title: Transcriptome analysis of iPSC-derived neurons from Rubinstein-Taybi patients reveals deficits in neuronal differentiation.

city: Cusano Milanino

first: Luciano

last: Calzari

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

summary: Rubinstein-Taybi syndrome (RSTS) is a rare multisystem developmental disorder with moderate to severe intellectual disability caused by heterozygous mutations of either CREBBP or EP300 genes encoding CBP/p300 chromatin modifiers. We explored the gene programs and processes underlying the morphological and functional alterations shown by iPSC-derived neurons modeling RSTS to bridge the molecular changes resulting from defective CBP/p300 to cognitive impairment. By global transcriptome analysis we compared the differentially expressed genes (DEGs) marking the transition from iPSC-derived neural progenitors to cortical neurons (iNeurons) of five RSTS patients carrying private CREBBP/EP300 mutations manifesting differently graded neurocognitive signs with those of four healthy controls. Our data shows a defective and altered neuroprogenitor to neuron transcriptional program in the cells from RSTS patients as compared to controls. First, transcriptional regulation is weaker in RSTS as less genes than in controls are modulated, including genes of key processes of mature functional neurons, such as those involved in synaptic integration. Second, regulation is subverted as genes acting at pre-terminal stages of neural differentiation in cell polarity and adhesive functions (members of the cadherin family) and axon extension/guidance (members of the semaphorins and SLIT receptors families) are improperly upregulated. Impairment or delay of RSTS neuronal differentiation program is also evidenced by decreased modulation of the overall number of neural differentiation markers, significantly impacting the initial and final stages of the differentiation cascade. Last, extensive downregulation of genes for RNA/DNA metabolic processes confirms that RSTS is a global transcription disorder, consistent with a syndrome driven by chromatin dysregulation. Interestingly, the overall transcriptome changes validate the morphological and functional alterations previously appointed as biomarkers of RSTS iNeurons, accounting for patients’ cognitive deficit. The impact of RSTS transcriptome may go beyond RSTS as cross-comparison of dysregulated genes with other  modeled neurodevelopmental disorders could enhance to unveil the core genes of cognitive impairment.

overall_design: The expression profile of 5 RSTS patients and 4 healthy controls was analyzed. For each individual, RNA was extracted from cells collected at two time points: the first after 35 days (neural progenitor stage) from the start of differentiation of iPSCs  and the second after 70 days of differentiation (mature neuron stage).

first: Matteo

last: Barcella

first: Lidia

last: Larizza


title: Alzheimer's disease-related dysregulation of mRNA translation causes key pathological features with ageing

status: Public on Jun 29 2020

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

country: United Kingdom

institute: King's College London

type: Expression profiling by high throughput sequencing

summary: Primary rat cortical neurons and treated with AB for 24h. RNA-seq on total and ribosome-enriched sucrose cushion

first: Anshua

last: Ghosh

first: Rocio

middle: T


title: Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80

status: Public on Jun 23 2020

city: Ann Arbor

first: Kenneth

middle: Y

last: Kwan

state: MI

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Regenerative reprogramming of the intestinal stem cell state via Hippo signaling suppresses metastatic colorectal cancer [DSS_scRNAseq]

status: Public on Jun 24 2020

city: Boston

first: Priscilla

last: Cheung

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

summary: Although the Hippo transcriptional coactivator YAP is considered oncogenic in many tissues, its roles in intestinal homeostasis and colorectal cancer (CRC) remain controversial. Here, we demonstrate that the Hippo kinases LATS1/2 and MST1/2, which inhibit YAP activity, are required for maintaining Wnt signaling and canonical stem cell function. Hippo inhibition induces a distinct epithelial cell state marked by low Wnt signaling, a wound-healing response, and transcription factor Klf6 expression. Notably, loss of LATS1/2 or overexpression of YAP is sufficient to reprogram Lgr5+ cancer stem cells to this state and thereby suppress tumor growth in organoids, patient-derived xenografts, and mouse models of primary and metastatic CRC. Finally, we demonstrate that genetic deletion of YAP and its paralog TAZ promotes the growth of these tumors. Collectively, our results establish the role of YAP as a tumor suppressor in the adult colon and implicate Hippo kinases as therapeutic vulnerabilities in colorectal malignancies.

overall_design: Single-cell mRNA profiles of colonic epithelial cells isolated from C57BL/6J mice treated with or without 3.5% dextran sulfate sodium (DSS) in drinking water for 5 days followed by normal water for 3 days.

first: Jordi

last: Xiol

first: Raffaele

middle: A

last: Calogero

first: Fernando

middle: D

last: Camargo


title: Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80 [ATAC-seq]

summary: Chromatin regulates spatiotemporal gene expression during neurodevelopment, but it also mediates DNA damage repair crucial to proliferating neural progenitor cells (NPCs). Here, we uncover molecularly dissociable roles for nucleosome remodeler INO80 in chromatin-mediated transcriptome and genome maintenance in corticogenesis. We find that conditional Ino80 deletion from cortical NPCs impairs DNA double-strand break repair, triggering p53 activation, robust apoptosis, and microcephaly, whereas co-deletion of Trp53 with Ino80 leads to remarkable reversal of these phenotypes. Using an in vivo DNA repair assay, we find that Ino80 is selectively required for homologous recombination (HR) DNA repair, which is mechanistically distinct from INO80 function in YY1-associated transcription. Unexpectedly, sensitivity to loss of INO80-mediated HR is dependent on the mode of NPC division: Ino80 deletion causes extensive DNA damage and apoptosis in symmetric NPC-NPC divisions, but not in asymmetric neurogenic divisions. Thus, distinct modes of NPC division have divergent requirements for Ino80-dependent HR DNA repair.

overall_design: We analyzed a total of 2 samples of genomic DNA from E13.5 mouse cortex using ATAC-seq to assess chromatin accessibility. Libraries were generated from 50,000 nuclei per sample following the ATAC-seq protocol from Buenrostro et al. 2015. One control sample and one Emx1-Cre Ino80 conditional mutant sample were used.

first: Jason

middle: M

last: Keil

first: Daniel

middle: J

last: Doyle

first: Adel

last: Qalieh

first: Mandy

last: Lam

first: Owen

middle: H

last: Funk

first: Yaman

first: Lei

last: Shi

first: Nitesh

last: Mohan

first: Alice

last: Sorel


title: Mammary gland tumor immunoinfiltrate analysis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: In this experiment we compare the gene expression profile using two different models of mammary gland tumors (M/D-induced or AT3) each of them have been treated or not with NAM.

overall_design: In this experiment we compare the gene expression profile of 8 mice M/D-driven mammary gland tumors and 6 AT3 mice mammary gland tumors, each of them treated or not with NAM for 10 days.

first: Aitziber

last: Buque

first: Lorenzo

last: Galluzzi

first: Guido

last: Kroemer


title: LN immunoinfiltrate analysis

summary: In this experiment we compare the expression profile of genes present in the lymph node or spleens of control mice vs mice treated with NAM in the drinking water for either 1, 3 or 14 days.

overall_design: Expression profile of 13 mice lymph nodes (LN) and 20 spleens (S) of animals under 4 different nutritional conditions: control (LN n=3; S n=5), 1 day NAM administration in the drinking water (LN n=2; S n=5),  3 days NAM administration in the drinking water (LN n=4;  S n=5),  14 days NAM administration in the drinking water (LN n=4;  S n=5)


title: Expression data from RAW264.7 murine cell line

city: Indianapolis

first: Rebecca

last: Davidson

state: IN

address: 5042 Melrose Ave

department: Biochemistry and Molecular Biology

institute: IUSM

summary:
Appropriate bone mass is maintained by the actions of the main cells in the bone, osteoclasts and osteoblasts. The Stat3 transcription factor is known to have an effect on maintaining bone mass, but it is not known whether its key actions are in osteoblasts, osteoclasts, or both. Preliminary data indicated that Stat3 plays a role in osteoclast differentiation, but the mechanisms of this role are not yet understood.
We performed a microarray analysis to understand what key players in osteoclast differentiation are affected by Stat3 transcriptional activity

overall_design: We performed a transient siRNA knockdown of Stat3 in the RAW264.7 cell line and differentiated these cells towards an osteoclast fate with RANKL stimulation.

middle: K

first: Jiliang

last: Li


title: Context-dependent IL-1 mRNA-destabilization by TTP prevents dysregulation of immune homeostasis

city: Wien

first: Pavel

last: Kovarik

address: Dr.-Bohr-Gasse 9/4

department: Max Perutz Labs

country: Austria

institute: University of Vienna

summary: We report that TTP exhibits context-dependent target destabilisation and that such context-defined mRNA decay is essential for maintaining steady state IL-1 levels in the physiological range

overall_design: mRNA profiles of untreated and LPS-stimulated WT and TTP-/- murine bone marrow-derived dendritic cells

first: L

last: Sneezum

first: P


title: Early precursor T cells establish and propagate T cell exhaustion in chronic infection

city: Clayton

first: Wei

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University


title: Gene expression of Abhd11 knock-out or over-expression embryonic stem cells

city: Chongqing

first: Rui

last: Jian

address: Gaotanyan Street

department: Department of Histology and Embryology

country: China

institute: Third Military Medical University

summary: Abhd11 is previously identified as a conserved lipase in lipid metabolism. However, its physiological functions in embryonic stem cells (ESCs) are unknown. Based on the construction of ESC lines with conditional Abhd11 expression, we analyst the transcriptome profiling of ESCs upon Abhd11 knock-out (KO) or over-expression (OE). In Abhd11 KO ESCs, differentially expressed genes were enriched in metabolic genes while Abhd11 OE ESCs elicited a smaller transcriptional response compared to that of Abhd11 KO ESCs.

