title: Recapitulation of Prostate Tissue Cell Type-specific Transcriptomes by an in vivo Primary Prostate Tissue Xenograft Model

city: Buffalo

first: Yue

last: Wu

state: Ny

address: 665 Elm St

institute: Roswell Park Cancer Institute Dept or Urology

summary: Purpose: Validate the cell type specific (Epithelial, Endothelial, and Stromal) transcriptome profile between prostate primary tissue xenografts and of fresh prostate tissue.  Nude-Fox1nu mice were castrated and silastic tubing containing dry testosterone (T) was inserted providing “humanized” levels of circulating T.  5-8 pieces of fresh human prostate tissue was then inserted subcutaneously along the flank of the animal.  After 30 days the animal was euthanized and tissue was harvested.  Tissue from xenograft and from fresh human prostate was then enriched into endothelial, epithelial and the remaining stromal compartments using magnetic bead enrichment.  RNA-Seq was then preformed on cell types from both origins and the results compared to show the primary tissue xenograft model faithfully recapitulates transcriptomic profile of the human prostate for epithelial, endothelial and stromal cell types.

overall_design: total of 40 samples from 7 fresh human prostate tissue specimens and from primary tissue xenografts established from 9 fresh human prostate tissue specimens were used.

first: Nelson

last: Gross

first: Jianmin

last: Wang

first: Michael

middle: V

last: Fiandalo

first: Eduardo

middle: C

last: Gomez

first: Anica

last: Watts

first: Alejandro

last: Godoy

first: Gary


title: Placental microarray profiling reveals common mRNA and lncRNA expression patterns in Preeclampsia and Intrauterine Growth Restriction

status: Public on May 31 2020

city: Mexico City

first: Ivan

last: Salido-Guadarrama

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

summary: Preeclampsia (PE) and Intrauterine Growth Restriction (IUGR) are major contributor of perinatal morbility and mortality, these pregnancy disorders associated with placental ischemia and share many similar pathophysiological features. The aim of this study was to compare the placental gene expression profiles including mRNA and lnRNAs from pregnant women from four study groups; PE, IUGR, PE-IUGR and normal pregnancy (NP). Gene expression microarray analysis was performed on placental tissue obtained at the moment of delivery and results were validated using RTq-PCR. Differential gene expression analysis revealed that the largest transcript variation was observed in the IUGR samples compared to NP (n=461; 314 mRNAs: 252 up-regulated and 62 down-regulated) and 133 lncRNAs: 36 up-regulated and 98 down-regulated). We also detected a group of differentially expressed transcripts shared between the PE and IUGR samples compared to NP (n=39), including 9 lncRNAs with a high correlation degree (P <0.05). Functional enrichment of these shared transcripts showed that cytokine signaling pathways, protein modification and regulation of JAK-STAT cascade are over-represented in both placental ischemic diseases. These findings contribute to the molecular characterization of placental ischemia showing common epigenetic regulation implicated in the pathophysiology of  preeclampsia and Intrauterine Growth Restriction

overall_design: Gene expression profiles from placental samples obtained at the moment of delivery from four study groups were determined usign Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarrays (G4851C, Agilent Technologies). Group distribution consisted in: Intrauterin Growth restriction (n=7), Preeclampsia (n=7), Preeclampsia and Intrauterine Growth Restriction (n=6) and Normal Pregnancy (n=8). Diagnosis was stablished according to the ACOG, 2013 criteria. All samples were obtained from pregnant women with intact membranes, no clinical evidence of intrauterine infection, with singleton pregnancy and who delivered by cesarean section (C-section) with no evidence of active labor. RNA was extracted righ after colletion of fresh rinsed and washed fullthickness placental tissue  using RNeasy Fibrous Tissue Mini Kit (Quiagen). All RNA samples were evaluated for RIN and showed values ≧7.

first: Diana

last: Medina-Bastidas


title: RNA-seq analysis of the kidneys from WT and Tet2-/- mice

status: Public on May 28 2020

city: Shanghai

first: Hao

address: 180 Fenglin Road

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of Tet2 deficiency on the gene expression in mouse kidney tissues under baseline and ischemia reperfusion injuried conditions, we collected the healthy control and IR-insulted kidney tissues from WT and Tet2-/- male mice and performed RNA-seq analysis.

overall_design: Comparison of the mRNA profiles of the normal and ischemia reperfusion-insulted kidneys from 6-week-old WT and Tet2-/- male mice

first: Tan

last: Li


title: Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

city: New York

first: Steven

middle: Zvi

last: Josefowicz

state: NY

address: 1300 York Ave, Box 69

department: Laboratory of Epigenetics and Immunity

country: USA

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Complex organisms are able to rapidly induce select genes among thousands in response to diverse environmental cues. This occurs in the context of large genomes condensed with histone proteins into chromatin. The macrophage response to pathogen sensing, for example, rapidly engages highly conserved signaling pathways and transcription factors (TF) for coordination of inflammatory gene induction.  Enriched integration of histone H3.3, the ancestral histone H3 variant, is a feature of inflammatory genes and, in general, dynamically regulated chromatin and transcription. However, little is known of how chromatin is regulated at rapidly induced genes and what features of H3.3, conserved from yeast to human, might enable rapid and high-level transcription. The amino-terminus of H3.3 contains a unique serine residue as compared with alanine residues found in “canonical” H3.1/2. We find that this H3.3-specific serine residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along the gene-bodies of rapidly induced response genes in mouse macrophages responding to pathogen sensing. Further, this selective mark of stimulation-responsive genes directly engages histone methyltransferase (HMT) Setd2, a component of the active transcription machinery. Our structure-function studies reveal that a conserved positively charged cleft in Setd2 contacts H3.3S31ph and specifies preferential methylation of H3.3S31ph nucleosomes. We propose that features of H3.3, including H3.3S31ph, engage delegated mechanisms to afford selective and rapid transcription.

overall_design: Primary mouse bone marrow derived macrophages (BMDM) were used for NGS experiments. Briefly, BMDM were used unstimulated or following stimulation with S.typhosa LPS (100ng/mL) for the indicated period of time. Included in this submission are RNA-seq data for control DMSO treated BMDM in triplicate (60' and 120' LPS stimulation) as well as wild type, hypomorphic macrophage-like RAW264.7 cell lines, and CRISPR-generated H3f3a/H3f3b double knockout lines in duplicate (60' and 120' LPS stimulation). Included is also ChIP-seq data for time course in LPS stimulated BMDM (0', 60', 120') for H3S31ph, H3S28ph, H3K36me3, H3K36me2, H3K27ac, and H3.3.

first: Anja

last: Armache

middle: Z


title: Single-cell copy number analysis in melanoma

status: Public on May 29 2020

city: Los Angeles

first: Enrique

last: Velazquez-Villarreal

state: CA

address: 1450 Biggy Street

department: Translational Genomics

institute: USC

summary: We performed shallow single-cell copy number analysis across 1,475 cells from a melanoma COLO829 line, to resolve overall tumor complexity and clonality. We identified at least four major sub-clones by discriminant analysis of principal components (DAPC). Re-analysis of previous spectral karyotyping data recapitulated these sub-clone hallmark features and explains why previous experiments generated conflicting results. Overall, our results demonstrate how single cell sequencing can uncover significant hidden insights in a melanoma sample.

overall_design: Copy number of analysis of 1,475 cells from COLO829 melanoma

middle: I

first: David

middle: W

last: Craig


title: Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells [ATAC-seq]

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

summary: We purified seven different cell populations and performed RNA sequencing to profile transcriptional similarities and differences between them. The seven cell types were 1) Atoh1-GFP positive cochlear hair cells from the organ of Corti of postnatal day one mice, 2) Atoh1-GFP negative cells from the organ of Corti of postnatal day one mice, 3) Atoh1-GFP positive induced hair cells generated by overexpression of Six1, Atoh1, Pou4f3, and Gfi1, 4) dsRed transduced control mouse embryonic fibroblasts, 5) Atoh1-GFP positive Merkel cells from postnatal day 1 mice, 6) Atoh1-GFP positive Cerebellar granule precursor cells from postnatal day 1 mice, and 7) Atoh1-GFP positive Gut secretory cells from postnatal day one mice.

overall_design: Compare chromatin accessibility of induced hair cells generated by direct reprogramming of mouse embryonic fibroblasts to control mouse embryonic fibroblasts and primary P1 cochlear hair cells.

first: Louise

last: Menendez

first: Talon

last: Trecek

first: Litao

last: Tao

first: Justin

last: Ichida


title: Genome-wide epigenetic analysis of Japanese immigrant plantation workers with Parkinson’s Disease

city: Honolulu

first: Maarit

last: Tiirikainen

state: HI

address: 701 Ilalo St, Genomics Shared Resource

institute: UHCC

summary: Parkinson’s Disease (PD) is a disease of the central nervous system that progressively affects the motor system.  Epidemiological studies have provided evidence that exposure to agriculture-related occupations or agrichemicals elevate a person’s risk for PD. Here, we sought to examine the possible epigenetic changes associated with working on a plantation on Oahu, HI and/or exposure to organochlorines (OGC) in PD cases. We measured genome-wide DNA methylation using the Illumina Infinium HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n=20) assessed for years of plantation work and presence of organochlorines in brain tissue. The comparison of 10+ to 0 years of plantation work exposure detected 7 and 123 differentially methylated loci (DML) in brain and blood DNA, respectively (P<0.0001). The comparison of cases with 4+ to 0-2 detectable levels of OGC, identified 8 and 18 DML in brain and blood DNA, respectively (P <0.0001). Pathway analyses revealed links to key neurotoxic and neuropathologic pathways related to impaired immune and proinflammatory responses as well as impaired clearance of damaged proteins, as found in the predominantly glial cell population in these environmental exposure-related PD cases.

overall_design: Genome-wide DNA methylation was analyzed using the Illumina HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n=20) assessed for years of plantation work and presence of organochlorines (OGC count) in brain tissue.

