title: Expression data of HUVEC exposed to an atheroprotective shear stress waverform in the presence of Doxorubicin

first: Guillermo

last: Garcia-Cardena

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School / Brigham and Women's Hospital

summary:
Doxorubicin suppresses flow-dependent vasoprotective programs triggering a dysfunctional endothelial cell phenotype.
Microarrays were used to profile the transcriptome of Doxorubicin treated endothelial cells exposed to atheroprotective flow

overall_design: HUVEC were exposed to atheroprotective flow for 48h, of which the second 24h with Doxorubicin added to the culture media. Static cultures and non-treated atheroprotective flow cultures were kept as controls. 3 biological replicates were analyzed for a total of 9 samples.

first: Bendix

last: Slegtenhorst


title: Human marginal zone B cell development from early T2 progenitors [MZBTraj]

status: Public on Jan 31 2021

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

country: United Kingdom

institute: King's College London

type: Expression profiling by high throughput sequencing

summary: B cells emerge from the bone marrow as transitional (TS) B cells that differentiate through T1, T2 and T3 stages to become naïve B cells. We have identified a bifurcation of human B cell maturation from the T1 stage forming IgMhi and IgMlo developmental trajectories. IgMhi T2 cells have higher expression of a4b7 integrin and lower expression of IL4 receptor (IL4R) compared to the IgMlo branch and are selectively recruited into gut-associated lymphoid tissue. IgMhi T2 cells also share transcriptomic features with marginal zone B cells (MZB). Lineage progression from T1 cells to MZB via an IgMhi trajectory is identified by pseudotime analysis of scRNA-sequencing data. Reduced frequency of IgMhi gut homing T2 cells is observed in severe SLE and is associated with reduction of MZB and their putative IgMhi precursors. The collapse of the gut-associated MZB maturational axis in severe SLE affirms its existence in health.

overall_design: Single cell transcriptomic analysis of B cells from human blood

first: Thomas

last: Tull

first: Michael

last: Pitcher

first: Mats

last: Bemark


title: A novel DNA methylation disruption contributes to ALKi resistance in NSCLC

status: Public on Feb 01 2021

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

summary: Acquired resistance to ALKi in NSCLC patients is attributed to gain of mutations in the ALK-EML4 fusion gene and an enhancement of the EGFR and/or IGF1R pathways. Here, we explain the epigenetic change that drives the EGFR and IGF1R reactivation in the absence of the appearance of an ALK-EML4 mutated scenario.

overall_design: The NSCLC cell line H3122 (positive for ALK-EML4 translocation) was used for deriving resistant clones to ALK inhibitors TAE684 and crizotinib.

first: Miguel

last: Vizoso

first: Manel

last: Esteller


title: Effect of restricted glycolysis on gene expression in MCF-7 cells

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

institute: University of Southampton

summary:
Cultured breast cancer cells in standard media are highly glycolytic
To determine the effect of glycolysis on gene expression in MCF-7 we adapted cells to cuture in mediae containing 10 mM fructose, and compared the gene expression to cells cutured in standard high glucose (25 mM) DMEM

overall_design: Cells were adapted to growth in the different sugars for 25 days prior to analysis. Biological replicates represent separately adapted batches of cells.

middle: P


title: Pathogenic LMNA variation disrupts a tissue-specific lamina-chromatin signature, resulting in loss of cellular identity

city: Philadelphia

first: Parisha

last: Shah

state: PA

address: 3400 Civic Ctr. Blvd

department: Medicine, Cell and Developmental Biology, Cardiovascular Institute

country: USA

institute: University of Pennsylvania Perelman School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We demonstrate that a normal function of lamina-associated chromatin is to maintain silencing of undesired lineages, and laminopathies, like LMNA T10I and R541C, may specifically target these regions, resulting in predictable tissue-specific nuclear architecture changes during development.

overall_design: Mapping of LB1 and H3K9me2 domains in control and LMNA T10I iPSC-derived cardiac myocytes at day 25 and 45 post-differentiation; mapping of LB1 and H3K9me2 domain in control and LMNA R541C iPSC-derived cardiac myocytes; mapping LB1 and H3K9me2 domains in control, LMNA T10I, and R541C iPSC-derived hepatocytes; mapping LB1 and H3K9me2 domains in control, LMNA T10I, and R541C iPSC-derived adipocytes; RNAseq of d25 control, T10I, and R541C iPSC-derived cardiac myocytes; RNAseq of control, T10I, and R541C iPSC-derived adipocytes.

first: Wenjian

last: Lv

first: Joshua

middle: H

last: Rhoades

first: Andrey

last: Poleshko

first: Deepti

last: Abbey

first: Matthew

middle: A

last: Caporizzo

first: Julie

middle: G

last: Heffler

first: Nazish

last: Sayed

first: Dilip

last: Thomas

first: Ricardo

last: Linares-Saldana

first: Qiaohong

last: Wang

first: Liam

middle: J

last: Stanton

first: Kenneth

last: Bedi

last: Morley

last: Cappola

first: Anjali

middle: T

last: Owens

middle: B

last: Margulies

first: David

last: Frank

first: Joseph

middle: C

last: Wu

first: Daniel

last: Rader

first: Wenli

last: Yang

first: Benjamin

middle: L

last: Prosser

first: Kiran

last: Musunuru

first: Rajan

last: Jain


title: Effect of knockdown of CtBP proteins on gene expression in MCF7 breast cancer cells, under normoxia and hypoxia

first: Jeremy

last: Blaydes

summary:
Regulation of gene expression by the CtBP family of NADH-sensitive transcriptional regulators, in MCF7 cells under normoxia and hypoxia.
To determine the effect of CtBP knockdown on gene expression in MCF7 we transfected cells with an siRNA (5′-GGGAGGACCUGGAGAAGUUdTdT-3′/3′-dTdTCCCUCCUGGACCUCUUCAA-5′, obtained from Ambion) targetting both CtBP1 and CtBP2 (versus control siRNA).  After 48 hours cells were either transferred to a hypoxic chamber (1% oxygen), or maintained in normoxia, for 18 hours.

overall_design: siRNA knockdown followed by hypoxia. Biological replicates represent separately transfected batches of cells.


title: Expression data from rat hippocampus

city: Seongnam

first: So Young

last: Kim

address: Yatapro 59

country: South Korea

institute: CHA University

summary:
Changes in the gene expression profiles of the inferior colliculus following unilateral cochlear ablation in adult rats
To explore gene expression changes in the inferior colliculus (IC) after single-sided deafness

overall_design: Twenty rats underwent right-side cochlear ablation, and IC tissues were harvested after 2 weeks (SSD 2-week group). Twenty rats underwent a sham operation and were sacrificed after 2 weeks (control group).

first: Hog

middle: K

last: Kil

first: Da-hye

last: Lee

first: So

middle: M

first: Chang

middle: Y


title: Expression data from primary vascular smooth muscle cells (VSMCs) from 5 unrelated patients - comparing different treatments versus untreated controls

city: Oxford

first: Nadia

last: Akawi

address: Headley Way

institute: John Radcliffe Hospital

summary: This study explores the effect of WNT5A signaling on the vascular redox state in obesity.

overall_design: VSMCs isolated from five unrelated patients were incubated with Wnt5a or Polyethylene glycol-conjugated superoxide dismutase (PEG-SOD) or both. We generated the following pairwise comparisons using Affymetrix Transcritome Analysis Console (TAC 4.0): WNT5A vs untreated-control; PEG-SOD vs untreated-control; WNT5A/PEG-SOD combination vs untreated-control.

first: Charalambos

last: Antoniades

first: Ioannis

last: Akoumianakis

first: Fabio

last: Sanna


title: Saturated fat diet induces transintestinal cholesterol excretion in mice

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Intake and absorption of cholesterol (the latter determined by double labeled cholesterol methodology) were nearly unchanged in mice fed the saturated fat diet, but the fecal excretion of neutral sterols (i.e. cholesterol and its microbial conversion products) was increased compared with control diet(+80%; p<0.01).