overall_design: Abhd11 was deleted under the inducible overexpression (iOE) of exogenous Abhd11 using “tetR-Krab-tetO” conditional gene expression system and CRISPR/Cas9 technology. To start with, we generated a stable tetR-Krab-Cas9 expressing cell line, which was hereafter used as a control cell lines. Next, we obtained Abhd11 iOE ESCs by transducing inducible expression cassette of Abhd11 targeted with Red fluorescent protein (Abhd11-RFP) into the tetR-Krab-Cas9 expressing cells. The subcloned Abhd11 iOE ESCs was induced to express Abhd11-RFP and used as Abhd11 OE ESCs in the presence of 1000ng/ml doxycycline (Dox). Finally, we generated Abhd11 iOE/KO ESCs by transducing lentivirus carrying sgRNAs that mapped to the Abhd11 genomic sequence spanning an intron-exon junction and only targeted endogenous Abhd11 into the Abhd11 iOE ESCs. Hence, endogenous Abhd11 depleted Abhd11 iOE/KO ESCs were used as Abhd11 KO  ESCs in the absence of Dox while used as Abhd11 rescued (Abhd11 RES) ESCs in the presence of 1ng/ml Dox.

first: Gaoke

last: Liu


title: The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

institute: Henry Ford Health System


title: M/D-tumors vs non´-tumor mammary gland tissues

status: Public on Jun 22 2020

city: New York

last: Buque Martinez

state: New York

address: 1300 York Avenue

department: Radiation Oncology

institute: Weill Cornell Medical College

summary:
The main goal of this experiment was to contrast the gene expression of  mammary gland tissues at three different tumoral stages : M/D-driven mammary gland small tumors vs mammary gland tissues that have been exposed to M/D but they did not develop a tumor (hyperplastic mammary gland) vs mammary gland tissues that were NOT expossed to M/D (normal mammary gland).
Expression profile of 18 mice mammary gland tissues at 3 differents neoplastic stages before and after M/D expossure

overall_design: Aitziber,Buque


summary: The project in which this experiment is included demostrate that the developtment and growth of breast tumors are under immunosurveillance. We perform as screaning of multiple nutritional interventions to observe the impact of each of them in the tumor incidence, tumor growth and overall survival of the animasls. We concluded that safe nutritional measures including nicotinamide (NAM) supplementation efficiently mediates immunotherapeutic effects against established transplantable BC.  In particular, the aim of this experiment was to analyse the effect that NAM has in the immune cells that infiltrate the breast tumors, more specifically the TSA mammary gland tumors.    Our findings identify NAM as a potential strategy for the prevention and treatment of HR+ BC.

overall_design: In this experiment we performed single cell RNAseq of the immunoinfiltrate of TSA mammary gland tumors that have been treated or not with NAM for 10 days.


title: CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Chromatin organization is critical for cell growth, differentiation, and disease development, however, its functions in peripheral myelination and myelin repair remain elusive. Here we observed a global diminution of chromatin accessibility during Schwann cell differentiation and demonstrated that the chromatin organizer CCCTC-binding factor (CTCF) is critical for Schwann cell myelination and myelin regeneration after nerve injury. Inhibition of Ctcf or its deletion blocked Schwann cell differentiation at the pre-myelinating stage, whereas overexpression of CTCF promoted the myelination program. CTCF establishes the chromatin interaction loop between promoters and regulatory elements to promote expression of key pro-myelinogenic factors such as EGR2. In addition, CTCF interacts with SUZ12, a component of polycomb-repressive-complex 2, to repress expression of immature Schwann cell-associated regulators including HES1, RSPO2, and CALCA. Together, our findings reveal the dual role of CTCF-dependent chromatin organization in promoting myelinogenic programs and recruiting chromatin-repressive complexes to block differentiation inhibitors to control peripheral myelination and myelin repair.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-seq: 2 Control and 2 Ctcf cKO mouse sciatic nerves; 3 siControl and 3 siCtcf rat Schwann cell cultures.  ChIP-seq: 1 proliferating and 1 differentiating samples for CTCF ChIP-seq; 1 siControl and 1 siCtcf samples for H3K27ac ChIP-seq.  ATAC-seq: 2 siControl and 2 siCtcf samples.

first: Jincheng

last: Wang

first: Jiajia

first: Lijun

last: Yang

first: Qinjie

last: Weng

first: Q

middle: R


title: Early precursor T cells establish and propagate T cell exhaustion in chronic infection [ATAC-seq]

last: Shi

summary: TCF1+ precursors of exhausted T cells maintain T cell immunity during chronic infection and cancer and mediate the response to immune checkpoint inhibition; however, their developmental requirements are poorly understood. Here, we demonstrate that high antigen load promoted the differentiation of TCF1+ precursor T cells, which acquired hallmarks of T cell exhaustion such as impaired production of IFN? within the first days after infection. Transcriptional profiling revealed that exhaustion was established first in precursor T cells while early effector cells retained a polyfunctional profile. Early precursor T cells exposed to high amounts of antigen showed epigenetic imprinting of T cell receptor-dependent transcription factor binding, were dependent on BACH2 and restricted to the generation of T cells displaying features of exhaustion. Overall, we demonstrate that T cell exhaustion manifests first in TCF1+ precursor T cells and is propagated subsequently to the pool of antigen-specific T cells.

overall_design: ATAC sequencing of ID3GFP+ and ID3GFP- P14 T cells obtained from early and late LCMV Armstrong and Docile infected mice.

first: Daniel

last: Utzschneider

first: Sarah

middle: S

last: Gabriel

first: David

last: Chisanga

first: Patrick

last: Gubser

first: Axel

last: Kallies


title: Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

status: Public on Jun 20 2020

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

institute: IGH

summary: R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, we have mapped RNA:DNA hybrids, replication stress markers and DNA double strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids were found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR was only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also cumulated at TTS, leading to persistent checkpoint activation, spreading of -H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.

overall_design: NGS-based analysis of the effect of R-loops on replication stress and genomic instability in human cells

first: Alexy

last: Promonet

first: Ismael

last: Padioleau

first: Yaqun

first: Lionel

last: Sanz

first: Magdalena

last: Skrzypczak

first: Krzysztof

last: Ginalski

first: Frédéric

last: Chedin

first: Malgorzata

last: Rowicka

first: Chunlong

last: Chen

first: Yea-Lih

last: Lin

first: Philippe

last: Pasero


title: In Vivo Chimeric Alzheimer’s Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons

city: San Francisco

first: Kelly

last: Zalocusky

state: CA

address: 1650 Owens Street, Gladstone Center for Translational Advancement

institute: Gladstone Institutes

summary: Despite its clear impact on Alzheimer’s Disease (AD) risk, apolipoprotein (apo) E4’s contributions to AD etiology remain poorly understood. Progress in answering this and other questions in AD research has been limited by an inability to model human-specific phenotypes in an in vivo environment. Here we transplanted human induced pluripotent stem cell (hiPSC)-derived neurons carrying normal apoE3 or pathogenic apoE4 into human apoE3 or apoE4 knock-in mouse hippocampi, enabling us to disentangle the effects of apoE4 produced in human neurons and in the brain environment. Using single nucleus RNA-sequencing (snRNA-seq), we identified key transcriptional changes specific to human neuron subtypes in response to endogenous or exogenous apoE4. We also found that Aβ from transplanted human neurons formed plaque-like aggregates, with differences in localization and interaction with microglia depending on the transplant and host apoE genotype. These findings highlight the power of in vivo chimeric disease modeling for studying AD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA Sequencing data from human induced pluripotent stem cell (hIPSC) derived neurons. hIPSC-derived neurons have an APOE4 genotype or are isogenic wth an APOE3 genotype. hIPSC-derived neurons were transplanted  into and matured for 7 months in human APOE4-KI or human APOE3-KI mice.

first: Ramsey

last: Najm

first: Yanxia

last: Hao

first: Yadong

last: Huang


title: The transcriptional repressor, BCL11A, promotes breast cancer metastasis

city: Cleveland

first: Darcie

last: Seachrist

address: 2109 Adelbert Rd,, Pharmacology Department SOM RT300

institute: Case Western Reserve University

summary: Identification of the BCL11A-regulated transcriptome and spliceosome and determination of MBNL1-dependent splicing changes by RNA-Seq

overall_design: Two/Three replicates were analyzed for each experimental condition.

first: Molly

last: Hannigan

first: Donny

last: Licatalosi

first: Ruth

last: Keri


title: Altered activity-dependent nascent transcription in Rai1-knockdown mature mouse cortical cultures

first: Patricia

last: Garay

address: 1137 Catherine St 5815 Med Sci II

summary: We performed the nascent RNA-seq technique, Bru-Seq, and chromatin immunoprecipitation sequencing (ChIP-seq) for Retinoic acid induced 1 (RAI1) using a custom antibody, on mouse neuronal cultures treated with control or Rai1-targeted shRNA, with 4 hour treatment of vehicle, tetrodoxin (TTX) or bicuculline (BIC) and 20 minute labeling of bromouridine.

overall_design:
2-3 biological replicates, each consisting of cortices and hippocampi pooled from sex-ratio matched groups of E18 mouse embryos. Cells were plated and cultured for 14 days in Neurobasal + B27 medium, at which point lentiviral delivery of control or Rai1-targeted shRNA was performed. 3 days later, cells were treated with TTX, Bicuculline, or vehicle (water) for 4 hours.
For Bru-seq: In the last 20 minutes, bromouridine was applied to the cells to label nascent RNA. Follow RNA purification,  bromouridine-immunoprecipitation was performed to isolate nascent RNAs, preceding cDNA library synthesis. Pooled stranded libraries were run on Illumina Hiseq, single-end, 50 bp reads.
For RAI1 ChIP-seq: Cells were harvested, fixed, and RAI1-bound chromatin isolated. Pooled libraries were run on Illumina NextSeq, single-end, 75 bp reads.

first: Shigeki

last: Iwase


title: Single-cell RNA sequencing (scRNAseq) data from Ventricular-Subventricular Zone (V-SVZ) and Olfactory Bulb (OB) cells, and Scope-Seq data from Ventricular-Subventricular Zone (V-SVZ)

status: Public on Jun 21 2020

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

summary: We performed large-scale single cell profiling of dissociated V-SVZ and OB cells from the same animal carrying either the hGFAP::CreERT2; Rosa26LSL-TdTomato (GCERT2) reporter, or ratNes::FLPOER; Rosa26FSF-TdTomato (NesFLPO) reporter. Scope-Seq profiling was performed on dissociated V-SVZ cells from C57BL/6J animals.

overall_design: Using automated microwell array platforms and mRNA capture beads, we generated single-cell RNA-seq profiles of dissociated V-SVZ and OB cells without any prior cell sorting.

first: Peter

last: Sims


title: Immunoinfiltrate analysis

first: Pierre

last: de la Grange

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

overall_design: Refer to individual Series


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [BS]

status: Public on Jun 18 2020

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

type: Methylation profiling by high throughput sequencing

summary:
Background: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia.

