title: Kinetics of Xist-induced gene silencing depends on combinations of epigenetic and genomic features

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: To initiate X-chromosome inactivation (XCI), the long non-coding RNA Xist mediates chromosome-wide gene silencing of one X chromosome in female mammals to equalize gene dosage between the sexes. The efficiency of gene silencing, however is highly variable across genes, with some genes even escaping XCI in somatic cells. A gene’s susceptibility to Xist-mediated silencing appears to be determined by a complex interplay of epigenetic and genomic features; however, the underlying rules remain poorly understood. We have quantified chromosome-wide gene silencing kinetics at the level of the nascent transcriptome using allele-specific Precision nuclear Run-On sequencing (PRO-seq). We have developed a Random Forest machine learning model that can predict the measured silencing dynamics based on a large set of epigenetic and genomic features and tested its predictive power experimentally. While the genomic distance to the Xist locus is the prime determinant of the speed of gene silencing, we find that also pre-marking of gene promoters with polycomb complexes is associated with fast silencing. Moreover, a series of features associated with active transcription and the O-GlcNAc transferase Ogt are enriched at rapidly silenced genes. Our machine learning approach can thus uncover the complex combinatorial rules underlying gene silencing during X inactivation.

overall_design: In this study we set out to identify the genetic and chromatin features of X-linked loci, or more precisely the enrichment or depletion of certain features, that predispose genes on the chromosome X to be efficiently silenced or avoid silencing. For this, we measured chromosome-wide silencing dynamics of X-linked genes following induction of Xist expression, using allele-specific Precision nuclear Run-On sequencing (PRO-seq) or RNAseq. 8 Timepoints after Dox induced Xist expression in undifferentiated ES cells were included in the PROseq analysis, of which the uninduced and 24 hrs induced samples were performed in replicate. For mRNAseq analysis, two dox-induced Xist time courses were performed: One in undifferentiated cells, over 6 timepoints, all in replicate, to measure the silencing rates of X-linked genes without interference of differentiation, and the second in differentiating cells, over 6 timepoints, all in replicate, to measure the effect of differentiation on the Xist induced silencing of X-linked genes.

first: Lisa

last: de Andrade e Sousa

first: Iris

last: Jonkers

first: Laurene

last: Syx

first: Julie

last: Chaumeil

first: Christel

last: Picard

first: Benjamin

last: Foret

first: Chong-Jian

last: Chen

first: John

last: Lis

first: Edda

middle: G

last: Schulz

first: Annalisa

last: Marsico

first: Edith

last: Heard


title: ATACseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

status: Public on Jun 06 2019

city: Oxford

first: Florian

last: Bonkhofer

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: Oxford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study is to analyse the open chromatin regions  via ATACseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. 2000-3000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.   Genomic control DNA was isolated from 30.000 cells using the DNeasy Blood & Tissue kit (Qiagen) and eluted with EB buffer. Tagmentation was performed as described. Fragments were amplified for 9 cycles. Sequencing was performed on a NextSeq machine. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).

overall_design: Analysis of 5 different cell types; DN (double negative), SP-kdrl (single positive), DP-R1lo (double positive runx1 low expression), DP-R1med (runx1 medium expressionand) and DP-R1hi (runx1 high expression) in  TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, in triplicates, NextSeq  with a 75 bp paired end

first: Rossella

last: Rispoli


title: Transcriptional profiling of healthy, eutopic and ectopic endometrial organoids

status: Public on Jun 05 2019

city: Leuven

first: Matteo

last: Boretto

address: Herestraat 49

country: Belgium

institute: KU Leuven

type: Expression profiling by high throughput sequencing

summary: We performed RNA-seq on RNA samples of organoids derived from healthy, eutopic (endometrium of patients with endometriosis) and ectopic (endometriosis) endometrium

overall_design: RNA-seq was performed on 4 RNA samples of healthy endometrial organoids, 4 eutopic endometrial organoids and 7 ectopic endometrial organoids using the Illumina NextSeq 500


title: Calibrated ChIP-seq for Xist-mediated polycomb recruitment

status: Public on Jun 17 2019

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary:
Calibrated ChIP-seq was employed to quantitatively address the questions of how and where Xist recruits polycomb modifications (H2AK119ub and H3K27me3) to the inactive chromosome. 'Dox' samples were performed after 24 hours of induced Xist expression.
Suz12 is the core enzymatic component of PRC2 while Pcgf3/5 are non-canonical PRC1 components which initiate the polycomb cascade in Xist-mediated chromosome inactivation. Xist PID region, encompassing the B-repeat and part of C-repeat, was characterized to bind hnRNPK directly, then recruit the Pcgf3/5. Notably, Suz12 KO does not affect Xist-dependent H2AK119ub deposition too much in a 24hour Xist induction.

overall_design:
H3K27me3 and H2AK119ub calibrated ChIP-seq for Xist and XistDelPID-induced chromosome inactivation [endogenous Xist model].
H3K27me3 and H2AK119ub calibrated ChIP-seq for WT, Pcgf3/5 acute double knockout, and Suz12KO [transgenic Xist model].

first: J

middle: S

last: Bowness

first: G

last: Pintacuda

first: T

middle: B

last: Nesterova

first: N

last: Brockdorff


title: KLRG1 and NKp46 discriminate subpopulations of human CD117+ CRTH2- ILCs biased toward ILC2 or ILC3

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

summary: Recently, circulating multi- and uni-potential human ILC precursors (ILCP) have been found in a lymphocyte population that expresses CD117 and CD127 but lack CRTH2 and NKp44. However, these ILCPs have not been extensively characterized. We performed an unbiased Hierarchical Stochastic Neighbor Embedding (HSNE) analysis of the phenotype of peripheral blood CD117+ ILCPs which revealed the presence of three major subsets; the first expressed NKp46, the second expressed both NKp46 and CD56 and the third expressed KLRG1. Analysis of the differentiation potential of these cells on bulk and clonal levels, cytokine production and the transcriptome revealed that the NKp46+ ILCPs contain high frequencies of ILC3 precursors whereas a minority can differentiate into ILC1/NK-like cells. In contrast KLRG1+ ILCPs are biased to the ILC2 lineage, but are highly plastic and epigenetically poised to differentiate to other ILC subsets depending on the activation signals they receive.

overall_design: 24 samples of 5 different cell types 6 replicates for 3 cell types and 3 replicates for 2 cell types

first: Maho

last: Nagasawa

middle: A

first: Ralph

last: Stadhouders

first: Chantal

middle: M

last: Kradolfer

first: Lisette

last: Krabbendam

first: Korneliusz

last: Golebski

first: Rudi

middle: W

last: Hendriks

first: Hergen

last: Spits

first: Suzanne

last: Bal


title: RNA-seq of tumor cells following angiopellosis extravasation

status: Public on Jun 04 2019

city: Raleigh

first: Tyler

last: Allen

state: North Carolina

address: 1001 William Moore Drive

country: USA

institute: NC State University

summary: Tumor cells were observed to undergo extravasation through intrivital imaging and immediately following the extravasation they were isolated and compared to control cells using RNA-seq.

overall_design: Examination of extravasating cells in comparison to conrol cells.

first: Ke

last: Cheng


title: MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Promoter architecture, shape and usage play an important role in the regulation of eukaryotic gene expression. Several promoter profiling techniques have been developed to detect transcription start sites and alternative promoter usage between tissues or during development. However promoter profiling has not been utilized in studies that demand quantification of expression changes between developmental stages, tissues and conditions. In this study, we combine promoter profiling and differential expression analysis in a single setup, using a fast and simple protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with a new software “icetea” (https://bioconductor.org/packages/icetea). The use of random molecular barcodes and spike-ins in MAPCap enables accurate quantification of expression from promoters. We detected sex-specific promoter usage in the brains of Drosophila melanogaster larvae. Comparison of male and female mutant flies of the male-less helicase (MLE), a protein known to be essential for the dosage compensation of the male X-chromosome, indicated that the sensitivity of promoters to dosage compensation depends on their genomic location. Our results expand the scope of promoter profiling methods to differential expression analysis and provide quantitative insights into promoter usage during dosage compensation.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
To evaluate MAPCap data and compare with other protocols, we performed MAPCap on stage 15 Drosophila embryos in four replicates, 5uG RNA per-replicate. Files are multiplexed in the same fastq. Further, for analysis of dosage compensation, we performed MAPCap on RNA isolated from brains of maleless (MLE) RNA helicase mutant (also referred as knock-outs/KOs) Drosophila Melanogaster L3 larvae, in three replicates each (5uG RNA per replicate). For the L3 larvae, we also independently performed a ribo-depleted Illumina RNA-seq.

To evaluate MAPCap TSS enrichment at various RNA concentration, we performed MAPCap on RNA isolated from S2 cells, at starting RNA concentrations of 5ug, 1ug, 500ng, and 100ng. To compare MAPCap with nAnTiCAGE, we performed MAPCap from 5ug RNA isolated from female mouse ESCs where the nAnTiCAGE data was available online

first: Vivek

last: Bhardwaj

first: Giuseppe

last: Semplecio

first: Niyazi

last: Umut Erdogdu


title: Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [miRNA-seq]

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: The extensive molecular characterization of the transcriptional regulatory landscape within the LCLs of a 3-generation, 17-member kindred was performed to allow for the identification of functional variants. A variant associated with changes in multiple molecular phenotypes was selected for validation through precise CRISPR/Cas9 editing. Edited clones were subsequently tested for reconstitution of function through CRISPR/dCas9 targeted TF activation.

overall_design: small RNA expression within a 3-generation,17-member kindred were assayed from two different cultures; thus, producing two biological replicates.

middle: D

first: Claudia

last: Simoes-Pires

first: Taylor

middle: V

last: Thompson

first: Masako

last: Suzuki

first: John

last: Greally


title: Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: DNA methylation within a 3-generation,17-member kindred were assayed using a strand sensitive library construction


title: Adipocyte-Derived Exosomal microRNAs in subject serum samples

status: Public on Jun 03 2019

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

summary:
Affymetrix miRNA 4.0 array profiling of adipocyte-derived exosomes from lean and obese subjects.
We used miRNA arrays to profile FABP4+ (adipocyte-derived) exosomes isolated from serum of lean and obese subjects.

overall_design: We isolated FABP4+ (adipocyte-derived) exosomes from human subjects profiled them to determine correlations between microRNAs and cholesterol efflux.

first: Robert

last: Freishtat


title: Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [dirRNA-seq]

overall_design: RNA expression within a 3-generation,17-member kindred were assayed using a strand sensitive library construction


title: Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding.

