title: The long non-coding RNA LUCAT1 is a negative feedback regulator of the Interferon Response in humans (LPS dataset)

summary: Long non-coding RNAs (lncRNAs) are important regulators of biological processes including immune responses. In the immune system, the immunoregulatory functions of lncRNAs have been revealed in murine studies with limited understanding of lncRNAs and the immune response in humans. Here, we identified  lncRNA LUCAT1 as amongst the most dynamically regulated non-coding transcripts in human myeloid cells stimulated with lipopolysaccharide (LPS) and other activators of the innate immune response.

overall_design: samples were prepared from 3 individual donors, and treated with LPS for 0, 1, 2, 6 hours. Total RNA was extracted for RNA-seq

first: Jennie

last: Chan

first: Kate


title: The long non-coding RNA LUCAT1 is a negative feedback regulator of the Interferon Response in humans (IAV and HSV dataset)

status: Public on Feb 19 2020

city: Worcester

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

country: USA

institute: Umass Chan Medical

type: Expression profiling by high throughput sequencing

overall_design: samples were prepared from 2 individual donors, and infected with IAV PR8 or HSV 7134 for 0,  2, 6 hours. Total RNA was extracted for RNA-seq

first: Shiuli

last: Agarwal


title: Impaired tumor death receptor signaling drives resistance to CAR T cell therapy

status: Public on Feb 17 2020

city: St. Louis

first: Nathan

last: Singh

state: MO

institute: Washington University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: LSM2-8 and XRN-2 contribute to the silencing of H3K27me3 marked genes through targeted RNA decay II

status: Public on Feb 12 2020

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary:
The LSM2-8 complex specifically targets nuclear RNAs generated from loci bearing histone H3K27me3 for degradation through the exonuclease XRN-2
In fission yeast and plants RNA-processing pathways including co-transcriptional degradation of nuclear mRNAs contributes to heterochromatic gene silencing additionally to the well-known transcriptional repression, but it was not knownunclear if this extra level of regulation also to occur in metazoans. Here we report the discovery of a related pathway in somatic cells of the flatworm C. elegans. The highly conserved, RNA binding LSM2-8 complex is shown to silence selectively heterochromatic reporters and endogenous genes bearing the Polycomb mark H2K27me3. LSM2-8-mediated silencing is independent of H3K9me2/me3 but depends on mes-2, the Polycomb-like histone methyl transferase. LSM2-8-mediated silencing is detectable from early embryonic stages through adulthood. The LSM2-8 complex works cooperatively with XRN-2, a 5’-3’ exonuclease, and disruption of the pathway leads to stabilized targeted mRNAs. Developmental defects and premature death were observed in worms lacking LSM-8, and levels of H3K27me3 dropped slightly at Pc-targeted loci. LSM2-8-mediated silencing of H3K27me3-bound regions defines a new mechanism of selective heterochromatin gene silencing not previously shown for higher eukaryotes.

overall_design: Total RNA-seq in syncrhonized and sorted L1 larval stage of C.elegans with the genotypes:  wild-type, lsm-8 mutant. 50 bp single-end sequencing was done on an Illumina HiSeq 2500.

first: Anna

last: Mattout

first: Jan

last: Padeken

first: Christoph

middle: D

last: Schmid

first: Florian

last: Aeschlimann

first: Véronique

last: Kalck

first: Susan

middle: M

last: Gasser


title: Transcriptional profiling of CART19 cells exposed to WT and BIDko Nalm6 cells

summary: Cellular immunotherapy using T cells engineered to express chimeric antigen receptors targeting CD19 (CART19) leads to long-term remission in patients with B-cell malignancies1-5. Unfortunately, a significant fraction of patients demonstrate primary resistance to CART19 or experience relapse after achieving remission. Beyond loss of target antigen, the molecular pathways governing CART19 failure are unknown. Here we demonstrate that death receptors, cell surface signaling molecules that induce target cell apoptosis, are key mediators of leukemic resistance and CART19 failure. Using a functional CRISPR/Cas9-based genome-wide knockout screen6 in B-cell acute lymphoblastic leukemia (ALL), we identified the death receptor signaling pathway as a central regulator of sensitivity to CART19-induced cell death. In the absence of the pro-apoptotic death receptor signaling molecules BID or FADD, ALL cells were resistant to CART19 cytotoxicity, resulting in rapid disease progression in mice. We found that this initial resistance to cytotoxicity led to persistence of tumor cells, which drove the development of T cell dysfunction that further compromised anti-tumor immunity and permitted tumor outgrowth. We validated these findings using clinical samples collected from patients with ALL treated with CD19-targeted CAR T cells and found that expression of pro-apoptotic death receptor pathway genes in pre-treatment tumor samples correlated with CAR T cell expansion and persistence, as well as patient response and overall survival. Our findings indicate that tumor-intrinsic death receptor signaling directly contributes to CAR T cell failure.

overall_design:
Here we report whole transcriptome data of CART19 cells cultured with either WT or BIDko Nalm6 cells
CART19 cells were co-cultured with WT or BIDko Nalm6 cells for 15 days and then underwent RNA sequencing.


title: Colonic gene expression in healthy and C. rodentium-infected mice lacking epithelial MHCII

status: Public on Feb 08 2020

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

summary: We generated conditional knockout of MHCII in intestinal epithelial cells in C57BL/6 mice (I-AbΔIEC) and compared their colonic transcriptome in control and Citrobacter rodentium infected mice. I-AbWT or I-AbΔIEC mice were orally gavaged with Citrobacter rodentium DBS100

overall_design: Two genotypes (I-AbWT = Vil-Cre-negative I-Abfl/fl; I-AbΔIEC = Vil-Cre-positive I-Abfl/fl) x two treatments (non-infected vs. infected) (n=3 per group)

middle: R


title: Open chromatin landscape of pancreatic endocrine progenitors

status: Public on Apr 01 2020

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

summary: During embryonic development, islet progenitors are specified from pancreatic duct cells by transient expression of Neurog3, a transcription factor necessary and sufficient for initiation of islet development. To understand the dynamics of Neurog3-dependent endocrine cell fate determination, in this study we  used ATAC-Seq to identify accessible genomic regions of  purified duct, endocrine progenitor, and endocrine cells isolated from mice with varying Neurog3 dosage

overall_design: We bred mice that are wild type, heterozygous or null for Neurog3. In het and null animals, at least one wild type allele of Neurog3 has been replaced with a green fluorescent protein (GFP). Using flow cytometry we purified GFP expressing progenitor cells, endocrine cells, and duct cells from different genotypes and performed ATAC-Seq. We obtained on average 25 million paired-end reads that mapped uniquely to the genome. Our analysis revealed substantial reorganization of accessible regions in progenitor cells when Neurog3 is present. We found "footprints" in the regions that transition from closed to open state during endocrine differentiation and identify targets of Neurog3.

first: H

middle: E

last: Arda

first: Eliza

last: Duvall


title: LSM2-8 and XRN-2 contribute to the silencing of H3K27me3 marked genes through targeted RNA decay


title: Interleukin-4 induces neural stem cell plasticity by antagonizing Serotonin/HTR1 signaling that suppresses BDNF/NGFRA in adult zebrafish Alzheimer's disease model

status: Public on Jan 24 2020

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: In Alzheimer’s disease (AD), reduced neural stem cell (NSC) plasticity causes reduced neurogenesis. Therefore, supplying the brain with new neurons using endogenous neurogenic reservoir – NSCs - might counteract the progression of AD. However, the mechanisms that enhance NSC plasticity are unknown. We recently generated an AD model in adult zebrafish brain where NSCs could react by enhanced plasticity and neurogenesis, and identified Interleukin-4 (IL4) as a key factor underlying this ability. Although IL4 directly regulated NSCs through its receptor IL4R, it was not clear how IL4R-negative NSCs would enhance their proliferation. Here, by performing whole tissue and single cell transcriptomics, we report that IL4 regulates IL4R-negative NSCs through modulating tryptophan metabolism by reducing the availability of Serotonin (5-HT) that suppresses NSC plasticity. 5-HT receptor htr1+ is only expressed in periventricular neurons where 5-HT balances the expression of brain-derived neurotrophic factor (bdnf), which promotes NSC proliferation through its receptor NGFRA, which is predominantly expressed in IL4R-negative NSCs. AD conditions induce IL4 that reduce 5-HT levels, and suppresses the suppressive effect on BDNF levels. Elevated levels of BDNF activate, through NGFRA, the proliferative output of the IL4R-negative NSCs. 5-HT overexpression dramatically reduces BDNF and proliferative ability of NSCs. Our results identify a novel IL4-dependent balancing mechanism on NSC proliferation by 5-HT through an intermediary regulatory cascade via HTR1, and BDNF/NGFRA signaling between periventricular neurons and NSCs. Our findings mark the heterogeneity of NSCs in response to direct or indirect regulation by IL4 – a biomarker for neurodegeneration-induced NSC plasticity.

overall_design: 6 months old Tg(her4.1:EGFP) adult fish brains were injected with CPP or AB42 using CVMI method (Kizil etal, 2013). 48 hpi brains were dissected, dissocited and non-GFP (GFP-N) and GFP positive (GFP-P) cells were sorted with FACS. Following total RNA isolation, samples were sequenced with triple replicates on Illumina HiSeq 2000 platform (75 bp end-read).

first: Prabesh

last: Bhattarai

first: Mehmet

middle: I

last: Cosacak


title: LSM2-8 and XRN-2 contribute to the silencing of H3K27me3 marked genes through targeted RNA decay I

overall_design: Total RNA-seq in sorted L3 larval stage of C.elegans with four different genotypes:  wild-type, lsm-8 mutant , the double met-2 set-25 mutant (no H3K9me) and the triple lsm-8; met-2 set-25 mutant. 50 bp single-end sequencing was done on an Illumina HiSeq 2500.


title: ATAC profiling of CART19 cells exposed to WT and BIDko Nalm6 cells

overall_design:
Here we report ATAC sequencing data of CART19 cells cultured with either WT or BIDko Nalm6 cells
CART19 cells were co-cultured with WT or BIDko Nalm6 cells for 15 days and then underwent ATAC sequencing.