The saturated fat diet did neither significantly affect biliary cholesterol secretion nor intestinal cholesterol absorption (49% vs. 65% in controls, double labeled water methodology, p>0.1). Thus, the increased fecal neutral sterol excretion was primarily due to increased net transintestinal cholesterol excretion (+89% versus control; p<0.05). Since a major fraction of TICE cholesterol absorption is normally reabsorbed (J Lipid Res 2019 Sep;60(9):1562-1572), the increased fecal cholesterol excretion could be due to more transintestinal excretion of cholesterol into the intestinal lumen and/or to its decreased reabsorption.
The saturated fat diet increased jejunal expression of genes involved in cholesterol synthesis (Srebf2 and target genes), but did not affect whole body de novo cholesterol synthesis.

Conclusion This proof-of-principle study shows that increasing the saturation of the dietary fat can stimulate fecal cholesterol excretion. Individual components of saturated fat diets are to be explored to address the responsible molecular mechanisms

overall_design: Total RNA optained for intestine ( 12 samples) , where compaired in the 2 different groups , consisting out of 6 biological replicates

first: V

middle: W

last: Bloks

first: J

last: Jonker

first: H

last: Verkade


title: Human marginal zone B cell development from early T2 progenitors

first: Jo

last: Spencer

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

overall_design: Refer to individual Series


title: Peroxisomal multifunctional protein 2 deficiency perturbs lipid homeostasis in the retina causing visual dysfunction in mice

city: Leuven

first: Myriam

last: Baes

state: Belgium

address: Herestraat 49, ON II, mailbox 823

department: Department of Pharmaceutical and Pharmacological Sciences

country: Belgium

institute: KU Leuven

summary: Patients lacking multifunctional protein 2, the central enzyme of the peroxisomal β-oxidation pathway, develop retinopathy. This metabolic pathway is involved in the metabolism of very long chain (VLCFAs) and polyunsaturated (PUFAs) fatty acids, which are enriched in the photoreceptor outer segments (POS). The molecular mechanisms underlying the retinopathy remain however elusive. Here, we report that Mfp2-/- mice display decreased retinal function already at the age of 3 weeks, which is accompanied by a profound shortening of the photoreceptor outer and inner segments, but with preserved photoreceptor ultrastructure. Furthermore, Mfp2-/- retinas exhibit severe changes in gene expression with downregulation of genes involved in the phototransduction pathway and upregulation of inflammation related genes. Lipid profiling of the retina of Mpf2-/- mice revealed a profound reduction of DHA-containing phospholipids. This was likely due to a hampered systemic supply and retinal traffic of this PUFA, although we cannot exclude that the local defect of peroxisomal β-oxidation contributes to this DHA decrease. Moreover, VLC-PUFAs were also reduced, except those containing ≥34 carbons that accumulated. The latter suggests that there is an uncontrollable elongation of retinal PUFAs. In conclusion, we showed that intact peroxisomal β-oxidation is indispensable for retinal integrity, most likely by maintaining PUFA homeostasis.

overall_design: RNA sequencing of neural retinas 3-weeks-old control and Mfp2-/- mice

first: Yannick

last: Das


title: Induction of Multiple Alternative Mitogenic Signaling Pathways Accompanies Emergence of Slowly Growing Drug-Tolerant Cancer Cells

city: Stony Brook

first: Frank

middle: Vincent

last: Celeste

state: NY

address: 101 Nicolls Road

department: Pathology

institute: Stony Brook University

summary: Drug resistance continues to be a major obstacle to curing cancer.  Resistance can evolve from a subpopulation of cancer cells that initially survive drug treatment and then gradually form a pool of slowly growing drug-tolerant cells.  Several studies have pinpointed activation of a specific bypass pathway that appears to provide the critical therapeutic target for preventing drug tolerance. Here we take a systems-biology approach using proteomics and genomics to examine the development of drug tolerance to EGFR inhibitors in EGFR-mutant lung adenocarcinoma cells and BRAF inhibitors in BRAF-mutant melanoma cells. We found that there are numerous alternative mitogenic pathways that become activated in both cases, including YAP, STAT3, IGFR1, and phospholipase C (PLC)/protein kinase C (PKC) pathways. Our results suggest that an effective therapeutic strategy to prevent drug tolerance will need to take multiple alternative mitogenic pathways into account rather than focusing on one specific pathway.

overall_design: Overall dataset consists of 8 single-cell RNA-seq datasets generated on 10X Genomics Chromium 3' platform (two cell lines each treated with a drug for three time points and an untreated control), and 18 bulk RNA-seq datasets generated with KAPA mRNA HyperPrep Kit (two cell lines each treated with a drug for two time points plus an untreated control, with three replicates for each).

middle: V

first: Scott

last: Powers


title: Human marginal zone B cell development from early T2 progenitors [Pooled]

summary: B cells emerge from the bone marrow as transitional (TS) B cells that differentiate through T1, T2 and T3 stages to become naïve B cells.  We have identified a bifurcation of human B cell maturation from the T1 stage forming IgMhi and IgMlo developmental trajectories. IgMhi T2 cells have higher expression of a4b7 integrin and lower expression of IL4 receptor (IL4R) compared to the IgMlo branch and are selectively recruited into gut-associated lymphoid tissue. IgMhi T2 cells also share transcriptomic features with marginal zone B cells (MZB). Lineage progression from T1 cells to MZB via an IgMhi trajectory is identified by pseudotime analysis of scRNA-sequencing data.  Reduced frequency of IgMhi gut homing T2 cells is observed in severe SLE and is associated with reduction of MZB and their putative IgMhi precursors. The collapse of the gut-associated MZB maturational axis in severe SLE affirms its existence in health.

first: Thomas

last: Tull

first: Michael

last: Pitcher

first: Mats

last: Bemark


title: miR-127-3p is an epigenetic activator of myofibroblast senescence situated within the miRNA enriched Dlk1-Dio3 imprinted domain on mouse chromosome 12 [miRNA array]