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

overall_design: Refer to individual Series


title: Generating Patterned Kidney Organoids for Studying Development and Diseases

status: Public on Jun 01 2019

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry


title: IGH VDJ-RNA-seq of circulating plasma cells at day zero and seven relative to experimental vaccination dosing

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: IGH VDJ-RNA-sequencing of CD19+IgD-CD27+CD71+CD38+CD20- circulating plasma cells prior to vaccination (day 0) and seven (day 63) days after the third vaccination.

overall_design: Blood samples were taken from healthy volunteers taking part in a Phase 1b clinical trial. RNA was isolated from flow sorted CD19+IgD-CD27+CD71+CD38+CD20- circulating plasma cells and IGH VDJ-RNA-sequencing performed on cells from days 0 and 7 relative to vaccination

first: Michelle

last: Linterman

first: Wim

last: Pierson

first: Danika

last: Hill

first: Edward

last: Carr

first: Steven

last: Wingett

first: Daniel

last: Bolland


title: Generating Patterned Kidney Organoids for Studying Development and Diseases [scRNA-Seq]

summary: Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. By single cell RNA-sequencing, we identify a subset of nephron progenitor cells as a potential source of the vasculature. Upon implantation into host mice, these kidney organoids undergo further structural and functional maturation, as demonstrated by the size-selective handling of dextran. Based on this differentiation platform, we establish an in vitro model of autosomal recessive polycystic kidney disease (ARPKD) by differentiating induced PSCs (iPSCs) from an ARPKD patient into 3D kidney organoids that develop tubule cysts in response to cAMP upregulation. The cystogenesis phenotype can be effectively prevented by gene correction or drug treatment. Our studies provide a versatile platform for studying human kidney development and diseases, and opens new avenues for modeling disease pathogenesis and performing patient-specific drug screening.

overall_design: Examination of transcriptome in human pluripotent stem cells-derived vascularized three-dimensional kidney organoids. Day 10 organoid (technical duplicate), Day 12 organoid, Day 14 organoid (technical duplicate).

first: Yun

last: Xia


title: Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [ATAC-Seq]

overall_design: The accessible regions of chromatin from a 3-generation,17-member kindred were assayed from two different cultures; thus, producing two biological replicates.


title: DNMT3B maintains mCA landscape and regulates mCG status of bivalent promoters in human embryonic stem cells

status: Public on Jun 02 2019

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: In mammalian cells, DNMT3B is known as a de novo DNA methyltransferase. However, its preferential target sites for DNA methylation are largely unknown. By studying CA methylation (mCA) and various histone mark distributions in human embryonic stem cells (hESC), we set up a connection between mCA, H3K36me3, and DNMT3B. We found that mCA, H3K36me3 and DNMT3B signals in hESC are distributed in a 3-level pattern: low level at promoter region, intermediate level before first splicing junction and high level afterward. Knocking out DNMT3B (KO) in hESC demolished mCA, and this further confirmed that DNMT3B is the main enzyme which maintains mCA. Furthermore, the mCA could not be maintained after we deleted the H3K36me3 binding domain, PWWP domain, in DNMT3B. This observation suggests that DNMT3B maintains mCA through its histone interaction. This is the first study that describes the detailed landscape of mCA and its connection with DNMT3B. In contrast to mCA, we only observed a minor reduction of global mCG level from 83.7% to 79.2% after DNMT3B KO. 5256 de novo hypomethylated regions (dnHMRs) were found in the KO cell, in which 57.8% overlapped annotated promoter sites. Intriguingly, most of these promoter dnHMRs were bivalent, possessing both H3K4me3 and H3K27me3. We call them spurious bivalent promoters. Gene ontology (GO) analysis associated spurious bivalent promoters with development and cell differentiation. Overall, we found the importance of DNMT3B for shaping mCA landscape and maintaining the fidelity of bivalent promoter landscape in hESC.

overall_design: DNMT3B is either knock-out or mutated in H1 hESC by CRISPR-Cas9 gene editing strategy. DNA methylation were profiled through WGBS. DNMT3B binding and histone mark status were profiled by ChIP-seq.

first: Hong

middle: K

last: Tan

first: Chan-shuo

last: Wu

first: Li

last: Jia

first: Henry

last: Yang

first: Annalisa

last: Di Ruscio

last: Tenen


title: RNA-seq of circulating Tfh like cells at day zero and seven and 28 relative to experimental vaccination dosing

summary: Total RNA-sequencing on 150-200 ICOS+CD38+ cTfh cells per person prior to vaccination (day 0), and seven (day 63) and 28 (day 84) days after the third vaccination.

overall_design: Blood samples were taken from healthy volunteers taking part in a Phase 1b clinical trial. mRNA was isolated from flow sorted circulating Tfh cells (CD4+CD45RA-CXCR5+PD1+ICOS+CD38+ cells) and RNA-sequencing performed on cTfh from days 0, 7 and 28 reletive to vaccination


title: RNA-sequencing of human lymph node and peripheral blood T follicular helper cells

summary: Total mRNA-sequencing on memory T helper cell populations from human blood and lymph nodes.

overall_design: Paired blood and lymph node samples were taken from patients recruited from the renal transplant live donor program at Cambridge University Hospitals NHS Foundation Trust, and who provided informed consent. All patients were either receiving or within 6 months of requiring renal replacement therapy. Patients taking immunosuppressive medication prior to transplant were excluded. mRNA was isolated from flow sorted CD4+ T cell populations and RNA-sequencing performed.


title: De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD


title: Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression (CD8+ T cells)

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Background  Multiple Sclerosis (MS) is a chronic inflammatory disease and a leading cause of progressive neurological disability among young adults. DNA methylation, which intersects genes and environment to control cellular functions on a molecular level, may provide insights into MS pathogenesis.   Methods  We measured DNA methylation in CD4+ T cells (n=31), CD8+ T cells (n=28), CD14+ monocytes (n=35) and CD19+ B cells (n=27) from relapsing-remitting (RRMS), secondary progressive (SPMS) patients and healthy controls (HC) using Infinium HumanMethylation450 arrays. Monocyte (n=25) and whole blood (n=275) cohorts were used for validations.   Findings  B cells from MS patients displayed most significant differentially methylated positions (DMPs), followed by monocytes, while only few DMPs were detected in T cells. We implemented a non-parametric combination framework (omicsNPC) to increase discovery power by combining evidence from all four cell types. Identified shared DMPs co-localized at MS risk loci and clustered into distinct groups. Functional exploration of changes discriminating RRMS and SPMS from HC implicated lymphocyte signaling, T cell activation and migration. SPMS-specific changes, on the other hand, implicated myeloid cell functions and metabolism. Interestingly, neuronal and neurodegenerative genes and pathways were also specifically enriched in the SPMS cluster.    Interpretation  We utilized a statistical framework (omicsNPC) that combines multiple layers of evidence to identify DNA methylation changes that provide new insights into MS pathogenesis in general, and disease progression, in particular.

overall_design: 28 CD8 samples with either  relapsing-remitting (RRMS), secondary progressive (SPMS) patients and healthy controls (HC)

first: Maja

last: Jagodic


title: De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ [ChIP-seq]

summary: Adenovirus-transformed cells have a de-differentiated phenotype. Eliminating E1A in transformed human embryonic kidney cells de-repressed ~2600 genes, generating a gene expression profile closely resembling mesenchymal stem cells (MSC). This was associated with a dramatic change in cell morphology from one with scant cytoplasm and a globular nucleus to one with increased cytoplasm, extensive actin stress fibers and actomyosin-dependent flattening against the substratum. E1A-induced histone hypoacetylation by p300/CBP at H3K27/18 was reversed. Most of the increase in H3K27/18ac was near TEAD transcription factors associated with their co-activators YAP and TAZ regulated by the Hippo pathway. E1A causes YAP/TAZ cytoplasmic sequestration. After eliminating E1A, YAP/TAZ were transported into nuclei where they associated with poised enhancers with DNA-bound TEAD4 and H3K4me1. This activation of YAP/TAZ required RHO-family GTPase signaling and caused histone acetylation by p300/CBP, chromatin remodeling, and cohesin loading to establish MSC-associated enhancers and then super-enhancers. Consistent results were also observed in rat embryo kidney cells, human fibroblasts and human respiratory tract epithelial cells. These results together with earlier studies suggest that YAP/TAZ function in a developmental check-point controlled by signaling from the actin cytoskeleton that prevents differentiation of a progenitor cell until it is in the correct cellular and tissue environment.

