskanen

first: Salaheddine

last: Ali

first: Stefan

last: Mundlos

first: Alexander

last: Meissner


title: Gene expression of Lymphoblastoid Cell Lines–LCLs from Depressed Patients after in-vitro treatment with citalopram–CTP

city: Bonn

first: Abdul Karim

last: Barakat

address: Kurt-Georg-Kiesinger-Allee 3

institute: Federal Institute for Drugs and Medical Devices

summary: We used whole gene gene expression profiling to identify potential gene expression biomarkers associated for the treatment individualization of unipolar depression.

overall_design: Gene expression was measured after 24 and 48 hours of in-vitro treatment with 3 µM CTP in n=17 LCLs derived from depressed patients with documented clinical treatment outcome to SSRIs.

first: Abdul-Karim

first: Catharina

last: Scholl

first: Michael

last: Steffens

first: Kerstin

last: Brandenburg

first: Marcus

last: Ising

first: Susanne

last: Lucae

first: Florian

last: Holsboer

first: Gonzalo

last: Laje

first: Ganna

middle: V

last: Kalayda

first: Ulrich

last: Jaehde

first: Julia

last: Stingl


title: ATR inhibition potentiates ionizing radiation-induced interferon response via cytosolic nucleic acid-sensing pathways

first: Junjie

last: Chen

address: 6565 MD Anderson Blvd

department: ERO

institute: UT MD Anderson Cancer Center

summary: Mechanistic understanding of how ionizing radiation induces type I interferon signaling and how to amplify this signaling module should help to maximize the efficacy of radiotherapy. In the current study, we report that inhibitors of the DNA damage response kinase ATR can significantly potentiate ionizing radiation-induced innate immune responses. Using a series of mammalian knockout cell lines, we demonstrate that, surprisingly, both the cGAS/STING-dependent DNA-sensing pathway and the MAVS-dependent RNA-sensing pathway are responsible for type I interferon signaling induced by ionizing radiation in the presence or absence of ATR inhibitors. The relative contributions of these two pathways in type I interferon signaling depend on cell type and/or genetic background. We propose that DNA damage-elicited double-strand DNA breaks releases DNA fragments, which may either activate the cGAS/STING-dependent pathway or-especially in the case of AT-rich DNA sequences-be transcribed and initiate MAVS-dependent RNA sensing and signaling. Together, our results suggest the involvement of two distinct pathways in type I interferon signaling upon DNA damage. Moreover, radiation plus ATR inhibition may be a promising new combination therapy against cancer.

overall_design: Examination of total RNA profiles with DMSO, AZD6738, IR, and AZD6738+IR treatments in MCF10A cells.

first: Xu

last: Feng

first: Chunchao

last: Zhang


title: Peripherally-induced brain tissue resident memory CD8 T cells  [RNA-seq]

city: Iowa City

first: Isaac

last: Jensen

state: IA

institute: University of Iowa

summary: OT-I CD8 T cell transcriptome of cells isolated from Spleen, IV+ brain, and IV- brain of DCLM immunized mice

overall_design: OT-I T cells were transferred into mice and DC(ova) primed and LM(ova) boosted. At a memory time point, OT-I cells (Thy1.1+, CD8+ and IV+ or IV-) were sorted from the Spleen, IV+ brain, or IV- brain in duplicate.  Sorted cells were used for RNAseq analysis

first: Stina

last: Urban

first: John

last: Harty


title: Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (ChIP-Seq)

first: Thomas

last: Quertermous

department: Medicine Cardiology

overall_design: Human coronary artery smooth muscle cells (HCASMC) grown in serum.Approximately 20M HCASMC, 0.3M from 65 different cell lines were pooled and fixed with 1 % formaldehyde and quenched by glycine.