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

summary: During wound healing, fibroblasts differentiate into non-proliferative contractile myofibroblasts, contribute to skin repair, and eventually undergo apoptosis or become senescent. MicroRNAs (miR) are posttranscriptional regulators of gene expression networks that control cell fate and survival and may also regulate senescence. Here we determined regulated miRs in myofibroblasts isolated from wounds and analyzed their role in senescent myofibroblast formation. Transcriptome profiling showed that a 200 kbp region of the Dlk1-Dio3 imprinted domain on mouse chromosome 12 encodes for most of the upregulated miRs in the entire genome of mouse myofibroblasts. Among those, miR-127-3p induced a myofibroblast-like phenotype associated with a block in proliferation. Molecular analysis revealed that miR-127-3p induced a prolonged cell-cycle arrest with unique molecular features of senescence, including the activation of the senescence-associated ß-galactosidase, increase in p21 levels, inhibition of lamin B1, proliferation factors, and the production of senescence-associated inflammatory and extracellular matrix -remodeling components. Hence, miR-127-3p emerges as an epigenetic activator regulating the transition from repair to remodeling during skin wound healing, but may also induce age-related defects, pathological scarring and fibrosis, all linked to myofibroblast senescence.

overall_design: Non-hematopoietic (CD45-)/non-endothelial (CD31-) cell populations with low expression of SMA-GFP from dermis (SMA-GFP+) and with high expression from wounds 7 days post injury  (SMA-GFP+++) were isolated by cell sorting from transgenic SMA-GFP mice. Total RNA of was isolated with TRIZOL (Life Technologies) and RNA quality was confirmed using micro capillary electrophoresis (2100 Bioanalyzer, Agilent).   ~50ng of RNA was amplified, labeled and hybridized to Sureprint G3 human GE 8x60K or whole genome mRNA microarray according to the manufacturer’s specifications (Low input Quick Amp Labeling kit, Agilent). The arrays were scanned (Agilent G2595C scanner), data extracted and processed to create a generic gene level experiments from two technologies using the Genespring 14.5 software (Agilent).


title: Expanding Hematopoietic Stem Cell pool through Fine tuning of Tpo receptor with diabodies.

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

summary: Class I cytokine receptors such as Thrombopoietin receptor (MPL) are dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Thrombopoietin (TPO) and its receptor (TpoR), to dimerize TpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism. Here we describe a single-cell transcriptome analysis of 659 human Hematopoietic Stem Cells cultured with different DA. We find several difference between differentiation and activation of signaling pathways compared to TPO.

overall_design: Examination of single cells transcriptome of HSC culture treated with different TPO agonists or antagonists.

first: Lu

last: Cui


title: Role of IgG autoantibodies in the pathogenesis of IgA nephropathy assessed in a passive mouse model

city: Birmingham

first: Colin

middle: Robert

last: Reily

state: Alabama

department: Medicine

institute: University of Alabama at Birmingham

summary: IgA nephropathy (IgAN), the most common primary glomerulonephritis worldwide, is characterized by IgA1-containing glomerular immunodeposits. These immunodeposits are thought to originate from the circulating immune complexes consisting of aberrantly glycosylated IgA1 (galactose-deficient IgA1; Gd-IgA1) bound by IgG autoantibodies. This hypothesis is supported by the findings that renal immunodeposits of IgA nephropathy patients are enriched for IgG autoantibodies specific for galactose-deficient  IgA1 (Rizk et al., J. Am. Soc. Nephrol. 30(10), 2017-2026, 2019). However, experimental proof is needed. This study provides in vivo data in mice that support the pathogenic role of IgG autoantibodies in IgAN.

overall_design: Kidneys of female CB-17 SCID (Balb/c background) were harvested after 3 doses of IgG-Gd-IgA1 immune complexes (administered i.v., one dose every other day, harvest one day after the third injection). Tissue was frozen in RNAlater. RNA extraction and RNA-Seq was performed by and sent to GeneWiz.

first: Zina

last: Moldoveanu

first: Hitoshi

last: Suzuki

first: Jan

last: Novak


title: Deletion of the Alzheimer’s Disease-associated CD33 results in increased phagocytosis, oxidative burst and inflammation

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

summary: In this study, wild type and CD33 knockout human THP1 macrophages were treated with control shRNA or shRNA against the CD33 signaling-associated protein tyrosine phosphatase PTPN6 and analyzed by mRNA sequencing. Whole genome transcriptome analysis showed that knockout of CD33 as well as knockdown of PTPN6 led to constitutive activation of inflammation-related pathways. On the other hand, PTPN6 knockdown was associated with changes in cell cycle and mitosis-related pathways in a CD33-deficient background.

overall_design: Examination of mRNA profiles of THP1 macrophages after knockout of CD33 and/or knockdown of PTPN6 by RNA-Seq (6 samples per group).

first: Jannis

last: Wißfeld

first: Ichiro

last: Nozaki

first: Mona

last: Mathews

first: Tamara

last: Rascka

first: Christian

last: Ebeling

first: Veit

last: Hornung

first: Oliver

last: Brüstle


title: Systematic Characterization of Mutations Altering Protein Degradation in Human Cancers

city: Boston

first: Collin

last: Tokheim

state: MA

address: 3 Blackfan Circle, CLS 11007

department: Data Science

institute: Dana-Farber Cancer Institute

summary: The Ubiquitin-Proteasome System (UPS) is the primary route for selective protein degradation in human cells. We implicate transcription factors as important substrates. By developing a deep learning model (deepDegron) to identify mutations that result in degron loss, and experimentally validated predictions that gain-of-function truncating mutations in GATA3 result in increased protein stability.  We profiled the DNA binding by ChIP-seq of GATA3 in response to point mutations of the implicated degron. We found an increase in DNA binding, with up-regulating peaks preferentially found near estrogen signaling related genes. To serve as control, we include GATA3 with a c-terminal FLAG-tag that would stabilize GATA3 regardless of mutation status. No significant enrichment was observed in the control.

overall_design: Examination of GATA3 ChIP-seq under three condtions in MDA-MB-231 cells: wildtype, p.A442M point mutation, and p.G444E point mutation. Additionally, the three conditions were also assayed with a FLAG-tag at the c-terminus, which stabilizes GATA3 protein levels, regardless of mutation status. Two replicaters per condition.

first: Xiaoqing

last: Wang

first: Richard

last: Timms

first: Boning

last: Zhang

first: Elijah

last: Mena

first: Binbin

first: Cynthia

last: Chen

first: Jun

last: Ge

last: Chu

first: Wubing

first: Stephen

last: Elledge

first: Myles

last: Brown

first: Xiaole

middle: S

last: Liu


title: miR-127-3p is an epigenetic activator of myofibroblast senescence situated within the miRNA enriched Dlk1-Dio3 imprinted domain on mouse chromosome 12

first: Bent

last: Brachvogel

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


title: Comparison of CGD transgene-expressing and non-expressing tumor cells from a MPNST allograft model