overall_design: Examination of YAP, H3K18ac, H3K27ac, H3K4me1, TEAD1, TEAD4, RAD21, chromatin accessibility and mRNA by ChIP-seq, ATAC-seq, and mRNA-seq

first: Nathan

middle: R

last: Zemke

first: Arnold

last: Berk


title: Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression (CD4+ T cells)

overall_design: 31 CD4 samples with either  relapsing-remitting (RRMS), secondary progressive (SPMS) patients and healthy controls (HC)


title: De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ [RNA-seq]


title: Gene expression signatures of chemotherapy-induced neuropathy induced by cisplatin and oxaliplatin

city: St Lucia

first: Alexander

last: Mueller

state: Queensland

address: 306 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary: Vincristine, oxaliplatin, and cisplatin are commonly prescribed chemotherapeutic agents for the treatment of several cancer types. However, a main side-effect is chemotherapy-induced peripheral neuropathy (CIPN), which may lead to decreased quality of life, changes in chemotherapeutic treatment or even treatment cessation. Although painful symptoms associated with CIPN are faithfully recapitulated by mouse models, there is limited knowledge of how these drugs affect the expression of genes in peripheral sensory neurons. The present study carried out a transcriptomic analysis of dorsal root ganglia isolated from mice treated with vincristine, oxaliplatin, and cisplatin with a view to gain insight into the comparative pathophysiological mechanisms of CIPN. RNA-Seq using 75-nucleotide single end runs revealed 368, 295 and 256 differential expressed genes (DEGs) induced by treatment with vincristine, oxaliplatin and cisplatin, respectively. Although there were many similarities in DEGs between chemotherapeutic agents, only 5 genes were dysregulated in all groups. Cell type enrichment analysis (CTEA) and gene set enrichment analysis (GSEA) showed predominant effects on genes associated with the immune system after treatment with vincristine, while oxaliplatin treatment affected mainly neuronal genes. Treatment with cisplatin resulted in a mixed inflammatory and neuropathic gene expression signature. Only ‘regulation of transport’ and ‘response to external stimuli’ were gene ontology terms shared between all treatments. These results provide insight into the recruitment of innate and adaptive immune responses to DRG tissue and indicate enhanced neuro-inflammatory processes following administration of vincristine, oxaliplatin, and cisplatin. These gene expression signatures may provide insight into novel drug targets for treatment of CIPN.

overall_design: RNA was extracted from Dorsal Root Ganglia L3, L4 and L5 tissue from wild type C57BL/6 mice treated with either vehicle or with cisplatin or oxaliplatin, in triplicates, and sequenced using Illumina NextSeq 500 as 75-nucleotide single-end runs

first: Hana

last: Starobova

first: Irina

last: Vetter


title: RNA-seq assessment of quadriceps muscle and brown adipose tissue in PPARGC1A uORF-TAA mice

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

summary: We report a mutant mouse in which the uORF encoded by the PPARGC1A gene is disrupted via mutation of its start codon (uORF-TAA mutation).  RNA-seq was used to assess differential gene expression in uORF-TAA versus wild-type mice in two metabolically important tissues that express PPARGC1A: skeletal mucle and brown adipose tissue.

overall_design: mRNA was purified from quadriceps or brown adipose tissue of 10-week old male mice.  Wild-type mice (n=4) and littermate uORF-TAA homozygous mice (n=4) were compared.

first: P

first: D

middle: F

last: Egan

first: B

last: Spiegelman


title: Effects of Maize Organ-specific Drought Stress Response on Yields from Transcriptome Analysis

city: qingdao

first: wang

last: baomei

state: shandong

address: school of life science，shandong university，72 binhai road， aoshanwei town， jimo city

department: school of  life science

country: China

institute: zea maize

summary:
Results: In this study, the ears at the V9 stage, kernels and ear leaf at the 5DAP (days after pollination) stage of maize were used for morphological, physiological and comparative transcriptomics analysis to understand the different features of “sink” or “source” organs and the effects on kernel yield under drought stress conditions. The ABA-, NAC-mediate signaling pathway, osmotic protective substance synthesis and protein folding response were identified as common drought stress response in the three organs. Tissue-specific drought stress responses and the regulators were identified, they were highly correlated with growth, physiological adaptation and yield loss under drought stress. For ears, drought stress inhibited ear elongation, led to the abnormal differentiation of the paired spikelet, and auxin signaling involved in the regulation of cell division and growth and primordium development changes. In the kernels, reduced kernel size caused by drought stress was observed, and the obvious differences of auxin, BR and cytokine signaling transduction appeared, which indicated the modification in carbohydrate metabolism, cell differentiation and growth retardation. For the ear leaf, dramatically and synergistically reduced the expression of photosynthesis genes were observed when suffered from drought stress, the ABA- and NAC- mediate signaling pathway played important roles in the regulation of photosynthesis.
Conclusions: Transcriptomic changes caused by drought were highly correlated with developmental and physiological adaptation, which was closely related to the final yield of maize, and a sketch of tissue- and developmental stage-specific responses to drought stress in maize was drafted.

overall_design: Examination of 3 different organs (ears at the V9 stage, kernels and ear leaf at the 5DAP )of B104 maize inbed line  under normal and drought conditions

first: Baomei

last: Wang

first: Can

last: Liu

first: Dengfeng

last: Zhang

first: Chunmei

last: He

first: Juren

first: Zhaoxia

last: Li


title: Genome-wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between CpG methylation and histological subtypes.

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary: Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development and may also lead to colorectal cancer (CRC) formation. While gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and non-recurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set (n=72) of formalin-fixed paraffin-embedded (FFPE) primary colorectal adenomas without recurrence (n=30), primary adenomas with recurrence at the same location (n=19), so-called “matched pair samples” (n=10; comprising the primary adenoma and the recurrent adenoma) and normal mucosa specimens (n=3). We aimed to unveil differentially methylated CpG positions (DMPs) across the methylome of the selected samples using the Illumina HumanMethylation 450K BeadChip array. Unsupervised hierarchical clustering exhibited a significant association of methylation patterns with the histological subtypes. No significant DMPs were identified comparing primary adenomas with and without recurrence. Despite that, a total of 5,094 DMPs (FDR<0.05, fold change>10%) were identified in the comparisons of recurrent adenomas vs. (non-) matched primary adenomas with recurrence (674; 98% hypermethylated), recurrent adenomas vs. primary adenomas with and without recurrence (241; 99% hypermethylated) and adenomas vs. normal mucosae (4,179; 46% hypermethylated). DMPs in CpG islands were frequently hypermethylated whereas open sea and shelves exhibited hypomethylation. Gene ontological analysis demonstrated enrichment of genes associated with the immune system, inflammatory processes, and cancer-pathways. We conclude that methylation data is helpful to contribute to a more stable and reproducible histological adenoma classification which is a prerequisite to establishing profound surveillance guidelines

overall_design: Bisulphite-converted DNA from the 72 samples were hybridized to the Illumina Infinium 450K Human Methylation Beadchip. Samples included colorectal adenomas without recurrence (n=30), colorectal adenomas with recurrence (n=29), matched pair (n=10) samples (each consisting of primary and the corresponding recurrent adenoma), and normal mucosa (n=3).

first: David

last: Fiedler

first: Daniela

last: Hirsch

first: Nady

last: El Hajj

first: Howard

last: Yang

first: Carsten

last: Sticht

first: Indrajit

last: Nanda

first: Sebastian

last: Belle

first: Maxwell

last: Lee

first: Josef

last: Rueschoff

first: Thomas

last: Ried

last: Haaf

first: Timo

last: Gaiser


title: Gene expression signatures of chemotherapy-induced neuropathy induced by vincristine

first: Alexander

last: Mueller

overall_design: RNA was extracted from Dorsal Root Ganglia L3, L4 and L5 tissue from wild type C57BL/6 mice treated with either vehicle or with vincristine, in triplicates, and sequenced using Illumina NextSeq 500 as 75-nucleotide single-end runs

first: Hana

last: Starobova

first: Irina

last: Vetter


title: Transcriptomic changes in wild-type and Phlpp1-/- mice following KLA stimulation

first: Christopher

last: Glass

department: School of Medicine

institute: University of California, San Diego

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) of bone marrow derived macrophages from wild-type and PHLPP1 knock-out mice and how Inflammatory stimulation affects those profiles.

overall_design: Bone marrow derived mRNA profiles of wild-type and Phlpp1-/- mice were generated in duplicate.

first: Ksenya

last: Cohen Katsenelson

first: Joshua

last: Stender

first: Alexandra

middle: C

last: Newton


title: RNAseq - scERαWT vs. scERαKO

city: Minneapolis

first: Dawn

last: Lowe

state: MN

address: 420 Delaware St SE, MMC 388

department: Rehabilitation Medicine

institute: University of Minnesota

summary: RNAseq performed on isolated satellite cells from scERαWT and scERαKO mice

overall_design: Generate mice, cre induction via tamoxifen, isolation of satellite cells via flow cytometry, RNA isolation, and submission of samples to UMGC for RNAseq

first: Alexie

last: Larson

first: Ning

last: Xie

first: Brittany

last: Collins


title: Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated with Altered Stress Response in Adulthood

status: Public on May 31 2019

city: New York

first: Nathan

last: Einhorn

address: 1230 York Avenue

department: Laboratory of Neuroendocrinology

institute: The Rockefeller University

summary: Using a protocol of chronic early-life stress (ELS) induced by limited bedding and nesting material followed by acute-swim stress (AS) in adulthood, we show that mice with a history of ELS display a blunted CORT response to AS, altered levels of the repressive histone marker H3K9me3 in several hippocampal regions, and a restricted translational response to stress in CA3 neurons

overall_design:
Examination of the HPA, genetic, and epigenetic effects of AS in the hippocampus of control mice and mice subjected to ELS
ELS = Early Life Stress, AS/FST = Acute Stress, Forced Swim Test

first: Jordan

last: Marrocco

first: Jason

last: Gray

first: Bruce

last: McEwen


title: Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids

city: Miami

first: Pei-Ciao

last: Tang

state: FL

address: 1501 NW 10th Avenue, Miami, FL 33136, 926 F2

department: Otolayrngology

institute: University of Miami

summary: The role of TMPRSS3 in hair cell (HC) remains unclear. Nelson and colleagues generated stem cell-derived inner ear organoids with Tmprss3-mutations to show that 1) inner ear organoids exhibit comparative effects of the genetic abnormality to its in vivo counterparts, 2) Tmprss3-mutations lead to apoptosis and reduced BK channels in HCs, and 3) cell membrane-bound TMPRSS3 is localized in HCs.

overall_design: Single-cell RNA sequencing (scRNA-Seq) was performed with day 25 and day 35 organoids from R1/E (WT) and R1/E-Tmprss3KO-GFPKI (KO).