title: Structural clusters of histone H3 and H4 residues regulate chronological lifespan in Saccharomyces cerevisiae [RNA-seq]

status: Public on Dec 13 2019

city: Stellenbosch

first: Hugh

last: Patterton

address: Merriman Street

department: Center for Bioinformatics and Computational Biology

country: South Africa

institute: Stellenbosch University

summary: We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast.  Residues where substitution resulted in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres.  Other residues that had a more modest effect on lifespan extension were concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame.  Residues implicated in a reduced lifespan were buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the disk and that caused lifespan extension are known to interact with Sir3.  We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1 or Abf1 binding sites, whereas H3E50 does not.  The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan.  The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response.  This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that different clusters of H3 and H4 residues are involved in either binding to non-histone proteins, or in destabilizing the association of the nucleosome DNA, or disrupting binding of a H3-H4 dimer in the nucleosome, or disturbing the structural stability of the octamer, each category impacting on chronological lifespan through a different path.

overall_design: RNA-seq was performed on 16h cultures of WT H3, WT H4, H4K16Q, H4H18A and H3E50A mutant strains

middle: G


title: Single cell analyses of Amyloid-beta42 and Interleukin-4 on neural stem cell plasticity I

status: Public on Dec 04 2019

summary: The neural stem cell (NSC) reservoir can be harnessed for stem cell-based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid-β-42 (Aβ42)-induced experimental Alzheimer’s disease (AD) model. Interleukin-4 (IL-4) is also critical for AD-induced NSC proliferation. However, the mechanisms of this response have remained unknown. Using single-cell transcriptomics in the adult zebrafish brain, we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell-cell communication is altered through ligand-receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro-regenerative ability at single-cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro-regeneration in humans.

overall_design: Single cell analyses of zebrafish telencephalon by 10X Genomics

first: Andreas

last: Dahl


title: Stromal cell signature associated with response to neoadjuvant chemotherapy in locally advanced breast cancer

status: Public on Jan 18 2020

city: São Paulo

first: Maria Lucia

middle: Hirata

last: Katayama

state: São Paulo

address: Av Dr Arnaldo

department: Radiology and Oncology

country: Brazil

institute: Faculty of Medicine University São Paulo

summary: Background. There is evidence that the stromal compartment may influence breast cancer responsiveness to chemotherapy. Our aim was to detect a stromal cell signature (using a direct approach of microdissected stromal cells) associated with response to neoadjuvant chemotherapy in locally advanced breast cancer, considering tumor down staging (to at least ypT1a/b,ypN0), as the best response. Patients and methods. Forty four patients diagnosed with locally advanced breast cancer (29 classified as estrogen receptor (ER) positive and 15, as ER negative) were included. Neoadjuvant chemotherapy consisted of doxorubicin/cyclophosphamide, followed by paclitaxel. Response was defined as downstaging to maximum ypT1a-b/ypN0. Stromal cells were microdissected from fresh frozen tumor samples and gene expression profile was determined using Agilent SurePrint G3 Human Gene Expression Microarrays. Expression levels were compared using MeV (MultiExperiment Viewer) software, applying SAM (Significance analysis of microarrays). Gene set enrichment analysis was used to identify gene sets correlated with the phenotype downstaging. Results: After chemotherapy, nine patients presented disease downstaging to maximum ypT1a-b/ypN0. Using SAM test (FDR 17), 11 sequences were differentially expressed, all of which (except for H2AFJ) more expressed in responsive tumors. Gene list enrichment analysis revealed three genes involved in abnormal cytotoxic T cell physiology: TOX, LY75 and SH2D1A. Gene sets correlated with tumor downstaging (FDR < 0.01), were mainly involved in immune response or lymphocyte activation, both in ER positive and ER negative samples. Conclusion: In locally advanced breast cancer, stromal cells may present specific features of immune response that may be associated with chemotherapy response.

first: Maria-Lucia

middle: H

first: Rosimeire

last: Roela

first: Pedro-Adolpho

last: Serio

first: Maria-Aparecida

last: Folgueira


title: Structural clusters of histone H3 and H4 residues regulate chronological lifespan in Saccharomyces cerevisiae [Sir3 ChIP-seq]

status: Public on Dec 03 2019

overall_design: ChIP-seq analysis of Sir3 binding to WT, H3E50A, H4K16Q and H4H18A substitution mutations yeast strains after 1d and 6d stationary phase culture


title: Structural clusters of histone H3 and H4 residues regulate chronological lifespan in Saccharomyces cerevisiae


title: Identification of osteoclast coupling factors in humans reveals links between bone remodeling and energy metabolism II

status: Public on Dec 07 2019

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

summary:
Purpose:  Identification of osteoclast derived coupling factors using Denosumab as a biological probe
Method: harvested RNA from centrifuged bone biopsies (heterogeneous population containing bone lining cells, osteoblasts, osteoclasts and osteocytes, without in vitro culture
Results:  Identification of genes differentially regulated in denosumab treated participants that correlate with bone remodeling indices
Conclusions:  Using this approach we identified denosumab regulated genes that correlate with bone remodeling in the untreated participants and may represent novel osteoclast derived coupling factors. Of interest, we identified DPP4 to be suppressed in denosumab treated participants, providing a novel link between bone remodeling and energy metabolism.

overall_design: Examination of gene expression of centrifuged bone biopsies isolated three months after treatment with placebo or denosumab in post-menopausal women

first: Megan

last: Weivoda


title: Structural clusters of histone H3 and H4 residues regulate chronological lifespan in Saccharomyces cerevisiae [ChIP-seq]

overall_design: ChIP-seq analysis of Rap1 binding in 16h and 14d stationary phase culture


title: Profiling open chromatin regions in human myometrial tissues

status: Public on Nov 28 2019

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: The open chromatin regions of nonpregnant and term pregnant human myometrial tissues were assessed by ATAC-seq to gain insight on potential genome regulatory elements in vivo. patterns of accessible genome change between NP and TP myometrium, leading to altered enrichment of binding motifs for hormone and muscle regulators such as the progesterone receptor (PGR), Krüppel-like factors and MEF2A transcription factors.

overall_design: Three nonpregnant and three term pregnant myometrial specimens were subject to ATAC-seq analysis. Viable tissues were taken from myometrial margins at the time of hysterotomy performed for clinically indicated cesarean section. After washing each specimen briefly in phosphate buffered saline (PBS), pieces of myometrium are flash frozen. All specimens are stored at <-80°C until use. ATAC-seq was performed by the Active Motif.

first: San-Pin

last: Wu

first: Matthew

middle: L

last: Anderson

first: Tianyuan

last: Wang

first: Lecong

last: Zhou

first: Olivia

last: Emery

first: Xilong

last: Li

first: Francesco

middle: J

last: De Mayo


title: Transcriptomic profiles of nonpregnant and term pregnant human myometrial tissues

summary: The myometrium undergoes structural and functional remodeling during pregnancy. We hypothesize that myometrial genomic elements alter correspondingly in preparation for parturition. Human myometrial tissues from nonpregnant (NP) and term pregnant (TP) human subjects were subject to RNAseq, ATAC-seq and PGR ChIP-seq assays to profile transcriptome, assessible genome and PGR occupancy.

overall_design: Three nonpregnant and three term pregnant myometrial specimens were subject to RNA-seq analysis. Viable tissues were taken from myometrial margins at the time of hysterotomy performed for clinically indicated cesarean section. After washing each specimen briefly in phosphate buffered saline, pieces of myometrium are preserved by plunging them into ice-cold RNALater. All specimens are stored at <-80°C until use.


title: Endometrial transcriptome and PGR cistrome in cycling fertile women

status: Public on Nov 27 2019


title: Small RNA analysis from megakarocyte, platelet and their microparticles

status: Public on Nov 30 2019

city: Newark

first: Chen-Yuan

last: Kao

state: DE

address: 15 Innovation Way, Rm 243

institute: University of Delaware

type: Non-coding RNA profiling by high throughput sequencing

summary: Identify the key small RNAs in megakaryocytic microparticles (MkMPs) in MkMP-induced megakaryocytic differentiation

overall_design: Examination of small RNA profile of human megakaryocyte, platelet, megakaryocytic microparticle, and megakaryocyte-derived platelet-like particles via small RNA-Seqencing

first: Jinlin

last: Jiang

first: Eleftherios

middle: T

last: Papoutsakis


title: Endometrial transcriptome and PGR cistrome in cycling fertile women [ChIP-seq]

summary: We report the transcriptomic profile and PGR cistromic profile for endometrial biopsies obtained from fertile women during the proliferative and mid-secretory phase of the menstrual cycle

overall_design: RNA-seq analyses were conducted on whole-endometrium and epithelium during the proliferative and mid-secretory phases. In parallel, PGR ChIP-seq was conducted on whole endometrium during rhe proliferative and mid-secretory phases.

first: Ru-pin

last: Chi

first: Nyssa

last: Adams

first: San-pin

first: Steven

last: Young

first: Thomas

last: Spencer


title: Endometrial transcriptome and PGR cistrome in cycling fertile women [RNA-seq]


title: Genome-wide CRISPR/Cas9 guide library knockout screening in Nalm6 ALL cells under CART19 selective pressure

first: Nathan

last: Singh

overall_design:
We report the results of a genome-wide screen using the Brunello guide RNA library to edit the Nalm6 ALL cell line and then subject these cells to CART19 selective pressure to identify regulators of sensitivity to CART19 cytotoxicity.
Sequencing of Brunello-edited Nalm6 ALL after 24h (short-term) or 36 days (long-term) of co-culture (NTD) with control T cells or CART19 cells, each condition performed in duplicate.


title: Complementary transcriptomic analysis of human medullary thymic epithelial cells

status: Public on Nov 20 2019

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. We are using a proteogenomic approach, combining RNA-Sequencing and mass spectrometry, to discover TSAs. We performed RNA-Sequencing on human medullary thymic epithelial cells (mTECs) to use them as a "normal control" because they express most known genes and orchestrate T cell selection to induce central tolerance to MHC peptides coded by their vast transcriptome.

overall_design: Transcriptomic analysis of 2 human samples of medullary thymic epithelial cells  using Illumina Next seq 500.

first: Leslie

last: Hesnard

first: Claude

last: Perreault


title: Noncoding regions are the main source of targetable tumor-specific antigens

summary:
Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies.
Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq200. Using those RNA-Sequencing data to build a global cancer database for each sample, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs.
Results: We identified a total of 30 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, most of these TSAs derived from non-mutated yet cancer-restricted transcripts that can be shared by multiple tumors.
Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

overall_design: Transcriptomic analysis of 2 human samples of thymic epithelial cells and 4 human samples of medullary thymic epithelial cells  using Illumina Next seq 500.