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We devised a transgene that expresses in the neural crest lineage cells at embryonic stage day 13.5. The transgene has an inducible Cre cassette and was used to induce Trp53 and Nf1 gene recombination in the cells of dorsal root ganglia and boundary cap of nerve roots (DRG&BC) at E13.5. The malignant peripheral nerve sheath tumor (MPNST) allograft model was generated by sciatic nerve injection using the recombined E13.5 DRG&BC cells. The nuclear localized eGFP from the transgene was used to facilitate the florescence activated cell sorting (FACS) of GFP+ and GFP- tumor cells after removal of wildtype cells from the dissociated tumors, including immune cells, endothelia cells and blood cells. GFP+ and GFP- tumor cells were harvested from 5 different allograft MPNSTs. Total RNA were prepared from 10 samples were sequenced on Hiseq4000 sequencer. The data was to support the transgene-labeled cancer stem cell population in MPNST mouse models.

overall_design: GFP+ and GFP- tumor cell populations were sorted out from 5 MPNST allograft models. The paired comparison was performed to obtain differentially expressed genes between the GFP+ and GFP- cells.

first: Luis

middle: F

last: Parada


title: NdpA2 & TprA regulon in PA14:  ICE PAPI-1 transference induced (M0) vs PAPI-1 transference inactivated (M0-59060-stop)

city: Marseille cedex 20

first: Gauthier

last: Dangla-Pélissier

state: PACA

address: 31 chemin Joseph Aiguier

department: IMM

country: France

institute: CNRS

summary:
Transcriptional profiling of Pseudomonas aeruginosa PA14 comparing T4SS-GI induced biosynthesis M0 strain with control T4SS-GI induced biosynthesis M0-59060-stop strain.
The PA14_59050-59120 locus was overexpressed through chromosomal insertion of ptac promoter within PA14_59030 gene.

overall_design: Two-condition experiment, M0 vs. M0-59060-stop PA14 strains. Biological replicates: 3 PAPI-1 inactivated transference replicates, 3 PAPI-1 induced transference replicates.

first: Nicolas

last: Roux

first: Victoria

last: Schmidt

first: Gaël

last: Chambonnier

first: Moly

last: Ba

first: Corinne

last: Sebban-Kreuzer

first: Sophie

last: de Bentzmann

first: Caroline

last: Giraud

first: Christophe

last: Bordi


title: Bi-directional c-Kit–mKitL signalling promotes tumour endothelial cell differentiation and triple-negative breast cancer progression

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

summary: Transcriptomic analysis of lineage traced KitL+ endothelial cells from naive, small and large tumour bearing mammary gland tissue

overall_design: Mice were treated with tamoxifen by oral gavage 10 times over 12 days (5 days gavage, 2 days pause, 5 days gavage) to induce stable EYFP labelling of KitL+ endothelial cells. Afterwards mice were either mock treated or received intramammary EO771 cell injection. FACS sorted EYFP+ (7AAD-CD45-Ter119-Epcam-Pdgfra-CD31+) endothelial cells were processed for single cell RNA sequencing according to the 10x Chromium Single Cell 3' protocol

first: Mario

last: Buono

first: Bostjan

last: Marklec


title: Deciphering the molecular alterations sustaining an inverted apicobasal polarity phenotype in colorectal cancer clusters (Tumour Spheres with Inverted Polarity, TSIPs)

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
Colorectal cancer (CRC) is the second deadliest form of cancer and most of patients die from their metastases. As previously shown by our team, in serrated CRC patients, metastases are due to spherical clusters of epithelial cancer cells displaying an inverted apicobasal polarity. We called them TSIPs for Tumor spheres with inverted polarity.
In this study, we investigated the alterations sustaining this remarkable phenotype using PDXs and organoids techniques. In particular, we compared a model that respond normally to its microenvironment (mainly 3D collagen-I networks) to two models that keep their inverted polarity. A whole transcriptome investigation allowed us to better understand the mechanisms of such a topology.

overall_design: Each CRC PDX model was processed in triplicates in two culture conditions: in suspension or in a 3D collagen-I network. On each biological triplicate for the three models, total RNA was processed to perform a whole transcriptome experiment by Clariom S human microarray.

first: Jérôme

last: Cartry

first: Charlotte

last: Canet-Jourdan

first: Fanny

last: Jaulin

last: Desterke


title: Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: The 5-carbon position on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). Genomic locations enriched for 5mC contribute to the regulation of chromatin structure and gene expression. While largely stable, massive waves of DNA demethylation are observed in key developmental windows in mammals. Additionally, DNA methylation is therapeutically targeted in cancer via DNA methyltransferase inhibition, in part to reverse abnormal silencing of tumor suppressor genes. DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). These oxidized cytosine forms have reported function in gene regulation and also serve as intermediates in an active 5mC removal process that involves the base excision repair pathway. 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. Distinguishing active versus passive 5mC removal on a genome-wide scale remains a challenge. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.

overall_design: Cells were treated with 1X PBS, 1 mM 5'aza-2'deoxycytidine (DAC), or 1 mM DAC plus 57 mM Vitamin C (VitC). DAC treated cells were pulsed with DAC for 24 hours and then with 1X PBS for the remaining 48 hours. VitC treated cells were treated every 24 hours. Cells were harvested at 72 hours post initial treatments. Extracted gDNA was converted with upstream modifications to bisulfite conversion to aid in distinguishing 5mC from 5hmC. Tet-assisted bisulfite (TAB) conversion was done to observe 5hmC, oxidative bisulfite (OxBS) conversion was done to observe 5mC,  and bisulfite conversion (BS) was done to observe both 5mC and 5hmC. ZYMO indicates bisulfite conversion was done with the ZYMO EZ DNA methylation kit (Catalog #:D5001) and NUGEN indicates bisulfite conversion was done with NuGEN TrueMethyl oxBS Module, Tecan Genomics, Inc. (Catalog #: 0414-32).

first: Rochelle

last: Tiedemann

first: Hope

middle: E

last: Eden

first: Zhijun

last: Huang

first: Keith

middle: D

last: Robertson


title: Transcriptome dynamics of rice spikelets under heat stress treatment

city: New Delhi

first: Amitha Mithra

last: Sevanthi

address: LBS Centre, Pusa Campus

country: India

institute: ICAR - National Institute for Plant Biotechnology

summary:
Rice reproductive development is highly sensitive to high temperature stress. In rice flowering occurs over a period of at least 5 days. Heat stress alters the global gene expression dynamics in panicle especially during pollen development, anthesis and grain filling. Some of the rice genotypes like Nagina 22 show better spikelet fertility and grain filling compared to high yielding and popular rice cultivars like IR 64.
We carried out microarray analysis of 8 days heat stressed panicles of Nagina22, heat and drought tolerant aus rice cultivar and IR64, a heat susceptible indica genotype along with unstressed samples of Nagina22 and IR64 so as to understand the transcriptome dynamics in these two genotypes under heat stress and to identify the genes important for governing heat stress tolerance in rice.

overall_design: Both the genotypes were grown in temperature controlled phenotyping facility and staggered planting was used to synchronize their flowering time. Once the plants entered the booting stage they were tagged and the temperature inside the facility was increased to 5 °C more than the atmospheric temperature prevailing. The panicles from the tagged main tillers were collected after 8 days of heat stress. For control, samples grown in the open adjacent field and tagged on booting were collected on the same day. All possible comparisons of the data were made to understand the differentially expressed genes under heat stress that are specific to Nagina 22.

first: P

last: Shanmugavadivel

first: V

last: Sureshkumar

first: Kapil

last: Tiwari

first: M

last: Ramkumar

first: Amitha

first: N

last: Singh

first: T

last: Mohapatra

first: Ratan


title: Disruption of the MSL complex inhibits tumor maintenance by exacerbating chromosomal instability

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

type: Genome variation profiling by high throughput sequencing

summary:
Identification of gene expression changes induced after loss of a functional MSL complex in Transformed Dermal Fibroblast cells.