first: Rick

last: Nelson


title: Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

summary: In breast cancer, the increased stiffness of the extracellular matrix (ECM) is a key driver of malignancy. Yet little is known about the epigenomic changes that underlie the tumorigenic impact of ECM mechanics. Here, we show in a 3D culture model of breast cancer that stiff ECM induces a tumorigenic phenotype through changes in chromatin state. We found that increased stiffness yielded cells with more wrinkled nuclei and with increased lamina-associated chromatin, that cells cultured in stiff matrices displayed more accessible chromatin sites, which exhibited footprints of Sp1 binding, and that Sp1 acts along with histone deacetylases (HDAC) 3 and 8 to regulate the induction of stiffness-mediated tumorigenicity. Just as cell culture on soft environments or in them rather than on tissue-culture plastic better recapitulates the acinar morphology observed in mammary epithelium in vivo, mammary epithelial cells cultured on soft microenvironments or in them also more closely replicate the in vivo chromatin state. Our results emphasize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a critical mediator of mechanotransduction.

overall_design: Examination of chromatin accessibility profiles of mammary epithelial cells in hydrogel culture of different stiffness

first: Ryan

last: Stowers

first: Anna

last: Shcherbina

first: Johnny

last: Israeli

last: Gruber

first: Julie

last: Chang

first: Sungmin

last: Nam

first: Atefeh

last: Rabiee

first: Mary

last: Teruel

first: Michael

last: Snyder

first: Anshul

last: Kundaje

first: Ovijit

last: Chaudhuri


title: c-Myc drives nab-paclitaxel resistance in pancreatic cancer

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary:
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited and very often, ineffective medical and surgical therapeutic options. The treatment of patients with advanced unresectable PDAC is restricted to systemic chemotherapy, a therapeutic intervention to which most eventually develop resistance. Recently, nab-paclitaxel has been added to the arsenal of first line therapies, and the combination of gemcitabine and nab-paclitaxel has modestly prolonged median overall survival. However, patients almost invariably succumb to the disease, and little is known about the mechanisms underlying nab-paclitaxel (n-PTX) resistance. Using the conditionally reprogrammed (CR) cell approach, we established and verified continuously growing cell cultures from treatment-naive PDAC patients. To study the mechanisms of primary drug resistance, nab-paclitaxel-resistant (n-PTX-R) cells were generated from primary cultures and drug resistance was verified in vivo, both in zebrafish and in athymic nude mouse xenograft models. Molecular analyses identified the sustained induction of c-MYC in the nab-paclitaxel-resistant cells. Depletion of c-Myc restored nab-paclitaxel sensitivity, as did treatment with either the MEK inhibitor, trametinib, or a small molecule activator of protein phosphatase 2a (SMAP).
Implications: The strategies we have devised, including the patient-derived primary cells and the unique drug resistant isogenic cells, are rapid and easily applied in vitro and in vivo platforms to better understand the mechanisms of drug resistance and for defining effective therapeutic options on a patient by patient basis

overall_design: Four samples included from two patients, one from each parental sample, one from the conditionally reprogrammed cell line derived from each sample. Original samples were from patients with disparate treatment regimens. This experiment was designed to determine major gene expression changes both between patients with different treatment regimens as well as confirm that pathway activation was consistent between original samples and derived cell lines.

first: Erika

last: Parasido

first: George

last: Avetian

first: Aisha

last: Naeem

middle: T

middle: J

last: Pishvaian

first: Eric

last: Glasgow

first: Shaila

last: Mudambi

first: Yichien

last: Lee

first: Chukwuemeka

last: Ihemelandu

first: Muhammad

middle: U

last: Choudhry

first: Ivana

last: Peran

first: Partha

middle: P

last: Banerjee

first: Maria

last: Avantaggiati

first: Kirsten

last: Bryant

first: Elisa

last: Baldelli

first: Mariaelena

last: Pierobon

first: Lance

last: Liotta

first: Emanuel

last: Petricoin

first: Stanley

last: Fricke

first: Aimy

last: Sebastian

first: Joseph

last: Cozzitorto

first: Gabriela

last: Loots

first: Deepak

last: Kumar

first: Stephen

last: Byers

last: London

first: Analisa

last: DiFeo

first: Goutham

last: Narla

last: Winter

first: Jonathan

last: Brody

first: Olga

last: Rodriguez

first: Chris

last: Albanese


title: Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [ATAC-Seq]

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

type: Genome variation profiling by high throughput sequencing

summary: We comapre mRNA expression level TOX and TOX2 CAR TILS and WT CAR TILs

overall_design: 5x105 B16-OVA-huCD19 tumor cells were inoculated into C57BL/6N mice, the mice were adoptively transferred with the indicated CAR T cells (1.5x106) 12 days later, and GFP+CD8+Thy1.1+ CAR T cells were sorted on day 24 from tumors

first: Hyungseok

last: Seo

first: Edahí

last: González-Avalos

first: Daniela

last: Samaniego-Castruita


title: Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion

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

overall_design: Refer to individual Series


title: Distinct immune responses and pruritic mechanisms in oxazolone- and urushiol- induced ACD (Allergic contact dermatitis) models.

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary:
The mechanisms underlying pruritus and skin inflammation of poison ivy ACD remain poorly understood,due to limited clinical data and animal studies. Most of the mechanistic understanding of ACD is based upon animal models using experimental allergens not present in the environment, such as oxazolone,DNFB or SADBE . Recently, it has become evident that different allergens elicit widely divergent immune responses in both human and animals, suggesting these models may not be representative of environmental forms of ACD . Given the high incidence and public health impact of poison ivy-induced ACD, it is necessary to establish and characterize a clinically relevant animal model using the actual allergen urushiol.
In this study we applied transcriptome microarray to evaluate the cutaneous immune response in urushiol ACD model.

overall_design: 4 hours after the last challenge, mice were sacrificed and neck skins were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Boyi

last: Liu

first: Yan

last: Tai

first: Boyu

first: Ana

middle: I

last: Caceres

first: Chenyu

first: Sven

middle: E

last: Jordt


title: Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [RNA-Seq]


title: Transnuclear mice reveal a population of Peyer’s patch iNKT cells that regulate B cell class switching to IgG1

first: Stephanie

last: Dougan

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: Tissue resident iNKT cells maintain tissue homeostasis and peripheral surveillance against pathogens; however, studying these cells is challenging due to low abundance and poor recovery from tissues. To increase the number of tissue resident iNKT cells, we used transnuclear mice cloned from iNKT nuclei. We detected iNKT cells from tissues where they are rare, including adipose, lung, skin-draining lymph nodes, and a previously undescribed population in Peyer’s patches (PP). We characterized the transcriptional profile of this novel population by bulk RNA-Seq.

overall_design: Nine samples were analyzed: 3 samples of iNKTs isolated from Peyer's patches (PPs), 3 of iNKTs isolated from spleens, and 3 of CD4+ T-cells from PPs.

first: Eleanor

last: Clancy-Thompson

first: Gui

middle: Z

last: Chen

first: Nelson

middle: M

last: LaMarche

first: Lestat

last: Ali

first: Hee-Jin

last: Jeong

last: Crowley

first: Kelly

last: Boelaars

first: Michael

middle: B

last: Brenner

first: Lydia

last: Lynch


title: C. elegans KLF-1 promoter binding sites

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

summary: Here we report CHIP-Seq DATA on KLF-1 pulldown in C. elegans N2 wild type and isp-1(qm150);ctb-1(qm189) mutant strain.

overall_design: KLF-1-YFP was expressed under gut-specific vha-6 promoter in the N2 and isp-1(qm150);ctb-1(qm189) animals. The worms were collected at the first day of adulthood and the CHIP-seq experiment was performed using GFP-TRAP (Chromotek).

first: Marija

last: Herholz

first: Prerana

last: Wagle


title: RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: enhancing the retinal microarray datasets from GeneNetwork

city: Munich

first: Felix

last: Struebing

address: Feodor-Lynen-Str. 23

department: Center for Neuropathology and Prion Research

institute: Ludwig Maximilian University of Munich

summary:
Purpose: The goal of the present study is to provide an independent assessment of the retinal transcriptome signatures of the C57BL/6J (B6) and DBA/2J (D2) mice and to enhance existing microarray datasets for accurately defining the allelic differences in the BXD recombinant inbred strains.
Methods: Retinas from both B6 and D2 mice (3 of each) were used for the RNA-seq analysis. Transcriptome features were examined for both strains. Differentially expressed genes between the 2 strains were identified and bioinformatic analysis was performed to analyze the transcriptome differences between B6 and D2 strains, including Gene ontology (GO) analysis, Phenotype and Reactome enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The RNA-seq data were then directly compared with one of the microarray datasets (DoD Retina Normal Affy MoGene 2.0 ST RMA Gene Level Microarray Database) hosted on GeneNetwork (www.genenetwork.org).
Results: RNA-seq provided an in-depth analysis of the transcriptome of the B6 and D2 retina with a total of more than 30,000,000 reads per sample. Over 70% of the reads were uniquely mapped, resulting in a total of 18,100 gene counts for all 6 samples. 1,665 genes were differentially expressed, with 858 of these more highly expressed in B6 and 807 more highly expressed in D2.  Several molecular pathways were differentially active between the two strains, including the retinoic acid metabolic process, endoplasmic reticulum lumen, extracellular matrix organization, and PI3K-Akt signaling pathway. The most enriched KEGG pathways were the pentose and glucuronate interconversions pathway, the cytochrome P450 pathway, protein digestion and absorption pathway and the ECM-receptor interaction pathway. Each of these pathways had a more than 4-fold enrichment. The DoD normal retina microarray database provided expression profiling for 26,191 annotated transcripts for B6 mouse, D2 mouse and 53 BXD strains. A total of 13,793 genes in this microarray dataset were comparable to the RNA-seq dataset. For both B6 and D2, the RNA-seq data and microarray data were highly correlated with each other (Pearson's r = 0.780 for B6 and 0.784 for D2). Our results suggest that the microarray dataset can reliably detect differentially expressed genes between the B6 and D2 retinas, with a positive predictive value of 45.6%, and a negative predictive value of 93.6%. Examples of true positive and false positive genes are provided.
Conclusions: Retinal transcriptome features of B6 and D2 mouse strains provide a useful reference for a better understanding of the mouse retina. Generally, the microarray database presented on GeneNetwork shows good agreement with the RNA-seq data, while we note that any allelic difference between B6 and D2 should be verified with the latter.