first: Rodney

last: Go

first: Michael

middle: J

last: Corley

first: G

last: Ross

first: Helen

last: Petrovitch

first: Kamal

middle: H

last: Masaki

first: Alika

middle: K

last: Maunakea

first: Qimei

last: He


title: Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells [RNA-seq]

overall_design: Compare induced hair cells generated by direct reprogramming of mouse embryonic fibroblasts to additional cell types (primary P1 cochlear hair cells, control mouse embryonic fibroblasts, P1 Merkel cells, P1 cerebellar granule precursors, and P1 gut secretory cells).


title: Argonaute Binding within 3’-Untranslated Regions Does Not Predict Gene Repression

status: Public on May 27 2020

city: DALLAS

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

summary: Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: 1) Knockout of argonaute (AGO) variants; 2) RNA sequencing analysis of gene expression changes; and 3) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identify potential microRNA (miRNA) binding sites. We find that knocking out AGO1, AGO2, and AGO3 are necessary to achieve full impact on gene expression. eCLIP-seq reveals several hundred significant AGO2 associations within 3’-untranslated regions. The standard mechanism of miRNA action would suggest that these associations repress gene expression. Contrary to this expectation, associations between AGO and RNA are poorly correlated with gene repression in wild-type versus knockout cells. Many clusters are associated with increased gene expression in wild-type versus knock out cells, including the strongest cluster within the MYC 3’-UTR. Our results suggest that assumptions about miRNA action should be re-examined.

overall_design: Total 23 samples, including 15 for standard transcriptome-type RNA-seq and 8 for eCLIP-seq

first: Yongjun

last: Chu

first: Audrius

last: Kilikevicius

first: Jing

last: Liu

first: Krystal

last: Johnson

first: Shinnichi

last: Yakota

middle: R


title: Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells [ChIP-seq]

first: Neil

last: Segil

overall_design: Examine primary P1 cochlear hair cells H3K27 acetylation.

first: Louise

last: Menendez

last: Trecek


title: Enhancer Regulation in Kidney Repair [RNA-Seq 2]

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: The endogenous repair process of the mammalian kidney allows rapid recovery after acute kidney injury (AKI) through robust proliferation of tubular epithelial cells. There is currently limited understanding of which transcriptional regulators activate these repair programs and how transcriptional deregulation leads to maladaptive repair. Here we investigate the existence of enhancer dynamics in the regenerating mouse kidney.

overall_design: RNA-Seq and ChIP-Seq (H3K27ac, H3K4me3, BRD4, POL2) were performed on samples from repairing kidney cortex 2 days after ischemia/reperfusion injury (IRI) to identify activated genes, transcription factors, enhancer and super-enhancers associated with kidney repair.

first: Julia

last: Wilflingseder


title: Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells

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

overall_design: Refer to individual Series


title: Enhancer Regulation in Kidney Repair


title: Effects of repetitive Iodine Thyroid Blocking on the Foetal Brain and Thyroid in rats: a Systems Biology approach

status: Public on May 30 2020

city: Fontenay-aux-Roses

first: Maâmar

last: Souidi

address: 31 Avenue de la Division Leclerc

country: France

institute: IRSN


title: Enhancer Regulation in Kidney Repair [ChIP-seq]

overall_design: RNA-Seq and ChIP-Seq (BRD2, BRD3, GR, HNF4A, STAT3, STAT5) were performed on samples from repairing kidney cortex 2 days after ischemia/reperfusion injury (IRI) to identify activated genes, transcription factors, enhancer and super-enhancers associated with kidney repair.


title: Inhibition of ABL1 tyrosine kinase reduces HTLV-1 in peripheral blood mononuclear cells from HTLV-1-associated myelopathy/tropical spastic paraparesis patients

status: Public on May 26 2020

city: Kagoshima-Shi

first: Daisuke

last: Kodama

state: Kagoshima-Ken

address: Sakuragaoka 8-35-1

department: Joint Research Center for Human Retrovirus Infection, Kagoshima University Campus

country: Japan

institute: Kagoshima University

summary: Human T-cell leukemia virus type 1 (HTLV-1) causes incurable adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Patients with HAM/TSP have increased levels of HTLV-1-infected cells compared with asymptomatic HTLV-1 carriers. However, the roles played by cellular genes in HTLV-1-infected CD4+ T cells await discovery. We combined microarray data and pathway analysis, and found that the ABL1 tyrosine kinase gene is a critical gene in HAM/TSP. ABL1 is a known survival factor for T- and B-lymphocytes. ABL1 is also part of the fused gene (BCR-ABL) known to be responsible for chronic myelogenous leukemia (CML), and tyrosine kinase inhibitors (TKI), including imatinib, nilotinib, and dasatinib, are in safe clinical use for treating CML. To evaluate whether ABL1 is indeed critical for the pathogenesis of HAM/TSP, we investigated the effect of ABL1 inhibitors on HTLV-1-infected cells. We developed a propidium monoazide-HTLV-1 viability quantitative PCR assay, which distinguishes DNA from live cells and DNA from dead cells. Using this method, we were able to measure the HTLV-1 proviral load (PVL) in live cells alone when peripheral blood mononuclear cells (PBMCs) from HAM/TSP cases were treated with TKI. Treating the PBMCs with nilotinib or dasatinib produced significant reductions in the PVL (21.0% and 17.5%, respectively) in live cells. Furthermore, a retrospective survey based on our clinical records found a rare case of HAM/TSP, where the patient also suffered from CML. The patient showed an 84.2% PVL reduction after CML treatment with imatinib. We conclude that inhibiting the ABL1 tyrosine kinase specifically reduced the PVL in PBMCs from patients with HAM/TSP, suggesting that ABL1 is a significant gene for the survival of HTLV-1-infected cells and that TKI may be a potential therapeutic agent for HAM/TSP.

overall_design: Human T-cell virus type 1 (HTLV-1) causes adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). We performed microarray experiments using GPL4133 Platform Agilent-14850 Whole Human Genome cDNA microarray G4112F (Feature number version, 85 columns x 532 rows) 1-color protocol (Cy3) and total RNA from HTLV-1 main reservoir, CD4+ T cells taken from patients with HAM/TSP (N=4), asymptomatic carriers (N=4), and HTLV-1 negative controls (N=4). Following to GeneSpring GX ver 7.3.1 manual, raw signal intensities data were filtered on flags and raw signal intensities less than 5.0 were set to 5.0. All signal intensities were transformed with base 2 log. For the per chip normalization, 50 percentile of transformed data were normalized to 1.0. By combination of differentially expressed genes up-regulated greater or less than 2-fold change only in HAM/TSP compared with NC and significant genes by 3 group comparison with one-way ANOVA (P < 0.01), we refined 310 genes. Furthermore, we identified 177 genes up-regulated only in HAM/TSP from these 310 genes by Venn mapping. Furthermore, these genes were mapped to pathway database TRANSPATH and performed Fisher’s exact test, we extracted 12 significant pathways. Eleven among these 12 pathways included ABL1 tyrosine kinase gene in common, therefore we decided this gene as the target to assay. Finally, we demonstrated that inhibition of ABL1 tyrosine kinase reduced HTLV-1 proviral loads in peripheral blood mononuclear cells from patients with HAM/TSP.

first: Masakazu

last: Tanaka

first: Toshio

last: Matsuzaki

first: Kimiko

last: Izumo

first: Nobuaki

last: Nakano

first: Eiji

last: Matsuura

first: Mineki

last: Saito

first: Masahiro

last: Nagai

first: Masahisa

last: Horinouchi

first: Atae

last: Utsunomiya

first: Hiroshi

last: Takashima

first: Ryuji

last: Kubota

first: Shuji


title: Transcriptome of ansamitocin P-3 producer Actinosynnema pretiosum ATCC 31280

status: Public on May 25 2020

first: yuanting

last: wu

address: 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: In submerged cultivation of filamentous microbes, including actinomycetes, complex morphology is one of the critical process features for secondary metabolites production. Ansamitocin P-3 (AP-3), an antitumor agent, is a secondary metabolite produced by Actinosynnema pretiosum ATCC 31280. An excessive mycelial fragmentation of A. pretiosum ATCC 31280 was observed during the early stage of fermentation. In order to identify genes involved in the early mycelial fragmentation, the total RNAs of mycelia collected at 15, 18, and 24 h were extracted and subjected to transcriptome sequencing using RNA-seq technology.Through comparative transcriptomic analysis, a subtilisin-like serine peptidase encoded gene APASM_4178 was identified to be responsible for the mycelial fragmentation. Mutant WYT-5 with the APASM_4178 deletion showed increased biomass and improved AP-3 yield by 43.65%.

overall_design: Exploration of the expression profile of genes in different mycelial morphology and search for mycelial fragmentation related genes. Three samples are analyzed.

first: Yuanting

last: Wu

first: Linquan

last: Bai


title: Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis via SYK activation

city: Leiden

first: Tom

last: van der Wel

address: Einsteinweg 55

department: Molecular Physiology

country: Netherlands

institute: Leiden University

summary: Comparative transcriptome profiling reveals that wild-type and CRISPR/Cas9-engineered FES_S700C HL-60 cells have highly similar transcript levels.

overall_design: Wild-type or FES_S700C mutant HL-60 cells, differentiated towards macrophages, followed by TempO-Seq analysis (Biospyder).


title: Elimination of rNMPs from mitochondrial DNA has no effect on its stability

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

summary: Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA), although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse lifespan and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1−/− mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their lifespan. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.