Identification of copy number changes induced after loss of a functional MSL complex in Transformed Dermal Fibroblast cells.

overall_design:
RNA-seq analysis of Transformed Dermal Fibroblast cells transduced with 4-7sgRNAs against members of the MSL complex (MSL1, MSL2, MSL3), control gene (GFP) or non-transduced (WT), and treated with doxycycline to induce Cas9 expression and target gene KO. RNA was collected 14 days post-induction. Grouped samples were compared: MSL KO (MSL1, MSL2 and MSL3 KO) and control (GFP KO, WT).

DNA-seq analysis of Transformed Dermal Fibroblast cells transduced with sgRNAs against MSL3, GFP as a control gene (cntr-KO) or non-transduced (WT), and treated with doxycycline to induce Cas9 expression and target gene KO. RNA was collected 14 days post-induction. Grouped samples were compared: MSL KO (MSL1, MSL2 and MSL3 KO) and control (GFP KO, WT).

first: Josep

last: Monserrat

first: Harshil

last: Patel


title: PAX5 promotes progression of neuroendocrine prostate cancer

city: Tianjin

first: Zhe

last: LIU

address: 22 Qixiangtai Road

department: Department of Immunology

country: China

institute: TIanjin Medical University

summary: Analysis of prostate adnocarcinoma cell line LNCaP cells overexpression pair box 5 (PAX5) for up to 4 days. The goals of this study are to compare PAX5 overexpression in LNCaP cell drives transcriptome profiling (RNA-seq) changes.

overall_design: Examination of 6 samples of LNCaP cells including 3 vector lines and 3 overexpression PAX5 lines

first: Xuemiao

last: Yan

first: Xiaobo

last: Li


title: Sources of Transcription Variation in Plasmodium falciparum

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

summary: The parasite strains HB3 and Dd2 were cloned via limiting dilution and then sub-cloned. The uncloned parental line, 4 clones and 4 sub-clones were thawed in two different culture batches using different media lots and RBC donors but were otherwise maintained in identical standard culture conditions and synchronized by 3 rounds of sorbitol synchronization. Total RNA samples were collected at 24 hours post invasion (hpi).

first: Lindsey

last: Turnbull

first: Katrina

middle: A

last: Button-Simons


title: Expression data from normal human spheroid-forming keratinocytes in monolayer mass culture and from corresponding cornified-like spheroid ring structures.

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary:
3-D suspension culture differs considerably from monolayer culture in regards to cell architecture, cell to cell contact, and cell to matrix interactions. These factors play a regulatory role in epithelial stem cell homeostasis and influence epidermal stem cells on their decision to remain quiescent or to activate self-renewal.
We used microarrays to determine the global programme of gene expression underlying spheroid ring formation and identified distinct gene programs involved in this process.

overall_design: Normal human keratinocytes primary cultures were stablished from neonatal foreskin epidermis. Multicellular spheroid cultures of normal human keratinocytes were generated and then plated into an uncoated polystyrene culture dish. Spheroid-derived cells were allowed to migrate until a cornified ring formed. RNA was extracted from the cornified ring and corresponding mass cultured line.  All cells used in the experiment originated from the same individual.

first: Yvon

last: Woappi

first: Lucia

last: Pirisi-Creek


title: Transcriptome profile of peritoneal lavage in response to adjuvants Alum and the polysaccharide from the roots of Actinidia eriantha (AEPS)

city: Hangzhou

first: Xiangfeng

last: Chen

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

summary: Analysis of peritoneal lavage from BALB/c mice 2 hours after intraperitoneal injection with PBS, AEPS, OVA, OVA+AEPS, or OVA+Alum. Results provide insight to explore the potential role of mRNAs and lncRNAs in adjuvant-induced innate immune response.

overall_design: BALB/c mice were injected intraperitoneally with PBS, AEPS(50 μg), OVA(25 μg), OVA(25 μg)+AEPS(50 μg), or OVA(25 μg)+Alum(200 μg). The peritoneal cells were harvested 2 h after injection for RNA extraction.

first: Hong

middle: X

last: Sun

first: Jing

last: Du

first: Xiang


title: Stress Responses in Bacteria Induced by a Giant Channel

city: Palmerston North

first: Jasna

last: Rakonjac

address: Riddet Road

department: Institute of Fundamental Science

country: New Zealand

institute: Massey University

summary: Pathogenic bacteria export large proteins and protein complexes, including virulence factors, using dedicated trans-envelope multi-protein machineries, collectively called secretion systems. Four of these protein export machines found in Gram-negative bacteria: type 2 and 3 secretion systems, the type 4 pilus biogenesis system and the filamentous phage assembly-secretion system (FFSS), contain large homologous gated channels in the outer membrane, called secretins. These channels are radially symmetrical homomultimers (luminal diameter 6-8 nm) interrupted by an internal septum, which blocks the channel in its resting state. By analyzing the transcriptome of Escherichia coli producing the FFSS secretin pIV and an isogenic leaky-gate variant, we have expanded the known secretin responses to include the Sox, Cpx, Rcs and RyhB regulons, in addition to the known secretin responder, the Psp regulon. Furthermore, we show that responses dependent on transcriptional regulators CpxR, SoxS and RcsB (in addition to PspF) are required for survival of E. coli producing the leaky-gate variant of secretin pIV, while CpxR, SoxS and PspF are required for survival of cells producing wild-type T3SS secretin InvG. Our analysis shows that secretins induce three out of six envelope stress responses and responses to oxidative stress. Identification of the key stress response regulators required for survival of secretin stress suggests pathways that may be of interest in developing strategies for control of secretin-expressing pathogenic bacteria.

overall_design: mRNA profiles for E. coli cultures expressing either vector control, wildtype pIV or pIV-E292K were deep sequenced in triplicate on 2 lanes of the Illumina HiSeq 2000 platform

first: J

last: Spagnuolo

first: S

last: Khanum

first: M

last: Russel

middle: P

last: Cox


title: GeoChip and environmental data of soil microbial communities of three subtropical broad-leaved forests

status: Public on Jan 29 2021

city: Biejing

first: Jingmin

last: Cheng

address: NO. 30 Shuangqing Road, Haidian District

department: School of Environment

institute: Tsinghua University

summary:
A comparision of soil microbial functional genes of three types of subtropical broad-leaved forests
Microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher alpha-diversity of functional genes but lower beta-diversity, and showed more complex functional gene networks.

overall_design:
Soil microorganisms play important roles in the ecosystem functioning of subtropical broad-leaved forests (SBFs). However, the patterns and environmental indicators of soil microbial functional structure remain unclear in SBFs.