title: Genes significantly down or Up-regulated upon RNF219 knockdown. [RNA-Seq]

status: Public on Nov 15 2019

city: Toulouse

first: Aude

last: Guenole

address: Université de Toulouse, UT3, Toulouse 31062, France

department: Centre de Biologie Integrative

country: France

institute: CNRS

summary: Purpose : to decipher the role a newly identified protein, RNF219, we performed a knock down of this protein and try to determine how it affect the global mRNA expression of the cells.

overall_design: mRNA expression in RNF219 Si-depleted Hela cells against control Hela Cells.

last: Guenolé

first: Fabien

last: Velilla

first: Aymeric

last: Chartier

last: Sardet

first: Martine

last: Simonelig

first: Bijan

last: Sobhian


title: A MYC/GCN2/eIF2alpha negative feedback loop limits protein synthesis to prevent MYC-dependent apoptosis in colorectal cancer

status: Public on Nov 04 2019

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: Tumours depend on altered rates of protein synthesis for growth and survival, suggesting that mechanisms controlling mRNA translation may be exploitable for therapy. Here, we show that loss of APC, which occurs almost universally in colorectal tumours, strongly enhances the dependence on the translation initiation factor eIF2B5. Depletion of eIF2B5 induces an integrated stress response and enhances translation of MYC via an internal ribosomal entry site. This perturbs cellular amino acid and nucleotide pools and strains energy resources and causes MYC-dependent apoptosis. eIF2B5 limits MYC expression and prevents apoptosis in APC-deficient murine and patient-derived organoids and in APC-deficient murine intestinal epithelia in vivo. Conversely, the high MYC levels present in APC-deficient cells induce phosphorylation of eIF2alpha via the GCN2 and PKR kinases. Pharmacological inhibition of GCN2 phenocopies eIF2B5 depletion and has therapeutic efficacy in tumour organoids, demonstrating that a negative MYC/eIF2alpha feedback loop constitutes a targetable vulnerability of colorectal tumours.

overall_design: RNA-seq analysis in a human colorectal cancer cell line with doxycycline-inducible restoration of full-length APC expression. Riboseq (samples titled Riboseq_Ribo*) and corresponding RNA-seq (samples titled Riboseq_RNA*) of shEIF2B5-3 and shCTR in SW480TetOnAPC cells. To identify genes that are required for the growth of APCdef, but not of APCres cells, a drop-out screen was performed in which SW480TetOnAPC cells were infected with a lentiviral shRNA library that targets 5,000 potentially druggable genes using 27,500 shRNAs.

first: Stefanie

last: Schmidt

first: David

last: Gay

first: Friedrich

middle: W

last: Uthe

first: Sarah

last: Denk

first: Madelon

last: Paauwe

first: Niels

last: Matthes

first: Markus

last: Diefenbacher

first: Sheila

last: Bryson

first: Fiona

middle: C

last: Warrander

first: Florian

last: Erhard

first: Carsten

middle: P

last: Ade

first: Apoorva

last: Baluapuri

first: Susanne

last: Walz

first: Rene

last: Jackstadt

first: Catriona

last: Ford

first: Georgios

last: Vlachogiannis

first: Nicola

last: Valeri

first: Christoph

last: Otto

first: Christina

last: Schülein-Völk

first: Katja

last: Maurus

first: Werner

last: Schmitz

first: John R

last: Knight

first: Elmar

last: Wolf

first: Douglas

last: Strathdee

first: Almut

last: Schulze

first: Christoph-Thomas

last: Germer

first: Andreas

last: Rosenwald

first: Owen

last: Sansom

first: Armin

last: Wiegering


title: Structural clusters of histone H3 and H4 residues regulate chronological lifespan in Saccharomyces cerevisiae [Other]

status: Public on Nov 09 2019

first: Hugh

last: Patterton

overall_design: Quantitation of yeast strain barcodes to determine level of each yeast strain in mixed pool


title: Early-life microbial exposure imprints the abundance of mucosal-associated invariant T cells and subsequent interactions modulate their function

status: Public on Oct 28 2019

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: How early exposure to the microbiota impacts long-term host immunity remains poorly understood. Here we show that the development of mucosal-associated invariant T (MAIT) cells depends on early-life exposure to microbes that synthesize riboflavin, such as Enterobacteriaceae. This microbial imprinting relies on a specific temporal window, after which MAIT cell development is permanently impaired. In adults, MAIT cells are a dominant population of IL-17A-producing lymphocytes within the skin that can subsequently respond to skin commensals in an IL-1 and antigen-dependent manner. Consequently, local activation of cutaneous MAIT cells promotes wound healing and limits skin inflammation. Together, our work uncovers a privileged interaction between defined members of the microbiota and MAIT cells that sequentially controls both tissue-imprinting and subsequent response to injury and inflammation.

overall_design:
Examination of CD4+CD25- T cells and MAIT T cells from skin of control  or S. epidermidis LM061-exposed mice.
Examination of MAIT cells from different tissues.

first: Michael

last: Constantinides

first: Yasmine

last: Belkaid


title: Modeling of aniridia-related keratopathy by CRISPR/Cas9 genome editing of human limbal epithelial cells and rescue by recombinant PAX6 protein

status: Public on Oct 22 2019

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

summary: Heterozygous PAX6 gene mutations leading to haploinsufficiency are the main cause of congenital aniridia, a rare and progressive panocular disease characterized by reduced visual acuity. Up to 90% of patients suffer from aniridia-related keratopathy (ARK), caused by a combination of factors including limbal epithelial stem-cell (LSC) deficiency, impaired healing response and abnormal differentiation. It usually begins in the first decade of life, resulting in recurrent corneal erosions, sub-epithelial fibrosis and corneal opacification. Unfortunately, there are currently no efficient treatments available for these patients and no in vitro model for this pathology. We used CRISPR/Cas9 technology to introduce into the PAX6 gene of LSCs a heterozygous nonsense mutation found in ARK patients. Nine clones carrying a p.E109X mutation on one allele were obtained with no off-target mutations. Compared to the parental WT-LSCs, heterozygous mutant LSCs displayed reduced expression of PAX6 and marked slow-down of cell proliferation, migration and detachment. Remarkably, addition to the culture medium of recombinant PAX6 protein fused to a cell penetrating peptide was able to activate the endogenous PAX6 gene and to rescue phenotypic defects of mutant LSCs, suggesting that administration of such recombinant PAX6 protein could be a promising therapeutic approach of congenital aniridia. More generally, our results demonstrate that introduction of disease mutations into LSCs by CRISPR/Cas9 genome editing allows creating relevant cellular models of ocular disease that should greatly facilitate screening of novel therapeutic approaches.

overall_design: Genome editing of aniridia-related keratopathy and rescue. Gene expression comparison between normal and genome-edited PAX6 mutation containing T-limba cells

first: Lauriane

middle: N

last: Roux

first: Isabelle

last: Petit

first: Romain

last: Domart

first: Jean-Paul

last: Concordet

first: Jieqiong

last: Qu

first: Huiqing

first: Alain

last: Joliot

first: Olivier

last: Ferrigno

first: Daniel

last: Aberdam


title: Deregulated Adhesion Program in Palatal Keratinocytes of Orofacial Cleft Patients

summary: Orofacial clefts (OFCs) are the most frequent craniofacial birth defects. An orofacial cleft (OFC) occurs as a result of deviations in palatogenesis. Cell proliferation, differentiation, adhesion, migration and apoptosis are crucial in palatogenesis. We hypothesized that deregulation of these processes in oral keratinocytes contributes to OFC. We performed microarray expression analysis on palatal keratinocytes from OFC and non-OFC individuals. Principal component analysis showed a clear difference in gene expression with 24 and 17% for the first and second component respectively. In OFC cells, 228 genes were differentially expressed (p<0.001). Gene ontology analysis showed enrichment of genes involved in β1 integrin-mediated adhesion and migration, as well as in P-cadherin expression. A scratch assay demonstrated reduced migration of OFC keratinocytes (343.6 ± 29.62 μm) vs. non-OFC keratinocytes (503.4 ± 41.81 μm, p<0.05). Our results indicate that adhesion and migration are deregulated in OFC keratinocytes, which might contribute to OFC pathogenesis.

overall_design:
We performed microarray expression analysis and QPCR on palatal keratinocytes from OFC and non-OFC individuals. In addition a functional scratch assay was performed.
Microarray expression study, cultured keratinocytes, QPCR, scratch assay

first: Aysel

last: Mammadova

first: Carine

last: Carels

first: Jie

first: Christian

last: Gilissen

first: Maria

last: Helmich

first: Zhuan

last: Bian

first: Johannes

last: Von den Hoff


title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a-deficient mice

status: Public on Oct 09 2019

first: Joseph

last: Gogos

address: 3227 Broadway, JGL Science Bldg, Quad 4A, Room L4-005

institute: Columbia University

summary: SETD1A, a histone methyltransferase, is a key schizophrenia susceptibility gene. Mutant mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics, accompanied by specific deficits in working memory that recapitulates SCZ-related alterations. We show that Setd1a targets mostly enhancers and reveal a striking overlap between Setd1a and Mef2 chromatin targets. Setd1a targets are highly expressed in pyramidal neurons and enriched for genes with postnatally-biased expression involved in synaptic structure and function. Notably, evolutionary conserved Setd1a binding sites and target genes are strongly associated with neuropsychiatric genetic risk burden. Reinstating Setd1a expression in adulthood rescues working memory deficits. We identify LSD1 as a major demethylase counteracting the effects of Setd1a methyl transferase activity and show that LSD1 antagonism in adult Setd1a-deficient mice results in a full rescue of the  behavioral abnormalities and axonal branching deficits. Our findings advance our understanding of how SETD1A mutations predispose to SCZ and point to therapeutic interventions.