Results: Here, we report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modelling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid-down by the differential expression and binding of other transcription factors under normoxia control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumours with high immune checkpoint expression, but not in tumours with low immune checkpoint expression, where they would compromise tumour immunotolerance. In a low-immunogenic tumour model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumour growth.

Conclusions: Our data elucidate the mechanism underlying cell-type specific responses to hypoxia, and suggest DNA methylation and hypoxia to underlie tumour immunotolerance.

overall_design: Examination of the methylation level of DNA fragments in human cancer cell lines, upon exposure to acute hypoxia

first: Flora

last: D’Anna

first: Laurien

last: Van Dyck

first: Hui

last: Zhao

first: Rebecca

middle: V

last: Berrens

first: Junbin

last: Qian

first: Pawel

last: Bieniasz-Krzywiec

first: Vikas

last: Chandra

first: Luc

last: Schoonjans

first: Jason

last: Matthews

first: Julie

last: De Smedt

first: Liesbeth

last: Minnoye

first: Ricardo

last: Amorim

first: Sepideh

last: Khorasanizadeh

first: Qian

last: Yu

first: Liyun

first: Marie

last: De Borre

first: Savvas

middle: N

last: Savvides

first: Celeste

last: Simon

last: Carmeliet

first: Wolf

last: Reik

first: Fraydoon

last: Rastinejad

first: Massimiliano

last: Mazzone

first: Bernard

last: Thienpont

first: Diether

last: Lambrechts


title: Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

summary: Viral infection outcomes are governed by the complex and dynamic interplay between the infecting virus population and the host response. It is increasingly clear that both viral and host cell populations are highly heterogeneous, but little is known about how this heterogeneity influences infection dynamics or viral pathogenicity. To dissect the interactions between influenza A virus (IAV) and host cell heterogeneity, we examined the combined host and viral transcriptomes of thousands of individual cells, each infected with a single IAV virion. We observed complex patterns of viral gene expression and the existence of multiple distinct host transcriptional responses to infection at the single cell level. We show that human H1N1 and H3N2 strains differ significantly in patterns of both viral and host anti-viral gene transcriptional heterogeneity at the single cell level. Our analyses also reveal that semi-infectious particles that fail to express the viral NS can play a dominant role in triggering the innate anti-viral response to infection. Altogether, these data reveal how patterns of viral population heterogeneity can serve as a major determinant of antiviral gene activation.

overall_design: Examination of the combined host and viral transcriptomes of thousands of individual transformed human lung cells singly-infected by influenza A virus Cal07 (H1N1) or Perth09 (H3N2).

first: Jiayi

last: Sun

first: Juan

middle: C

last: Vera

first: Jenny

last: Drnevich

first: Yen

last: Lin

first: Ruian

last: Ke

first: Christopher

middle: B

last: Brooke


title: Urine-derived podocytes from Alport patients as a model for glomerular filtration barrier defects

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Alport syndrome (AS) is a genetic defect involving mutations of collagen IV α3, α4 or α5 genes, resulting in distinctive clinical features: kidney disease, hearing loss and eye abnormalities. Podocytes are responsible of production and correct assembly of the collagen IV isoforms, however, specific alterations of podocyte phenotype are currently scarce. We here generated immortalised AS urine-derived podocyte from three different patients. AS podocytes expressed a typical podocyte signature when compared to normal urine-derived podocytes, with comparable expression of podocyte markers. Each AS cell line showed a collagen IV profile that reflected the typical patient mutation. Furthermore, by RNA-sequencing 348 genes were found differentially expressed in Alport podocytes. Gene Ontology analysis underlined enrichment in genes involved in cell motility, adhesion, survival and angiogenesis. In parallel, AS podocyte motility was reduced. In conclusion, our data clearly indicate that AS podocytes display altered features connected but distinct from the collagen alterations.

overall_design: RNA-sequencing was performed on urine-derived podocytes from three Alport syndrome patients (three immortalized clones  for each patient) and one control healthy subject (three different passages): AS patient 1 (AS216P1, AS213P1, AS212P1: col4a3 mutation), AS patient 2 (AS612P2, AS611P2, AS610P2: col4a5 mutation), AS patient 3 (710P3, 71P3, 72P3: col4a5 mutation), Urine-derived podocytes (control). Total RNA isolated from control podocytes and AS podocyte cell lines.

first: C

last: Iampietro

first: L

last: Bellucci

first: FO

last: Arcolino

first: M

last: Arigoni

last: Alessandri

first: R

last: Van Den Heuvel

first: E

last: Levtchenko

first: B

last: Bussolati


title: The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage [RNA-Seq]

first: Qing-Sheng

last: Mi

summary: Tissue-resident macrophages (TRMs) play central roles in local tissue development and immunity. However, how to control TRM ontogeny and maintenance remains unclear. We performed transcriptional and histone modification analyses of alveolar macrophages in mice with myeloid-specific (Csf1rCre) deletion of HDAC3 using bulk RNA-seq, single-cell RNA-seq and ChIP-seq. We report that HDAC3 deficiency results in metabolic disorders and increased cell death of the fetal lung TRMs, which is partially regulated through directly targeting PPAR-γ. Although the loss of AMs in the absence of HDAC3 is not AM subset specific, the transcriptome changes in HDAC3 deficient AM subsets are different. We propose that HDAC3 serves a key epigenetic regulator that controls embryonic TRM ontogeny and maintenance.

overall_design: RNA-sequencing of Csf1rCre+HDAC3fl/fl and Csf1rCre-HDAC3fl/fl fetal preAMs at E18.5

first: Yi

last: Yao

first: Queping

last: Liu

first: Indra

last: Adrianto

first: James

last: Glassbrook

first: Xiaojun

last: Wu

first: Congcong

last: Yin

first: Yu

last: Wang

first: Jun

last: Zhang

first: Hongmei

last: Peng

last: Yang

first: Zheng

last: Dong

first: Frederic

last: Geissmann

first: Li

last: Zhou


title: Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome

city: Trieste

first: Giannino

last: Del Sal

state: TS

address: Padriciano 99 - ed. F3 - Area Science Park

institute: LNCIB

summary: miR-30d has been identified in this study as a novel onco-miRNA downstream of mutant p53. Here we report the microarray data obtained in MDA-MB-231 in which miR-30d levels and function were stably inhibited by a decoy construct (dy_30d)

overall_design: Microarray analysis was performed on MDA-MB-231 stably transduced with the decoy construct for miR-30d (dy_30d) and the matching control cells, each in biological triplicate.

first: V

last: Capaci

first: L

last: Bascetta

first: M

last: Fantuz

first: S

last: Piazza

first: G


title: Single-cell analysis uncovers inter- and intra-organ fibroblast heterogeneity and provides criteria for fibroblast identification and discrimination from vascular mural cells [bladder]

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Many important cell types in adult vertebrates have a mesenchymal origin, including fibroblasts and vascular mural cells (pericytes and smooth muscle cells). Although their biological importance is undisputed, the level of mesenchymal cell heterogeneity within and between organs, while appreciated, has not been analysed in detail. Here, we compare single-cell transcriptional profiles of fibroblasts and vascular mural cells across four murine muscular organs: heart, skeletal muscle, intestine and bladder. We reveal gene expression signatures that demarcate fibroblasts from mural cells across these four as well as other organs and provide molecular signatures for cell subtype identification. Striking inter- and intra-organ heterogeneity and specialization were observed amongst the fibroblasts, primarily reflecting differences in the expression of extracellular matrix components. In comparison, mural cells appeared more homogenous. Fibroblast subtypes localize to discrete anatomical positions in all four organs, offering novel predictions about physiological function(s) and regulatory signalling circuits. Our data shed new light on the diversity and relationships between hitherto poorly defined classes of cells and provide a foundation for improved understanding of their roles in physiological and pathological processes.

overall_design: single-cell transcriptomes were generated of individual cells captured from adult male mice (10-20 weeks of age) by single-cell RNA-sequencing

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Jianping

last: Liu

first: Liqun

last: He

first: Giuseppe

last: Mocci

first: Ying

last: Sun

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Indira

last: Chivukula

first: Åsa

last: Segerstolpe

first: Elisabeth

last: Raschperger

first: Emil

last: Hansson

first: Johan

middle: L

last: Björkegren

first: Xiao-Rong

first: Michael

last: Vanlandewijck

first: Urban

last: Lendahl

first: Christer

last: Betsholtz


title: Single-cell analysis uncovers inter- and intra-organ fibroblast heterogeneity and provides criteria for fibroblast identification and discrimination from vascular mural cells [heart]

first: Lars

last: Muhl

first: Guillem

last: Peng


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [WGBS]

first: Jieyi

last: Xiong

overall_design: Examination of genome wide DNA methylation in mouse ES (mES) cells triple knock out for Ten eleven translocation (Tet-TKO), mES Arnt WT and KO at 10X coverage

first: Flora

last: D’Anna

first: Laurien

last: Van Dyck

first: Hui

last: Zhao

first: Rebecca

last: Berrens

first: Junbin

last: Qian

first: Pawel

last: Bieniasz-Krzywiec

first: Vikas

last: Chandra

first: Luc

last: Schoonjans

first: Jason

last: Matthews

first: Julie

last: De Smedt

first: Liesbeth

last: Minnoye

first: Ricardo

last: Amorim

first: Sepideh

last: Khorasanizadeh

first: Qian

last: Yu

first: Liyun

first: Marie

last: De Borre

first: Savvas

last: Savvides

first: Celeste

last: Simon

first: Peter

last: Carmeliet

first: Wolf

last: Reik

first: Fraydoon

last: Rastinejad

first: Massimiliano

last: Mazzone

first: Bernard

last: Thienpont

first: Diether

last: Lambrechts


title: Single-cell analysis uncovers inter- and intra-organ fibroblast heterogeneity and provides criteria for fibroblast identification and discrimination from vascular mural cells (skeletal muscle)