overall_design: Retinal mRNA profiles of 2 strains of mice, C57BL/6J and DBA/2J, were generated by deep sequencing, in triplicate, using Illumina TruSeq Stranded Total RNA kit.

first: Jiaxing

last: Wang

first: Eldon

last: Geisert

middle: L


title: Human pleural fluid elicits pyruvate and phenylalanine metabolism in Acinetobacter baumannii to enhance cytotoxicity and immune evasion

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

summary:
Analysis of the effect of human pleural fluid on the transcriptome of Acinetobacter baumanii A118
Acinetobacter baumannii (Ab) is one of the most treacherous pathogens among those causing hospital-acquired pneumonia (HAP). A. baumannii possesses an adaptable physiology, seen not only in its antibiotic resistance and virulence phenotypes, but also in its metabolic versatility. In this study, we observed that A. baumannii undergoes global transcriptional changes in response to human pleural fluid (PF), a key host-derived environmental signal. Differential gene expression analyses combined with experimental approaches revealed changes in A. baumannii metabolism, affecting cytotoxicity, persistence, bacterial killing and chemotaxis. Over 55% of the differentially expressed transcriptomic genes corresponded to metabolic processes, including the up regulation of glutamate, short chain fatty acid, and styrene metabolism. We observed an up regulation of the pyruvate dehydrogenase complex and found that pyruvate (PYR), in conjunction with PF, triggers an A. baumannii pathogenic behavior that adversely impacts human epithelial cell viability. Interestingly, PF also amplified A. baumannii cytotoxicity against murine macrophages, suggesting an immune evasion strategy implemented by A. baumannii. Moreover, we uncovered opposing metabolic strategies dependent on the degree of pathogenicity of the strains, where less pathogenic strains demonstrated greater utilization of PYR to promote persister formation in the presence of PF. Additionally, our transcriptomic analysis and growth studies of A. baumannii suggest the existence of an alternative phenylalanine (PA) catabolic route independent of the phenylacetic acid pathway, which converts PA to phenylpyruvate (PP) and shuttles intermediates into styrene metabolism. This alternative route promoted a neutrophil-evasive state, as PF-induced degradation of PP significantly reduced overall human neutrophil chemotaxis in ex vivo chemotactic assays. Taken together, these data highlights A. baumannii pathoadaptabililty in response to host signals and provide further insight into the role of bacterial metabolism in virulence traits, antibiotic persistence strategies, and host innate immune evasion.

overall_design: Total RNA of Acinetobacter baumanii A118 was isolated from bacteria incubated in LB with or without 4% human pleural fluid. Four biological replicates of each treatment were submitted to rRNA removal, Illumina RNA-seq library preparation, and Illumina HiSeq 2500 sequencing.

first: Maria

middle: S

first: Rodrigo

last: Sieira


title: Interferon signature in patients with STAT1 gain-of-function mutation is epigenetically determined

city: Tartu

first: Epp

last: Kaleviste

state: no

address: Ravila 19

department: Institute of biomedicine and translational medicine

country: Estonia

institute: University of Tartu

summary: STAT1 gain-of-function (GOF) variants lead to defective Th17 cell development and chronic mucocutaneous candidiasis (CMC), but frequently also to autoimmunity. STAT1 GOF mutations result in hyperphosphorylation and delayed dephosphorylation of STAT1. However, how the delayed dephosphorylation exactly causes the increased expression of STAT1-dependent genes, and how the intracellular signal transduction from cytokine receptors is affected, remains unknown. In this study we show that the circulating levels of IFN-α in STAT1 GOF patients were not persistently elevated. Nevertheless, the interferon signature was evident even in the patient with low or undetectable IFN-α levels. Chromatin immunoprecipitation (ChIP) experiments showed that the active chromatin mark H3K4me3, was significantly enriched in areas associated with interferon-stimulated genes in STAT1 GOF cells in comparison to normal cells. This suggests that GOF STAT1, while binding to chromatin, promotes epigenetic changes compatible with higher gene expression and elevated reactivity to type I interferons, and interferon-related autoimmunity. We suggest that epigenetic rewiring may be responsible for treatment failure of JAK1/2 inhibitors in certain patients. We also found that after IL-21 stimulation the balance of p-STAT3/p-STAT1 was significantly impaired in patients, which could potentially be applied as a diagnostic test for STAT1 GOF.

overall_design: ChIP-seq of 4 patient and 6 healthy control PBMC samples

first: Mario

last: Saare

first: Timothy

last: Leahy

first: Winnie

last: Ip

first: E Graham

last: Davies

first: Vincent

last: Bondet

first: Darragh

last: Duffy

first: Trine

last: Mogensen

first: Sofie

last: Jørgensen

first: Helke

last: Nurm

first: Sascha

last: Sauer

first: Ann-Christine

last: Syvänen

first: Lili

last: Milani

first: Pärt

last: Peterson

first: Kai

last: Kisand


title: Relative timing of type I interferon response and virus replication determines disease outcome during MERS-CoV infection

status: Public on May 30 2019

city: Iowa City

first: Stanley

last: Perlman

state: Iowa

address: Dept. Microbiology, BSB 3-712, 51 Newton Road

institute: University of Iowa

summary: Type 1 interferons (IFN-I) generally protect mammalian hosts from virus infections, but in some cases, IFN-I is pathogenic. Because IFN-I is protective, it is commonly used to treat virus infections for which no specific approved drug or vaccine is available. The Middle East respiratory syndrome-coronavirus (MERS-CoV) is such an infection, yet little is known about the role of IFN-I in this setting. Here we show that IFN-I signaling is protective during MERS-CoV infection. Blocking IFN-I signaling resulted in delayed virus clearance, enhanced neutrophil infiltration and impaired MERS-CoV-specific T cell responses. Notably, IFN-I administration within 1-day post infection (before virus titers peak) protected mice from lethal infection, despite a decrease in ISG (interferon stimulated gene) and inflammatory cytokine gene expression. In contrast, delayed IFN-I treatment failed to effectively inhibit virus replication, increased infiltration and activation of monocyte-macrophages and neutrophils into the lungs and enhanced pro-inflammatory cytokine expression, resulting in fatal pneumonia in an otherwise sub-lethal infection. Together, these results suggest that the relative timing of the IFN-I response and maximal virus replication is key in determining outcomes, at least in infected mice. By extension, IFN-I or combination therapy may need to be used cautiously to treat virus infections in clinical settings.

overall_design: Examination of gene expression in early and late IFN treated lungs after MERS-CoV infection.

first: Rudragouda

last: Channappanavar


title: Exome sequencing identified mutations in clpex mouse mutants

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

summary: 3 mutants from the clpex mouse mutant line were exome sequenced to identify candidate causal variants.

overall_design: 3 independent mutants were sequenced

first: Marshall

last: Lukacs


title: Quantitative Analysis of OxyS regulatory Transcriptomes

city: Busan

first: Kwang-sun

last: Kim

address: 63 beon-gil 2, Jangjeon-dng, Geumjeong-gu

department: Chemistry

country: South Korea

institute: Pusan National University

summary:
Purpose: The identification of genes and regulatory pathways by OxyS sRNA in Escherichia coli.

Methods: mRNA profiles of OxyS overexpression in wild-type and knockout of hfq strains using Illumina sequencing. Ribosomal RNA depletion from total RNA was performed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Illumina) according to manufacturer protocols. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) by the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using a pair-end 50 bp sequencing. The sequence data for the reference genome (E. coli K-12 MG1655) was retrieved from the NCBI database. Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2 software.
The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM). All data processing were further performed by CLRNASeq V.1.00 (Chunlab, South Korea).

Results: Using an optimized data analysis workflow, about 1 million sequence reads per sample to the E. coli K-12 genome were mapped and identified 4,224 and 4,303 transcripts in wild-type and hfq- strains, respectively. After TMM (Trimmed Mean of M-value) normalization and elmination of <100 reads in control and OxyS overexpression, 3,524 or 2,748 genes in hfq+ or hfq- strain, respetively, were utilized as a set to screening of candidates related to OxyS phenotype.

Conclusions: Our study represents the first detailed analysis of OxyS transcriptomes in hfq+ and hfq- strains, generated by RNA-seq technology. The optimized data analysis workflows reported here could comparative investigate the expression profiles of sRNA in different background strains. We conclude that RNA-seq based transcriptome characterization of sRNAs would unravel genetic network in complex biologic functions.

overall_design: mRNA profiles of OxyS overexpression in  wild type (WT) and hfq- were generated by deep sequencing using Illumina HiSeq 2500.


title: Gene expression signatures of chemotherapy-induced neuropathy induced by vincristine, cisplatin and oxaliplatin

first: Alexander

last: Mueller

address: 306 Carmody Rd

department: Institute for Molecular Bioscience

institute: University of Queensland


title: Targeting kidney proximal tubules by protein nanocages via glomerular filtration

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: Nature exploits cage-like proteins for a variety of biological purposes from molecular packaging and cargo delivery to catalysis. These cage-like proteins are of immense importance in nanomedicine due to their propensity to self-assemble from simple identical building blocks to highly-ordered architecture and the design flexibility afforded by protein engineering. However, delivery of protein nanocages to the renal tubules remains a major challenge because of the glomerular filtration barrier, which effectively excludes conventional size nanocages. Here we show that DNA-binding Protein from Starved cells (Dps)—the extremely small archaeal antioxidant nanocage—is able to cross the glomerular filtration barrier and is endocytosed by the renal proximal tubules. Using a model of endotoxemia, we present an example of the way in which proximal tubule-selective Dps nanocage can limit the degree of endotoxin-induced kidney injury. This was accomplished by amplifying the endogenous antioxidant property of Dps with addition of a dinuclear manganese cluster. Dps is the first-in-class, protein cage nanoparticle that can be targeted to renal proximal tubules through glomerular filtration. In addition to its therapeutic potential, chemical and genetic engineering of Dps will offer a novel nanoplatform to advance our understanding of the physiology and pathophysiology of glomerular filtration and tubular endocytosis.

overall_design: C57BL/6J male mice were subjected to vehicle (control), Dps (18 mg/kg iv), or MnDps (18 mg/kg iv) for indicated durations.