overall_design: Setd1a-deficient mice

first: Stavros

last: Lomvardas

first: Jun

last: Mukai

first: Enrico

last: Cannavo


title: Villitis of unknown etiology in the human placenta

status: Public on Sep 30 2019

first: Alexey

middle: Aleksandrovich

last: Leontovich

address: 200 First street

department: Health Science Research

summary: Human placentas were collected following birth and formalin fixed paraffin embedded. Villitis of unknown etiology (VUE) cases were microdissected by laser capture microscopy for areas of high and low immune cell inflitration. RNA was extracted by Qiagen's RNeasy and run on Affymetrix U133 plus 2.0 arrays.

overall_design: 1:1 gestational aged matched cases (VUE) and controls

middle: A

first: Elizabeth-Ann

last: Enninga


title: Human Transcriptome Array 2.0 (HTA) from healthy colonic, colorectal adenoma and colorectal cancer tissue

status: Public on Sep 13 2019

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary: Whole transcriptome expression levels of healthy colonic, colorectal adenoma and colorectal cancer biopsy samples were analyzed by HTA 2.0 microarrays

overall_design: Biopsy samples were collected from 20 healthy colonic, 20 colorectal adenoma and 20 colorectal cancer tissue during routine colonoscopy. HTA 2.0 microarray experiments were performed according to the manufacturer’s instructions. 100 ng input total RNA samples were applied as staring material. For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix). Microarrays were washed and stained with GeneChip® Hybridization, Wash, and Stain Kit reagents according to FS450_0001 protocol using the Fluidics Station 450 instrument (Affymetrix). Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

first: Alexandra

last: Kalmár

first: Zsófia

last: Brigitta Nagy

first: Orsolya

last: Galamb

first: István

last: Csabai

first: András

last: Bodor

first: Barnabás

last: Wichmann

first: Gábor

last: Valcz

first: Barbara

last: Kinga Barták

first: Zsolt

last: Tulassay

first: Péter

last: Igaz

first: Bela

last: Molnar


title: Progesterone Receptor A Isoform Specific ChIP-Seq

status: Public on Aug 29 2019

first: Franco

last: Demayo

summary: Chromatin immunoprecipitation for the progesterone receptor (PGR) and sequencing was performed on Pgrcre/-mPRALsL/+ mice. These mice exhibit no endogenous PGR expression, yet exhibit constitutive expression of the PGR-A isoform in PGR positive tissues due to the presence of a conditional expression allele. Mice were ovariectomized, rested for two weeks, and treated with progesterone for 1 hour before harvesting and freezing whole uterine tissue.

overall_design: PGRA isform expressing mice were ovariectomized, rested for two weeks, and treated with progesterone for 1 hour before harvesting of whole uterine tissue.


title: Neuronal impact of patient-specific aberrant NRXN1α splicing [whole]

status: Public on Sep 10 2019

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

summary: We performed targeted long-read and short-read RNA sequencing to identify and quantify NRXN1 isoforms in human post-mortem dlPFC and hiPSC-neurons derived from controls and NRXN1+/- individuals. We also performed whole transcriptome RNA seuqencing and 10x genomics single cell sequencing to determine transcriptional changes in NRXN1+/- hiPSC-neurons compared to controls.

overall_design: To investigate transcriptomic changes in NRXN1+/- neural cells, whole transcriptome short-read RNAseq was performed  on hiPSC-NPCs and 6 week forebrain neurons (hiPSC-neurons) differentiated from multiple hiPSC clones derived from four control and four NRXN1+/- individuals totaling 40 unique samples. To examine the expression level of NRXN1 in the human brain, short-read RNAseq with three adult and one fetal human dlPFC sample. To examine specific hiPSC-derived neural cell types  short-read RNAseq was performed on NGN2-induced neurons (3 weeks of differentiation) and ASCL1/DLX2-induced GABAergic neurons (5 weeks of differentiation) from control and NRXN1+/- donors. We also examined changes in cell type composition and neuronal maturation using 10X Genomics single-cell sequencing of two control hiPSC-neuron and three NRXN1+/- hiPSC-neuron samples.

first: Erin

last: Flaherty

first: Gang

last: Fang

first: Kristen

last: Brennand


title: A male infertility mutation switches NANOS1 activity from anti-apoptotic to pro-apoptotic

status: Public on Aug 01 2019

city: Poznan

first: Jadwiga

last: Jaruzelska

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: While Nanos-mediated maintenance of germ cells in Drosophila and mice has been related to regulation of apoptosis, the relevance of these findings to human physiology is uncertain. We show here that the NM_199461.4(NANOS1_v001):c.[100C>A;240_242del]; NM_199461.4(NANOS1_i001):p.[(Pro34Thr);(Ser83del)] double mutation, which has previously been associated with a lack of germ cells in the testes of infertile patients, causes NANOS1 to functionally switch from being anti-apoptotic to pro-apoptotic in the human male germ cell line TCam-2.

overall_design: Transcriptome-wide analysis of apoptosis-related genes upon NANOS1 or NANOS3  overexpression in comparison to empty vector overexpressing Tcam-2 cells

first: D

middle: M

last: Janecki

first: E

last: Ilaslan

first: M

last: Smialek

last: Sajek

last: Kotecki

first: B

last: Ginter-Matuszewska

first: A

last: Spik

first: P

last: Krainski

first: J

first: K

last: Kusz-Zamelczyk


title: Circular RNAs expression profiles in canine mammary tumours

status: Public on Sep 23 2019

city: Guangzhou

first: Kun

last: Jia

address: Wushan Street

department: College of Veterinary Medicine

country: China

institute: South China Agricultural University

summary: We explored the expression profile of circRNAs in canine mammary tumours using high-throughput sequencing technology. In our study, we analysed the expression profiles of 3 pairs of canine mammary tumours and their adjacent normal tissues. The total RNA was extracted, and a RNA library was constructed. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses revealed that these genes were mainly concentrated in 14 biological pathways. We selected 11 validated circRNAs and further confirmed the existence of these circRNAs by qRT-PCR. The circRNA-miRNA network diagram was constructed by using Cytoscape software. We found a total of 14851 circRNAs and 106 differentially expressed circRNAs in canine mammary tumours and their adjacent normal tissues (fold change ≥ 2, P ≤ 0.05). There were 64 upregulated circRNAs and 42 downregulated circRNAs. The main GO functions were the regulation of the regulated secretory pathway, the regulation of neurotransmitter secretion and the positive regulation of phagocytosis. Most of these pathways were related to the cGMP-PKG (cyclic guanosine monophosphate) signalling pathway, the cAMP (cyclic adenosine monophosphate) signalling pathway and the OXYTOCIN signalling pathway. CircRNAs have the function of adsorbing miRNA, similar to a sponge, and we further constructed the interaction network of circRNAs and miRNAs. The screened source genes closely related to canine mammary tumours included RYR2, PDE4D, ROCK2, CREB3L2 and UBA3. The screened circRNAs related to canine mammary tumours included chr27:26618544-26687235-, chr26:8194880-8201833+, and chr17:7960861-7967766-.In conclusion, our study uncovered circRNA expression profiles in canine mammary tumours. Moreover, some circRNAs may be used as potential biomarkers for screening dogs with high-risk canine mammary tumours.

overall_design: Examination of the circRNAs  of 3 pairs of canine mammary tumours and their adjacent normal tissues.

first: Hebi

last: Chen

first: Huizhen

last: Li


title: High-throughput suppressor selection of a type I toxin-antitoxin system in Helicobacter pylori

status: Public on Aug 30 2019

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

institute: University of Bordeaux

summary: As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin–antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations. To fill this gap, we developed a systematic approach called FASTBAC-Seq (Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep Sequencing). Combining life/death phenotypic selection with next-generation sequencing, FASTBAC-Seq allows the rapid identification of loss-of- function (toxicity) mutations in toxin-encoding genes belonging to TA loci with nucleotide resolution. Here, we apply this new tool to study aapA3/IsoA3, a member of a new family of type I TA systems hosted on the chromosome of the major human gastric pathogen Helicobacter pylori.

overall_design: Amplicon DNA sequencing of strains transformed with PCR products of a wild-type or mutated toxin-antitoxin system; in both cases three biological replicate samples were sequenced (6 samples in total)

first: Sara

last: Masachis

first: Claire

last: Lays

first: Marion

last: Faucher

first: Sandrine

last: Chabas

first: Isabelle

last: Iost

first: Fabien

last: Darfeuille


title: The Bone Marrow Protects and Optimizes Immunological Memory during Dietary Restriction

status: Public on Aug 22 2019

first: Verena

last: Link

summary: Mammals evolved in the face of fluctuating food availability. How the immune system adapts to transient nutritional stress remains poorly understood. Here, we show that memory T cells collapsed in secondary lymphoid organs in the context of dietary restriction (DR) but dramatically accumulated within the bone marrow (BM), where they adopted a state associated with energy conservation. This response was coordinated by glucocorticoids and associated with a profound remodeling of the BM compartment, which included an increase in T cell homing factors, erythropoiesis, and adipogenesis. Adipocytes and CXCR4-CXCL12 and S1P-S1P1R interactions contributed to enhanced T cell accumulation in BM during DR. Memory T cell homing to BM during DR was associated with enhanced protection against infections and tumors. Together, this work uncovers a fundamental host strategy to sustain and optimize immunological memory during nutritional challenges that involved a temporal and spatial reorganization of the memory pool within ‘‘safe haven’’ compartments.

overall_design: Examiniation of T cells and whole tissue of dietary restriction versus normal condition with RNA-seq

first: Nicholas

last: Collins

first: Seong-Ji

last: Han

first: Michel

last: Enamorado

first: Yasmine

last: Belkaid


title: Induction of Pluripotency by Alternative Factors (RNA-Seq)

status: Public on Jun 18 2019

first: dongwei

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides  a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals.  Here we apply this logic to the design a seven factor combination, Jdp2, Jhdm1b, Mkk6, Glis1, Nanog, Essrb and Sall4 (7F), that reprogram MEFs to chimera competent iPSCs efficiently.  RNA- and ATAC-seq reveal differences between 7F and Yamanaka induced pluripotency, 7IP and YIP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

overall_design: Seven factor combination, Jdp2, Jhdm1b, Mkk6, Glis1, Nanog, Essrb and Sall4 (7F)

first: Bo

last: Wang


title: Directly Reprogrammed Human Neurons Identify a Pathogenic Mechanism of Valproic Acid at Early Developmental Stages

status: Public on May 28 2019

city: STANFORD

first: Cheen Euong

last: Ang

address: 265 Campus Drive

institute: Stanford

summary: Human pluripotent stem cells can be rapidly converted into functional neurons by ectopic expression of proneural transcription factors. Here we show that directly reprogrammed neurons, despite their rapid maturation kinetics, can model teratogenic mechanisms that specifically affect early neurodevelopment. We delineated distinct phases of in vitro maturation during reprogramming of human neurons and assessed the cellular phenotypes of valproic acid (VPA), a teratogenic drug. VPA exposure caused chronic impairment of dendritic morphology and functional properties of developing neurons, but not those of mature neurons. These pathogenic effects were associated with VPA-mediated inhibition of the histone deacetylase (HDAC) and glycogen synthase kinase-3 (GSK-3) pathways, which caused transcriptional downregulation of many genes, including MARCKSL1, an actin-stabilizing protein essential for dendritic morphogenesis and synapse maturation during early neurodevelopment. Our findings identify a developmentally restricted pathogenic mechanism of VPA and establish the use of reprogrammed neurons as an effective platform for modeling teratogenic pathways.