first: Quanyi

last: Zhao

last: Dacre

first: Trieu

last: Nguyen

first: Milos

last: Pjanic

first: Boxiang

last: Liu

first: Dharini

last: Iyer

first: PoSheng

last: Cheng

first: Robert

last: Wirka

first: Juyong

last: Kim

first: Hunter

last: Fraser


title: RNA sequencing of WNK1 and SLUG co-overexpressed LNCaP cells

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Human prostate cancer LNCaP cells Overexpressed with rat WNK 1 and human SLUG cDNA

overall_design: To understand the role of co-overexpression of SLUG and WNK1 in Human prostate cancer cells above experiments were performed. RNA sequencing were were analysed by Partek  flow

first: Goutam

last: Chakraborty

first: Philip

last: Kantoff


title: Combined loss of BRCA2 and RB1 leads to aggressive prostate cancer mediated by WNK1


title: RNA sequencing of BRCA2 and/or RB1 knockout LNCaP cells

summary: Human prostate cancer LNCaP cells infected with Lentivirus carried huamn BRCA2 gRNA alone or in combination with lentivirus carrying human RB1 shRNA. Infected cell were selcted by drug selection and the knockdown were confirm by westernblot or qPCR

overall_design: To understand the role of co-loss of BRCA2 and RB1 in Human prostate cancer cells. RNA sequencing were were analysed by Partek  flow


title: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in ARP-1 cells treated with DMSO and carfilzomib (Cfz)

first: Qiang

last: Wang

summary: The goals of NGS-derived retinal transcriptome profiling (RNA-seq) is to identify the signaling pathways in multiple myeloma (MM) cells affected by Cfz treatment. We treated ARP-1 MM cells with DMSO or 6nM Cfz for 16 hours (each group has 3 replicates) and extracted the total RNA using RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to BGI genomics for RNA-seq followed by data analysis.

overall_design: Examination of gene-profiling data in MM cells repsonse to control or Cfz treatment.


title: Differential Gene Expression Upon PFN1 Deletion

status: Public on May 06 2020

city: Gainesvile

first: Kristen

last: Skruber

state: Florida

address: 1333 Center Drive

institute: university of florida

summary: The actin binding protein profilin1 (PFN1) was deleted using CRISPR/Cas9 in Cath.a differentiated cells.

overall_design: CRISPR/Cas9 with guide RNAs targeting the gene for PFN1.

first: Eric

last: Vitriol


title: Altered regional progenitor dynamics in the neocortex of a BBSOA disease mouse model

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: The relationships between impaired cortical development and consequent malformations in neurodevelopmental disorders, as well as the genes implicated in these processes, are not fully elucidated to date. In this study, we report six novel cases of patients affected by BBSOAS (Boonstra-Bosch-Schaff Optic Atrophy Syndrome), a newly emerging rare neurodevelopmental disorder, caused by loss-of-function mutations of the transcriptional regulator NR2F1. Young patients with NR2F1 haploinsufficiency display mild to moderate intellectual disability and show reproducible polymicrogyria-like brain malformations in the parietal and occipital cortex. Using a recently established BBSOA mouse model, we found that Nr2f1 regionally controls long-term self-renewal of neural progenitor cells via modulation of cell cycle genes and key cortical development master genes, such as Pax6. In the human foetal cortex, distinct NR2F1 expression levels encompass gyri and sulci and correlate with local degrees of neurogenic activity. In addition, reduced NR2F1 levels in cerebral organoids affect neurogenesis and PAX6 expression. We propose NR2F1 as an area-specific regulator of mouse and human brain morphology and a novel causative gene of abnormal gyrification.

overall_design: Transcriptional profile of cortex in wt and Nr2f1 KO mice.