first: Lars

last: Muhl

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Jianping

last: Liu

first: Liqun

last: He

first: Giuseppe

last: Mocci

first: Ying

last: Sun

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Indira

last: Chivukula

first: Åsa

last: Segerstolpe

first: Elisabeth

last: Raschperger

first: Emil

last: Hansson

first: Johan

last: Björkegren

first: Xiao-Rong

last: Peng

first: Michael

last: Vanlandewijck

first: Urban

last: Lendahl

first: Christer

last: Betsholtz


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance

first: Jieyi

last: Xiong


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [ChIPSeq]

overall_design: Examination of genome wide HIF1b binding sites in 4 human cancer cell lines, one demethylated cancer cell line and mouse ES Dnmt-WT and Dnmt-TKO cell lines by HIF1b ChIP-seq

first: Flora

last: D’Anna

first: Laurien

last: Van Dyck

first: Hui

last: Zhao

first: Rebecca

last: Berrens

first: Junbin

last: Qian

first: Pawel

last: Bieniasz-Krzywiec

first: Vikas

last: Chandra

first: Luc

last: Schoonjans

first: Jason

last: Matthews

first: Julie

last: De Smedt

first: Liesbeth

last: Minnoye

first: Ricardo

last: Amorim

first: Sepideh

last: Khorasanizadeh

first: Qian

last: Yu

first: Liyun

first: Marie

last: De Borre

first: Savvas

last: Savvides

first: Celeste

last: Simon

first: Peter

last: Carmeliet

first: Wolf

last: Reik

first: Fraydoon

last: Rastinejad

first: Massimiliano

last: Mazzone

first: Bernard

last: Thienpont

first: Diether

last: Lambrechts


title: Transcriptomic characterisation of ALDH+ cells in therapy resistant breast cancer patient samples

status: Public on Jun 19 2020

city: Liverpool

first: Eva

last: Caamano-Gutierrez

address: Crown Street

department: Technology Directorate

institute: University of Liverpool

summary:
This study is part of a larger multidisciplinary study entitled A dormant sub-population expressing interleukin-1 receptor characterises anti-estrogen resistant ALDH+ breast cancer stem cells.
In particular these data were generated to gain understanding of the development of resistance to AE therapies in ER+ breast cancer patients by comparing the gene expression pattern between ALDH+ and ALDH- cells in 9 metastatic ER+ patient samples.

overall_design: 18 tissue samples of 9 patients were analysed separating tissue cells into ALDH+ and ALDH- populations and using the RNA for microarray analysis.

first: Aida

last: Sarmiento-Castro

first: Bruno

last: Simoes

first: Robert

last: Clarke

first: Andrew

last: Sims

first: Sacha

last: Howell

first: Max

last: Wicha


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [SeqCapEpi]

first: Jieyi

last: Xiong

overall_design: Examination of genome wide DNA methylation in 3 human cancer cell lines, at least in duplicate

first: Flora

last: D’Anna

first: Laurien

last: Van Dyck

first: Hui

last: Zhao

first: Rebecca

last: Berrens

first: Junbin

last: Qian

first: Pawel

last: Bieniasz-Krzywiec

first: Vikas

last: Chandra

first: Luc

last: Schoonjans

first: Jason

last: Matthews

first: Julie

last: De Smedt

first: Liesbeth

last: Minnoye

first: Ricardo

last: Amorim

first: Sepideh

last: Khorasanizadeh

first: Qian

last: Yu

first: Liyun


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [ChIPBS]

overall_design: Examination of the methylation level of the DNA fragment immunoprecipitate by HIF1b antibody in  one human breast cancer cell line (MCF7) and mES Tet-TKO cell line, upon exposure to hypoxia

first: Marie

last: De Borre

first: Savvas

last: Savvides

first: Celeste

last: Simon

first: Peter

last: Carmeliet

first: Wolf

last: Reik

first: Fraydoon

last: Rastinejad

first: Massimiliano

last: Mazzone

first: Bernard

last: Thienpont

first: Diether

last: Lambrechts


title: TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing.

status: Public on Jun 17 2020

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

institute: University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: The PIWI protein MIWI2 and its associated PIWI-interacting RNAs (piRNAs) instruct DNA methylation of young active transposable elements (TEs) in the male germline. Here we show that MIWI2 associates with TEX15 in foetal gonocytes. TEX15 is predominantly a nuclear protein that is not required for piRNA biogenesis but is essential for piRNA-directed TE de novo methylation and silencing. In summary, TEX15 is an essential executor of mammalian piRNA-directed DNA methylation.

overall_design: Examination of piRNA expression profiles in control (Tex15+/-) and Tex15-/- foetal testes, RNA expression profiles in wildtype and Tex15-/- P20 testis, and RNA expression profiles in control (Tex15+/-) and Tex15-/- E16.5 gonocytes.

first: Theresa

last: Schöpp


title: Transcriptome profiling of guinea pig cytomegalovirus infected cells

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

summary: We report the transcriptome profiles of guinea pig cytomegalovirus (Caviid betaherpesvirus 2 ; GPCMV) infected and uninfected cells. RNA was harvested at an early time post-infection. Data sets from a lung fibroblast cell line (JH4), primary amnion derived cells (1° AECs), and HPV16 E6/E7-transduced amniotic epithelial cells (AECD) is shared.

overall_design: Confluent guinea pig lung fibroblasts (JH4 clone 1), primary guinea pig amnion derived cells (1° AECs), or HPV16 E6/E7-transduced amniotic epithelial cells (AECD) were infected with guinea pig cytomegalovirus (GPCMV, Caviid betaherpesvirus 2) or mock infected in triplicate. RNA was extracted from these cells at 24 hours post-infection and sequenced by Illumina RNA-Seq. Data represents three expreiments and eightteen total samples.

first: Claudia

last: Fernández-Alarcón

first: Juan

middle: E

last: Abrahante

first: Mark

last: Schleiss


title: Immune phenotyping of diverse syngeneic murine brain tumors identifies immunologically distinct types

status: Public on Jun 16 2020

city: Boston

first: Khalid

last: Shah

state: Massachusetts

address: 60 Fenwood Road

institute: Harvard Medical School

summary: Whole tissue RNA-seq analysis of end-stage brain tumor tissue collected from 4 different syngenic murine glioblastoma models at end-stage compared with naïve brain tissue.

overall_design: To perform expression profiling comparison between 4 different brain tumor models, tumor cells were implanted in brain of C57/Bl6 mice and brains were harvested when mice reached humane end-point. Tissues were collected from 3 mice in each group.

first: Jasneet

last: Khalsa


title: Single-cell analysis uncovers inter- and intra-organ fibroblast heterogeneity and provides criteria for fibroblast identification and discrimination from vascular mural cells (Colon)

first: Lars

last: Muhl

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Jianping

last: Liu

first: Liqun

last: He

first: Giuseppe

last: Mocci

first: Ying

last: Sun

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Indira

last: Chivukula

first: Åsa

last: Segerstolpe

first: Elisabeth

last: Raschperger

first: Emil

last: Hansson

first: Johan

last: Björkegren

first: Xiao-Rong

last: Peng

first: Michael

last: Vanlandewijck

first: Urban

last: Lendahl

first: Christer

last: Betsholtz


title: Altered 3D chromatin structure permits inversional recombination at the IgH locus

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

summary: We report that in the absence of intergenic control region 1 (IGCR1), a regulatory sequence that specifies the RAG scanning domain on WT IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA.

overall_design: Chromatin accessibility of different pro-B cell lines were analyzed by ATAC-Seq method

first: Mingming

last: Zhao

first: Lily

last: Shipp

first: Angela

first: Arun

last: Dutta

first: Supriyo

last: De

first: William

last: Wood III

first: Kevin

middle: G

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

last: Atchison

first: Ranjan

last: Sen


title: Expansion of human iPSC-derived ureteric bud organoids with repeated branching potential [CDP & TIP]

city: Kyoto

first: Makoto

last: Ryosaka

address: 53 Kawahara-cho, Shogoin,

country: Japan

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

summary: Ureteric bud (UB) is the embryonic kidney progenitor tissue that gives rise to the collecting duct and lower urinary tract. UB-like structures generated from human pluripotent stem cells by previously reported methods show limited developmental ability and limited branching. Here we report a new method to generate UB organoids that possess epithelial polarity and tubular lumen and repeat branching morphogenesis. We also succeeded in monitoring UB tip cells by utilizing the ability of tip cells to uptake very-low-density lipoprotein, cryopreserving UB progenitor cells and expanding UB tip cells that can reconstitute the organoids and differentiate into collecting duct progenitors. Moreover, we successfully reproduced some phenotypes of multicystic dysplastic kidney (MCDK) using the UB organoids. These methods will help elucidate the developmental mechanisms of UB branching and develop a selective differentiation method for collecting duct cells, contributing to the creation of disease models for congenital renal abnormalities.

overall_design: mRNA profiles of collecting duct progenitor (CDP) cells and tip colomies (TIP) derived from human iPSCs

first: Shin-Ichi

last: Mae

first: Satoko

last: Sakamoto

first: Kyoko

last: Matsuse

first: Aya

last: Nozaki

first: Maiko

last: Igami

first: Ryotaro

last: Kabai

first: Akira

last: Watanabe

first: Kenji

last: Osafune


title: E. coli transcriptional response to mammalian histone H2A

city: Irvine

first: Albert

last: Siryaporn

address: 4129 Reines Hall

institute: University of California Irvine

summary: RNAseq analysis of MG1655 in response to calf thymus H2A treatment.