overall_design:
Examination of global transcriptional changes by chronic Valproic acid-exposure.
Article reference: STEM2658
NIHMS ID: NIHMS 1528543

first: C

first: Soham

last: Chanda

first: Thomas

last: Südhof


title: Neuronal impact of patient-specific aberrant NRXN1α splicing [targeted]

first: Shijia

last: Zhu

summary: We performed targeted long-read and short-read RNA sequencing to identify and quantify NRXN1 isoforms in human post-mortem dlPFC and hiPSC-neurons derived from controls and NRXN1+/- individuals.

overall_design: To identify and quantify NRXN1 isoforms targeted long-read (pacific biosciences) and targeted short-read (Illumina) was performed on 6 week forebrain hiPSC-neurons, adult and fetal dlPFC and NGN2-induced neurons (3 weeks of differentiation) and ASCL1/DLX2-induced GABAergic neurons (5 weeks of differentiation).

first: Erin

last: Flaherty

first: Gang

last: Fang

first: Kristen

last: Brennand


title: Epimutations in developmental genes underlie the onset of domestication in farmed European sea bass

status: Public on Jul 09 2019

city: Barcelona

first: Dafni

last: Anastasiadi

address: Pg. Marítim de la Barceloneta 37-49

department: Renewable Marine Resources

country: Spain

institute: Institute of Marine Sciences-CSIC

type: Methylation profiling by high throughput sequencing

summary: Domestication of wild animals induces a set of phenotypic characteristics collectively known as the domestication syndrome. However, how this syndrome emerges is still not clear. Recently, the neural crest cell deficit hypothesis proposed that it is generated by a mildly disrupted neural crest cell developmental program, but clear support is lacking due to the difficulties of distinguishing pure domestication effects from preexisting genetic differences between farmed and wild mammals and birds. Here, we use a farmed fish as model to investigate the role of persistent changes in DNA methylation (epimutations) in the process of domestication.We show that early domesticates of sea bass, with no genetic differences with wild counterparts, contain epimutations in tissues with different embryonic origins. About one fifth of epimutations that persist into adulthood are established by the time of gastrulation and affect genes involved in developmental processes that are expressed in embryonic structures, including the neural crest. Some of these genes are differentially expressed in sea bass with lower jaw malformations, a key feature of domestication syndrome. Interestingly, these epimutations significantly overlap with cytosine-to-thymine polymorphisms after 25 years of selective breeding. Furthermore, epimutated genes coincide with genes under positive selection in other domesticates. We argue that the initial stages of domestication include dynamic alterations in DNA methylation of developmental genes that affect the neural crest. Our results suggest a role for epimutations during the beginning of domestication that could be fixed as genetic variants and suggest a conserved molecular process to explain Darwin’s domestication syndrome across vertebrates.

overall_design: We analyzed genome-wide methylation and gene expression differences between wild European sea bass captured by speargun in the North-Eastern coast of Spain and European sea bass born in a hatchery and reared under farming conditions until adulthood. Genome-wide methylation patterns were analyzed by performing Reduced Representation Sequencing (RRBS) of four tissues representative of the embryonic layers: brain (ectoderm), muscle (paraxial mesoderm), testis (intermediate mesoderm) and liver (endoderm) from three wild and three farmed fish. In addition, we performed RRBS for three pools of five eggs each at 27-30 hours post fertilization spawned and fertilized by captive fish. Gene expression patterns were analyzed by RNA-seq in the brain, muscle, testis and liver of five wild and five farmed fish (seven testes of farmed fish). The RRBS and RNA-seq data of muscle and testis of wild fish are already published under the GEO Series accession number GSE104366.

first: Francesc

last: Piferrer


title: Induction of Pluripotency by Alternative Factors (ATAC-Seq)

last: Li


title: Identification of LncRNAs and mRNAs involved in renal ishchemia reperfusion injury

status: Public on May 21 2019

city: Shanghai

first: Ping

last: Jia

address: No. 180, Fenglin Road

department: Department of Nephrology

institute: Zhongshan Hospital, Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The identification of the expression patterns of long non‑coding RNAs (lncRNAs) and mRNAs in the kidney under normal and renal ischemia/reperfusion (IR) conditions is essential for understanding the genetic mechanisms underlying the pathogenesis of renal IR injury. Here, we have carried out a genome-wide long non-coding RNA  and mRNA microarray analysis in mice kidneys with IR. The data revealed that the expression profiles of lncRNAs and mRNAs in the kidneys differed markedly between the Sham group and IR group, and in total 276 differentially expressed (>2‑fold) lncRNAs (201 upregulated, 75 downregulated) and 267 mRNAs (192 upregulated, 75 downregulated) were identified. qRT-PCR analysis was performed to verify the expression patterns of several lncRNAs and mRNAs.We found a specific and strongly differentially expressed lncRNA, an renal ischemia-reperfusion (IR) injury associated RNA, termed lncRNA-IRAR, which was mainly located in tubular epithelia cells. In vitro and in vivo gain- or loss-of-function studies were performed to investigate the role of  lncRNA-IRAR during renal IRI. Moreover, an expression volcano map of the differentially expressed mRNAs showed that UCP1 was the most dramatically downregulated gene, and its role in oxidative stress and apoptosis was assessed both in vitro and in vivo. Genetic deletion of UCP1 was used to investigate the effects of UCP1 on ischemia -indued acute kidney injury in mice.

overall_design: Renal IRI was induced by bilateral renal pedicle clamping for 30 min (IR group). Sham-operated mice underwent the same surgical procedures but without occlusion of renal pedicle. Kidneys were harvested 24 h after renal IR. Three kidney samples from each group (Sham group and IR group) were analyzed.

first: Xiaoqiang

last: Ding

first: Xiaoli

last: Wu


title: A Phase II Randomized Trial of Neoadjuvant Trastuzumab or Lapatinib or the Combination of Trastuzumab and Lapatinib, Followed by Docetaxel and Carboplatin with Trastuzumab and/or Lapatinib in Patients with HER2+ Breast Cancer

status: Public on May 08 2019

city: Santa Monica

first: HSIAOWANG

last: CHEN

address: 2825 Santa Monica Blvd

institute: UCLA

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

overall_design: Refer to individual Series


title: A Phase II Randomized Trial of Neoadjuvant Trastuzumab or Lapatinib or the Combination of Trastuzumab and Lapatinib, Followed by Docetaxel and Carboplatin with Trastuzumab and/or Lapatinib in Patients with HER2+ Breast Cancer [Baseline]

summary: Adjuvant docetaxel, carboplatin, and trastuzumab (TCH) is a standard regimen for HER2+ breast cancer. Dual HER2-blockade with lapatinib (L) and trastuzumab demonstrated significant activity in the metastatic and neoadjuvant settings. This study evaluates neoadjuvant TC plus trastuzumab (H) and/or lapatinib (L). This study demonstrated a similar pCR rate with TCH and TCHL and a lower rate of pCR with TCL.  Treatment-related toxicity limited the ability for participants to receive protocol-specified chemotherapy and HER2-targeted therapy in the TCHL Arm.

overall_design:
Microarray experiments were conducted using the 2-color Agilent Whole Human Genome platform. Samples were collected before treatment at the time of diagnosis (baseline samples). Every adequate baseline sample was profiled against a breast tumor mixed reference pool. 110 patients had baseline samples which passed QC.  Samples were also taken after two weeks of treatment with the HER2-targeted biologic. (run-in samples). Each run-in sample was compared to the baseline sample from the same patient. 89 patients had adequate baseline and run-in samples. The Agilent feature extracted data was processed using the Rosetta Resolver Gene Expression system V 7.2.0 SP2.12. Data is available for each unique probe on the Agilent platform (total of 41000) and expressed as log 10 ratio of experimental to reference sample.  In the 110 baseline experiments the reference sample is the untreated breast tumor collected at diagnosis and the reference sample is the mixed breast tumor reference.  In the 89 run-in experiments, the experimental sample is the run-in sample taken after two weeks of treatment and the reference sample is the baseline sample taken at diagnosis from the same patient.