overall_design: Mapping ribonucleotides in DNA from mouse proficient and deficient in SAMHD1 with HydEn-seq (5´end sequencing of genomic fragments)

first: Paulina

last: Wanrooij

first: Phong

last: Tran

first: Liam

last: Thompson

first: Sushma

last: Sharma

first: Katrin

last: Kreisel

first: Clara

last: Navarrete

first: Anna-Lena

last: Feldberg

first: Danielle

last: Watt

first: Anna

last: Nilsson

first: Martin

last: Engqvist

first: Anders

first: Andrei

last: Chabes


title: GPSeq Reveals the radial organization of chromatin in the cell nucleus

city: Solna

first: Gabriele

last: Girelli

state: Stockholm

address: Tomtebodavägen 23A

department: MBB

institute: Karolinska Institutet / Science for Life Laboratory

summary: In eukaryotes, a significant portion of the genome consists of lamina-associated domains, which are preferentially located at the periphery of the cell nucleus. However, how exactly the remaining parts of the genome are radially organized in the nucleus remains largely unknown. Here, we describe a method named Genomic loci Positioning by Sequencing (GPSeq), which allows genome-wide measurements of the distance of genomic loci to the nuclear periphery. Using GPSeq, we generated reproducible maps of radial genome organization in human cells, at various resolutions, which revealed radial gradients of genetic and epigenetic features, gene expression, as well as A/B compartments and chromatin loops. We assessed the contribution of various features in predicting radiality, and found GC content to have the strongest predictive power. Finally, we show that by combining Hi-C with GPSeq information to radially position intra- and inter-chromosomal contacts revealed by Hi-C, we are able to make 3D genome structure predictions much more accurately than it was possible thus far. We conclude that GPSeq is able to reveal fundamental aspects of genome architecture.

overall_design:
4 GPseq experiments (Exp1-4) were performed in HAP1 cells. 2 experiments (Exp1-2) using HindIII enzyme and the following digestion times: 10 min, 15 min, 30 min, 1 h, 2 h. 2 experiments (Exp3-4) using MboI enzyme and the following digestion times: 1 min, 5 min, 10 min, 30 min. Additional times were performed for Exp1: 45 min and 6 h. Additionally, 2 GPSeq experiments (Exp5-6) were performed on GM06990 cells using HindIII enzyme and the following digestion times: 10 min, 15 min, 30 min, 2 h. Deposited GPSeq scores were calculated using the gpseqc (v2.3.6) pipeline, available on github: https://github.com/ggirelli/gpseqc . "estimated.tsv"; raw GPSeq score (prob_g column) estimated by gpseqc pipeline. "rescaled.tsv"; rescaled GPSeq score (prob_g column) estimated by gpseqc pipeline.

All deposited structures were generated starting from Hi-C data available from the 4DN project (accession #: 4DNFI1E6NJQJ); either (*10000.zip and *10000_intra.zip) using only Hi-C data, or (*10000G.zip and *10000G_intra.zip) integrating Hi-C and GPSeq data coming from the first experiment (Exp1) in this series (as briefly described in the chromflock.README file). The chromflock pipeline is available on github: https://github.com/elgw/chromflock

first: Joaquin

last: Custodio

first: Tomasz

last: Kallas

first: Federico

last: Agostini

first: Erik

last: Wernersson

first: Bastiaan

last: Spanjaard

first: Ana

last: Mota

first: Solrun

last: Kolbeinsdottir

first: Eleni

last: Gelali

first: Nicola

last: Crosetto

first: Magda

last: Bienko


title: Tumor invasion in draining lymph nodes is associated with Treg accumulation in breast cancer patients.

status: Public on May 22 2020

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary: Tumor-draining lymph node (TDLN) invasion by metastatic cells in breast cancer correlates with poor prognosis and is associated with local immunosuppression, which can be partly mediated by regulatory T cells (Tregs). Here, we study Tregs from matched tumor-invaded and non-invaded TDLNs, and breast tumors. We observe that Treg frequencies increase with nodal invasion, and express higher levels of co-inhibitory/stimulatory receptors than effector cells. Also, while Tregs show conserved suppressive function in TDLN and tumor, conventional T cells (Tconvs) in TDLNs proliferate and produce Th1-inflammatory cytokines, but are dysfunctional in the tumor. We describe a common transcriptomic signature shared by Tregs from tumors and nodes, including CD80, which is significantly associated with poor patient survival. TCR RNA-sequencing analysis indicates trafficking between TDLNs and tumors and ongoing Tconv/Treg conversion. Overall, TDLN Tregs are functional and express a distinct pattern of druggable co-receptors, highlighting their potential as targets for cancer immunotherapy.

overall_design: TCR-β sequencing of sorted CD4+ Tconv (CD4+FOXP3-CD45RA-) and Treg (CD4+FOXP3hiCD45RA-) from breast cancer patients. Tconvs and Tregs were purified and processed from matched non-invaded lymph node (N=5) and invaded lymph node (N=5), as well as tumors when possible (N=3 for Tconvs and N=2 for Tregs).

first: Nicolas

middle: G

last: Núñez

first: Jimena

last: Tosello

first: Rodrigo

middle: N

last: Ramos

first: Jeremy

last: Bigot

first: Olivier

last: Lantz

first: Eliane

last: Piaggio


title: Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cell through super-enhancers [ChIP-seq 1]

status: Public on May 24 2020

city: Guangzhou

first: Zhijun

last: Ren

address: 74 Zhongshan Rd.2

institute: Sun Yat-sen University

summary: Hippo-YAP signaling pathway is a highly conserved pathway during evolution. It involves in a broad spectrum of physiological and pathological procedure. It also functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. Our previous research revealed that knockout of Mst1 and Mst2, the key components of Hippo signaling in mouse embryonic stem cells (ESCs), led ESCs preferentially differentiate into ectoderm lineage, and the differentiation to mesoderm and endoderm lineage was disturbed. To uncover the underlying regulatory mechanisms, we performed ChIP-seq experiments with antibodies against Yap, master transcription factors and some characterized histone modification markers. Combined with RNA-seq assays of wild type and Mst KO ESCs and day 4 embryoid bodies (EBs), we found that YAP is preferentially enriched at Nanog, Sox2, Oct4 and H3K27Ac co-marked super-enhancers (SEs) in ESCs. The upregulation of YAP in Mst KO ESCs resulted in the formation of new super-enhancers on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Hence, our study revealed a super-enhancer related ESC lineage differentiation mechanism which can be shaped by Hippo-YAP signaling.

overall_design: Examination of 4 different histone modifications and 4 different TF in 2 cell types.

first: Sun

last: Xiang


title: Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cell through super-enhancers [RNA-seq]

overall_design: Examination of ES and EB in 2 cell types.


title: Enhancer Regulation in Kidney Repair [RNA-seq]

first: Michaela

last: Willi

first: Julia

last: Wilflingseder


title: Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers


title: Regulation of neurogenesis by FGF signaling and Neurogenin in the invertebrate chordate Ciona

status: Public on May 21 2020

city: Atlanta

first: Alberto

last: Stolfi

state: GA

address: 950 Atlantic Dr

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: To profile gene expression associated with BTN neurogenesis we performed RNAseq of isolated BTN lineage cells in which BTN neurogenesis was enhanced or suppressed by perturbing Neurog function.

overall_design: Bulk RNAseq of FACS-isolated cells from embryos electroporated with molecular perturbartion constructs

first: Wei

last: Wang


title: Changes in Shewanella baltica transcriptome upon cold stress

city: Gdansk

first: Pawel

last: Olszewski

address: Debinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdansk

summary: In this work we analyzed changes in gene espression in Shewanella baltica upon cold stress. In order to imitate natural environment, we cultured bacteria in the Instant Ocean medium in a chemostat. Samples were collected after 90 and 180 minutes of cold stress and analyzed by RNA sequencing. The transcriptomic response could be characterized as global downregulation of gene expression (613 genes downregulated) and we found only 242 genes which were upregulated. We randomly tested 11 transcripts with RT-qPCR to confirm changes observed in RNA seq experiment. We observed change in expression of sigma factors namely, downregulation of the housekeeping sigma 70 encoded by rpoD and upregulation of ECF subfamily RNA polymerase sigma 24 factor rpoE2, indicating global transcription reprogramming. Analysis of metabolic pathways revealed common changes observed in other bacteria such as change in fatty acid metabolism toward synthesis of unsaturated fatty acids and upregulation of flagellar assembly genes after 90 minutes of cold stress. A novel observation was downregulation of genes encoding components of the type II secretion system. In summary,

overall_design: Bacteria were cultured in Instant Ocean medium in a chemostat, at 20C and cold stress was induced by shifting to 8C. Experiment composed of five samples: single control sample (before stress) and samples collected after 90 and 180 minutes (in duplicates).

first: Anna

last: Kloska

first: Agnieszka

last: Szalewska-Palasz

first: Grzegorz

last: Cech


title: Transcriptomic analysis of airway macrophages from a murine experimental allergic airway disease model

status: Public on May 20 2020

city: London

first: Clare

middle: Margaret

last: Lloyd

address: Inflammation, Repair and Development, National Heart and Lung Institute, Sir Alexander Fleming Building

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: Airway macrophages (AMs) are the most abundant leukocytes in the healthy airway lumen and have a highly specialised but plastic phenotype that is governed by the local microenvironment. AMs are thought to maintain immunological homeostasis in the steady state, but have also been implicated in the pathogenesis of allergic airway disease (AAD). To better understand these potentially contrasting AM functions, bulk RNA sequencing was performed on murine AMs obtained during experimental AAD driven by repeated house dust mite inhalation (AM[HDM]s), comparing to control AMs from non-allergic mice. AM[HDM]s showed increased expression of genes associated with antigen presentation, inflammatory cell recruitment and tissue repair, including several chemokines and matrix metalloproteinases. This was accompanied by increased expression of mitochondrial electron transport chain subunit genes and the retinoic acid biosynthetic enzyme gene Raldh2. Conversely, AM[HDM]s displayed decreased expression of a number of cell cycle genes, genes related to cytoskeletal functions and a subset of genes implicated in antimicrobial innate immunity, such as Tlr5, Il18 and Tnf. Differential gene expression in AM[HDM]s was consistent with upstream effects of the cytokines IL-4 and IFN-γ, both of which were at increased concentrations in lung tissue after HDM treatment. These data highlight diverse gene expression changes in the total AM population in a clinically relevant mouse model of AAD, overall suggestive of contributions to inflammation and tissue repair/remodelling, but decreases in certain steady state cellular and immunological functions.