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

overall_design: 4 experimental groups: untreated, 10 μg/mL H2A, 50 μg/mL H2A, and 100 μg/mL H2A. Experiments were performed in biological triplicate. Untreated samples serve as controls.

first: Tory

last: Doolin

first: Henry

last: Amir

first: Leora

last: Duong

first: Rachel

last: Rosenzweig

last: Pol

first: Steven

middle: P

last: Gross

first: Lauren

last: Urban

first: Marta

last: Bosch


title: Expansion of human iPSC-derived ureteric bud organoids with repeated branching potential [DiI-VLDL]

first: Makoto

last: Ryosaka

overall_design: mRNA profiles of DiI+ and DiI- cells of induced UB organoids

last: Mae


title: Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [ChIP-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Chromatin modifiers affect the spatiotemporal expression of gene expression programs that underlie organismal development. The Polycomb repressive complex 2 (PRC2) has  emerged as a crucial player in executing neurodevelopmental programs. Here we show that the nucleic acid–binding protein Ybx1 interacts with PRC2 in human and mouse neural progenitor cells (NPCs). During early neural development in vivo, Ybx1 is required for forebrain specification and modulates mid/hindbrain growth. In NPCs, Ybx1 controls the self-renewal and neuronal differentiation. Mechanistically, Ybx1 binds PRC2 gene targets, reduces the levels of PRC2-mediated H3K27me3, and promotes the expression of genes in forebrain specification, cell proliferation, or neuronal differentiation. In Ybx1-knockout NPCs, H3K27me3 reduction by PRC2 enzymatic inhibitor or genetic depletion partially rescues the control of gene expression, self-renewal, and neuronal differentiation. Our findings suggest that Ybx1 modulates H3K27me3 by PRC2 to regulate spatiotemporal gene expression in embryonic neural development and uncover a crucial epigenetic mechanism balancing forebrain–hindbrain lineages and selfrenewal-differentiation choices in NPCs.

overall_design: Examination of YBX1, Ezh2, H3K4me3, H3K27me3 in WT and YBX1 KO mouse neural progenitor. Intergrated analysis with transcriptome.

first: Myron

last: Evans

first: Yurika

last: Matsui

first: Jamy

last: C. Peng


title: Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [RNA-seq]

last: Peng


title: Identification of total and subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

status: Public on Jun 15 2020

city: EDINBURGH

first: Kathryn

middle: Alexandra

last: Jackson-Jones

address: Institute of Genetics and Molecular Medicine, Crewe Road South

department: MRC Human Genetics Unit

overall_design: Refer to individual Series


title: DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [RNA]

first: Jieyi

last: Xiong

overall_design: Examination of differentially expressed genes upon exposure to 0.5% O2 in 3 human cancer cell lines, one demethylated cancer cell line and mouse  Hif1b-WT and Hif1b-KO cell lines by RNA-seq

first: Flora

last: D’Anna

first: Laurien

last: Van Dyck

first: Hui

last: Zhao

first: Rebecca

last: Berrens

first: Junbin

last: Qian

first: Pawel

last: Bieniasz-Krzywiec

first: Vikas

last: Chandra

first: Luc

last: Schoonjans

first: Jason

last: Matthews

first: Julie

last: De Smedt

first: Liesbeth

last: Minnoye

first: Ricardo

last: Amorim

first: Sepideh

last: Khorasanizadeh

first: Qian

last: Yu

first: Liyun

first: Marie

last: De Borre

first: Savvas

last: Savvides

first: Celeste

last: Simon

first: Peter

last: Carmeliet

first: Wolf

last: Reik

first: Fraydoon

last: Rastinejad

first: Massimiliano

last: Mazzone

first: Bernard

last: Thienpont

first: Diether

last: Lambrechts


title: Identification of total gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

first: Kathryn

last: Jackson-Jones

summary: Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs.

overall_design: Profiling of HeLa cells when NMD factors NBAS or UPF1 depleted, in quintuplicate, using Illumina sequencing

middle: A

first: Robert

last: Young

first: Martin

last: Taylor

first: Dasa

last: Longman

first: Magdalena

last: Maslon

first: Laura

last: Murphy

first: Jack

last: Stoddart

first: Dimitrios

last: Papadopoulos

first: Javier

middle: F

last: Caceres


title: Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803

city: Roscoff

first: Laurence

last: Garczarek

address: Place Georges Teissier

department: UMR7144-Adaptation and Diversity in Marine Ecosystems

institute: Station Biologique (Sorbonne University and CNRS)

summary: Understanding how microorganisms adjust their metabolism to maintain their ability to survive to short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here WH7803, the best physiologically characterized marine Synechococcus strain was submitted to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem II (PSII) quantum yield, PSII repair rate, pigment and lipid content as well as whole transcriptomes. This notably revealed that cells previously acclimated to HL seem to be better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of this key component of marine ecosystems. Our data also highlighted important specificities of the stress responses compared to model freshwater cyanobacteria.

overall_design: Whole transcriptome responses of Synechococcus sp. WH7803 under modulated light/dark cycles at two temperatures or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. For stress experiments, three biological replicates are available for each timepoint and differential expression data are normalized to T0. For light/dark cycles experiments,  four biological replicates are available for each timepoint and differential expression data are normalized either to 6 a.m. (corresponding to the dark-to-light transition) for each temperature dataset analyzed individually, or to  the corresponding time point at 21 °C when comparing the two temperature datasets

first: Ulysse

last: Guyet

first: Ngoc

last: N'guyen

first: Hugo

last: Doré

first: Julie

last: Haguait

first: Justine

last: Pittera

first: Maël

last: Conan

first: Morgane

last: Ratin

first: Erwan

last: Corre

first: Gildas

last: Le Corguillé

first: Loraine

last: Brillet-Guéguen

first: Mark

last: Hoebeke

first: Christophe

last: Six

first: Claudia

last: Steglich

first: Anne

last: Siegel

first: Damien

last: Eveillard

first: Frédéric

last: Partensky


title: BRD4 Prevents the Accumulation of R-loops and Protects Against Transcription-Replication Collision Events and DNA Damage

city: Cambridge

first: Michael

last: Yaffe

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Brd4 is essential in enhancing productive polII elongation along gene bodies. Inhibition of Brd4 leads to transcription-replciation conflicts and DNA damage.

overall_design: ChIP-seq were performed for anti-Brd4, anti-gH2AX, anti-RNApolIIser2,  and anti-IgG from HeLa cells treated with DMSO or JQ-1 for 16 hours.

first: Fred

last: Lam


title: DNA sequencing for multiple rounds of the pMHC-yeast display selection for 2W, Yae and Fat TCR

city: Stanford

first: Ricardo

last: Fernandes

state: California

address: 279 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

summary: A peptide library was displayed on Ab MHC class II allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.

overall_design: A naive pMHC-yeast display library was selected with biotinylated TCRs of interest present on magnetic beads (Miltenyi) or fluorescently labelled streptavidin. After 4 rounds of TCR selection, DNA was extracted using zymolase for all rounds of selected yeast, enriched for cognate pMHC, as well as the naive library. Isolated DNA/plasmid was amplified by PCR with appropriate barcodes and sequencing was performed using a Miseq.

first: K

last: Garcia


title: ATAC-seq on mouse embryonic stem cells for asynchronous cells, mitotic cells and purified mitotic chromosomes.

status: Public on Jun 14 2020

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: E14Tg2a mouse embryonic stem cells (ESCs) were cultured on gelatin coated plates in KO-DMEM medium supplemented with 15% FCS and 1000 U/ml leukaemia inhibitory factor. Rapidly dividing cultures of ESCs were arrested in metaphase using demecolcine (0.1 μg/ml for 6 h), achieving samples where most (85-90%) cells were in M-phase as judged by propidium iodide labelling. Condensed chromosomes were released using polyamine buffer, stained with Hoechst 33258 and Chromomycin A3 and purified by flow cytometry using a Becton Dickinson Influx equipped with specialised air-cooled lasers.

overall_design: ATAC-seq was performed in duplicate on nuclei from asynchronous cells (5x10^4) or directly on mitotic cells (5x10^4) or flow-sorted mitotic chromosomes (2x10^6). Libraries were sequenced on the Illumina NextSeq system (75 bp, paired end). ATAC-seq performed in duplicate in three conditions.

first: Dounia

last: Djeghloul

first: Andrew

last: Dimond

first: Amanda

last: Fisher


title: Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

summary: Reactive astrocytes have been implicated in the pathogenesis of neurodegenerative diseases, including a non-cell autonomous effect on motor neuron survival in ALS. We previously defined a mechanism by which microglia release three factors, IL-1α, TNFα, and C1q, to induce neurotoxic astrocytes. Here we report that knocking out these three factors markedly extends survival in the SOD1G93A ALS mouse model, providing evidence for gliosis as a potential ALS therapeutic target.

overall_design: Isolated astrocyte and microglia RNA samples were first assayed on an Agilent 2100 Bioanalyzer System to quantify RNA quality and total RNA abundance. mRNA libraries were then prepared for Illumina paired-end sequencing using the Agilent SureSelect Strand Specific RNA-Seq Library Preparation kit (G9691B) on the Agilent Bravo Automated Liquid Handling Platform. Libraries were sequenced on an Illumina HiSeq 4000. Alignment of RNA-sequencing reads to the mouse mm10 reference genome and transcriptome was performed using STAR v2.7.3a27 following ENCODE standard options, read counts were generated using rsem, and differential expression analysis was performed in R v3.6.1 using the DESeq2 package v1.38.028 (detailed pipeline v2.0.1 and options available on https://github.com/emc2cube/Bioinformatics/).

first: Kevin

last: Guttenplan

first: Shane

last: Liddelow

first: Aaron

middle: D

last: Gitler

first: Ben

last: Barres


status: Public on Jun 13 2020

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

summary: The gut-brain axis, a reciprocal interaction between the central nervous system (CNS) and peripheral intestinal functions, is conceptually feasible from recent clinical and experimental evidence showing mutual interactions between the CNS and gut microbiota that are closely associated with the bidirectional effects of inflammatory bowel diseases (IBDs) and CNS disorders. Despite recent advances in our understanding of neuroimmune interactions, it remains unclear how the gut and brain communicate to maintain gut immune homeostasis, including induction and maintenance of peripheral regulatory T cells (pTregs) and what environmental cues prompt the host to protect host from development of IBDs. Here, we report a novel liver-brain-gut neural arc that ensures proper differentiation and maintenance of peripheral regulatory T cells (pTregs) in the gut. The hepatic vagal sensory afferents were responsible for indirectly sensing the gut microenvironment and relaying the sensory inputs to the nucleus tractus solitarius (NTS) of the brainstem, and ultimately to the vagal parasympathetic nerves and enteric neurons. Surgical and chemical perturbation of the vagal sensory afferents at the hepatic afferent level significantly impaired colonic pTregs, which was attributed to impairment of aldehyde dehydrogenase (ALDH) expression and retinoic acid (RA) synthesis by intestinal antigen-presenting cells (APCs). Muscarinic Ach receptor (mAChR) activation directly induced ALDH gene expression both in human and mouse colonic APCs, whereas genetic ablation of mAChRs abolished APC excitement in vitro. Disruption of left vagal sensory afferents from the liver to the brainstem in colitis models reduced the colonic pTreg pool, resulting in increased susceptibility to colitis. These results demonstrate that the novel vago-vagal liver-brain-gut reflex arc tunes the number of pTregs and maintains the gut homeostasis. Intervening in this autonomic feedback feed-forward system could help develop new therapeutic strategies to treat or prevent immunological disorders of the gut.