title: Induction of alpha cell-restricted Gc in dedifferentiating beta cells contributes to stress-induced beta-cell dysfunction [RNA-seq]

first: Taiyi

middle: Diana

last: Kuo

address: 1150 St Nicholas Ave., Ste. 237

institute: Columbia University

summary: To identify effector genes of pancreatic beta cell dedifferentiation and dysfunction, we performed RNA expression in beta cells sorted from mice with multiparity-induced diabetes.

overall_design: We performed RNAseq in FAC-sorted beta cells from female mice. There are a total of 6 conditions: 3-month-old nulliparous WT and RIP-Cre/FoxO1 floxed (IKO) mice, 12-month-old nulliparous WT and IKO mice, and 12-month-old multiparous WT (labeled as NGT) and IKO (labeled as DM) mice.

middle: D


title: Identification of monocyte-like precursors of granulocytes as a mechanism for accumulation of PMN-MDSC in cancer [microarray]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) inhibit immune responses in cancer, limit the effects of therapies and promote tumor cell metastasis. Here, we have identified a new precursor that differentiates into granulocytes in vitro and in vivo yet belong to the monocytic lineage. We have termed these cells monocyte-like precursors of granulocytes (MLPG). Under steady state conditions MLPG were absent in the spleen and barely detectable in the bone marrow (BM). In contrast, these cells significantly expanded in tumor-bearing mice. Selective depletion of monocytic cells had no effect on the number of granulocytes present in naïve mice but decreased the population of PMN-MDSC in tumor-bearing mice by 50%. The expansion of MLPG was found to be controlled by the down-regulation of the protein Rb1 and not the IRF8 transcription factor that is known to regulate the expansion of PMN-MDSC from classical granulocytes precursors. In cancer patients, putative MLPG were found within the population of CD15 CD14+HLA-DR-/lo M-MDSC. CXCR1+CD15 CD14+HLA-DR-/lo cells lacked immune suppressive activity but had potential to differentiate to neutrophils in contrast to monocytes and CXCR1- suppressive M-MDSC. These findings describe a mechanism of abnormal myelopoiesis in cancer and suggest potential new approaches for selective targeting of MDSC.

overall_design: Microarray gene expression of monocyte-like precursors of granulocytes (MLPG) and granulocytic progenitors (GP)

first: Jerome

last: Mastio

first: Dmitry

last: Gabrilovich


title: Generating Patterned Kidney Organoids for Studying Development and Diseases [bulk RNA-Seq]

status: Public on May 29 2019

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

summary: Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. By single cell RNA-sequencing, we identify a subset of nephron progenitor cells as a potential source of the vasculature. Upon implantation into host mice, these kidney organoids undergo further structural and functional maturation, as demonstrated by the size-selective handling of dextran. Based on this differentiation platform, we establish an in vitro model of autosomal recessive polycystic kidney disease (ARPKD) by differentiating induced PSCs (iPSCs) from an ARPKD patient into 3D kidney organoids that develop tubule cysts in response to cAMP upregulation. The cystogenesis phenotype can be effectively prevented by gene correction or drug treatment. Our studies provide a versatile platform for studying human kidney development and diseases, and opens new avenues for modeling disease pathogenesis and performing patient-specific drug screening.

overall_design: Examination of transcriptome in human pluripotent stem cells-derived vascularized three-dimensional kidney organoids. Day 0 organoid (technical duplicate), Day 10 organoid (technical duplicate), Day 24 organoid (technical duplicate), 2-week implanted organoid (technical triplicate), 4-week implanted organoid (technical triplicate).

first: Yun

last: Xia


title: Induction of alpha cell-restricted Gc in dedifferentiating beta cells contributes to stress-induced beta-cell dysfunction [ChIP-seq]

summary: To identify effector genes of pancreatic beta cell dedifferentiation and dysfunction, we integrated analyses of histone methylation as a surrogate of gene activation status and RNA expression in beta cells sorted from mice with multiparity-induced diabetes.

overall_design: We performed H3K4me3 ChIPseq and H3K27me3 ChIPseq in FAC-sorted beta cells from female mice. There are a total of 6 conditions: 3-month-old nulliparous WT and RIP-Cre/FoxO1 floxed (IKO) mice, 12-month-old nulliparous WT and IKO mice, and 12-month-old multiparous WT (labeled as NGT) and IKO (labeled as DM) mice.


title: Expression data from bladder cancer cells T24 - treated with G9a siRNA or negative control siRNA

city: Shanghai

first: Jingya

last: Sun

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary:
Target genes regulated by G9a in bladder cancer cells T24
In this dataset, we include the expression data obtained from bladder cancer cells T24 treated with G9a siRNA or negative control siRNA. These data are used to obtain genes that are differentially expressed in response to G9a konckdown.

overall_design: 6 Total samples were analyzed. We generated the following pairwise comparisons: siNC and siG9a. Genes with P≤0.001 and a fold-change ≥1.5 were selected.

first: Jun

last: Yan


title: Selective Disruption of Core Regulatory Transcription [RNA-seq]

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs. Surprisingly, we find histone deacetylases (HDAC) to be an indispensable component of SE-driven transcription. While histone acetylation is a marker for active genes, over accumulation of acetylation selectively halts core regulatory transcription. We show this conundrum may in part be explained by a SE-specific need for resetting histones to maintain SE boundaries, to facilitate enhancer-promoter looping and high levels of transcription.

overall_design: RNA-seq data for FP-RMS cells treated with various concentrations of various small molecules modulators of epigenetic processes.

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Gene expression profiles of non-recurrent human glioblastoma tissues

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

institute: The Catholic University of Korea

summary: Samples were obtained from 52 non-recurrent GBM patients treated at Severance Hospital

first: Seok-Gu

last: Kang


title: Transcriptome profiling of Embryonic day 9.5 WT and Clpex mutant mice

first: Rolf

last: Stottmann

summary: Purpose: To determine the differentially expressed genes in the whole E9.5 Clpex mutant embryo, a hypomorph of Pgap2 of the glycosylphosphatidylinositol biosynthetic pathway.

overall_design: 5 WT and 5 Clpex mutant E9.5 embryos were snap frozen on dry ice. RNA was isolated and pooled samples of each genotype were used for paired-end bulk-RNA sequencing (BGI-Americas, Cambridge, MA). RNA-Seq analysis pipeline steps were performed using CSBB [Computational Suite for Bioinformaticians and Biologists: https://github.com/csbbcompbio/CSBB-v3.0]. CSBB   has multiple modules, RNA-Seq module is focused on carrying out analysis steps on sequencing data, which comprises of quality check, alignment, quantification and generating mapped read visualization files. Quality check of the sequencing reads was performed using FASTQC  (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). RNA-Seq reads for the mutant and wildtype were paired-end and had ~43 and ~31 million reads respectively.Differential expression analysis was carried out by EBSeq [https://www.biostat.wisc.edu/~kendzior/EBSEQ/]. Differential transcripts are filtered based on LogFC and p-value. Filtered DE transcripts are used for functional and pathway enrichment using toppgene [https://toppgene.cchmc.org/]

first: Lukacs

last: Marshall

first: Praneet

last: Chaturvedi


title: NanoString mRNA Profiling of Aptamer- and Antibody-Isolated CD8 Mock and CAR T Cells

city: Seattle

first: Suzie

last: Pun

state: WA

department: Bioengineering

institute: University of Washington

summary: The goal of this study was to see if isolating CD8 T cells from PBMCs with a DNA aptamer versus an antibody would have 1) any immediate transcriptional affect on freshly isolated T cells and 2) any downstream transcriptional affect on a manufactured CD19 CAR T cell product.

overall_design: There are a total of 18 samples, divided into three groups of 6 by day and cell type (D0, S1R1D14 mocks, S1R1D14 CD19 CAR). Within each group of 6, there are 3 biological replicates (i.e. separate donors) for both aptamer- and antibody-isolated cells. Furthermore, the 3 separate donors are the same between aptamer- and antibody-isolated cells and across the groups, enabling pair-wise comparisons. The antibody-isolated samples were thus considered the control/reference samples to which the aptamer-isolated samples were compared (donor-by-donor within each group) to.

first: Ian

last: Cardle

middle: H

first: Michael

last: Jensen


title: Gene expression profiling of the canine placenta during normal and antigestagen-induced luteolysis.

status: Public on May 27 2019

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Next-generation sequencing (RNA-Seq) was performed on canine placenta Placental samples collected at natural prepartum luteolysis were compared with those samples obtained from dogs at mid-pregnancy stage. Furthermore, in order to better understand the involvement of P4 and PGR-dependent downstream regulatory mechanisms during initiation of parturition in the dog, samples derived from dogs in which prepartum luteolysis/abortion was induced with the antigestagen aglepristone at mid-pregnancy, were included. With this approach the aim was to acquire new information that could be translated to clinical and breeding practice for more accurate patient management. The sample set derived from antigestagen-treated dogs was compared with mid-pregnant non-treated group that served as non-treated control. Finally, to identify differences in molecular events occurring in the placenta prior to natural parturition and/or abortion, placental transcriptomes of both groups were compared.

overall_design: Placentae from nine (n=9) clinically healthy, cross-breed bitches (aged 2-8 years) were included in this study. Animals were assigned to following experimental groups: 1) mid-gestation (days 35-40 of pregnancy; n=3); 2) natural prepartum luteolysis (n=3); 3) antigestagen-induced luteolysis (n=3). Dogs were mated 2 days after ovulation, which was determined by vaginal cytology and measurements of serum P4 concentrations (> 5ng/ml). Day of mating represented Day 0 of gestation. The time of natural prepartum luteolysis (Group 2) was ascertained by measurements of serum P4 beginning on day 58 of pregnancy, in 6h intervals. Under physiological conditions, parturition in dogs occurs 12-42h following the luteolytic P4 drop. Thus, when P4 levels dropped below 3ng/ml in three consecutive measurements indicating its prepartum decrease, the surgery was performed and the tissue samples were collected. Additionally, abortion was induced in bitches at mid-pregnancy (Group 3) using P4-receptor (PGR) blocker, aglepristone (Alizine®, Virbac, Bad Oldesloe, Germany) in dosage of 10 mg/kg bw, 2 times in 24h interval. The surgery and tissue collections were done 24h after the second treatment. All dogs used for the study were subjected to routine ovariohysterectomy. Following surgery, placentae were separated from uteri, rinsed with phosphate-buffered saline (PBS) and immersed in RNAlater® for 24h at +4°C. After 24h, tissue material was stored at -80°C until RNA isolation.