overall_design: CD11c+ CD64+ Siglec F+ AMs were flow cytometry sorted from bronchoalveolar lavage of adult female C57BL/6J mice after 3 weeks of intranasal exposures to either house dust mite (HDM) allergen (AM[HDM]s, N=4) or PBS control (control AMs, N=5). RNA was extracted and converted to mRNA libraries before performing Illumina paired end sequencing. Reads were aligned to the Mm10 genome using COBWeb. Transcripts were quantified from aligned reads using DESeq. Low abundance transcripts were filtered (normalised expression <8 in  >25 % of samples in both groups) and differential expression analysis performed by moderated t-test with Benjamini-Hochberg false discovery rate correction. Differentially expressed genes were hierarchically clustered using Ward's method and pathway analysis performed to predict changes in AM function during HDM-driven allergic airway disease.

first: William

last: Branchett

first: Anne

last: O'Garra

middle: M


title: Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cell through super-enhancers [ChIP-seq 2]

overall_design: Examination of 1 histone modification in 2 cell types.


title: Antifungal agent 4-AN changes the genome-wide expression profile, down-regulates virulence-associated genes, and induces necrosis in Candida albicans cells

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

institute: Poznan University of Technology

summary: In the light of the increasing occurrence of antifungal resistance, there is an urgent need to search for new therapeutic strategies to overcome this phenomenon. One of the applied approaches is the synthesis of small-molecule compounds showing antifungal properties. Here we present a continuation of the research on the recently discovered anti-Candida albicans agent 4-AN. Using next generation sequencing and transcriptional analysis, we revealed that the treatment of C. albicans with 4-AN can change the expression profile of a large number of genes. The highest up-regulation was observed in the case of genes involved in cell stress, while the highest down-regulation was shown for genes coding sugar transporters. Real-time PCR analysis revealed 4-AN mediated reduction of the relative expression of genes engaged in fungal virulence (ALS1, ALS3, BCR1, CPH1, ECE1, EFG1, HWP1, HYR1, and SAP1). The determination of the fractional inhibitory concentration index (FICI) showed that the combination of 4-AN with Amphotericin B is synergistic. Finally, flow cytometry analysis revealed that the compound induces mainly necrosis in Candida albicans cells.

overall_design: Examination of genome-wide expression profile in Candida albicans under treatment with the compound 4-AN

last: Martyna

first: Maciej

last: Masłyk

first: Monika

last: Janeczko

first: Elżbieta

last: Kochanowicz

first: Bartłomiej

last: Gielniewski

last: Świercz

first: Oleg

last: Demchuk

first: Konrad

last: Kubiński


title: DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

sample_organism:
Sus scrofa
Bos taurus

platform_organism:
Sus scrofa
Bos taurus


title: Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription

city: Bronx

first: PABITRA

last: PARUA

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both are enriched in coding regions, and H2Bub1 levels are directly proportional to those of phospho-Spt5. Cdk9-dependence of antisense suppression correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Combined reduction of Cdk9 activity and loss of H2Bub1 prevent recruitment of the histone deacetylase Clr6-CII to transcribed genes, and lead to decreased histone occupancy and increased histone acetylation within gene coding regions. These results uncover new pathways linking regulators of RNAPII transcription elongation to suppression of aberrant antisense transcription, and demonstrate novel interactions between co-transcriptional histone modification pathways.

overall_design:
ChIP-seq: Data represent eighteen different ChIP-seq experiments in S. pombe, performed in biological replicates. There are raw sequencing files for all biological replicates and processed files after combining the replicates.

Please note that the *Combined.bigwig processed data was generated from both rep1 and rep2 data combined and is available as Series supplementary files.

first: Pabitra

last: Parua

first: Miriam

last: Sansó

first: Jason

last: Tanny


title: Rehabilitative Impact of Exercise Training on Human Skeletal Muscle Transcriptional Programs in Parkinson’s Disease

city: New York

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: We performed transcriptional profiling to test the hypotheses that a) type I myofiber grouping severity in Parkinson's disease skeletal muscle is linked to distinct gene expression networks and b) high-intensity resistance exercise rehabilitation training influences the skeletal muscle transcriptome in individuals with Parkinson's disease.

overall_design: Bulk poly-A RNAseq was performed on skeletal muscle from 12 individuals with Parkinson's Disease, 12 age and sex-matched old adults, and 12 sex-matched young adults. Five of the 12 subjects with Parkinson's disease were also profiled following 16-wk of resistance training.

first: Kaleen

last: Lavin

first: Stuart

last: Sealfon

first: Merry-Lynn

last: McDonald

first: Katarzyna

last: Wilk

first: Venugopalan

middle: D

last: Nair

first: Jeremy

middle: S

last: McAdam

first: Preeti

middle: L

last: Kumar

first: Samuel

middle: T

last: Windham

first: Marcas

last: Bamman


title: DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [BS-Seq]

summary: Preimplantation embryos experience profound resetting of epigenetic information. Genome-wide analysis at single-base resolution had shown relevant species differences between human and mouse preimplantation embryos. Thus, we have extended such analysis to two key livestock species, the pig and the cow. We generated data showing the genome-wide DNA methylation landscape and whole-transcriptomes from gametes to blastocysts in both species. Detailed analysis revealed species specific differences and new insights in biological paradigms. An oocyte-like pattern of methylation in the cleavage stages, albeit with some reduction in methylation level, appears to persist even in cow blastocysts. Hypermethylated domains were prevalent over hypomethylated domains in pigs and cows, similar to human, while in the mouse the pattern is reversed. Interestingly, the behaviour of the oocyte hypo-domains in cleavage embryos revealed a complex dynamic of methylation reprogramming. It shows a pronounced increase in methylation at the 8-16 cell stage in pigs, similar to human, concomitant with ZFP57 expression.   Even it is widely accepted that imprinted genes are established in the parental germline and robustly maintained through early development, our data show a greater dynamic of methylation in germline differentially methylated regions and few appear to maintain the expected 50% methylation from the 2-4 cell stage to blastocyst stage. It reveals that an active period of imprint stabilization until the blastocyst stage is required

overall_design: DNA methylation analysis on genome-wide scale was performed using germ cells or early embryos from porcine or bovine specie

first: Elena

last: Ivanoa

first: Sebastian

last: Canovas

first: Soledad

last: Garcia-Martinez

first: Raquel

last: Romar

first: Jordana

last: Lopes

first: Dimitrios

last: Rizos

first: Maria

last: Sanchez-Calabuig

first: Simon

last: Andrews

first: Fernando

last: Perez-Sanz

first: Gavin

last: Kelsey

first: Pilar

last: Coy


title: ChIP-Seq melanoma PDX TM00702

status: Public on May 18 2020

city: Duarte

first: Haiqing

last: Li

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

summary: H3K4me3 ChIP-seq from melanoma PDX tumours fed with different diets

overall_design: H3K4me3 peak changes in melanoma tumours as a result of glutamine supplementation in diet

first: Mari

middle: B

last: Ishak Gabra

first: Ying

last: Yang

first: Eric

middle: A

last: Hanse

first: Parijat

last: Senapati

first: Xazmin

last: Lowman

first: Thai

middle: Q

last: Tran

first: Linda

last: Doan

first: Xiangdong

last: Xu

first: Dustin

middle: E

last: Schones

first: David

last: Fruman

first: Mei

last: Kong


title: Sequencing of serum exosomal circRNAs in colorectal cancer

status: Public on May 15 2020

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary:
CircRNA sequencing for 10 samples
To assess the serum exosomal circular RNAs (circRNAs) expression profile and explore the potential functions in human colorectal cancer (CRC).The differentially expressed circRNAs profiles of CRC (n=5) and age-matched healthy controls(n=5) were analyzed using RNA-seq profiling. Quantitative real-time PCR was used to validate the expression pattern of circRNAs.Bioinformatic tools including network analysis, Gene ontology, and KEGG pathway analysis were utilized.

overall_design: Sequence was performed on 5 colorectal cancer samples and 5 healthy control samples,each sequencing sample was a mixture of 10 serum from participant.

first: Chuanxin

last: Wang


title: A long-read RNA-seq approach to identify novel transcripts of very large genes

status: Public on May 17 2020

city: Washington

first: Prech

middle: Brian

last: Uapinyoying

state: District of Columbia

address: 111 Michigan Ave, NW

department: Genetic Medicine

institute: Children's National Medical Center

summary: RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon-junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts.  Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential expression studies. We used long-read isoform sequencing combined with a novel analysis approach to compare alternative splicing of large, repetitive structural genes in muscles. Analysis of muscle structural genes that produce medium (Nrap - 5kb), large (Nebulin - 22 kb) and very-large (Titin - 106 kb) transcripts in cardiac muscle, and fast and slow skeletal muscles identified unannotated exons for each of these ubiquitous muscle genes. This also identified differential exon usage and phasing for these genes between the different muscle types. By mapping the in-phase transcript structures to known annotations, we also identified and quantified previously unannotated transcripts. Results were confirmed by endpoint PCR and Sanger sequencing, which revealed muscle-type specific differential expression of these novel transcripts. The improved transcript identification and quantification demonstrated by our approach removes previous impediments to studies aimed at quantitative differential expression of ultra-long transcripts.

overall_design: Comparing mRNA isoform expression of three muscle structural genes from three types of muscle tissues in mice using PacBio Iso-Seq.

middle: P

last: Hoffman


title: Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth

status: Public on May 14 2020

summary: Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. We recently found, in melanoma, tumour cells often experience low glutamine levels, which induce histone hypermethylation, promote dedifferentiation, and increase resistance to BRAF inhibitors. These findings raise the possibility that increased glutamine levels can be detrimental to melanoma tumours. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in transgenic mouse model, and increases sensitivity to BRAF targeted inhibitors in both melanoma xenograft and patient-derived xenograft (PDX) models. Notably, metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine and its downstream metabolite, αKG, in serum and tumours, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome and suppresses expression of many melanoma-associated genes. Our data further demonstrate that increase in intra-tumoural αKG concentration, following glutamine supplementation, drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide important evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.