first: Francesco

last: Neri

first: Salvatore

last: Oliviero

first: Michele

last: Bertacchi

last: Studer


title: Zebrafish Retina thrb-/- RNA-seq

city: Saint Louis

first: Joseph

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Thyroid hormone (TH) signaling plays an important role in the regulation of long-wavelength vision in vertebrates. In the retina, thyroid hormone receptor β (thrb) is required for expression of long-wavelength-sensitive opsin (lws) in red cone photoreceptors; whereas in retinal pigment epithelium (RPE), TH regulates expression of a cytochrome P450 enzyme, Cyp27c1, that converts vitamin A1 into vitamin A2 to produce a red-shifted chromophore. To better understand how TH controls these processes, we analyzed the phenotype of zebrafish with mutations in the three known TH nuclear receptor transcription factors (thraa, thrab, and thrb). We found that no single TH nuclear receptor is required for TH-mediated induction of cyp27c1 but that deletion of all three (thraa-/-;thrab-/-;thrb-/-) completely abrogates its induction and the resulting conversion of A1- to A2-based retinaldehydes. In the retina, loss of thrb resulted in an absence of red cones at both larval and adult stages without disruption of the underlying cone mosaic. RNA-seq analysis revealed significant downregulation of only five genes in adult thrb-/- retina, of which three (lws1, lws2, and miR-726) occur in a single syntenic cluster. In the larval thrb-/- retina, retinal progenitors destined to become red cones were transfated to ultraviolet (UV) cone opsin (sws1)-expressing cells and cells resembling horizontal cells. Taken together, our findings demonstrate cooperative regulation of cyp27c1 by TH receptors and a requirement for thrb in red cone fate determination. Thus, TH signaling coordinately regulates both spectral sensitivity and sensory plasticity.

overall_design: 6-month-old WT and clutch-matched thrb stl628/stl628 zebrafish retina were isolated. Two retinas from a male and two retinas from a female zebrafish were combined to make one sample. Three WT and thrb stl628/stl628 samples were collected and RNA extracted.

first: L

middle: I

last: Volkov

first: J

last: Kim-Han

last: Saunders

first: D

last: Parichy

middle: C


title: ASEP: gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing

first: Chenyi

last: Xue

summary: Allele-specific expression (ASE) quantifies the relative expression of two alleles in a diploid individual, and such expression imbalance potentially contributes to phenotypic variation and disease pathophysiology among individuals. We developed ASEP, a method that is able to detect gene-level ASE under one condition, as well as, ASE difference between two conditions (e.g., pre- vs post-treatment) across individuals. Application of ASEP to human macrophage RNA-seq dataset has illustrated its ability to uncover ASE / differential ASE genes related to cardiometabolic traits.

overall_design: Human peripheral blood mononuclear cell (PBMC)-derived macrophages (HMDM) and M1-polarized HMDM were sequenced by Illumina HiSeq 2500 with poly-A selection

first: Hanrui

last: Zhang


title: SETD5-coordinated chromatin reprogramming regulates adaptive resistance to targeted pancreatic cancer therapy

city: stanford city

first: Or

last: Gozani

state: California

address: 371 Serra Mall, Room 208A Stanford, CA 94305-5020

department: Department of Biology

summary: Oncogenic KRAS signaling is a hallmark of pancreatic ductal adenocarcinoma (PDAC), a lethal malignancy with few treatment options. A major roadblock in deploying therapies targeting the KRAS-MAPK pathway is the rapid emergence of resistant cancer cells. However, molecular mechanisms underlying adaptive targeted therapy resistance in PDAC are poorly understood. Here we find SETD5 (SET domain containing 5) as a major epigenetic driver of PDAC resistance to MEK1/2 inhibition (MEKi). SETD5 is identified in a genetic screen of annotated methyltransferases that mediate MEKi toxicity in PDAC cells. SETD5 expression is induced upon PDAC cells and tumors acquring MEKi-resistance and SETD5 deletion restores vulnerability of refractory PDAC to MEKi therapy in mouse models and patient-derived xenografts (PDX). SETD5 lacks intrinsic histone methyltransferase activity and rather scaffolds a distinct corepressor complex that regulates HDAC3 and G9a catalytic behaviors to couple selective deacetylation with methylation of histone H3 at lysine 9 (H3K9). Gene silencing by the SETD5 complex regulates a network of known drug resistance pathways to reprogram cellular responses to MEKi, a resistance program disrupted by G9a and HDAC3 blockade. Combinatorial pharmacological targeting of MEK1/2, G9a, and HDAC3 results in sustained tumor growth inhibition in murine and human models of PDAC. Together, our work uncovers SETD5 as a master epigenetic regulator of acquired MAPK-pathway therapy resistance and suggests an efficacious clinical path for MEKi in PDAC.