DBF = Saiwudang forest
EBF = Badagongshan forest
MBF = Houhe forest

first: Yuguang

last: Zhang

last: Cong

first: Jingjing

last: Yu


title: Annual transcriptome dynamics of Japanese cedar (Cryptomeria japonica) and effects of photoperiod and temperature on dormancy induction

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

country: Japan

institute: Forest Tree Breeding Center

summary: To investigate the mechanism of annual rhythms in Japanese cedar, annual time series samples were collected from the cuttings planted in natural condition. Also, to investigate the effects of photoperiod and temperature during transition to dormancy, the samples of cuttings grown in the controlled-environmental chamber were analyzed by a microarray.

overall_design:
Annual time series samples were collected at 8:00 at 12 intervals covering a year (Jun 24, Aug 5, Sep 30, Oct 30, Nov 26, Dec 24, 2013, Jan 30, Feb 21, Mar 11, Apr 9, May 9, Jun 18, 2014) from cuttings of a Japanese cedar clone (Goudai-1) planted in 1999 at the Forest Tree Breeding Center, Forestry and Forest Products Research Institute (Hitachi, Ibaraki, Japan) (Season; 24 samples).
To investigate the effects of photoperiod, the potted cuttings were transferred to short day (SD; 8 hours of light and 16 hours of dark at 25 °C) and long day conditions (LD; 16 hours of light and 8 hours of dark at 25 °C), and the samples was collected from two cuttings at 0, 7, 21, 35, 49 and 70 days after transfer (experiment 1; 22 samples). Also, to investigate the effect of temperature, the cuttings were transferred to high (25 °C) and low (15 °C) temperature in long day conditions, and the samples were collected from two cuttings at 0, 7, 21, 42, 63 and 90 days after transfer (experiment 2; 22 samples).

first: Atsushi

last: Watanabe


title: The analysis of gene transcription and the effect of drug resistance of Radix Paeoniae Rubra Decoction on Staphylococcus aureus

status: Public on Jan 30 2021

city: Beijing

first: Zhao

last: Xiaomng

address: Beinong Road num 6

institute: Beijing university of agriculture

summary: To study the effect of Radix Paeoniae Rubra decoction on tolerance of Staphylococcus aureus.The effect of Radix Paeoniae Rubra on the resistance of Staphylococcus aureus to oxacillin sodium was studied by millipore dilution method in this experiment.At the same time ,conducted on transcriptome analysis of Staphylococcus aureus related genes in Radix Paeoniae Rubra.And to detect the expression level of related genes of Staphylococcus aureus under the action of Radix Paeoniae Rubra by PCR technology.The tolerance of Staphylococcus aureus was decreased obviously when the concentration of Radix Paeoniae Rubra decoction was above 1mg/ml.The effect of Radix Paeoniae Rubra decoction on the expression of tolerance genes femB,pvL and gluM when the concentration of Radix Paeoniae Rubra decoction was above 4mg/ml.When rhe concentration of Radix Paeoniae Rubra is more than 1mg/ml,it can effectively reduce the resistance of Staphylococcus aureus to oxacillin sodium.The reason may be due to the effect of Radix Paeoniae Rubra on the resistance gene of Staphylococcus aureus.

overall_design: ATCC-29213 was co-cultured with the concentration of Radix Paeoniae Rubra decoction was 1, 2, 4mg/ml for 12h. RNA was extracted and reverse transcribed into cDNA for examination the gene expression.

first: Yingjian


title: Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

institute: Institut Curie

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

overall_design: Refer to individual Series


title: Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish]

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

summary: Obesity, and visceral adiposity in particular, increases the risk of common metabolic diseases, including type 2 diabetes, cardiovascular disease, and several forms of cancer. However, the molecular mechanisms responsible for regional fat storage remain poorly characterized, preventing therapeutic innovation. We here applied a systematic genome-wide screen and translational approach, and discovered a novel role for the adipocyte-expressed neutral amino acid transporter SLC7A10/ASC-1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot-dependent and fat loss-dependent expression, 27 genes further showed significant correlations with waist-to-hip (WHR) ratio adjusted for BMI. Among these ASC-1 was expressed at the highest level in isolated visceral adipocytes. Further, we found decreased ASC-1 mRNA in visceral, and not subcutaneous adipose tissue, in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro, we found that ASC-1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly, radiometric amino acid uptake assays showed ASC-1 dependent uptake of the serine D-enantiomere. Using primary human and murine adipocyte models, we uncovered marked effects of inhibiting ASC-1 on mitochondrial respiratory capacity (within hours) and lipid accumulation (within days). Finally, Asc-1 knockout (KO) zebrafish had increased body weight and adipocyte enlargement upon eight-week overfeeding compared to wild-type (WT) fish. RNA sequencing data from zebrafish adipose tissue showed up-regulation of genes involved in fatty acid and lipid metabolism in the ASC-1 KOs, consistent with the increased lipid accumulation in the inhibitor-treated cell models. Additionally, duox, an enzyme involved in ROS generation, showed higher expression in the KOs compared to the WTs. Importantly, we confirmed increased reactive oxygen species (ROS) generation (within minutes and within hours) when inhibiting ASC-1 in our in vitro cell models. Our study points to increased ROS generation and reduced mitochondrial respiratory capacity as central early mechanisms in development of visceral adiposity, and a role for adipocyte D-serine transport via ASC-1 in these processes. Enhancing ASC-1 expression and/or activity in adipocytes, likely through primary effects on one-carbon metabolism and redox balance, is a promising therapeutic strategy for reducing visceral adiposity and related diseases.

overall_design: Total RNA-Seq of Zebrafish adipose tissue were sequenced on the Illumina HiSeq4000 platform

first: Simon

last: Dankel

first: Regine

last: Asen


title: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

institute: Huazhong Agricultural University

type: Methylation profiling by high throughput sequencing

summary: We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

overall_design:
Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues in B. napus.
WGBS: Total genomic DNA was extract from tissue with DNeasy plant mini kit (QIAGEN, 69104), library construction using EZ DNA Methylation-Gold kit (ZYMO, D5005), sequence was generated on Illumina HiSeq X Ten sequencer.

first: Qing

first: Pengpeng

last: Guan

first: Lun

last: Zhao


title: Single-cell RNA-sequencing of bovine fetal gonads using 10x Genomics

city: Davis

first: Pablo

middle: Juan

last: Ross

state: California

address: One Shields Ave

department: Animal Science

institute: University of California, Davis

summary: The germ cell lineage ensures the creation of new individuals perpetuating the genetic information across generations. Primordial germ cells (PGCs) are pioneers of gametes and exist transiently during development until they differentiate into oogonia in females, or spermatogonia in males. Little is known about the molecular characteristics of PGCs in cattle. By performing single-cell RNA-sequencing of bovine fetal gonads we evaluated the molecular signatures of bovine germ cells and their niche at 50 days of development. Our results indicate that PGCs and somatic cells were in very early stages of development, and that bovine and human germ cells share expression of transcriptional regulators of germline specification, and several genes coding for membrane-bound proteins. Additionally, the expression of members of Notch, Nodal/Activin, and BMP signaling cascades in the bovine fetal ovary, suggests that these pathways are involved in the interaction between germ cells and their niche. Results of this study provide insights into the mechanisms involved in the development of bovine PGCs and put in evidence similarities between the bovine and human germline.