overall_design: Comparison of mRNA and gene expression profiles in control versus glutamine high melanoma tumors.


title: NeuroD1-driven differentiation of medulloblastoma cells from Patched 1 deficient mice

status: Public on May 19 2020

city: Philadelphia

first: Zeng-jie

state: Pennsylvania

address: 333  Cottman Avenue

department: Cancer Biology Program

institute: Fox Chase Cancer Center

summary: Tumor cells are characterized with unlimited proliferation and perturbed differentiation. By single cell RNA sequencing, we demonstrate that tumor cells in medulloblastoma (MB) retain their capacity to differentiate in a similar way as their normal originating cells, cerebellar granule neuron precursors. Once they differentiate, MB cells permanently lose their proliferative capacity and tumorigenic potential. Differentiated MB cells highly express NeuroD1, a helix-loop-helix transcription factor, and forced expression of NeuroD1 promotes the differentiation of MB cells.  The expression of NeuroD1 in bulk MB cells is repressed by trimethylation of histone 3 lysine-27 (H3K27me3). Inhibition of the histone lysine methyltransferase EZH2 prevents H3K27 trimethylation, resulting in increased NeuroD1 expression and enhanced differentiation in MB cells, which consequently reduces tumor growth. These studies reveal the mechanisms underlying MB cell differentiation, and provide rationales to treat MB (potentially other malignancies) by stimulating tumor cell differentiation.

overall_design: Medulloblastoma cells were dissociated from Patched 1 deficient mice, which were used for single cell sequencing by 10X Genomics Chromium Controller. Data from a total of 9,164 cells that met quality control criteria (average 2,130 unique genes per cell) were used for transcriptomic analysis.


title: Multi-organ transcriptomic profiling of short-term fasted mice

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

summary: To investigate the global gene expression dynamics associated with short-term fasting, we used mRNA-seq to profile the transcriptomes of nine organs obtained from mice subjected to six different STF duration (0, 2, 8, 12, 18 and 22 hours of fasting; n=3 per time point; Fig. 1a). The nine organs profiled were: olfactory bulb (OB), brain (BRN, which includes the telencephalon and diencephalon), cerebellum (CBL), brainstem (BST, which consists of the mesencephalon, pons, and myelencephalon), stomach (STM), liver (LIV), interscapular brown adipose tissue (iBAT), perigonadal white adipose tissue (pgWAT), and posterior-subcutaneous white adipose tissue (psWAT).

overall_design: mRNA profiling of nine organs obtained from wild type (WT) mice subjected to six different short term fasting duration

first: Luis

last: Saraiva

first: SusieSY

last: Huang


title: S-phase independent silencing establishment in Saccharomyces cerevisiae

city: Berkeley

first: Davis

last: Goodnight

address: 440 Barker Hall

department: Molecular & Cell Biology

institute: UC Berkeley

summary: As part of a study of establishment of silencing in Saccharomyces cerevisiae, we performed ChIP-seq on myc-tagged Sir4 in several conditions. Included in those conditions are wild-type cycling cells, cycling sir3∆ cells, and various experiments during which silencing establishment was controlled using the inducible SIR3-EBD allele. Silencing establishment experiments were performed in both wild-type and dot1∆ cells.

overall_design: Sir4-13xMyc ChIP-seq, Sir3-EBD ChIP-seq and H3K79me3 ChIP-seq. For all key experiments, replicates were included.

first: Jasper

last: Rine


title: DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [RNA-Seq]

first: Felix

last: Krueger

overall_design: Total RNA was extracted using oocyte, 2-4 cell embryo, 8-16 cell embryo, morula and blastocyst from porcine and bovine species and used to generate whole genome transcriptomic RNA seq data

first: Elena

last: Ivanoa

first: Sebastian

last: Canovas

first: Soledad

last: Garcia-Martinez

first: Raquel

last: Romar

first: Jordana

last: Lopes

first: Dimitrios

last: Rizos

first: Maria

middle: J

last: Sanchez-Calabuig

first: Simon

last: Andrews

first: Fernando

last: Perez-Sanz

first: Gavin

last: Kelsey

first: Pilar

last: Coy


title: Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:DNA PT modification mapping

city: Singapore

first: Xiaolin

last: Wu

state: Singapore

address: 1 CREATE Way

country: Singapore

institute: Singapore-MIT Alliance for Research and Technology (SMART)

summary: Endogenous and exogenous chemical modifications in DNA have profound influences on genome function. We have developed a novel technology, Nick-seq, for mapping variety of DNA chemical modifications across the genomes at single-nucleotide resolution, by which we achieved quantitative profiling of single-strand breaks, phosphorothioate modifications, and oxidative DNA damage sites. This method is applicable for mapping of any DNA metabolism events that are involved in or can be converted, enzymatically or chemically, to DNA strand breaks such as DNA modifications, damages, genome replication, and chromatin structures.

sample_organism: Salmonella enterica subsp. enterica serovar Cerro

overall_design: One sample was used together with one negative control.Then for each sample, two library prep methods were ultilized.

first: Bo

last: Cao

first: Peter

middle: C

last: Dedon


title: HUMAN-VIRUS CHIMERIC PROTEINS GENERATED DURING INFECTION

city: Frederick

first: George

last: Pavlakis

state: MD

address: 535 Sultan St

department: Vaccine Branch

institute: NCI

summary: RNA viruses are a major threat to global human health. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, as viral polymerases cleave 5′m7G-capped host transcripts to prime viral mRNA synthesis (‘cap-snatching’). We hypothesized that start codons within cap-snatched host transcripts could drive the expression of chimeric human-viral coding sequences. Here, we report the existence of this mechanism of gene origination (‘start-snatching’), which creates, depending on the translatability of the viral UTRs, human-virus protein chimeras either as N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting.  We show that both types of chimeric proteins are made in IAV-infected cells, can generate T cell responses and contribute to virulence. Our results indicate that IAV, and likely a multitude of other human-, animal- and plant-viruses, use this host-dependent mechanism to expand their proteome diversity during infection.

overall_design: Ribosome profiling of influenza A infected cells

first: Jessica

last: Ho

first: Matthew

last: Angel

first: Yixuan

last: Ma

first: Elizabeth

last: Sloan

first: Guojun

last: Wang

first: Carles

last: Martinez-Romero

first: Marta

last: Alenquer

first: Laura

last: Campisi

first: Liliane

last: Chung

first: Simin

last: Zheng

first: Max

last: Chang

first: Yesai

last: Fstkchyan

first: Sara

last: Clohisey

first: Adam

last: Dinan

first: James

last: Gibbs

first: Robert

last: Gifford

first: Rosie

last: Shen

first: Quan

last: Gu

first: Nerea

last: Irigoyen

first: Vladimir

last: Roudko

first: Huang

last: Cheng

last: Zhao

first: Joshua

last: Jones

first: Ingeborg

last: van Knippenberg

first: Natasha

last: Moshkina

first: Léa

last: Meyer

first: Justine

last: Noel

first: Zuleyma

last: Peralta

first: Veronica

last: Rezelj

first: Robyn

last: Kaake

first: Brad

last: Rosenberg

first: Jiajie

last: Wei

first: Slobodan

last: Paessler

first: Helen

last: Wise

first: Jeffrey

last: Johnson

first: Alessandro

last: Vannini

last: Amorim

first: J

middle: K

last: Baillie

first: Emily

middle: R

last: Miraldi

first: Christopher

last: Benner

first: Ian

last: Brierley

first: Paul


title: Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:nickase mapping

first: Xiaolin

last: Wu

sample_organism: Escherichia coli str. K-12 substr. DH10B

overall_design: 2 sample treated by different nickase were used. For each sample, there is one negative control.Then for each sample, two library prep methods were ultilized.

first: Bo

last: Cao

first: Peter

last: Dedon


title: Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:DNA damage mapping

platform_organism: Escherichia coli str. K-12 substr. DH10B


title: Regulation of HLA II expression in acute myeloid leukemia by CIITA methylation

status: Public on May 13 2020

city: Helsinki

first: Olli

last: Dufva

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

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

overall_design: Refer to individual Series


title: Regulation of HLA II expression in acute myeloid leukemia by CIITA methylation (RRBS dataset)

summary: Acute myeloid leukemia cell lines were treated with the hypomethylating agent decitabine and interferon gamma to investigate if these treatments induce HLA II gene expression. Cells carrying either control or CIITA-targeting sgRNAs were used to tet

overall_design: Reduced representation bisulfite sequencing (RRBS) data were obtained from acute myeloid leukemia cell lines treated with decitabine and/or interferon gamma and subjected to CRISPR-mediated disruption of CIITA.

first: Petri

last: Pölönen

first: Merja

last: Heinäniemi

first: Satu

last: Mustjoki


title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [ChIP-Seq]

city: Tianjin

first: Bingxue

last: Lan

address: Qixiangtai road

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that HRP2-DPF3a-BAF complex coordinates histone H3 lysine 36 methylation (H3K36me) and ATP-dependent chromatin remodeling to regulate chromatin dynamic and gene transcription during myogenic differentiation. Mechanistically, through its HIV integrase binding domain (IBD), HRP2 associates with BRG1/BRM associated factor (BAF) chromatin remodeling complex by direct interaction with BAF45c (DPF3a) subunit. Through its Pro-Trp-Trp-Pro (PWWP) domain, HRP2 preferentially binds to H3K36me2. Consistent with the biochemical studies, genome-wide analyses show that HRP2 colocalizes with DPF3a at gene promoters enriched for H3K36me2.

overall_design: Examination of binding of Hrp2 in mouse myoblasts and myotubes by ChIP-seq.  Examination of binding of Dpf3a and H3K36me2 in mouse myotubes by ChIP-seq.