overall_design: RNA-seq was used for identifying signature genes of gut APCs including dendritic cells (DCs) and mononuclear phagocytes (MNPs). Specifically, RNA-seq libraries for splenic and colonic MHCII+ APCs and colonic CD11b+, CD11c+, CD11b+CD11c+ MNP/DC were generated from WT 8-wk-old mice.

first: Toshiaki

last: Teratani

first: Yuya

last: Hagihara

first: Nobuhito

last: Taniki

first: Takanori

last: Kanai


title: Sustained activation of AMPK enhances differentiation of human iPSC-derived cardiomyocytes via sirtuin activation

status: Public on Jun 12 2020

first: Mohsen

last: Sarikhani

address: 7 Divinity,Fairchild 159

department: Stem cell and regenerative biology

institute: Harvard University

summary: Lee and colleagues demonstrate that sustained activation of AMPK enhances differentiation of iPSC-derived cardiomyocytes. Sustained AMPK activation decreased histone acetylation at known target sites for nuclear-localized sirtuins, suggesting that AMPK activation enhances sirtuin activity. AMPK-induced sirtuin-mediated deacetylation of histone proteins may regulate chromatin accessibility and enhance cardiomyocyte differentiation.

overall_design: We have done the experiment in duplicate for NAM and AICAR treated iPSC-derived Cardiomyoytes.

first: Richard

middle: T

last: Lee


title: Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation

first: Beisi

last: Xu

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


city: Solna

first: Henrik

middle: J

last: Johansson

state: Stockholm

address: Tomtebodavägen 23A

department: Oncology-Pathology

summary:
Transciptome profiling of 18 breast cancer cell llines as part of a drug screen to identify mechanisms of response and resistance for each compound and find biomarkers
doi: 10.7554/eLife.57894

overall_design: 18 different breast cancer cell lines analysed in biological triplicates

first: Erik

last: Fredlund

first: Oliver

last: Frings


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation [RNA-seq]

first: Hemalvi

last: Patani

address: Charterhouse Square

institute: Barts Cancer Institute

summary: Aberrant DNA hypermethylation of promoter CpG islands in the context of a hypomethylated genome is a hallmark of cancer. Thus far there is no human experimental model available to mechanistically investigate this phenomenon. Here we show that upon reprogramming of human embryonic stem cells to the naïve state, the acquisition of a globally hypomethylated genome is accompanied by hypermethylation of a subset of bivalent promoter CpG islands, resulting in a DNA methylome comparable to the human inner cell mass. We show that de novo methylation is carried out by DNMT3A and coordinated by the transcription factor network. We further show that the subset of bivalent sites that become hypermethyated are functionally distinct, with an enrichment in developmental genes, and demonstrate that this is mirrored in DNA hypermethylation patterns across cancer types, suggesting that common mechanisms may be responsible. We propose a wider utility of this experimental system to understand pre-malignant cancer-associated processes.

overall_design: RNA-seq experiment with n=3 biological replicates of primed, early transition (72h), early transition (1 week), late transition and naïve human embryonic stem cells

first: Michael

last: Rushton

first: Gabriella

last: Ficz


title: Single-cell analysis uncovers inter- and intra-organ fibroblast heterogeneity and provides criteria for fibroblast identification and discrimination from vascular mural cells

first: Lars

last: Muhl

address: Blickagången 6


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation (data set 3)

type: Methylation profiling by genome tiling array

overall_design: EPIC array data for n=1 Primed and late transition: NS control, DNMT3A KD1, DNMT3A KD2 and DNMT3B KD1


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation (data set 2)

overall_design: EPIC array data for n=3 Primed, early transition, late transition (+PKCi), late transition (-PKCi) and naïve hESCs.


title: A frameshift variant in the specificity protein 1 triggers superactivation of Sp1-mediated transcription in familial bone marrow failure

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

summary: Inherited bone marrow failure (BMF) syndromes are a heterogeneous group of diseases characterised by defective hematopoiesis and often predispose to myelodysplastic syndrome (MDS) and acute myeloid leukemia. We have studied a large family consisting of several affected individuals with hematological abnormalities including one family member who died of acute leukemia. By whole exome sequencing, we identified a novel frameshift variant in the ubiquitously expressed transcription factor specificity protein 1  SP1). This heterozygous variant (c.1995delA) truncates the canonical Sp1 molecule in the highly conserved C-terminal DNA binding zinc finger domains. Functional characterisation of the truncated Sp1 molecule revealed compromised DNA binding ability and  educed stability. Transcriptomic analysis and gene promoter characterisation in patients’ blood revealed a hypermorphic effect of this Sp1 variant, triggering superactivation of Sp1-mediated transcription and driving a significant upregulation of Sp1 target genes.  his familial genetic study indicates a central role for Sp1 in causing autosomal dominant transmission of BMF, thereby confirming its critical role in hematopoiesis in humans.

overall_design: Examination of mRNA profiles from a family with mutation of SP1

first: Hemanth

last: Tummala

first: Tom

last: Vulliamy

first: Inderjeet

last: Dokal


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation (data set 4)

overall_design: EPIC array data for n=2 Early transition: NS control, DNMT3A KD (1&2), DNMT3B KD (1&2), DNMT3L KD (1&2)


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation


title: Investigating the epigentic and transciptional changes induced in tolerant T cells [RNA-seq]

status: Public on Jun 11 2020

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: Here we investigated the underlying mechanisms causing the suppression of normal immune responses when T cells are rendered anergic by tolerance induction. By performing an integrated analysis of signaling, epigenetic modifications and gene expression, we demonstrate that immunological tolerance is established when both signaling to and epigenetic priming of immune response genes are weakened. In parallel, epigenetic priming of immune-repressive genes is boosted, rendering them sensitive to low levels of signaling below the threshold needed to activate immune response genes.

overall_design: RNA-seq samples were generated in triplicate for CD4 naïve and tolerant T cells either untreated, treated in vivo by peptide stimulation or ex vivo with PMA and Calcium Ionophore

first: Sarah

last: Bevington

first: Sky

last: Ng

first: Peter

last: Keane


title: Investigating the epigenetic and transciptional changes induced in tolerant T cells [DNAse-seq]

overall_design: DNAse-seq samples were generated in duplicate for CD4 naïve and tolerant T cells either untreated, treated in vivo by peptide stimulation or ex vivo with PMA and Calcium Ionophore

last: Cockerill

first: David

last: Wraith


title: Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation (data set 1)

overall_design: EPIC array data for n=2 Primed, early transition, late transition and naïve hESCs.


title: Inter-strain epigenomic profiling reveals a candidate IAP master copy in C3H mice

status: Public on Jun 10 2020

city: Villeurbanne

first: rita

last: rebollo

address: Bat. 406/Louis Pasteur, 20, avenue Albert Einstein

institute: BF2i UMR INRA-INSA de Lyon

summary: Insertions of endogenous retroviruses cause a significant fraction of mutations in inbred mice but not all strains are equally susceptible. Notably, most new Intracisternal A particle (IAP) ERV mutagenic insertions have occurred in C3H mice. We show here that strain-specific insertionally polymorphic IAPs have accumulated faster in C3H/HeJ  mice relative to other strains and that IAP transcript levels are higher in C3H/HeJ embryonic stem (ES) cells compared to other ES cells. To investigate the mechanism for high IAP activity in C3H mice, we identified 61 IAP copies in C3H/HeJ ES cells enriched for H3K4me3 (a mark of active promoters) and, among those tested, all are unmethylated in C3H ES cells. Notably, 13 of the 61 are specific to C3H/HeJ and are members of the non-autonomous 1Δ1 IAP subfamily that is responsible for nearly all new insertions in C3H. One copy is full length with intact open reading frames and hence potentially capable of providing proteins in trans to other 1Δ1 elements. This potential “master copy” is present in other strains, including 129, but its 5’ long terminal repeat (LTR) is methylated in 129 ES cells. Thus, the unusual IAP activity in C3H may be due to reduced epigenetic repression coupled with the presence of a master copy.

overall_design: ChIP-seq examination of H3K4me3 in C3H/HeJ and TT2 (C57BL/6/CBA) mouse embryonic stem cells, and H3K9me3 in C3H/HeJ mES cells.

first: Rita

last: Rebollo

first: Mariana

last: Galvão Ferrarini

first: Liane

last: Gagnier

first: Ying

last: Zhang

first: Ardian

last: Ferraj

first: Christine

middle: R

last: Beck

first: Matthew

last: Lorincz

first: Dixie

last: Mager


title: Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: It is widely assumed that decreasing transcription factor DNA-binding affinity reduces transcription initiation by diminishing occupancy of sequence-specific regulatory elements. However in vivo transcription factors find their binding sites while confronted with a large excess of low affinity degenerate motifs. Here we show, using the melanoma lineage survival oncogene MITF as a model, that low affinity binding sites act as a competitive reservoir in vivo from which TFs are released by MAPK-stimulated acetylation to promote increased occupancy of their regulatory elements. Consequently a low DNA-binding affinity acetylation-mimetic MITF mutation supports melanocyte development and drives tumorigenesis, whereas a high affinity, non-acetylatable mutant does neither. The results reveal a paradoxical acetylation-mediated molecular clutch that tunes transcription factor availability via genome-wide titration and couples BRAF to tumorigenesis. Our results further suggest that genomic titration regulated by p300/CBP-mediated acetylation will represent a common mechanism to control TF availability.