overall_design: Gonads harvested from 2 female fetuses at aproximately day 50 of development. Each replicate was independently processed for single-cell RNA-sequencing.

first: Delia

last: Soto

middle: J


title: Targeting DNA damage repair functions of two histone deacetylases, HDAC8 and SIRT6, sensitizes acute myeloid leukemia to NAMPT inhibition

status: Public on Jan 27 2021

city: Columbus

first: Pu

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

summary: CRISPR knockout screening on MOLM-13 cells with KPT-9274

overall_design: MOLM-13 cells were transduced with geckov2 CRISPR knockout library (Addgene 1000000048   ) with: 1) baseline (7 days post library infection), 2) KPT-9274-treated, 3) DMSO control.

first: Lindsey

middle: T

last: Brinton

first: Rosa

last: Lapalombella

first: James

last: Blachly


title: The neuroendocrine stress response at single-cell resolution reveals adrenal ABCB1 as key regulator of stress adaptation

status: Public on Jan 28 2021

city: Munich

first: Alon

last: Chen

department: Department of Stress Neurobiology and Neurogenetics

institute: Max Planck Institute of Psychiatry

summary: Chronic activation and dysregulation of the neuroendocrine stress response has severe physiological and psychological consequences, including the development of metabolic and stress-related psychiatric disorders. Here, we provide the first unbiased, cell-type-specific, molecular characterization of all three components of the hypothalamic-pituitary-adrenal (HPA) axis, under baseline and chronic stress conditions, using single-cell RNA sequencing. Interestingly, the most prominent alterations were observed in the adrenal gland. We identified a population of Abcb1b+ cells involved in stress adaptation in the zona fasciculata of the adrenal. We validated our findings in a mouse stress model and human adrenal tissues from patients with ACTH-dependent Cushing’s syndrome. We demonstrated that transcriptional activity and variants of the ABCB1 gene underlie a dampened HPA axis response, using in-vitro adrenocortical cell lines and functional endocrine testing in depressed patients. Our findings raise the possibility for ABCB1 based stratification of patients with stress-related disorders and modulation of its function as a tailored treatment strategy.

overall_design: Single-cell RNA sequencing characterization of all three components of the HPA axis under baseline (unstressed) and chronic stress conditions.

first: Juan

last: Lopez

first: Simone

last: Roeh


title: NdpA2 & TprA regulon in PA14:  ICE PAPI-1 transference induced (M0) vs Control (Tn38)

city: Marseille cedex 20

first: Gauthier

last: Dangla-Pélissier

address: 31 chemin Joseph Aiguier

institute: CNRS

summary:
Transcriptional profiling of Pseudomonas aeruginosa PA14 comparing T4SS-GI induced biosynthesis M0 strain with control wild type phentoype Tn38 strain
The PA14_59050-59120 locus was overexpressed through chromosomal insertion of ptac promoter within PA14_59030 gene.

overall_design: Two-condition experiment, M0 vs. Tn38 PA14 strains. Biological replicates: 2 control replicates, 2 PAPI-1 induced transference replicates.

first: Nicolas

last: Roux

first: Victoria

last: Schmidt

first: Gaël

last: Chambonnier

first: Moly

last: Ba

first: Corinne

last: Sebban-Kreuzer

first: Sophie

last: de Bentzmann

first: Caroline

last: Giraud

first: Christophe

last: Bordi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mock- and Hydrogen peroxide (H2O2)-Treated Human Hepatocellular Carcinoma (HCC) Cell Transcriptomes

city: Seoul

first: Eunkyong

last: Ko

address: Gwanak ro

institute: Seoul National University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived H2O2-treated HCC transcriptome profiling (RNA-seq) to NGS-derived mock-treated HCC transcriptome profiling.
Methods: HCC mRNA profiles of mock-treated Huh7 cells and H2O2-treated Huh7 cells were generated by deep sequencing, in duplicate, using Illumina Pipeline (CASAVA) v1.8.2. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: RNA-seq data validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.90.
Conclusions: We conclude that our study represents the first detailed analysis of H2O2-treated HCC cells transcriptomes compared to mocke-treated HCC cells, with biologic replicates, generated by RNA-seq technology.

overall_design: Human HCC cell Huh7 mRNA profiles of 4 day following mock-treated and H2O2-treated cells were generated by deep sequencing, in duplicate, using Illumina Pipeline (CASAVA) v1.8.2.

first: Daekwan

last: Seo


title: Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer [scTCR-seq]

first: Paul

last: Gueguen

summary:
Purpose: The goal of this study is to delineate the processes of CD8+ T cell differentiation in primary NSCLC by integrating transcriptomic and tcr profiles.
Methods: A combination of single cell RNA and TCR sequencing (scRNA-seq and scTCR- seq) was used, in tumors, normal tissues adjacent to the tumor (juxta-tumor), and circulating blood derived from 11 patients with untreated, primary NSCLC.
Results: We show that precursor, memory-like CD8+ TILs include 2 main populations: one is also present in the blood (circulating precursors); the other is also present in juxta-tumor tissue and bears markers of memory resident T cells (resident precursors). Both precursor subtypes differentiate into a main population of terminal effectors through a similar “transitional” stage. Terminal effectors are not observed in blood or juxta-tumor tissue, are more clonally expanded, and express signatures of exhaustion. A significant proportion of transitional and terminal effectors also express cell cycle signatures and Ki67, suggesting that clonal expansion occurs in situ is part of the terminal differentiation process.

overall_design: 6 patients with early-stage, untreated NSCLC

first: Christina

last: Metoikidou


title: Dopamine Receptor Antagonists and Radiation Create a Metabolic Vulnerability in Mouse Models of Glioblastoma

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary:
Glioblastoma is the deadliest brain tumor in adults and the standard-of-care consists of surgery followed by radiation and treatment with temozolomide. Overall survival times for patients suffering from glioblastoma are unacceptably low indicating an unmet need for novel treatment options.
Using patient-derived glioblastoma lines and mouse models of glioblastoma we tested the effect of radiation and the dopamine receptor antagonist on glioblastoma self-renewal in vitro and survival in vivo. A possible resistance mechanism was investigated using RNA-Sequencing.
Treatment of glioma cells with the dopamine receptor antagonist quetiapine reduced glioma cell self-renewal in vitro and combined treatment of mice with quetiapine and radiation prolonged the survival of glioma-bearing animals. The combined treatment induced the expression of genes involved in cholesterol biosynthesis. This rendered the tumors vulnerable to simultaneous treatment with atorvastatin and further significantly prolonged the survival of the animals.
Our results indicate promising therapeutic efficacy with the triple combination of quetiapine, atorvastatin and radiation treatment against glioblastoma without increasing the toxicity of radiation. With both drugs readily available for clinical use our study could be rapidly translated into a clinical trial.