first: Xu

last: Zhu

first: Xianfu

last: Yi


title: Cholesterol metabolism drives regulatory B cell IL-10 through geranylgeranyl pyrophosphate

status: Public on May 12 2020

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

summary: Regulatory B cells restrict immune and inflammatory responses across a number of contexts. This capacity is mediated primarily through the production of IL-10. Here we demonstrate that the induction of a regulatory program in human B cells is dependent on a metabolic priming event driven by cholesterol metabolism. Synthesis of the metabolic intermediate geranylgeranyl pyrophosphate (GGPP) was required to specifically drive IL-10 production, and to attenuate Th1 responses. Furthermore, GGPP-dependent protein modifications controlled signaling through PI3Kd-AKT-GSK3, which in turn promoted BLIMP1-dependent IL-10 production. Inherited gene mutations in cholesterol metabolism result in a severe autoinflammatory syndrome, termed mevalonate kinase deficiency (MKD). Consistent with our findings, B cells from MKD patients induced poor IL-10 responses and were functionally impaired. Moreover, metabolic supplementation with GGPP was able to reverse this defect. Collectively, our data define cholesterol metabolism as an integral metabolic pathway for the optimal functioning of human IL-10 producing regulatory B cells.

overall_design: Comparison of human B cells stimulated with CpG (1uM) in the presence or absence of the geranylgeranyl pyrophosphate inhibitor GGTi-298

first: Andrew

last: Cope

first: Esperanza

last: Perucha


title: Regulation of HLA II expression in acute myeloid leukemia by CIITA methylation (RNA-seq dataset)

summary: Acute myeloid leukemia cell lines were treated with the hypomethylating agent decitabine and interferon gamma to investigate if these treatments induce HLA II gene expression. Cells carrying either control or CIITA-targeting sgRNAs were used to test the dependence of the HLA II induction on CIITA.

overall_design: RNA sequencing data were obtained from acute myeloid leukemia cell lines treated with decitabine and/or interferon gamma and subjected to CRISPR-mediated disruption of CIITA.


title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [RNA-Seq]

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that HRP2-DPF3a-BAF complex coordinates histone H3 lysine 36 methylation (H3K36me) and ATP-dependent chromatin remodeling to regulate chromatin dynamic and gene transcription during myogenic differentiation. To study the cellular and molecular function of HRP2-DPF3a-BAF complex during myogenic differentiation, we used RNA sequencing (RNA-seq) to generate gene expression profiling during myogenic differentiation under Hrp2/Dpf3a/Brg1 transient knockdown by siRNAs in C2C12. We identified multiple genes whose expression is significantly affected by Hrp2/Dpf3a/Brg1 levels.

overall_design: For knockdown condition, C2C12 myoblasts were transfected with siRNAs against Hrp2/Dpf3a/Brg1 or control 24h before start of differentiation. Cells were harvested for gene expression profiling when differentiation was induced (0h, confluent cells) and after 48h of differentiation in differentiation medium. Two replicates were performed per siRNA.


title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription


title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [ATAC-Seq]

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that HRP2-DPF3a-BAF complex coordinates histone H3 lysine 36 methylation (H3K36me) and ATP-dependent chromatin remodeling to regulate chromatin dynamic and gene transcription during myogenic differentiation. Mechanistically, through its HIV integrase binding domain (IBD), HRP2 associates with BRG1/BRM associated factor (BAF) chromatin remodeling complex by direct interaction with BAF45c (DPF3a) subunit. Through its Pro-Trp-Trp-Pro (PWWP) domain, HRP2 preferentially binds to H3K36me2. Integrative transcriptomic and cistromic analyses, coupled with ATAC-seq, reveal that HRP2 and DPF3a activate myogenic genes by increasing chromatin accessibility through recruitment of BRG1, the ATPase subunit of the BAF complex.

overall_design: ATAC-seq analysis from  C2C12 transfected with siRNAs against Hrp2/Dpf3a or control 24h before start of differentiation. Cells were harvested for chromatin accessibility profiling after 48h of differentiation in differentiation medium. Two replicates were performed per siRNA.


title: Transcriptome analysis of in vitro generated plasmablasts dervied from Waldenström macroglobulinemia (WM) or heathly control B-cells

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: The ability to model WM B-cell differentiation using an in vitro system was validated in comparison to healthy cells. The stimuli used initially were CD40L and F(ab’)2 anti-IgG/M, a combination which mimics T-cell dependent activation. Using these conditions, WM B-cells generated mature plasma cells that closely resemble those from healthy controls. Since WM cells harbour the characteristic gain-of-function MYD88L265P mutation, it was also of interest to determine the impact of TLR signals on the differentiation process. In contrast to the expectation of enhanced survival, WM cells exhibited a profoundly deleterious response to R848 + F(ab’)2 anti-IgG/M stimulation, with a sharp decline in population from the initiation of culture and a failure to generate plasma cells. RNA sequencing was performed on material harvested from differentiating cells at day 6 of culture within the in vitro system to assess the underlying gene expression changes that accompanied the two types of stimulation. The samples consisted of 3 healthy controls with matched samples for both CD40L and R848 stimulation and a total of 6 WM samples. Examination of the transcriptomes revealed that WM plasmablasts exhibit elevated expression levels of genes associated with TLR and NF-κB signaling, but reduced levels of genes associated with plasma cell re-programming. This is particularly pronounced in cells treated with the TLR7 agonist R848, suggesting an uncoupling of TLR signaling from plasma cell differentiation in WM.

overall_design: mRNA profiles of plasmablasts generated from CD40L or R848 stimulated B-cells derived from healthy donors or Waldenström macroglobulinemia (WM) patients

first: Gina

last: Doody


title: Evaluation of 5-Day In Vivo Rat Liver and Kidney with High-Throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes

city: Research Triangle Park

first: Will

last: Gwinn

state: NC

address: 111 Alexander Dr.

department: National Toxicology Program

institute: National Institute of Health Sciences

summary: The Division of the National Toxicology Program (DNTP) is currently evaluating high-throughput transcriptomics (HTT) as an approach to provide estimates of chemical exposure that may pose minimal risk. HTT was evaluated in a 5-day in vivo rat model (with repeated dosing) with the objective to determine if benchmark doses (BMD) values for transcriptional pathway changes in the liver and kidney could estimate BMD values for traditional toxicological (apical) endpoints. Eighteen chemicals, most having been tested by the NTP in 2-year bioassays, were chosen for this study. Some of these chemicals are known to be potent hepatotoxicants (e.g. DE71, PFOA, furan, and methyl eugenol) in rodents, some exhibit toxicity but have minimal effects on the liver (e.g. acrylamide and α,β-thujone), and some exhibit little overt toxicity (e.g. ginseng and milk thistle extract) based on traditional toxicological evaluations. Male Sprague Dawley rats were exposed daily for 5 consecutive days by oral gavage to 8 to 10 dose levels of each chemical. Liver and kidney were collected 24 hours after the final exposure and assayed using HTT with the rat S1500+ platform. HTT dose-response data were analyzed using BMD Express 2.2 to determine transcriptional BMD values for liver and kidney. BMDS Wizard was used to determine apical BMD values for histopathological effects from historical chronic or sub-chronic toxicity studies. For many of the chemicals, the lowest transcriptional BMDs from the 5-day assays were within a factor of 5 of the lowest histopathological BMDs estimated from the traditional toxicity studies. These data suggest that using HTT in a 5-day in vivo model provides reasonable estimates of BMD values for traditional apical endpoints. This approach may be useful to prioritize chemicals for further testing while providing actionable data in a timely and cost-effective manner.

overall_design: Male HSD rats were housed five animals per cage and randomly assigned to treatment and control groups. Animals were divided into five testing blocks each consisting of four test articles administered at eight or nine doses plus a control group. Four animals per dose group receive the test article via gavage for five consecutive days and euthanized 24 hours following the last dose. Dosing for a four-chemical block was conducted simultaneously in the same room. Kidney and liver were removed from each animal and up to three samples (~250 mg total) from the left liver lobe and right kidney were taken. Each sample was cut into smaller pieces (approximately 5 mm3) and aliquoted into screw-cap tubes. Two of the samples from each animal were preserved in RNA later, one of which was used for RNA extraction at Battelle and submission to BioSpyder for transcriptomic screening by TempO-Seq analysis as previously described (Yeakley, et al., 2017). The remaining samples from each animal were snap frozen in liquid nitrogen and stored at -80 degrees C.

first: William

middle: M

first: Scott

last: Auerbach

first: Fred

last: Parham

last: Stout

first: Suramya

last: Waidyanatha

first: Esra

last: Mutlu

first: Brad

last: Collins

first: Richard

last: Paules

first: B

last: Merrick

first: Stephen

last: Ferguson

first: Sreenivasa

last: Ramaiahgari

first: John

last: Bucher

first: Barney

last: Sparrow

first: Heather

last: Toy

first: Jenni

last: Gorospe

first: Nick

last: Machesky

first: Ruchir

last: Shah

first: Michele

last: Balik-Meisner

first: Deepak

last: Mav

first: Dhiral

last: Phadke

first: Georgia

last: Roberts

first: Michael

last: DeVito


title: Transcriptom profiling of in vitro induced exhauted CD8+ T cells

status: Public on May 09 2020

city: Rotterdam

first: Peter

last: Katsikis

state: Zuid Holland

address: Dr Molewaterplein 40

department: Department of Immunology

institute: Erasmus University Medical Center

summary: By comparing transcriptome profiling of in vitro repeated stimulated cells with without stimulation and single peptide stimulated cells, to evaluated if the transcriptome profiling of repeated stimulated cells meet the features of exhausted cells. CD8+ T cells purified from OT-I mice were stimulated daily for five days with 10ng/ml OVA(257-264) peptide in the presence of IL-15 and IL-7. As controls, cells were either left without stimulation or stimulated only once with OVA(257-264) peptide for 48 hours and then washed and cultured without peptide for an additional 3 days.  On day 5, cells were harvested. Live CD8+ T cells were sorted and RNAseq were performed after RNA isolation. It was found that the transcriptional prolife of the repeat peptide stimulated cells is clearly distinct to those of the single and non-stimulated cells. Among the upregulated genes, multiple inhibitory receptors encoding genes were presented on the top of this list. The genes for the markers of the terminal differentiated effector cells, like GzmB, GzmC and Prf1 were also significantly upregulated on the repeat peptide stimulated cells. The expression pattern of exhaustion specific transcription factors were identified in repeat stimulated cells. In vitro repeat peptide stimulation results in the transcriptional changes of in vivo exhausted CD8+ T cells from chronic viral infections which serve as the benchmark of CTL exhaustion.