overall_design: 501mel melanoma cell lines engineered to express ectopic-doxycycline-inducible-HA-epitope-tag-murine Mitf-WT or K243Q or K243R were treated with 20ng Dox prior to fixation and ChIP-sequencing

first: Colin

last: Goding


title: Investigating the epigenetic and transciptional changes induced in tolerant T cells

last: Varnai

overall_design: Refer to individual Series


title: Ephydatia muelleri methylome

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

summary: Ephydatia muelleri is a cosmopolitan freshwater demosponge, with potential to become a model system. We have participated in a large collaborative project to sequence the genome (PRJNA579531), methylome, transcriptome for this species, aiming to better understand the biology of this sponge species. In terms of DNA methylation, it presents relatively low methylation levels compared to the methylomes of other sponges (A. queenslandica and S. ciliatum), suggesting quite a lot of varation within the sponge phylum.

overall_design: Profiling of cytosine methylation for Ephydatia muelleri.

first: Ryan

last: Lister


title: Microarray-based Gene Expression Analysis of human cerebral organoids from urinary epithelial cells

city: Fort Worth

first: Yu-Chieh

last: Wang

state: TX

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

summary: Analysis of human cerebral organoids developed from both WA09 human embryonic stem cells and human urinary epithelial cell derived hiPSCs. The hypothesis tested was that organoids developed from human urinary epithelial cell derived hiPSC have similar gene expression patterns as WA09 derived organoids subjected to the same organoid development process.

overall_design: Total RNA obtained from human cerebral organoids developed using dual smad inhibitors (100nM LDN & 500nM A83). Organoid samples were collected along the development timeline from the pluripotent stem cell stage to day 80 or cerebral maturation

first: Victor

last: Lin

first: Yu-chieh


title: Single-cell RNA-seq of human peripheral blood NKT cells

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

summary: NKT cells are potent immune regulators and skew immune responses toward either inflammation or tolerance through quickly secreting either T helper (Th)1-, Th2-, Th17- or regulatory T-associated cytokines upon activation. Although the thymic development and functional differentiation of NKT cells is well defined in mice, it has not yet been studied in detail in humans.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq) of unstimulated and PMA/ionomycin-stimulated NKT cells from human peripheral blood mononuclear cells (PBMCs).

first: Jie

first: Xiaojun

last: Wu

first: Li

last: Zhou

first: Qing-Sheng

last: Mi


title: Gene expression variation during grape genome duplication

city: Beijing

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: RNA-seq was used to assess gene expression variation between 2X and 4X grape

overall_design: 4X vs. 2X

first: Wenwen

last: Liu


title: Genomic methylation variation during grape genome duplication

summary: WGBS was used to assess gene expression variation between 2X and 4X grape


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Human single cell RNA-seq blood)

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay fro Single-cell Transcriptome and Accessibility Regions).

overall_design: ASTAR scRNA libraries prepared from umblical cord blood cells undergoing differentiation to form erythroblasts


title: Mediator Med23 regulates adult hippocampal neurogenesis

city: Shanghai

first: Shuai

last: Zhang

state: Shanghai

address: 320 YueYang Road

institute: SIBCB

summary: we provide evidence that Med23 is involved in the regulation of adult hippocampal neurogenesis in mouse. Med23-deficient NSCs in the SGZ display faster self-renewal activity possibly by reducing cell cycle length, but neuroblasts, immature  and mature new-born neurons are reduced.

overall_design: Comparison of mRNA expression profile of between primary NSCs  from the hippocampus of 2-month-old Med23 CKO and littermate control mice.

first: Gang

first: Yu-Qiang

last: Ding

first: Chang-Jun

last: Su

first: Guo-Yan

last: Chen

first: Chong-Hui

last: Li

first: Cong-Cong

last: Qi

first: Ya-Zhou

first: Jia-Yin


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Human single cell ATAC-seq blood)

overall_design: ASTAR scATAC libraries prepared from umblical cord blood cells undergoing differentiation to form erythroblasts

first: Q

last: Xing

first: C

last: EL Farran

first: N

last: Gnanasegaran

first: H

first: Y

last: Loh


title: Mucosal immune response to persistent Mycobacterium avium ssp. Paratuberculosis (MAP) infection in bovine gut-associated lymphoid tissues

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

summary: Chronic enteric Mycobacterium avium subsp. paratuberculosis (MAP) infections are endemic in cattle worldwide but disease management is thwarted by a lack of therapeutics to prevent or control infection. A better understanding of the host-pathogen interactions occurring in Peyer’s patches (PP), the portal of MAP entry and site of infection, is required to develop effective vaccines. The ruminant small intestine possesses two structurally and functionally distinct PP (discrete [dPP] found in jejunum and continuous [cPP] found in ileum). Using RNA-Seq, we investigated the long-term outcome of persistent MAP infection in dPP compared to cPP in neonatal calves using surgically isolated intestinal segments containing draining mesenteric lymph nodes (MLN) and Peyer’s Patches (PP). At 12 months post-infection, MAP persisted at a detectable level in cPP (n=4), but was controlled in dPP (n=5). This study demonstrates a marked regional difference in both persistence of MAP infection and the mucosal immune responses that occur in dPP and cPP following infection.

overall_design:
Control uninfected gut-loops were inoculated with PBS, while MAP infected tissues were inoculated with MAP gc86
Ile_LN = draining mesenteric lymph nodes from ileum
Ile_PP = continuous Peyer's patches (PP) in ileum
Jej_LN = draining mesenteric lymph nodes from jejunum
Jej_PP = discrete Peyer's patches (PP) in jejunum

first: Antonio

last: Facciuolo

middle: H

first: Robert

last: Hancock

first: Philip

last: Griebel


title: Transcriptomic analysis of the effect of iron overload in human iPSC-CMs

status: Public on Jun 08 2020

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: We used human iPSC-CMs generated from healthy individuals and performed RNA-sequencing after 5 days of trastuzumab treatment to examine the mechanism associated with cardiac dysfunction in iPSC-CMs after iron treatment. Transcriptome analysis revealed broad changes in cardiovascular development and processes.

overall_design: RNA profiling of 6 samples of trastuzumab- and no drug (control)-treated human iPSC-CMs

first: June

last: Rhee

first: Hyoju

last: Yi

first: Joseph

last: Wu


title: PD-L1 ChIP-seq in MDA-MB-231 cells

status: Public on Jun 07 2020

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary: Although membrane-anchored PD-L1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether PD-L1 regulate oncogenic signaling pathways in tumor cells remains elusive. We found that a portion of PD-L1 could translocate to the nucleus and knockout of PD-L1 changed RNA profiles in MDA-MB-231 cells. To further explore potential role of PD-L1 in regulating gene expression in tumor cells, we performed ChIP-seq in HA tag-inserted (after the signal peptide) PD-L1 re-expressed MBA-MB-231cells (endogenous PD-L1 knockout background).  Methods: HA-insert-PD-L1 was re-introduced into MDA-MB-231 PD-L1 knockout cells using lentivirus and then the infected cells were selected with puromycin to make stable subclones. ChIP experiments were performed using HA antibody (Abcam, ab9110).  Conclusions: Our study indicates that nuclear PD-L1 has potential roles in regulating gene transcription. More efforts are needed to further dissect the exact working model.

overall_design: ChIP experiments were performed in two independent biological replicates using HA antibody (Abcam, ab9110). Sequecing data were respectively called for enriched peaks.

first: Aleksandra

last: Kolodziejczyk

first: Steve

last: Chan

first: Wei

last: Xu

first: Yang

last: Gao

first: Wenyi

last: Wei


title: RNA sequencing of PD-L1 knock out human MDA-MB231 cells and mouse CT26 cells

summary: Although membrane-anchored PD-L1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether PD-L1 regulate oncogenic signaling pathways in tumor cells remains elusive.  Methods: Total RNA from MDA-MB-231 wild type (WT) , MDA-MB-231 PD-L1 knock-out (KO), CT26 WT or CT26 Pd-l1 KO cells was purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed at the Molecular Genetics Core facility in Dana-Farber Cancer institute. RNA-seq data was aligned using STAR v2.5.4a.   Conclusions: Our study indicates that PD-L1 may regulate genes that are involved in immune response regulating pathways.

overall_design: Total RNA was extracted from MDA-MB-231 cells and CT26 cells for the following genotypes  PD-L1 wild type (PD-L1 WT) and  knock out (PD-L1  KO). Each group has four repeats.

first: Naoe

last: Nihira


title: RNA sequencing of mouse CT26 knockout Pd-l1 cells rescued with WT or K262Q Pd-l1

summary:
Although membrane-anchored Pd-l1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether Pd-l1 regulate oncogenic signaling pathways in tumor cells remains elusive. In this experiment, to further dissect roles of the K262 residue acetylation for Pd-l1 nuclear function, we profiled RNA expression of  WT or K262Q mutant mouse Pd-l1 re-expressed in CT26 KO Pd-l1 cells.
Methods: Total RNA fromCT26/Vector, CT26/WT or CT26 Pd-l1 KO cells was purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed by BGI-Hong Kong Co. Ltd.
Conclusions: Our study indicates that Pd-l1 acetylation modification may affect its function in nuclear.

overall_design: Total RNA was extracted from CT26 cells for the following genotypes   Pd-l1 knockout cells re-expressed wtih control vector; Pd-l1 knockout cells re-expressed wtih  wild type (WT) mouse Pd-l1; and Pd-l1 knockout cells re-expressed wtih  K262Q mutant mouse Pd-l1. All subclones are retrovirus infected and selected by puromycin to make stable polyclones. Each group has three repeats.