overall_design: mRNA profiles of KPCR cells (n = 3) (sgControl + Trametinib 0.2µM, sgSETD5 + Trametinib 0.2µM, or DMSO + Trametinib 0.2µM, UNC0638 0.6 µM + RGFP966 0.6µM + Trametinib 0.2µM).

first: Ruitu

last: Lyu

first: Zhengtian


title: The RNA helicase DDX5 supports mitochondrial function in small cell lung cancer

city: West Lafayette

first: Elizabeth

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

summary: DDX5 is a founding member of the DEAD-box RNA helicase family, which are a group of enzymes that regulate ribonucleoprotein (RNP) formation and function in every aspect of RNA metabolism. Our lab previously found that DDX5 is involved in energy homeostasis, a process altered in many cancers. Small cell lung cancer (SCLC) is an understudied cancer type that lacks effective treatment. Therefore, we investigated the roles of DDX5 in SCLC. We show here that DDX5 is overexpressed in SCLC cell lines. Depletion of DDX5 results in reduced growth and mitochondrial dysfunction in the chemoresistant SCLC cell line H69AR. The latter is evidenced by downregulation of genes involved in oxidative phosphorylation and impaired oxygen consumption,. Interestingly, depletion of DDX5 specifically leads to reduction of intracellular succinate, a TCA intermediate that serves as a direct electron donor to mitochondrial complex II. Taken together, we propose that the oncogenic role of DDX5 is at least in part manifested through upregulation of respiration to support the energy demands of cancer cells. This also suggests that defects in RNP remodeling are connected to energy metabolism and carcinogenesis.

overall_design: Six samples

first: Zheng

last: Xing

first: Matthew

last: Russon

first: Sagar

last: Utturkar


title: NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure (RNA-seq)

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: There is growing evidence that paternal pre-conception cigarette smoke (CS) exposure is associated with increased risk of behavioral disorders and cancer in offspring. To characterize the effects of CS exposure on the sperm epigenome and offspring neurodevelopment, we investigated the impact of pre-conception paternal CS exposure on mouse sperm DNA methylation and gene expression in offspring.  We further investigated the role of oxidative stress on sperm epigenetic changes using a mouse model (Nrf-/-) with impaired antioxidant capacity. Lastly, we evaluated the capacity for sperm DNA methylation to recover following removal of CS for 1-5 spermatogenic cycles (28-171 days). We found that smoking significantly impacts sperm DNA methylation as well as DNA methylation and gene expression in offspring. These changes were largely recapitulated in Nrf-/- mice independent of smoke exposure. Recovery experiments indicated that about half of differentially methylated regions returned to normal within 28 days of removal from smoke, however additional recovery following longer periods was not observed. Thus, we present strong evidence that cigarette smoke exposure induces paternally mediated, heritable epigenetic changes. Parallel studies performed in Nrf-/- mice provide evidence for oxidative stress as the predominant underlying mechanism for smoke-induced epigenetic changes to sperm as well as changes in the offspring of smoke-exposed sires. Lastly, recovery experiments indicate that while many epigenetic changes are corrected following removal from smoke exposure, aberrant methylation persists at a significant number of regions even after five spermatogenic cycles

first: Patrick

last: Murphy

first: Kenneth

last: Aston


title: NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mitral valve leaflet response to ischemic mitral regurgitation: From gene expression to tissue remodeling