overall_design: Examination RNA profiling of in vitro cultured CD8+ T cells from 3 different types of stimulation (no peptide; single peptide and repeat peptide). Each condition has 4-5 replicates.

first: Manzhi

last: Zhao


title: MYC-MIZ1 protein interaction in germinal center.

status: Public on May 08 2020

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

summary: Characterisation of the splenic light zone germinal center B cells in mice carrying WT endogenous mouse allele and mice carrying a mouse allele (Myc V394D) unable to bind its partner transcription factor Miz1 (Zbtb17). Characterisation of Myc WT memory B cells.

overall_design: Spleenic light zone B cells  and memory B cells were sorted by flow cytometry 10 days after immunisation of mice with sheep red blood cells

first: Amparo

last: Toboso-Navasa

first: Probir

last: Chakravarty


title: Dynamics in protein translation sustaining T cell preparedness

status: Public on May 07 2020

city: Bellinzona

first: Roger

last: Geiger

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

summary: In response to pathogenic threats, naïve T cells rapidly transition from a quiescent to activated state, yet the underlying mechanisms are incompletely understood. Using a pulsed SILAC approach, we investigated the dynamics of mRNA translation kinetics and protein turnover in human naïve and activated T cells. Our datasets uncovered that transcription factors maintaining T cell quiescence had constitutively high turnover, which facilitated their depletion upon activation. Furthermore, naïve T cells maintained a surprisingly large number of idling ribosomes as well as 242 repressed mRNA species and a reservoir of glycolytic enzymes. These components were rapidly engaged following stimulation, promoting an immediate translational and glycolytic switch to ramp up the T cell activation program. Our data elucidate new insights into how T cells maintain a prepared state to mount a rapid immune response, and provide a resource of protein turnover, absolute translation kinetics and protein synthesis rates in T cells (www.immunomics.ch).

overall_design: mRNA profiles of human naive, 6h and 24h activated CD4+ T cells


title: Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University

summary:
Purpose: The goals of this study are to identify Mutator insertion sites and determine the affect of these insertions on nearby genes
Methods: Wiseq-based Mu element profiling was performed as described previously using B73/Mo17 F1 hybrid progeny seedlings. The B73 parent was carried Mutator activity that had been introgressed into the B73 genetic background. The Mo17 parent lacked active Mu elements. Thus, all new insertions were into the B73 genome. Genomic DNA was extracted from 6-day-old seedlings of B73/Mo17 hybrid plants. Amplicon-based enrichment of Mu flanking DNA was then performed. The purified PCR products were subject to Miseq-based Wideseq pipeline at Purdue Genomics Core Facility (https://www.purdue.edu/hla/sites/genomics/wideseq-2/). Wideseq reads were mapped to the B73 reference genome as described previously. By identifying the Mu target site duplications (TSDs), a set of genes targeted by Mu insertions that segregated in hybrid progeny was obtained and those containing B73/Mo17 SNPs in their mRNA sequences were used for allele-specific expression analysis. Because new insertions were into the B73 genome, the effect of these insertions would be expected to be specific in all cases to the B73 allele. To quantify the allele frequency, we performed RT-PCR followed by Wideseq from the identical shoot tissues of the hybrid seedlings mentioned above. Total RNA was extracted using the RNA Extraction Kit (Zymo) and cDNAs were synthesized using Promega M-MLV Reverse Transcriptase. For for a subset of 16 genes that carried SNPs, RNA fragments containing B73/Mo17 SNPs were amplified by RT-PCR. Libraries were prepared using an mRNA preparation kit (Illumina) following a standard protocol (https://www.purdue.edu/hla/sites/genomics/wi-deseq-2/). The RT-PCR products were then sequenced by the “WideSeq” pipeline.
Results: A knockdown index was deduced by normalizing the observed ratio to that observed in genes that lacked Mu insertions in both genetic backgrounds for each insertion. We found that none of the four promoter insertions changed the expression of nearby genes. A quarter of 5’ UTR insertions (5 out of 20) caused knockout or strong knockdown effects and one of seven intronic insertions resulted in a knockout effect. Collectively, of a total of 33 Mu insertions, all of which were within 200 bp of genes, only 11 significantly reduced gene expression, and only two knocked it out completely.
Conclusions: These results indicate that that Mu element insertions near TSSs of host genes are often associated with quantitative and in many cases neglectable functional consequences on nearby gene expression.

overall_design: We aimed to examine the degree to which insertions of precision targeting TEs affect the expression of nearby genes. To do this, we evaluated the consequences of a list of de novo Mu element insertions, most of which are into promoter or 5’ UTRs, by experimentally testing the fold change of gene expression levels caused by Mu element insertions. A Mu-active maize line in the B73 background was crossed with a Mu-inactive line in the Mo17 background. The segregating Mu element insertions in the progeny were profiled using a Miseq-based amplicon-sequencing pipeline and the B73-Mo17 SNPs were called for quantifying relative transcript levels of both parental alleles with and without Mu element insertions using deep.

first: Xinyan

last: Zhang


title: Genome-wide ETS-1 binding profile to chromatin in human CD4+ T lymphocytes [ChIP-seq]

status: Public on May 11 2020

first: Samuele

last: Notarbartolo

address: Via Vela 6

summary: In response to pathogenic threats, naïve T cells rapidly transition from a quiescent to activated state, yet the underlying mechanisms are incompletely understood. We investigated the dynamics of mRNA translation kinetics and protein turnover in human naïve and activated T cells. Our datasets uncovered that transcription factors maintaining T cell quiescence had constitutively high turnover, which facilitated their depletion upon activation. Our data elucidate new insights into how T cells maintain a prepared state to mount a rapid immune response.

overall_design: ETS-1 binding profile (ChIP-seq) in human CD4+ T lymphocytes ex-vivo isolated from the peripheral blood of three healthy donors.

first: Federica

last: Sallusto


title: Global translation during early development depends on the essential transcription factor PRDM10 [RNA-Seq_2]

status: Public on May 06 2020

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

institute: Institute of Molecular and Cell Biology, A*STAR

summary: Members of the PR/SET domain-containing (PRDM) family of zinc finger transcriptional regulators play diverse roles in embryonic development and lineage differentiation. PRDM10 is a yet uncharacterized family member, with unknown functions in vivo. Here we report an essential requirement for PRDM10 in the pre-implantation embryo and embryonic stem cells (mESCs), where loss of PRDM10 results in severe cell growth inhibition. Genomic and biochemical analyses reveal that PRDM10 functions as a sequence-specific transcription factor which modulates gene expression by binding to target gene promoters. We identify Eif3b, which encodes a core component of the eukaryotic translation initiation factor 3 (eIF3) complex, as a key downstream target and demonstrate that growth inhibition in PRDM10-deficient mESCs is largely mediated through EIF3B-dependent effects on global translation. This work elucidates the molecular function of PRDM10 in maintaining global translation and establishes its essential role in early embryonic development and mESC homeostasis, offering novel insights into the functional repertoire of PRDMs as well as the transcriptional mechanisms regulating global translation.

overall_design: Single embryo RNA-seq analysis of gene expression in 8-cell stage PRDM10 KO vs control mouse embryos

middle: Y

first: Michelle

last: Seah

first: Imogen

last: Brooks

first: Delia

middle: H

last: Quek

first: Dominic

last: Huxley

first: Chuan-Sheng

last: Foo

first: Li

last: Lee

first: Heike

last: Wollmann

first: Huili

last: Guo

first: Daniel

last: Messerschmidt

first: Ernesto

last: Guccione


title: Cooperation of MYC and b-catenin in liver tumorigenesis requires Yap/Taz

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

summary: One of the transcriptional targets of b-catenin/TCF and a key downstream effector of the WNT/b-catenin pathway in several tissues is the MYC proto-oncogene, which encodes for a transcription factor that is a master regulator of proliferation- and growth-related genes. However, several evidences indicate that this epistatic relationship does not seem to occur in liver: indeed Myc was not induced upon b-catenin activation driven by APC loss, and Myc deletion in hepatocytes does not suppress the effects of APC loss on cell proliferation and liver zonation. Besides, there are indications that the two pathways can be independently activated, and cooperate during tumorigenesis. In particular, MYC amplification and b-catenin mutations showed a tendency toward co-occurrence in either adult HCC or aggressive childhood hepatoblastoma, and MYC-driven HCC in experimental mouse models frequently acquired activating mutations in b-catenin.   In order to address whether these observations reflect a functional cross-talk between the two pathways that may occur in a specific molecular subgroup of HCC patients, we generated a new mouse model allowing conditional activation of MYC and -catenin in hepatocytes. This model demonstrated a strong cooperativity between the two oncogenes in promoting liver tumorigenesis. Our data indicate that this cooperation occurs mainly through unrestrained proliferation of liver cells that requires the activity of the transcriptional co-factors Yap and Taz.

overall_design: Total RNA profiling of gene expression upon short term activation of MYC and/or b-catenin in hepatocytes by AAV8-TBG-CRE injection or in Myc or Myc/b-catenin driven mouse hepatocellular carcinomas

first: Andrea

last: Bisso


title: Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells [RNA-Seq]

city: PHILADELPHIA

first: Kai

last: Tan

state: PA

address: 3501 CIVIC CENTER BLVD.