first: Marta

last: Nowak

first: Mariusz

last: Kowalewski


title: Selenium Deficiency is Associated with Pro-Longevity Mechanisms

city: Boston

first: Sun Hee

last: Yim

address: 77 Ave Louis Pasteur, RM435

institute: BWH/Harvard Medical School

summary: Selenium deficiency in mice is associated with pro-longevity mechanisms due to reduced amino acid levels and altered nutrient signaling

overall_design: Mice were fed with 0, 0.1, 0.4, 2.25 ppm selenium diet and metabolome, transcriptome, microRNA profiling were performed

first: Sun

first: Clary

last: Clish

first: Vadim

middle: N

last: Gladyshev


title: Single cell RNA-Seq of sorted nephron progenitor cells from pooled mouse kidneys

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

institute: WEHI

summary: Kidneys from multiple litters of Six2GFP+ E14.5 mouse embryos were pooled into three replicate tubes and dissociated in parallel. Six2GFP+ cells were isolated and processed for single cell sequencing using 10x Genomics technology. This resulted in a dataset of 7844 single cells representing the nephron progenitor population of the mouse kidney.

overall_design: High resolution single cell analysis of the nephron progenitor population in Six2GFP+ mice.

first: B

first: A

last: Combes


title: RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

summary: The goal of this study is to analyse the transcriptome of control hearts vs hearts lacking SRSF3 expression and to analyse binding preferences of SRSF3 in cardiac myocytes.

overall_design: SRSF3 KO and control mice were treated with 3 inyection of 1 mg 4-hydroxytamoxifen in non-consequtive days. Hearts were extracted 5 days after the last inyection. Three different hearts were included for each condition. Neonatal cardiomyocytes were extracted from C57BL/6 mice at P0 or P1.23 A total of 8 million cells were plated in 10 cm2 plates. The following day, cells were transfected with 15 µg of SRSF3-GFP modRNA using 21 µL Lipofectamine 2000. At 48 h post-transfection, cells were irradiated once with 100 mJ UV light (254 nm), and iCLIP was performed

first: Paula

last: Ortiz-Sánchez

first: Michaela

last: Müller-McNicoll

first: Enrique

last: Lara-Pezzi


title: Effect of chronic oxycodone self administration (SA) on gene expression in the adult male mouse brain

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Examining changes in gene expression in the dorsal and ventral striatum following chronic oxycodone SA

overall_design:
Two groups of adult male mice: one group (n=5-6) were allowed to self administer oxycoodne, another group (n=5-6) served as yoked saline control.

*** Please note that the submitter was unable to provide the raw data files for the following samples:
GSM3124429: CPU5P
GSM3124430: CPU6P
GSM3124431: CPU7P

first: Yong

last: Zhang

first: Matthew

last: Ranesi

first: Orna

last: Levran

last: Yuferov

first: Mary

last: Kreek


title: The bipartite TAD organization of the X-inactivation centre ensures opposing developmental regulation of Tsix and Xist

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions within the Xic that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically up-regulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X-inactivation. Our study illustrates how genomic architecture can hardwire the potential for mammalian developmental regulation by cis-regulatory landscapes.

overall_design: Genomic deletions and inversions were genereated in the Xic of mouse male ES cells (E14Tg2a) and female ES cells (PGK#106, PGK12.1-derived). Consequences of these inversions were analysed using high-throughput Chromosome Conformation Capture (5C and Capture-C), RNAseq and RAP.

first: Joke

middle: G

last: van Bemmel

first: Rafael

last: Galupa

first: Chris

last: Gard

first: Christel

last: Picard

first: James

last: Davies

first: Anthony

last: Szempruch

first: Yinxiu

last: Zhan

first: Zylicz

last: Jan

first: Elphege

last: Nora

first: Sonia

last: Lameiras

first: David

last: Gentien

first: Sylvain

last: Baulande

first: Luca

last: Giorgetti

first: Mitchell

last: Guttman

first: Jim

last: Hughes

first: Douglas

middle: R

last: Higgs

first: Joost

last: Gribnau

first: Edith

last: Heard


title: The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation

status: Public on May 25 2019

first: Hui

last: Zhang

address: Rd, Fenglin

institute: SIPPE

summary: we performed Hi-C to probe the nuclear organization patterns after genome duplication in Arabidopsis, In connection with RNA-Seq data and ChIP-Seq data, we found that the transcription of a group of genes is specifically affected by the chromatin interactions with epigenome dynamics.

overall_design: Performed Hi-C on autotetraploid and wide type Arabidopsis; examination of 2 different histone modifications H3K4me3 and H3K27me3 in autotetraploid and wilde type Arabidopsis, and RNA-seq also used to check the transcriptional changes in these two samples.

first: Ruiqin

last: Zheng

first: Yunlong

last: Wang

first: Yuda

last: Fang

first: Guoliang

last: Li


title: MUC1-C represses the RASSF1A tumor suppressor and activated Kras signaling in human carcinoma cells

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: RASSF1A encodes a tumor suppressor that inhibits RAS’RAF’MEK’ERK signaling and is one of the most frequently inactivated genes in human cancers. MUC1-C is an oncogenic effector of the cancer cell epigenome that is overexpressed in diverse carcinomas. We show here that MUC1-C represses RASSF1A expression in multiple types of KRAS wild-type and mutant cancer cells. Mechanistically, MUC1-C occupies the RASSF1A promoter in a complex with the ZEB1 transcriptional repressor. In turn, MUC1-C/ZEB1 complexes recruit DNA methyltransferase 3b (DNMT3b) to the CpG island in the RASSF1A promoter. Targeting MUC1-C, ZEB1 and DNMT3b thus decreases methylation of the CpG island and derepresses RASSF1A transcription. We also show that targeting MUC1-C downregulates KRAS signaling with decreases in MEK/ERK activation, which is of importance for RAS-mediated tumorigenicity. These findings define a previously unrecognized role for MUC1-C in suppression of RASSF1A and support targeting MUC1-C as an approach for inhibiting KRAS signaling.

overall_design: Using Lentiviral vector, a control shRNA hairpin and shRNA against MUC1-C were used to generate the stably silenced MUC1-C and control cell lines of BT-549 and A549 cells respectively.  Total RNA were isolated from 3 different sets of control shRNA and MUC1-shRNA for both BT549 and A549 cell types and used for RNA-seq library preparation.

first: Hasan

last: Rajabi

first: Donald

last: Kufe


title: Transcriptome-wide expression profile of yeast under different carbon sources

status: Public on May 24 2019

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Carbon source is the basic nutrition and is essential for yeast growth. We grew the yeast cells (BY4741 strain) under different carbon sources including glucose with different concentration, galactose and raffinose. We generated bulk-cell RNA-seq data and investigated the dynamics of gene expression profiles under different growth conditions. We also generated single-cell RNA-seq data for yeast cells under 2% glucose, and explored the heterogeneity of gene expression within a cell population.

overall_design: Saccharomyces cerevisiae BY4741 strain was used. The bulk-cell RNA-seq and single-cell RNA-seq data were generated for yeast cells under different growth media.

first: Yunhao

first: Kin

middle: F


title: (p)ppGpp promotes Enterococcus faecalis virulence in a murine model of catheter-associated urinary tract infection

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: In Firmicutes, the nutrient-sensing regulators (p)ppGpp, the effector molecule of the stringent response, and CodY work in tandem to maintain bacterial fitness during infection. Here, we tested (p)ppGpp and codY mutant strains of Enterococcus faecalis in a catheter-associated urinary tract infections (CAUTI) mouse model and used global transcriptional analysis to investigate the (p)ppGpp and CodY relationship. Absence of (p)ppGpp or single inactivation of codY led to lower bacterial loads in catheterized bladders, and diminished biofilm formation on fibrinogen-coated surfaces under in vitro and in vivo conditions. Single inactivation of the bifunctional (p)ppGpp synthetase/hydrolase rel did not affect virulence supporting previous evidence that association of (p)ppGpp with enterococcal virulence is not dependent on activation of the stringent response. Inactivation of codY in the (p)ppGpp0 strain restored E. faecalis virulence in the CAUTI model as well as the ability to form biofilms in vitro. Transcriptome analysis revealed that inactivation of codY restores, for the most part, the dysregulated metabolism of (p)ppGpp0 cells. While a clear linkage between (p)ppGpp and CodY with expression of virulence factors could not be established, targeted transcriptional analysis indicate that a possible association between (p)ppGpp and c-di-AMP signaling pathways in response to the conditions found in the bladder may plays a role in enterococcal CAUTI. Collectively, this study identifies the (p)ppGpp-CodY network as an important contributor to enterococcal virulence in catheterized mouse bladder and supports that basal (p)ppGpp pools promote virulence through maintenance of a balanced metabolism during adverse conditions.

overall_design: Examination of genes that are directly or indirectly controlled by (p)ppGpp and CodY in E. faecalis

first: Cristina

last: Colomer-Winter

first: Jose

middle: A

last: Lemos


title: Human CD4+CD103+ cutaneous resident memory T cells are found in the circulation of healthy subjects

first: Daniel

middle: J

last: Campbell

state: Washington

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Tissue-resident memory T cells (TRM) persist locally in non-lymphoid tissues where they provide front-line defense against recurring insults. TRM at barrier surfaces express the markers CD103 and/or CD69 which function to retain them in epithelial tissues. In humans, neither the long-term migratory behavior of TRM nor their ability to re-enter the circulation and potentially migrate to distant tissue sites have been investigated. Using tissue explant cultures, we found that CD4+CD69+CD103+ TRM in human skin can downregulate CD69 and exit the tissue. Additionally, we identified a skin-tropic CD4+CD69-CD103+ population in human lymph and blood that is transcriptionally, functionally and clonally related to the CD4+CD69+CD103+ TRM population in the skin. Using a skin xenograft model, we confirmed that a fraction of the human cutaneous CD4+CD103+ TRM population can re-enter circulation, and migrate to secondary human skin sites where they re-assume a TRM phenotype. Thus, our data challenge current concepts regarding the strict tissue compartmentalization of CD4+ T cell memory in humans.