NOTE: the assigned treatment group and the final drug response is provided as sample characteristics; T=Docetaxel C=Carboplatin, H=trastuzumab, Ty=lapatinib,  RD=residual disease, PCR=Pathological complete Response defined as the absence of invasive cancer in the breast and axilla

first: Sara

last: Hurvitz

first: Chen

last: Hsiao-Wang

first: Dering

last: Judy

first: Slamon

last: Dennis


title: Unveil the transcriptional landscape at the Cryptococcus-host axis in mice and nonhuman primates

status: Public on Jun 28 2019

city: ShenYang

first: Li

last: Hailong

state: Liaoning

address: NO. 3-11, Wenhua Road, Heping District

institute: Northeastern University

summary: Pathogens and hosts require rapid modulation of virulence and defense mechanisms at the infection axis, but monitoring such modulations is challenging. In studying the human fungal pathogen Cryptococcus neoformans, mouse and rabbit infection models are often employed to shed light on the disease mechanisms but that may not be clinically relevant. In this study, we developed an animal infection model using the non-human primate cynomolgus monkey Macaca fascicularis. In addition, we systematically profiled and compared transcriptional responses between the infected mice and the cynomolgus monkey, using simultaneous or dual RNA next-generation sequencing. We demonstrated that there are shared but distinct transcriptional profiles between the two models following C. neoformans infection. Specifically, genes involved in immune and inflammatory responses are all upregulated. Osteoclastogenesis and insulin signaling are also significantly co-regulated in both models and disrupting an osteoclastogenesis-associated gene (OC-STAMP) or the insulin-signaling process significantly altered the host tolerance to C. neoformans. Moreover, C. neoformans was shown to activate metal sequestration, dampen the sugar metabolism, and control cell morphology during infection. Taking together, we described the development of a non-human primate model of cryptococcosis that allowed us to perform an in-depth analysis and comparison of transcriptome profiles during infections of two animal models and conceptually identify host genes important in disease responses. This study provides new insights in understanding fungal pathogenesis mechanisms that potentially facilitate the identification of novel drug targets for the treatment of cryptococcal infection.

sample_organism:
Macaca fascicularis
Mus musculus
Cryptococcus neoformans H99

overall_design: The paired-end dual RNA-seq was performed between Cryptococcus neoformans H99 and the rodent and primate host using three biological triplicates.

first: Hailong

first: Yanjian


title: A low level of expression of C-terminally truncated human FUS causes extensive changes in the spinal cord transcriptome of asymptomatic transgenic mice

status: Public on May 03 2019

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: A number of mutations in a gene encoding RNA-binding protein FUS was linked to the development of a familial form of amyotrophic lateral sclerosis known a FUS-ALS. C-terminal truncations of FUS by a nonsense or frameshift mutations lead to the development of FUS-ALS with a particularly early onset and fast progression. However, even in patients with this aggressive form of the disease the function of motor neurons is not noticeably compromised for at least a couple of decades suggesting that until accumulation in the cytoplasm of pathogenic FUS lacking its C-terminal nuclear localisation signal does not reach a critical threshold, motor neurons are able to tolerate its permanent production. In order to identify how the nervous system responds to low levels of pathogenic variants of FUS we produced and characterised a mouse line, L-FUS[1-359], with a low level of neuronal expression of a highly aggregation prone and pathogenic form of C-terminally truncated FUS. In contrast to mice with substantially higher level of expression of the same FUS variant that develop severe early onset motor neuron pathology, L-FUS[1-359] mice do not develop any sign of pathology even at old age. Nevertheless, we detected substantial changes in the spinal cord transcriptome of these mice comparing to the wild type littermates. We suggest that at least some of these changes reflect activation of cellular mechanisms compensating to potentially damaging effect of pathogenic FUS production. Further studies of these mechanism might reveal effective target for therapy of FUS-ALS and possibly, other forms of ALS

overall_design: Exploring differential gene expression between wild-type (4 samples) and transgenic samples (4 samples)


title: p63 cooperates with CTCF to modulate chromatin accessibility and architecture in skin keratinocytes

status: Public on Jun 21 2019

first: Jo Huiqing

last: Zhou

summary: Here we integrated multi-omics profiles including transcriptomics, DNA accessibility and capture Hi-C data to explore how p63 shapes local chromatin architecture in skin keratinocytes isolated from EEC syndrome patients. Surprisingly, we observed decreased chromatin accessibility in a number of DNA looping nodes which were co-mediated by p63 and CTCF. Our findings not only identified a new aspect of the bookmark function of p63, but also shed light on the disease mechanism underlined p63 dysfunction. Therefore, we propose p63 as a spatial genome organizer by modulating a subset of DNA loops with CTCF and therefore fine-tuning transcription programs required for skin keratinocytes.

overall_design: ATAC-seq, CTCF ChIP-Seq of both control and p63 mutant keratinocytes on the proliferation stage

first: Jieqiong

last: QU

first: Guoqiang

last: YI

first: Huiqing

last: ZHOU


title: Time-series reveals processes underlying colon inflammation and repair

status: Public on May 11 2019

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: To elucidated through an unbiased manner which genes and pathways are differentially regulated during mouse colonic inflammation followed by a tissue regeneration phase. In particular, we took advantage of the widely used dextran sodium sulfate (DSS)-induced model of colitis. This model is one of the few characterized by a phase of damage followed by a phase of regeneration. Therefore, this model gave the possibility to identify also sets of genes essential in the regeneration phase, a key step towards the resolution of the inflammation. In short, mice were exposed to DSS in the drinking water for 7 days, then allowed to recover for the following 7 days. During this period, we collected colonic tissue samples every second day to then be analyzed by RNA sequencing (RNA-seq). Next, we performed a RNA-seq analysis from colonic samples throughout the experiment and computed differentially expressed genes (DEGs) taking the complete kinetics of expression into consideration for p-value estimation using EdgeR.

overall_design: C57BL/6J female mice were treated with 2.5% DSS in order to induce colinic inflammation. 2-3 animals were sacrificed at different time points when the colonic tissue was collected.

first: Eduardo

last: Villablanca


title: Single-cell lymphocyte heterogeneity inadvanced Cutaneous T-Cell Lymphoma skin tumors

status: Public on May 10 2019

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Purpose: The heterogeneity of tumor cells presents a major challenge to cancer diagnosis and therapy. Cutaneous T cell lymphomas (CTCL) are a group of T lymphocyte malignanciesthat primarily affect skin. Lack of highly specific markers for malignant lymphocytes prevents early diagnosis, while only limited treatment options are available for patients with advanced-stage CTCL.Droplet-basedsingle-cell transcriptome analysis of CTCL skin biopsiesopens avenues for dissecting patient-specificT lymphocyte heterogeneity, providing a basis for identifying specific markers for diagnosis and cure of CTCL. Experimental Design: Single-cell RNA-sequencing was performed by Droplet-based sequencing (10X Genomics), focusing on 14,056 CD3+lymphocytes (448 cells from normal and 13,608 cells from CTCL skin samples) from skin biopsies of 5 patients with advanced-stage CTCL and 4 healthy donors.Protein expression of identified genes was validated in advanced-stage CTCL skin tumors byimmunohistochemistry and confocal immunofluorescence microscopy. Results: Our analysis revealed a large inter- and intra-tumor gene expression heterogeneity in the T lymphocyte subset, as well as a common gene expression signature in highly proliferating lymphocytes that was validated in multiple advanced-stage skin tumors. In addition, we established the immunological state of reactive lymphocytes and found heterogeneity in effector and exhaution programs across patient samples. Conclusions: Single-cell analysis of CTCL skin tumor samples reveals patient-specific landscapes of malignant and reactive lymphocytes within the local microenvironment of each tumor, giving anunprecedented view of lymphocyte heterogeneity and identifying tumor-specific molecular signatures, withimportant implications for diagnosis and personalized disease treatment.

overall_design:
5 CTCL samples were analyzed and 4 normal controls were analyzed.

***Raw data will be submitted to dbGaP***

first: Alyxzandria

last: Gaydosik

first: Tracy

last: Tabib

first: Larisa

last: Gerskin

first: Claire-Audrey

middle: Y

last: Bayan

first: James

middle: F

last: Conway

first: Robert

last: Lafyatis


title: Human dermal endothelial cells co-treated with dsRNA mimic poly IC and antimicrobial peptide LL-37

status: Public on Apr 02 2019

city: San Diego

first: Richard

last: Gallo

address: 9452 Medical Center Drive

department: Dermatology

institute: UCSD

summary: Next generation sequencing (RNA-seq) was used to study the global effects of co-treatment of endothelial cells with poly IC and LL-37. This lead to identification of differentially regulated genes and enriched pathways

overall_design: 2 samples

first: Nikhil

last: Kulkarni


title: Identification of genes whose expression is affected by ptc + dpp double RNAi in spider embryos

status: Public on Mar 15 2019

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

summary: In the spider Parasteatoda tepidariorum, Hedgehog (Hh) and Decapentaplegic (Dpp) signaling play key roles in the formation of the two major embryonic axes (Akiyama-Oda and Oda, 2010, Development 137, 1263-1273; Akiyama-Oda and Oda, 2006, Development 133, 2347-2357). Patched (Ptc), a receptor for Hh,functions as a negative regulator of Hh signaling. Double parental RNA interference (pRNAi) against spider homologs of ptc and dpp, Pt-ptc and Pt-dpp, respectively, results in severe defects in axis formation. In this microarray experiment, we attempted to identify candidate genes whose expressions are regulated by Hh and Dpp signaling during axis formation.

overall_design: The objective of this experiment was a screen for genes whose expressions might be affected by Pt-ptc + Pt-dpp double pRNAi in spider embryos. Oligonucleotide probes were designed based on accumulated P. tepidariorum EST and cDNA sequences and embedded in custom microarrays (12K x2). Total RNA was extracted from late stage 5 embryos derived from a mated female before and after injection of dsRNA targeted for Pt-ptc and Pt-dpp. Gene expression levels were compared between the untreated (normal) and the Pt-ptc + Pt-dpp pRNAi-treated (pd-RNAi) samples.  The same RNA sample was hybridized to the two different array platforms (GPL11390 and GPL11391).

first: Yasuko

last: Akiyama-Oda


title: NRF2 target gene expression profile in  primary human lung microvascular endothelial cells (HMVEC) and human erythroleukemia cells (K562) treated with dimethyl fumarate (DMF) and CDDO-Methyl Ester (CDDO-Me).

status: Public on Apr 30 2019

first: Chibueze

middle: Anthony

last: Ihunnah

state: Pennsylvania

address: Lothrop St, Pittsburgh, PA 15213

department: Medicine

type:
Expression profiling by array
Other

summary: We profiled  the expression of 104 NRF2 target genes in human erythroid progenitor cells and microvascular endothelial cells to assess spatiotemporal and drug-specific induction profiles for NRF2 target genes.

overall_design: Cells were treated with dimethyl fumarate or CDDO-Me for 6-12hrs. Total RNA was isolated according to standard methods. The gene expression profiling assay was conducted at the University of Pittsburgh Genomics Core with the nCounter gene expression system from Nanostring technologies.  The nCounter GX system is an automated platform designed by Nanostring which includes labeling, hybridization, data acquisition and processing.


title: Microarray Experiment for Swarnaprabha rice line in low light stress

status: Public on May 14 2019

city: Bhubaneswar

first: Madhusmita

last: Panigrahy

state: Orissa

address: Siksha O Anusandhan University

country: India

institute: Government

summary: To further understand the genomics of low light tolerance, Swarnaprabha rice line was subjected to low light or shade stress. The fully emerged panicles were samples at early grain filling stage and microarray was performed from the spikelets. Expression of 12 gene in different pathway were verified using real-time PCR reactions.