city: Austin

first: Michael

middle: S

last: Sacks

address: 201 East 24th St, Stop C0200

department: Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering

institute: The University of Texas at Austin

summary: Rationale: Ischemic mitral regurgitation (IMR) is frequently observed following myocardial infarction (MI) and is associated with higher mortality and poor clinical prognosis if left untreated. Accumulating evidence suggests that mitral valve (MV) leaflets actively remodel post-MI, yet the cellular mechanisms underlying these responses and how this affects tissue function remain largely unknown. Objective: We sought to elucidate MV remodeling post-MI at the tissue, cellular, and transcriptomic levels. Methods and Results: The mechanical behavior of ovine MV leaflets pre-MI and 8 weeks post-MI reveal a significant decrease in radial direction extensibility, which essentially eliminated the mechanical anisotropy typically observed in healthy MVs. Quantitative histology and ultrastructural assessment by transmission electron microscopy revealed altered leaflet composition and architecture at 8 weeks post-MI. Assessment of the MV interstitial cell (MVIC) nuclear aspect ratio, a metric of cellular deformation, revealed that MVICs were on average rounder following MI. RNA sequencing (RNA-seq) indicated that YAP-induced genes were elevated at 4 weeks post-MI and genes related to extracellular matrix organization were some of the most downregulated in sheep with IMR compared to sheep without IMR at 4 weeks post-MI. Additionally, RNA-seq revealed the possible recruitment of immune cells in this remodeling process due to the drastic elevation of CXCL9 and CLEC10A. Conclusions: This multiscale assessment revealed significant mechanical and microstructural changes due to MI. RNA-seq provided a baseline for global gene expression changes in response to MI with and without IMR and suggests YAP-induced mechanotransduction, altered expression of ECM-related genes, and recruitment of immune cells as mechanisms contributing to altered MV biomechanics post-MI. Conclusions: This multiscale assessment revealed significant mechanical and microstructural changes due to MI. RNA-seq provided a baseline for global gene expression changes in response to MI with and without IMR and suggests YAP-induced mechanotransduction, altered expression of ECM-related genes, and recruitment of immune cells as mechanisms contributing to altered MV biomechanics post-MI.

overall_design: Leaflets from 13 animals (pre-MI, n=3; 4 weeks post-MI, n=5; 8 weeks post-MI, n=4) were used for RNA isolation and quantification. Half of the animals at 4 and 8 weeks post-MI exhibited low-grade IMR, with the other half exhibiting no observable IMR. No animals exhibited IMR at the pre-MI time point.

first: Daniel

last: Howsmon

first: Bruno

last: Rego

first: Estibaliz

last: Castillero

first: Salma

last: Ayoub

first: Amir

last: Khalighi

first: Robert

last: Gorman

last: Gorman III

first: Giovanni

last: Ferrari


title: The Swi/Snf chromatin remodeling complex promotes Th17 differentiation by coordinating RORγt-driven epigenetic program

city: Seoul

first: Sungkyu

last: Lee

address: Gwanak-gu, Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: TH17 cells play a critical role in mucosal immunity and also in multiple autoimmune diseases. The differentiation of TH17 cells is dictated by a master transcription factor, RORγt; however, the mechanism by which RORγt controls target genes is poorly understood. Here we identify the Swi/Snf chromatin remodeling complex as an essential regulator of TH17 cell differentiation. Loss of the expression of SRG3/mBAF155, a core subunit of the Swi/Snf complex, results in a specific downregulation of RORγt target genes such as IL-17A, IL-17F and IL-23R. Importantly, the comparative transcriptional analysis reveals a high similarity between RORγt and the Swi/Snf complex in the control of TH17-related gene expression. Mechanistically, the Swi/Snf complex partners with RORγt and coordinates a variety of RORγt–mediated epigenetic modifications, including both permissive and repressive ones. These results provide a basis for the understanding of how a master transcription factor RORγt cooperates with the Swi/Snf complex to govern the Th17 cell differentiation.

overall_design: WT, SRG3-deficinet and RORγt-deficinet naïve CD4+ T cells were cultured under Th17(β) conditions.

first: Rho

last: Seong


title: NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure (RRBS)

overall_design: To characterize the effects of CS exposure on the sperm epigenome and offspring neurodevelopment, we investigated the impact of pre-conception paternal CS exposure on mouse sperm DNA methylation and gene expression in offspring.  We further investigated the role of oxidative stress on sperm epigenetic changes using a mouse model (Nrf-/-) with impaired antioxidant capacity. Lastly, we evaluated the capacity for sperm DNA methylation to recover following removal of CS for 1-5 spermatogenic cycles (28-171 days).