overall_design: RNA-seq was performed on 5 populations of CD4+CD45RA-CLA+ T cells  sorted from human blood and skin (from 5 distinct healthy donors) based on expression of CD103 and CCR7.  19 total samples passed quality control checks and were included in subsequent analyses.

first: D

first: I

last: Gratz

first: B

last: Höllbacher

first: M

last: Klicznik

first: P

last: Morawski

first: S

last: Motley


title: Clonal replacement of tumor-specific T cells following PD-1 blockade [bulk RNA]

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

summary: Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients. However, the clonal origin of tumor-specific T cells following checkpoint blockade in patients remains unclear. Here, we performed paired single-cell RNA- and T cell receptor (TCR)- sequencing on site-matched tumors from patients with basal cell carcinoma (BCC) pre- and post-anti-PD-1 therapy. Tracking TCR clonotypes and transcriptome phenotypes revealed a coupling of tumor-recognition, clonal expansion, and T cell dysfunction: the response to treatment was accompanied by a clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, this response was not accompanied by an expansion of pre-existing tumor-specific T cell clonotypes; rather, expanded T cell clones post-therapy comprised novel clonotypes, which were not previously observed in the same tumor. Clonal replacement of T cells was preferentially observed in tumor-specific exhausted CD8+ T cells, compared to other distinct T cell phenotypes, and was more evident in patients who exhibited a clinical response to treatment. These results, enabled by single-cell multi-omic profiling of clinical samples, demonstrate that the chronic activation of pre-existing tumor-infiltrating T cells may limit their re-invigoration following checkpoint blockade, and that a successful response relies on the expansion of a distinct repertoire of tumor-specific T cell clones.

overall_design: CD4+ T helper cells were sorted as naive T cells (CD4+CD25-CD45RA+), Treg (CD4+CD25+IL7Rlo), Th1 (CD4+CD25-IL7RhiCD45RA-CXCR3+CCR6-), Th2 (CD4+CD25-IL7RhiCD45RA-CXCR3-CCR6-), Th17 (CD4+CD25-IL7RhiCD45RA-CXCR3-CCR6+), Th1-17 (CD4+CD25-IL7RhiCD45RA-CXCR3+CCR6+), and Tfh subsets (CXCR5+ counterparts of each). RNA-seq cDNA library construction was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with 2 ng of input RNA. Sequencing libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).

first: Kathryn

middle: E

last: Yost

first: Ansuman

middle: T

last: Satpathy

last: Wells

first: Yanyan

last: Qi

first: Robin

last: Kageyama

first: Chunlin

first: Kavita

last: Sarin

first: Ryanne

last: Brown

first: Samantha

last: Bucktrout

first: Mark

last: Davis

first: Anne


title: Clonal replacement of tumor-specific T cells following PD-1 blockade

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

overall_design: Refer to individual Series


title: The anti-cancer effects of cordycepin in MA-10 mouse laydig tumor cells

city: Tainan

first: Bu-Miin

last: Huang

address: No. 1, University Rd.

department: Cell Biology and Anatomy

country: Taiwan

institute: National Cheng Kung University

summary: Cordycepin, a 3-deoxyadenosine, a traditional Chinese medicine. Studies have demonstrated that cordycepin could  modulate multiple signaling pathways to induce cancer cell death. This study aims to determine  the genes regulated by Cordycepin and clarify the possible molecular mechanism underlying their action.

overall_design: MA-10 cells treated with Cordycepin 100uM or PBS (vehicle control) for 3 hours.

first: Bumiin

first: Bo-Syong

last: Pan

first: Ming-Min


title: Peer pressure from a Proteus mirabilis self-recognition system controls participation in cooperative swarm motility

status: Public on May 23 2019

city: Cambridge

first: Murray

last: Tipping

address: 16 Divinity Ave

department: MCB

institute: Harvard University

summary: A resident of animal intestines, Proteus mirabilis is a major cause of catheter-associated urinary tract infections and can cause recurrent, persistent infections. Swarming, which is a collective behavior that promotes centimeter-scale population migration, is implicated in colonization of bladders and kidneys. A regulatory factor of swarming is kin recognition, which involves the transfer of a self-identity protein from one cell into a physically adjacent neighboring cell. However, how kin recognition regulates swarming was previously unclear. We have now shown a mechanism linking kin recognition, swarm migration, and antibiotics tolerance: cells induce a transient antibiotics-tolerant, persister-like state in adjacent non-identical cells which in turn prevents non-identical cells from continuing to participate in collective swarming. These affected non-identical cells continue to exhibit large-scale gene expression suggesting an active shift into a different expression state. These data provide two key insights for the field. First, kin recognition can be a regulatory mechanism that acts with spatial and temporal precision. Second, induction into an antibiotics-tolerant state, instead of occurring stochastically, can be physically and spatially regulated by neighboring cells. These insights highlight the importance of further developing four-dimensional (time and X-, Y-, Z-axes) model systems for interrogating cell-cell signaling and control in microbial populations.

overall_design: RNA-Seq of mRNA taken from six different bacterial strains isolated from consolidating swarm colonies. Two biological repeats of each isolate are included. Samples "dids" were compared against wildtype "BB", "966" against "dids", and "didsE" and "Dex" against "comp". See https://www.biorxiv.org/content/10.1101/490771v1 for detailed experimental design.

first: Karine

last: Gibbs


title: RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

city: Aurora

first: Rytis

last: Prekeris

state: CO

address: 12801 East 17th Ave, Bldg RC1 S, Room L18-12402C, None

institute: University of Colorado Denver

summary: RNAseq analysis of cells that have accumulated post-abscission midbodies

overall_design: HeLa MKLP1-GFP cells were sorted into a low GFP population and high GFP population, denoting accumulation (or lack of thereof) of midbodies. For fed condiions, midbodies were isolated, plated onto cells, and flow sorted 24 hours later.

first: Eric

last: Peterman


title: Transcriptomic analysis of Mtb Erdman, MtbΔvirS and  MtbΔvirSComplement  upon acidic stress of pH4.5

city: New Delhi

first: Garima

last: Khare

state: Delhi

address: Benito Juarez Road

department: Biochemistry

country: India

institute: University of Delhi

summary: Since VirS was shown to be upregulated in acidic conditions and MtbΔvirS displayed defect in growth at pH4.5, we performed microarray at pH 6.6 and pH 4.5 to study the role of VirS in regulating gene expression at acidic pH.

sample_organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

overall_design: Early log phase grown cultures of Mtb Erdman, MtbΔvirS and MtbΔvirSComp were exposed to 7H9 media supplemented with ADC-Tween of pH of 6.6 and pH 4.5 for one hour at 37 degree at 200rpm. Mtb Erdman and MtbΔvirS, each had three replicates while MtbΔvirSComp has two replicates at both pH conditions i.e. pH 6.6 and pH 4.5. MtB  Erdman and  MtbΔvirSComp served as control for MtbΔvirS which was the test sample.

first: Swati

last: Singh

first: Anil

last: Tyagi


title: RNA sequencing, chromatin accesibility and ChIP seq analysis of BAP1 -/- human liver organoids

status: Public on May 22 2019

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: Liver organoids were engineered by CRISPR/Cas9 to introduce mutation in the BAP1 gene and profiled for changes in RNA expression, chromatin accessibility and histone marks

overall_design:
We genereated RNA-seq data, ATAC-seq data and H3K4me3-, H3K27me3-, H3K9me3- ChIP-seq data from WT and BAP1-/- human liver organoids and BAP1-/- after 24 hr rescue of BAP1 expression

There are no raw data available for sample GSM3713198 due to a server failure.

first: Benedetta

last: Artegiani

first: Lisa

last: van Voorthuijsen

first: Daniëlle

last: Seinstra

first: Inha

last: Heo

first: Pablo

last: Tapia

first: Carmen

last: López-Iglesias

first: Daniel

last: Postrach

first: Talya

last: Dayton

first: Rurika

last: Oka

first: Huili

last: Hu

first: Ruben

last: van Boxtel

first: Johan

last: H. van Es

last: Offerhaus

first: Peter

last: Peters

first: Jacco

last: van Rheenen

first: Michiel

last: Vermeulen

first: Hans

last: Clevers


title: Transcriptome sequencing of two Lake Baikal endemic (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) transcriptome species from the Baikal region subjected to different stressors: quantification by full assemblies

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

summary: The project aims at describing the transcriptome composition and differential expression of genes in response to different stressors (elevated temperature, heavy metals (cadmium) and organic pollutants (phenanthrene)).

sample_organism:
Eulimnogammarus verrucosus
Gammarus lacustris
Eulimnogammarus cyaneus

overall_design: Individuals of three amphipod species were subjected to temperature or chemical stresses. Mixed samples from different conditions were used to create de novo transcriptome assemblies with Trinity. After that, transcript quantiifcation was performed with salmon and further processed with the DESeq2 package for R.

first: Daria

last: Bedulina

first: Lorena

last: Rivarola‐Duarte

first: Denis

last: Axenov‐Gribanov

first: Anton

last: Gurkov

first: Yulia

last: Lubyaga

first: Kseniya

last: Vereshchagina

first: Jörg

last: Hackermüller

first: Steve

last: Hoffmann

first: Christian

last: Otto

first: Frank

last: Jühling

first: Stephan

last: Schreiber

first: Ekaterina

last: Madyarova

first: Zhanna

last: Shatilina

first: Lena

last: Jakob

first: Magnus

last: Lucassen

first: Franz

last: Sartoris

first: Hans‐Otto

last: Pörtner

last: Stadler

first: Till

last: Luckenbach

first: Maxim

last: Timofeyev