overall_design: Two control (normal day night grown) and two test (shade) grown samples were used for the experiment. The samples were prepared from spikelets of two panicles on the mother tillers of individual rice plants. Oryza sativa, Agilent's Rice Gene Expression  4x44k Array (AMADID: 064815) designed by Gneotypic Technology Private Limited, Bangalore

first: Kishore

last: Panigrahi

first: Bipin

last: Chand


title: Open chromatin in Sox2-EGFP-sorted cells of the embryonic mouse cochlear duct

city: Seattle

first: Olivia

last: Bermingham-McDonogh

state: WA

address: 1959  NE Pacific St box 357420

department: Biological Structure

institute: University of Washington

summary: Hearing loss is often due to the absence or the degeneration of hair cells in the cochlea. Understanding the mechanisms regulating the generation of hair cells may therefore lead to better treatments for hearing disorders. To elucidate the transcriptional control mechanisms specifying the progenitor cells (i.e. prosensory cells) that generate the hair cells and support cells critical for hearing function, we compared chromatin accessibility using ATAC-seq in sorted prosensory cells (Sox2-EGFP+) and surrounding cells (Sox2-EGFP-) from E12, E14.5 and E16 cochlear ducts. In Sox2-EGFP+, we find greater accessibility in and near genes restricted in expression to the prosensory region of the cochlear duct including Sox2, Isl1, Eya1 and Pou4f3. Furthermore, we find significant enrichment for the consensus binding sites of Sox2, Six1 and Gata3—transcription factors required for prosensory development—in the open chromatin regions. Over 2,200 regions displayed differential accessibility with developmental time in Sox2-EGFP+ cells, with most changes in the E12-14.5 window. Open chromatin regions detected in Sox2-EGFP+ cells map to over 48,000 orthologous regions in the human genome that include regions in genes linked to deafness. Our results reveal a dynamic landscape of open chromatin in prosensory cells with potential implications for cochlear development and disease.

overall_design: ATAC-seq on 2 cell types (Sox2-EGFP+ and Sox2_EGFP- cells) isolated from the cochlear duct at 3 developmental stages (E12, E14.5 and E16)

first: Brent

last: Wilkerson


title: Melanoma GEMM Tumors, untreated or vemurafenib treated (scRNASeq)

status: Public on Mar 08 2019

city: South San Francisco

first: Dorothee

last: Nickles

address: 1 DNA Way

institute: Genentech

summary: Emerging research suggests that multiple tumor compartments can influence treatment responsiveness and relapse, yet the search for therapeutic resistance mechanisms remains largely focused on acquired genomic alterations in cancer cells. Here, we show how treatment-induced changes occur in multiple tumor compartments during tumor relapse and can reduce benefit of follow-on therapies. By utilizing serial biopsies, next generation sequencing and single cell transcriptomics, we tracked the evolution of multiple cellular compartments within individual lesions during first-line treatment response, relapse and second-line therapeutic interventions in an autochthonous model of melanoma. We discovered that while treatment-relapsed tumors remained genetically stable, they converged on a shared resistance phenotype characterized by dramatic changes in tumor cell differentiation state, immune infiltration and extracellular matrix (ECM) composition. Similar alterations in tumor cell differentiation were also observed in more than half of our treatment-relapsed patient tumors. Tumor cell state changes were coincident with ECM remodeling and increased tumor stiffness, which alone was sufficient to alter tumor cell fate and reduce treatment responses in melanoma cell lines in vitro. Despite the absence of acquired mutations in the targeted pathway, resistant tumors showed significantly decreased responsiveness to second-line therapy intervention within the same pathway. The ability to preclinically model relapse and refractory settings - while capturing dynamics within and crosstalk between all relevant tumor compartments - provides a unique opportunity to better design and sequence appropriate clinical interventions. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is NGS2034.

overall_design: RNA isolated from cells sorted from an untreated melanoma tumor, a tumor that regressed on vemurafenib treatment and one tumor that progressed on vemurafenib treatment (genetically engineered mouse model).

first: Melissa

middle: R

last: Junttila


title: Whole Sequencing Of The Mitochondrial Genome Of Breast Tumor Tissue In Mexican-Mestizo Postmenopausal Women, With Different Body Mass Index

status: Public on Mar 31 2019

city: Ciudad de México

first: Nishi

middle: Alan

last: Adams-Reyes

state: Cuidad de México

address: AV. UNIVERSIDAD 3000

department: Faculty of Medicine

country: Mexico

institute: Universidad Nacional Autónoma de México

type: Genome variation profiling by genome tiling array

summary:
Mitochondrial and oxidative stress have been related to obesity and breast cancer, and this cancer is more frequent and more aggressive in postmenopausal women with obesity.
To investigate if Mexican-Mestizo postmenopausal women with breast cancer and obesity presented different somatic mutations in the mitochondrial DNA (mtDNA) when compared to women with normal body mass index.

overall_design: The whole mtDNA sequence was determined by MitoChip v2.0 mitochondrial resequencing array, and the analysis of data was performed using the GeneChip Sequence Analysis Software. Mitochondrial tumor DNA sequence was compared with matched leukocyte mtDNA sequence.

first: Ramón

last: Coral-Vázquez

first: Juan

last: Méndez

first: Alberto

last: Tenorio

last: Znteno

first: Vanessa

last: Villegas-Ruiz

first: Patricia

last: Canto


title: Small RNA-sequencing of primary fibrolamellar carcinoma (FLC), FLC patient-derived xenograft, and maturational liver lineage stages

status: Public on Mar 07 2019

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006 Vet Research Tower

country: USA

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a rare liver cancer. Here we characterized the small RNA expression landscape of primary FLC, a FLC patient-derived xenograft model, and normal maturational liver lineage stages

overall_design: Small RNA expression profiles were generated by high throughput sequencing using the Illumina HiSeq2000 platform

first: Timothy

last: Dinh

first: Matthew

last: Kanke


title: Epigenomic and lipidomic changes in Multiple Sclerosis patients with high Body Mass Index enhance the neurotoxic function of monocytes

status: Public on Jun 20 2019

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: The growing obesity “epidemic” has shed light on its negative impact on overall health status, not only in relation to cardiovascular disorders and metabolic syndrome, but also in regard to its influence on a variety of other health conditions, including autoimmune diseases, such as Multiple Sclerosis (MS). High Body Mass index (BMI) is a risk factor for MS, however, it is not known whether and how it could impact disease course. Several studies, including those on the Dutch Famine, have highlighted the role of epigenetic modifications in mediating phenotypic changes in response to metabolic shifts, suggesting that epigenetic changes could be a potential mechanism for BMI-driven differences in disease course. Using the Illumina 450K array, we identified genome-wide differences in DNA methylation between blood monocytes from therapy-naïve RRMS patients with high BMI compared to low BMI. Differences were subtle, however, were heavily skewed in the positive direction in the high BMI group, indicative of overall DNA hypermethylation. Further curation of differentially methylated genes, using stringent criteria, revealed enrichment in anti-inflammatory functions among the top hypermethylated genes. Thus, epigenomic changes related to inflammatory processes of monocytes are detected in MS patients with high BMI compared to those with low BMI and could potentially impact disease course by modulating immune-driven neurotoxicity.

overall_design: 23 Multiple Sclerosis patients with high Body Mass Index (25 and over) and 26 Multiple Sclerosis patients with low Body Mass Index (under 25) were recruited for the study. Monocytes were isolated from the blood of patients using CD14 beads and DNA extracted and bisulfite converted from the sorted cells. Genome-wide DNA methylation levels were assessed using Illumina Infinium HumanMethylation450 BeadChip.

first: Yunjiao

last: Zhu

first: Corey

last: Watson

first: Jimmy

last: Huynh


title: Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

status: Public on Dec 23 2018

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University


title: Application a Next generation sequencing to analysis differential gene expression for CRFK cell infected by CPV isolate from LaoPDR

status: Public on Jan 08 2019

city: Chaingmai

first: Soulasack

last: Vanamahaxay

state: chaingmai

address: 155m2 Maehia Dormitory

department: Veterinary Medicine

country: Thailand

institute: ChaingMai University

summary: We use the Next generation sequencing (RNAseq) to profiling gene expression of CRFK cell.The purpose of this study are to comparison of CRFK gene expression between uninfected and infected by CPV isolated from Laos PDR

overall_design: The experiment are divide in 4 isolate of CRFK cell samples, and  separate in 2 group of treatment, group one are CRFK normal cell as: CO1; CO2 and CRFK cell infected by CPV as a C22;VTE034 respectively

last: Vannamahaxay

first: Phongsakorn

last: Chuammitri

first: Prapas

last: Patchanee

first: Kidsadagon

last: Pringproa


title: Human dermal endothelial cells treated with sno U1 dsRNA and antimicrobial peptide LL-37

first: Richard

middle: L

last: Gallo

state: CA

summary: Next generation sequencing (RAN-seq) was used to study the global effects of co-treatment of endothelial cells with U1 and LL-37. This lead to identification of differentially regulated genes and enriched pathways

overall_design: 4 samples

first: Nikhil

last: Kulkarni


title: ATAC-seq on 14-d-old WT col-0 Arabidopsis thaliana roots carrying INTACT

summary:
Background:   There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus the accessibility of these loci for TF binding is highly regulated and determines where and when TF bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana, and define organ-specific regulatory sites and binding motifs of transcription factors at these sites.

Results:   We coupled the recently described INTACT (Isolation of Nuclei TAgged in specific Cell Types) and ATAC-seq (Assay for Transposase-Accessible Chromatin with highthroughput sequencing) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis, based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions, but are correlated with root-specific expression of distant genes. Importantly these gene-distant sites are enriched for binding motifs of TFs important for root development, as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel genedistant regulatory elements.