institute: Children's Hospital of Philadelphia

overall_design: Examination of global gene expression during the ontogeny of hematopoietic stem cells

first: Changya

last: Chen

first: Peng

last: Gao


title: Analyzing Presymptomatic Tissue to Gain Insights into Late-Onset Degenerative Trinucleotide Repeat Disease

city: Dallas

first: Venkateswara

last: Mootha

state: Texas

address: 5323 Harry Hines

department: Ophthalmology

institute: UT Southwestern

summary: How genetic defects trigger late-onset disease is important for understanding disease progression and therapeutic development. Fuchs’ endothelial corneal dystrophy (FECD) is an RNA-mediated disease caused by a trinucleotide CUG expansion in an intron within the TCF4 gene. The mutant intronic CUG RNA is present at 1-2 copies per cell, posing a challenge to understand how a rare RNA can cause disease. Late-onset FECD is a uniquely advantageous model for studying how RNA triggers disease because; 1) Affected tissue is routinely removed during surgery; 2) The expanded CUG mutation is one of the most prevalent disease-causing mutations, making it possible to obtain pre-symptomatic tissue from eye bank donors to probe how gene expression changes precede disease; and 3)  The affected tissue is a homogeneous single cell monolayer, facilitating accurate transcriptome analysis. Here we use RNA sequencing to compare tissue from individuals who are pre-symptomatic (Pre_S) to tissue from patients with late stage FECD (FECD_REP). The abundance of mutant repeat intronic RNA in Pre_S and FECD_REP tissue is elevated due to increased half-life in a corneal cell-specific manner. In Pre_S tissue, changes in splicing and extracellular matrix gene expression foreshadow the changes observed in advanced disease and predict the activation of the fibrosis pathway and immune system seen in late-stage patients. The absolute efficiency of splicing changes are similar in presymptomatic and late stage tissue. Our data identify gene candidates for early drivers of disease and biomarkers that may represent diagnostic and therapeutic targets for FECD. We conclude that changes in alternative splicing and gene expression are observable decades prior to the diagnosis of late-onset trinucleotide repeat disease.

overall_design: Total 25 samples, including 9 for comtrol, 6 for FECD_REP and 6 pre-symptomatic

first: Yongjun

last: Chu

first: Jianxin

last: Hu

first: Hanquang

last: Liang

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Walter

last: Beebe

first: Charles

last: Bowman

first: Xin

last: Gong

first: David

last: Corey

first: Vinod


title: Transcriptomic changes in response to modulation of long-non-coding RNA LINC00473

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

summary: Human thermogenic adipose tissue mitigates metabolic disease, raising much interest in understanding its development and function. Here, we show that human thermogenic adipocytes specifically express a primate-specific long non-coding RNA, LINC00473 which is highly correlated with UCP1 expression and decreased in obesity and type-2 diabetes. LINC00473 is detected in progenitor cells, and increases upon differentiation and in response to cAMP. In contrast to other known adipocyte LincRNAs, LINC00473 shuttles out of the nucleus, colocalizes and can be crosslinked to mitochondrial and lipid droplet proteins. Up- or down- regulation of LINC00473 results in reciprocal alterations in lipolysis, respiration and transcription of genes associated with mitochondrial oxidative metabolism. Depletion of PLIN1 results in impaired cAMP-responsive LINC00473 expression and lipolysis, indicating bidirectional interactions between PLIN1, LINC00473 and mitochondrial oxidative functions. Thus, we suggest that LINC00473 is a key regulator of human thermogenic adipocyte function, and reveals a role for a LincRNA in inter-organelle communication and human energy metabolism.

overall_design: To elucidate the mechanisms involved in the generation of thermogenic adipocytes in humans, we searched for major gene expression differences between adipocytes generated from mostly non-thermogenic and thermogenic adipose tissue depots. Biopsies from abdominal subcutaneous (AbdSQ) and from supraclavicular (SClav) adipose tissue of non-diabetic subjects were obtained. Differentiated adipocytes were stimulated for 4h with norepinephrine (NE) prior to RNASeq.

first: Khanh-Van

last: Tran

first: Erin

middle: L

last: Brown

first: Tiffany

last: De Souza

first: Naja

middle: Z

last: Jespersen

first: Cecilie

last: Nandrup-Bus

first: Qin

last: Yang

first: Zinger

first: Anand

last: Desai

first: SoYun

last: Min

first: Raziel

last: Rojas-Rodriguez

first: Morten

last: Lundh

first: Amir

last: Feizi

first: Hanni

last: Willenbrock

first: Therese

last: Larsen

first: Mai

last: Severinsen

first: Kimberly

last: Malka

first: Anthony

last: Mozzicato

first: Atul

middle: S

last: Deshmukh

first: Brice

last: Emanuelli

first: Bente

last: Pedersen

first: Timothy

last: Fitzgibbons

first: Camilla

last: Scheele

first: Søren

last: Nielsen


title: Global translation during early development depends on the essential transcription factor PRDM10

first: Brenda

last: Han

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

overall_design: Refer to individual Series


title: Global translation during early development depends on the essential transcription factor PRDM10 [ChIP-seq]

overall_design: ChIP-seq analysis of PRDM10 binding in Prdm10F/F; Rosa26-CreERT2 treated with ethanol or 4-OHT; 3 replicate ChIP samples + 1 input sample per condition.

first: Michelle

last: Seah

first: Imogen

last: Brooks

first: Delia

last: Quek

first: Dominic

last: Huxley

first: Chuan-Sheng

last: Foo

first: Li

middle: T

last: Lee

first: Heike

last: Wollmann

first: Huili

last: Guo

first: Daniel

last: Messerschmidt

first: Ernesto

last: Guccione


title: Integrated single cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC sensitive cell lines

status: Public on May 04 2020

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

address: 1650 Orleans St - Rm 485

department: Oncology

institute: Johns Hopkins University

summary: The identification of the potential mechanisms of resistance while tumor cells still respond to therapy is critical to develop combination therapies to delay acquired resistance. Cetuximab, an anti-EGFR therapy, is the only targeted therapy available for head and neck squamous cell carcinoma (HNSCC). We generated the first comprehensive multi-omics, bulk and single cell data in sensitive HNSCC cells to identify relevant transcriptional and epigenetic changes that are an immediate response to cetuximab in sensitive cells. These changes include genes from two pathways potentially associated with resistance: regulation of growth factor receptors through the transcription factor TFAP2A, and epithelial-to-mesenchymal transition (EMT) process. Single cell RNA-sequencing demonstrates inter-cell lines heterogeneity, with cell specific expression profiles of TFAP2A and VIM gene expression in cetuximab treated and untreated clones, and an independent role of each pathway. RNA-seq and ATAC-seq demonstrate that there are global transcriptional and epigenetic changes within the first five days of anti-EGFR therapy. We also experimentally verified that lack of TFAP2A reduces HNSCC growth in vitro and that this effect is enhanced with cetuximab and a stronger effect is observed with JQ1, an inhibitor of alternative receptor tyrosine kinases. Corroborating our scRNA-seq observation, TFAP2A silencing does not affect cell migration, supporting the lack of interplay with the EMT pathway. Overall, our study shows that the immediate adaptive transcriptional and epigenetic changes induced by cetuximab include relevant pathways associated with acquired resistance. Although heterogeneous, these changes can be targeted by a multiple-target drug as JQ1 that in combination with cetuximab in the early stage of treatment present better efficacy in controlling tumor growth.

overall_design: 3 head and neck squamous cell carcinoma cell lines treated with cetuximab or PBS (untreated controls) each in triplicate.

first: Elana

last: Fertig


title: PolyA-miner: Accurate assessment of differential Alternative Poly-Adenylation from 3’Seq data using Vector projections and Non-negative matrix factorization

city: Houston,

first: Hari Krishna

last: Yalamanchili

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Integrated single cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC sensitive cell lines (scRNA-Seq)

overall_design: 3 head and neck squamous cell carcinoma cell lines treated with cetuximab or PBS (untreated controls) each in duplicate.


title: PolyA-miner: Accurate assessment of differential Alternative Poly-Adenylation from 3’Seq data using Vector projections and Non-negative matrix factorization [human]

summary: Plethora of misprimed and noisy APA sites are filtered out by PolyA-miner

overall_design: Non-silencing shRNA-infected WA09 human embryonic stem-cell derived excitatory neuron mRNA 3' end sequencing profiles generated by deep sequencing in triplicate

first: Hari

first: Callison

middle: E

last: Alcott

first: Huda

last: Zoghbi

first: Zhandong

last: Liu


title: Molecular Atlas of the Adult Mouse Brain

status: Public on May 03 2020

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavägen 9

department: Neuroscience

institute: Karolinska Institutet

summary: Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette – that is sufficient to spatially annotate the adult brain. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.

overall_design: We hybridized 75 coronal sections from one brain hemisphere of 3 adult mice with Spatial Transcriptomics and defined a molecular atlas using clustering algorithms.

first: Cantin

last: Ortiz

first: Jose

last: Fernandez Navarro

first: Aleksandra

last: Jurek

first: Antje

last: Märtin

first: Joakim

last: Lundeberg


title: Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells [scRNA-seq]

first: Kai

last: Tan

summary: Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.

overall_design: Examination of global gene expression during the ontogeny of hematopoietic stem cells.

first: Changya

last: Chen

first: Peng

last: Gao

first: Elizabeth

last: Howell


title: PolyA-miner: Accurate assessment of differential Alternative Poly-Adenylation from 3’Seq data using Vector projections and Non-negative matrix factorization [mouse]

overall_design: Wild-type, male, C57BL/6J mouse, left hippocampal mRNA 3' end sequencing profiles generated by deep sequencing in triplicate.


title: Respiratory supercomplexes provide metabolic efficiency in zebrafish

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

institute: University of Bern

summary: The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 (cox7a2l) is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III-IV complexes. Therefore the SCAF1 null allele model lack all III-IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources.

overall_design: Muscle from females SCAF1Δ1 after the 6 weeks of a regime of standard diet or double diet  were dissected and stored at -80°C.

first: Carolina

last: Garcia-Poyatos

first: José

middle: A

last: Enríquez

first: Marius-Alexandru

last: Botos