title: RNA sequence for macrodactyly ADSCs

status: Public on Jun 05 2020

city: shanghai

first: bin

last: sun

address: zhizaojulu

institute: Shanghai Jiaotong University School of Medicine

summary: Macrodactyly is a congenital malformation characterized by enlargement of bone and soft tissues in limbs, typically with excessive accumulation of adipose tissues. Although gain-of-function mutation of PIK3CA has been identified in macrodactyly, the mechanism of PIK3CA mutation in adipose accumulation is poorly understood. In this study, we found that adipocytes from macrodactyly were more hypertrophic than those observed in polydactyly. PIK3CA (H1047R) activating mutation and enhanced activity of PI3K/AKT pathway were detected in macrodactylous adipose-derived stem cells (Mac-ADSCs). To identify the key downstream effectors of PIK3CA activation-mediated adipogenesis in Mac-ADSCs, we examined the transcriptome of Mac-ADSCs, BYL-719 treated Mac-ADSCs  and Pol-ADSCs by RNA-Seq analysis.

first: Bin

last: Sun


title: Herpes Simplex Virus 1 and Adeno Associated Virus distribution in neurons of the murine trigeminal and superior cervical ganglia

city: Seattle

first: Pavitra

last: Roychoudhury

state: Washington

address: 1100 Fairview Ave N, PO Box 19024, E5-110

institute: University of Washington

summary: After initial infection at mucosa, herpes simplex virus (HSV) establishes lifelong latency in neurons of the peripheral nervous system, which represents the source of recurrent disease. Current antiviral therapies reduce symptoms and viral shedding, but do not cure the infection. In contrast, gene editing offers the possibility to lethally mutate or even eliminate latent viral genomes. Delivery of gene editing enzymes by Adeno Associated Virus (AAV) vectors represents a promising approach to functionally curing HSV infection. In order to optimize in vivo gene therapy approaches it is necessary to understand which neuronal subtypes within peripheral ganglia are infected by HSV and which subtypes are efficiently targeted by various AAV serotypes. Here we use single cell RNA sequencing (scRNA-seq) to identify neurons expressing HSV genes as well as reporter genes for AAV1, AAV8, AAV-PhP.s, and AAV-Rh10 serotypes.

overall_design: 12 adult female Swiss-Webster mice were infected with 10^5 PFU HSV syn17+ by corneal scarification. 3 mice were transduced with AAV1-mScarlet via intradermal injection into the wisker pad; 3 mice were transduced with AAV1-mScarlet via retro orbital IV injection. 3 mice were transduced with AAV8-mEGFP intravenously via retro-orbital injection; 3 mice were transduced with AAV-PHP.S-DsRed-Express2 intravenously via retro-orbital injection; and 3 mice were transduced with AAV-Rh10-mTagBFP-2 intravenously via retro-orbital injection. Trigeminal Ganglia were dissected out of each animal and pooled. Superior Cervical Ganglia were dissected out of each animal and pooled.

first: Martine

last: Aubert

first: Daniel

last: Strongin

first: Michelle

last: Loprieno

last: Stone

first: Keith

last: Jerome


title: ERK5 is required for tumor growth and maintenance through regulation of the extracellular matrix in triple negative breast cancer

status: Public on Jun 04 2020

city: New Orleans

first: Matthew

last: Burow

state: Louisiana

address: 1430 Tulane Ave

institute: Tulane University School of Medicine

summary: Depletion of ERK5 expression using the CRISPR/Cas9 system in MDA-MB-231 and Hs-578T cells resulted in loss of mesenchymal features, as observed through gene expression profile and cell morphology, and suppressed TNBC cell migration. In vivo xenograft experiments revealed ERK5 knockout disrupted tumor growth kinetics, which was restored using high concentration MatrigelTM and ERK5-ko reduced expression of the angiogenesis marker CD31. These findings implicated a role for ERK5 in the extracellular matrix (ECM) and matrix integrity. RNA-sequencing analyses demonstrated downregulation of extracellular matrix (ECM), integrin, and pro-angiogenic factors in ERK5-ko cells. Tissue decellularization combined with cryo-SEM and interrogation of biomechanical properties revealed that ERK5-ko results in loss of key ECM fiber alignment and mechanosensing capabilities in breast cancer xenografts compared to parental wild-type cells. In this study, we identified a novel role for ERK5 in tumor growth kinetics through modulation of the ECM and angiogenesis axis in breast cancer.

overall_design: Examination of ERK5-knockout and constitutively activated MEK5 compared to control gene expression in two cell lines in duplicate.

first: Kenneth

last: Nephew

first: Fang

last: Fang

first: Douglas

last: Busch

first: Aaron

last: Buechlein


title: Stimulation of glycolysis via the pyruvate dehydrogenase axis promotes cardiomyocyte proliferation after injury in adult zebrafish.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Cardiac metabolism plays a crucial role in producing sufficient energy to sustain cardiac contractions.  However, the role of metabolism in cardiomyocyte proliferation remains unclear.  Working with the adult zebrafish heart regeneration model, we first find an increase in the levels of mRNAs encoding enzymes regulating glucose and pyruvate metabolism, including pyruvate kinase M1/2 (Pkm) and pyruvate dehydrogenase kinases (Pdks), specifically in tissues bordering the damaged area.  We proceed to show that impaired glycolysis decreases the number of proliferating cardiomyocytes following cardiac injury.  These observations are further supported by analyses using loss-of-function models for the metabolic regulators Pkm2a and peroxisome proliferator-activated receptor gamma coactivator 1 alpha (Ppargc1a).  Cardiomyocyte-specific loss- and gain-of-function manipulations of pyruvate metabolism using Pdk3 and a catalytic subunit of the pyruvate dehydrogenase complex (PDC) reveal its importance in cardiomyocyte dedifferentiation and proliferation.  Furthermore, we find that PDK activity can modulate cell cycle progression and protrusive activity in mammalian cardiomyocytes in culture.  Our findings reveal new roles for cardiac metabolism and the PDK-PDC axis in cardiomyocyte behavior following cardiac injury.

overall_design: Mock and Pdk3 expressing samples (n=2)

first: Ryuichi

last: Fukuda

last: Guenther

first: Carsten

last: Kuenne


title: Essential role for CD30-Transglutaminase 2 axis in memory Th1 and Th17 cell generation.

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: Memory helper T (Th) cells are crucial for secondary immune responses against infectious microorganisms but also drive the pathogenesis of chronic inflammatory diseases. Therefore, it is of fundamental importance to understand how memory T cells are generated. However, the molecular mechanisms governing memory Th cell generation remain incompletely understood. Here, we identified CD30 as a molecule heterogeneously expressed on effector Th1 and Th17 cells, and CD30hi effector Th1 and Th17 cells preferentially generated memory Th1 and Th17 cells. We found that CD30 mediated signal induced Transglutaminase-2 (TG2) expression, and that the TG2 expression in effector Th cells is essential for memory Th cell generation. In fact, Cd30-deficiency resulted in the impaired generation of memory Th1 and Th17 cells, which can be rescued by overexpression of TG2. Furthermore, transglutaminase-2 (Tgm2)-deficient CD4 T cells failed to become memory Th cells. As a result, T cells from Tgm2-deficient mice displayed impaired antigen-specific antibody production and attenuated Th17-mediated allergic responses. Our data indicate that CD30-induced TG2 expression in effector Th cells is essential for the generation of memory Th1 and Th17 cells, and that CD30 can be a marker for precursors of memory Th1 and Th17 cells.

overall_design: Cell surface markers expressed on effector Th1, Th2, and Th17 cell are assessed by RNA-seq.

first: Akane

middle: S

last: Suzuki

first: Ryoji

last: Yagi

first: Motoko

middle: Y

last: Kimura

first: Chiaki

last: Iwamura

first: Kenta

last: Shinoda

first: Atsushi

last: Onodera

first: Kiyoshi

last: Hirahara

first: Damon

last: Tumes

first: Ryo

last: Koyama-Nasu

first: Siiri

last: Iismaa

first: Robert

middle: M

last: Graham

first: Shinichiro

last: Motohashi

first: Toshinori

last: Nakayama


title: Whole spleen transcriptome during acute phase of infection in a virulent Plasmodium chabaudi chabaudi CB infection

status: Public on Jun 03 2020

city: Chengdu

first: Jing-wen

last: Lin

address: No. 17, Section 3, People's South Road

institute: West China Second Hospital

summary:
Analysis of spleen samples taken throughout the acute phase of infection from mice infected with virulent P. chabaudi CB strain
spleen samples collected at 2-day intervals till parasite load were controlled

overall_design: Spleen samples collected from infected C57BL/6 mice at 2, 4, 6, 8, 9, 10, 12 days post infection. Naïve samples were collected from age matched mice at the beginning (day 0) and the end (day 12) of the experiment. 3-4 replicates per conditon

first: Jean

last: Langhorne


title: Gene expression profiling of striatum in Huntington's disease model mouse

city: Kyotanabe-shi

first: Haruko

last: Miyazaki

state: Kyoto

address: 1-3 Tatara Miyakodani

department: Graduate School of Brain Science

institute: Doshisha University

summary: Gene expression profiling of striatum in R6/2 Huntington’s disease (HD) model mouse. Striatum gene set contained gene expression alterations in other neuronal populations, such as oligodendrocyte, astrocyte, microglia and interneuron.

overall_design: Striatal samples were obtained from 4-week-old male R6/2 and control mouse. The following number of replicates was analysed for each genotype: 4 for R6/2, 4 for WT.

first: Fumitaka

last: Oyama

first: Yoshihiro

last: Kino

first: Masaru

last: Kurosawa

first: Mizuki

last: Yamada-Kurosawa

first: Tomoyuki

last: Yamanaka

first: Nobuyuki

last: Nukina


title: Gene expression profiling of FACS-purified striatal medium spiny neurons in Huntington's disease model mouse

summary: Gene expression profiling of purified medium spiny neurons (MSNs) in R6/2 Huntington’s disease (HD) model mouse. To purify MSNs by FACS, R6/2 was crossed with Scn4b-Venus transgenic mouse expressing Venus in MSNs. MSN gene set excluded gene expression alterations in other neuronal populations, indicating the gene set displays MSN-specific pathological changes in HD. We identified the dysregulated genes expression, which are associated with apoptosis and transcriptional regulation, and found considerable number of disease causative genes in MSN gene set.

overall_design: Purified-MSNs were obtained from 4-week-old male R6/2;Scn4b-Venus and control mouse. The following number of replicates was analysed for each genotype: 4 for R6/2;Scn4b-Venus, 4 for WT;Scn4b-Venus.