Conclusion:   By coupling the INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity, possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.

overall_design: Nuclei were isolated from transgenic Arabidopsis thaliana col-0 roots. Roots were harvested from 14-day old seedlings containing a single-plasmid INATCT system under the constitutive 35S promoter. ATAC-seq was performed on isolated nuclei.

first: Miriam

last: Tannenbaum

first: Avital

last: Sarusi-Portuguez

first: Ronen

last: Krispil

first: Michal

last: Schwartz

first: Olga

last: Loza

first: Jennifer

middle: I

last: Benichou

first: Assaf

last: Mosquna


title: Acetylation of cytidine in messenger RNA

status: Public on Nov 07 2018

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary:
Generation of the "epitranscriptome through post-transcriptional ribonucleoside modification embeds a layer of regulatory complexity into RNA structure and function. Here we describe N4-acetylcytidine (ac4C) as an mRNA modification that is catalyzed by the acetyltransferase NAT10. Transcriptome-wide mapping of ac4C revealed discretely acetylated regions that were enriched within coding sequences. Ablation of NAT10 reduced ac4C detection at the mapped mRNA sites and was globally associated with target mRNA down-regulation. Analysis of mRNA half-lives revealed a NAT10-dependent increase in stability in the cohort of acetylated mRNAs. mRNA acetylation was further demonstrated to enhance substrate translation in vitro and in vivo. Codon content analysis within ac4C peaks uncovered a biased representation of cytidine within wobble sites that was empirically determined to influence mRNA decoding efficiency. These findings expand the repertoire of mRNA modifications to include an acetylated residue and establish a role for ac4C in the regulation of mRNA translation.
Generation of the “epitranscriptome” through post-transcriptional ribonucleoside modification embeds a layer of regulatory complexity into RNA structure and function. Here we describe N4-acetylcytidine (ac4C) as a novel mRNA modification that is catalyzed by the acetyltransferase NAT10. Transcriptome-wide mapping of ac4C revealed discretely acetylated regions that were distributed across target mRNAs with the majority of peaks occurring within coding regions. Depletion of ac4C through NAT10 ablation revealed a relationship to gene expression wherein loss of ac4C was globally associated with transcript downregulation. The presence of ac4C within coding sequences was associated with elevated ribosome density and enhanced translation, as assessed in vivo and in vitro. In addition to expanding the repertoire of mRNA modifications to include an acetylated residue, these findings highlight a role for ac4C in the control of mRNA metabolism at the level of translation.

overall_design: Detection of acetylated cytide in RNA with immunoprecipitation (RIP), along with RNA-Seq, Ribo-Seq, and BRIC-Seq to analyze effects on RNA processing and stability.

first: Daniel

last: Arango

first: Najwa

last: Alhusaini

first: Allissa

last: Dillman

first: Thomas

middle: J

last: Sweet

first: Gavin

last: Hanson

first: Masaki

last: Hosogane

first: Wilson

last: Sinclair

first: Kyster

middle: K

last: Nanan

first: Mariana

middle: D

last: Mandler

first: Stephen

last: Fox

first: Thomans

middle: T

last: Zengeya

first: Thorkell

last: Andresson

first: Jordan

last: Meier

first: Jeffery

last: Coller

first: Shalini

last: Oberdoerffer


title: The  Tissue-Engineered Human Psoriatic Skin Substitute: A Valuable In Vitro Model to Identify Genes with Altered Expression in Lesional Psoriasis

status: Public on Sep 26 2018

city: Québec

first: Roxane

last: Pouliot

state: Québec

address: 1401, 18ème rue, aile R

institute: Centre de recherche en organogenese expérimentale de l'Université Laval/LOEX

summary:
Psoriasis is a chronic inflammatory skin disease for which no cure has emerged. Its complex etiology requires the development of an in vitro model representative of the pathology.
Various skin substitutes were produced by tissue-engineering using biopsies from normal, healthy donors, or from lesional or non-lesional skin samples from patients with psoriasis, and their gene expression profiles were examined by DNA microarray.

overall_design: Total RNA was isolated from five different healthy (18-, 22-, 23-, 38-, and 46-year old) and eight different psoriatic reconstructed skin substitutes (four lesional and four non-lesional (47-, 49-, 64-, and 70-year old))

first: Sylvain

last: Guérin

first: Jacques

last: Soucy

first: Manel

last: Benhassine

first: Mélissa

last: Simard

first: Claudia

last: Pouliot-Bérubé

first: Genevieve

last: Rioux


title: RNA-seq from roots of 14 day old col-0 Arabidopsis thaliana carrying INTACT

first: Ofir

last: Hakim

overall_design: Roots were harvested from 14-day old seedlings from transgenic Arabidopsis thaliana col-0 roots, containing a single-plasmid INATCT system under the constitutive 35S promoter. RNA was extracted using TRIZOL (Life Technologies) reagent and cleaned with RNA Clean & Concentrator™-5 (Zymo). Libraries were prepared for NGS sequencing with NEBNext RNA library prep kit (module E7530-E7490).

first: Miriam

last: Tannenbaum

first: Avital

last: Sarusi-Portuguez

first: Ronen

last: Krispil

first: Michal

last: Schwartz

first: Olga

last: Loza

first: Jennifer

last: Benichou

first: Assaf

last: Mosquna


title: Image-based profiling identifies compound induced phenotypes in patient-derived organoids

status: Public on Mar 03 2019

city: Heidelberg

first: Johannes

last: Betge

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

institute: German Cancer Research Center (DKFZ)

summary:
Patient derived organoids (PDOs) closely resemble individual tumor biology. They are thus promising models for drug discovery and precision medicine. Here, we describe high-throughput imaging and automated image analysis of PDOs. We generated PDOs from colorectal cancer patients. Subsequently, we treated them with >500 substances to capture almost 6 million images by confocal microscopy. We developed a software framework to analyze how perturbations alter the organization of multicellular PDOs. Therewith, we observed a rich spectrum of reoccurring phenotypes. Targeting cellular processes, including signaling by MEK, GSK3 or CDKs, led to distinct architectural changes. Also, we detected compound-induced phenotypes only present in subsets of PDOs with specific molecular alterations. Finally, PDO response to anticancer drugs matched the clinical course of corresponding patients. The presented high-throughput imaging workflow and data allow compound profiling with complex multicellular organoid models for drug discovery and personalized medicine.
We used microarrays to detail the global programme of gene expression underlying different lines of patient-derived colorectal cancer organoids.

overall_design: We measured total RNA from 16 human patient-derived colorectal cancer organoids.

first: Benedikt

last: Rauscher

first: Michael

last: Boutros


title: p63 controls the enhancer landscape during keratinocyte differentiation

status: Public on Dec 18 2018

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

institute: Radboud University

summary: Here we characterized the transcriptome and epigenome of control keratinocytes during differentiation. Epigenomic analyses showed that the temporal enrichment of p63 motifs in dynamic enhancers underscores the key role of p63 in orchestrating the enhancer landscape during keratinocyte differentiation. The cooperation between p63 and its co-regulating factors, such as RUNX1, is important for the finetuning of gene expression.

overall_design: RNA-Seq, H3K4me3 ChIP-Seq and H3K27me3 ChIP-Seq of keratinocytes during differentiation on day0(proliferation), day2(early differentiation), day4(mid differentiation) and day7(late differentiation). RUNX1 ChIP-Seq of keratinocytes at the proliferation stage(day0).

first: Jieqiong

last: Qu

first: Evelyn

middle: N

last: Kouwenhoven

first: Huiqing


title: Characterization of molecular response to Golimumab in Ulcerative Colitis by mucosal biopsy mRNA expression profiling: results from PURSUIT-SC induction study

status: Public on Dec 03 2018

city: Spring House

first: K

last: Li

address: 1400 McKean Road

institute: Janssen R&D

summary:
To evaluate the effects of induction treatment with an anti-TNF, golimumab (GLM), on gene expression in patients with moderately to severely active ulcerative colitis (UC), we performed mRNA microarray studies on colon biopsies from patients who participated in the PURSUIT-SC induction study and additional samples from 21 healthy subjects.  Comparisons were conducted between baseline UC (n=87) and healthy (n=21), and week 6 (n=75) vs. baseline (n=87) prior to treatment.
A significant difference was observed in mRNA expression between UC and healthy.
Significant expression modulations were identified in patients who responded to GLM at week 6, but not GLM-treated non-responders or placebo-treated subjects.

overall_design: Mucosal biopsy samples (162 UC from the PURSUIT-SC induction study and 21 healthy) were collected for RNA extraction and microarray analysis.

first: S

last: Telesco

first: Paul

last: Rutgeerts

first: William

last: Sandborn

first: C

last: Marano

first: Keying

last: Ma

first: Jewel

last: Johanns

first: Hongyan

last: Zhang

first: R

last: Strauss

first: Walter

last: Reinisch

first: J

last: Colombel

last: Brodmerkel


title: Drug synergy slows ageing and improves healthspan through IGF and SREBP lipid signaling

status: Public on Dec 17 2018

city: Singapore

first: Jan

last: Gruber

address: 5 Engineering Drive 1

department: Science/ Biochemistry

country: Singapore

institute: Yale-NUS College / NUS

summary: Pharmacological interventions directly modulating ageing would extend human healthspan, resulting in dramatic medical and economic benefits. Such interventions should be efficacious in adults and ideally repurpose drugs known to be safe. Here we show that dramatic lifespan extension can be achieved by targeting multiple, evolutionarily conserved ageing pathways using drugs already used in humans. Using this approach in C. elegans, we were able to slow ageing, improve healthspan and minimize trade-offs. We show that daf-2, daf-7 and sbp-1 (mammalian SREBP-1c) interact upstream of changes in lipid metabolism, resulting in increased monounsaturated fatty acid content and lifespan extension. For one combination, we observed evolutionary conservation in fruit flies. To the best of our knowledge, this is the largest lifespan effect ever reported for any adult-onset drug treatment in C. elegans. Drug repurposing approaches, by leveraging drugs already approved for humans, could lead to rapid translation of experimental results to clinical applications.

overall_design: A total of 53 samples are sequenced in three lanes. Lane one contains from sample 1 to sample 17 which includes all single drugs in triplicates and control in duplicate. Lane two contains from sample 18 to sample to sample 37 which includes six drug combinations in triplicates and control in duplicate. The third lane contains from sample 38 to sample 53 which includes  three drug combinations in triplicates, one drug combination in duplicate, eat-2 mutants in triplicates and control in duplicate.

first: Tesfahun

last: Dessale

first: Diogo

middle: G

last: Barardo


title: Sequential regulation of maternal mRNAs through a conserved cis-acting element in their 3'UTRs

status: Public on Sep 05 2018

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

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

overall_design: Refer to individual Series