overall_design: Cells were irradiated with 0 or 4 Gy and treated with solvent or Quetiapine at 10µM


title: Host transcriptome profile of children with respiratory virus infection

city: Melbourne

first: Clyde

last: Dapat

state: Victoria

address: 792 Elizabeth Street

country: Australia

institute: WHO Collaborating Centre for Reference and Research on Influenza

summary: Purpose: The aim of this study is to determine the expression profile in whole blood samples of children infected with respiratory syncytial virus and other respiratory viruses. Method: Host mRNA profiles in whole blood samples of children were generated by next-generation sequencing using Illumina Hiseq. Sequence reads were trimmed for adapter using skewer, mapped to reference human genome using STAR, and quantified using RSEM. Differential expression analysis was performed using DESeq2. Results: Transcriptional module analysis revealed dysregulation of genes related to inflammatory response, neutrophils, monocytes, B-cell and T-cell response. Conclusion: This study showed an imbalance in innate and adaptive immune responses in children with respiratory virus infections. This study also showed that NGS provides a comprehensive assessment of transcripts in whole blood samples.

overall_design: Whole blood samples from hospitalized children infected with respiratory syncytial virus (n=37), human rhinovirus (n=15), human metapneumovirus (n=4), influenza virus (n=2), enterovirus D68 (n=1), adenovirus (n=1); including respiratory syncytial virus and human rhinovirus mixed infection (n=5), respiratory syncytial virus and enterovirus D68 mixed infection (n=1); and virus negative (n=10).

first: Satoru

last: Kumaki

first: Hiroki

last: Sakurai

first: Hidekazu

last: Nishimura

first: Ryo

last: Funayama

first: Matsuyuki

last: Shirota

first: Keiko

last: Nakayama

first: Hannah

middle: K

last: Labayo

first: Mchiko

last: Okamoto

first: Mayuko

last: Saito

first: Hitoshi

last: Oshitani


title: YTHDF2 inhibits gastric cancer cell growth by regulating FOXC2 signaling pathway

city: Suzhou

first: Xudong

last: Sheng

address: 1055 Sanxing Road

institute: Soochow University

summary: We found that YTHDF2 has lower expression in GC tissues and GC cells, and promotes the growth, migration and invasion of GC cells. In addition, the analysis of clinical data found that the expression level of YTHDF2 was closely related to the stage of GC and the survival of patients with GC. RNA-seq showed that overexpression of YTHDF2 significantly reduced protein expression in the FOXC2 (Forkhead box protein C2, FOXC2) signaling pathway.

overall_design: The gene expression of Vector and MGC-803 cell lines overexpressing YTHDF2 were detected by RNA sequencing.

last: Shen

first: Kui

last: Zhao


title: RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

city: Grand Rapids

first: Gerd

last: Pfeifer

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: RNAseq was performed by to compare gene expression between wildtype and Smchd1 KO ES cells, the gene expression pattern in Dux KO mutants , Double KO mutant Tet-TKO mutants and Tet TKO plus SMCKHD1 KO mutants were analyzed by RNAseq.

overall_design: Three biological replicates per genotype; RNA was isolated individually from each replicate; three samples for WT, Smchd1 KO, Dux KO, Double KO(Smchd1 plus Dux KO), Tet-TKO and quadKO(Tet-TKO plus Smchd1 K) were sequenced individually; three samples for WT, Smchd1 KO were sequeced two technical repilacate.

first: Zhijun

last: Huang


title: Expression data of Tfe3/Tfeb- or GFP-knocked-down RAW264 macrophages treated with or without iron

city: Nagoya

first: Yohei

last: Kanamori

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary:
In an attempt to elucidate the role of MiT/TFE families in the iron-mediated phenotypic changes of macrophages, we performed DNA microarray analysis using ferric chloride-stimulated RAW264 cells transfected with Tfe3/Tfeb or GFP.
A number of genes upregulated by ferric chloride treatment in siGFP-transfected RAW264 cells were decreased in siTfe3/Tfeb-transfected cells, suggesting MiT/TFE families are involved in phenotypic changes of macrophages induced by iron.

overall_design: RAW264 macrophages transfected with or without siTfe3/Tfeb were stimulated with or without ferric chloride for 24 h. Microarray analysis was performed using SurePrint G3 Mouse 8x60K ver. 2 .0.

first: Miyako

last: Tanaka

first: Takayoshi

last: Suganami


title: Total paired-end RNA sequencing of bone marrow and peripheral blood MNCs from patients with Juvenile myelomonocytic leukemia and age-matched controls

city: Gent

first: Mattias

last: Hofmans

address: C. Heymanslaan 10

department: Department of pediatrics

institute: Ghent University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Dysregulation of the non-coding RNA transcriptome has been demonstrated in Juvenile myelomonocytic leukemia (JMML), a rare and aggressive disorder of early childhood. Currently, JMML treatment relies on hematopoietic stem cell transplantation resulting in long-term overall survival of only 50-60%. Consequently, there is need to develop novel treatments. In this study we investigated the therapeutic potential of targeting overexpressed long non-coding RNAs (lncRNAs) in JMML. Total RNA sequencing from 19 previously untreated JMML patients and 3 pediatric normal bone marrow samples revealed 202 differentially expressed lncRNA genes (144 upregulated and 58 downregulated). Molecular knockdown (≥ 70% compared to mock control) after 24h of incubation was observed for 6 out of 10 overexpressed lncRNAs for which LNA GapmeRs were designed. For 3 lncRNAs (lnc-THADA-4-1, lnc-ACOT9-1 and NRIR) knockdown resulted in a significant effect on cell viability after 96h or 72h of incubation in cell lines or in primary JMML cells, respectively. Importantly, the extend of cellular damage correlated well with the expression of the lncRNA of interest. In conclusion, we provided proof-of-concept that knockdown of overexpressed lncRNAs such as lnc-THADA-4-1, lnc-ACOT9-1 and NRIR is a feasible therapeutic strategy in vitro in haematopoietic cell lines and in primary JMML cells. These results will need further validation in JMML xenograft models.

overall_design:
We report long non-coding RNA transcriptome in patients with Juvenile Myelomonocytic Leukemia. To this end, total paired-end RNA sequencing identified 38117 non-coding RNA genes of which 202 differentially expressed between JMML and age-matched healthy controls.
Examination of total paired-end RNA sequencing data between bone marrow and peripheral blood MNCs from JMML and bone marrow MNCs from healthy age-matched controls.

first: Tim

last: Lammens

first: Jan

last: Philippé

first: Barbara

last: DeMoerloose


title: WGBS of WT and Smchd1-KO ES cells

summary: We performed the whole genome bisulfite sequencing to detect the DNA methylation between the wild type ES cells and Smchd1 mutant ES cells

overall_design: Three biological replicates per genotype; DNA was isolated individually from each replicate; three samples for WT and Smchd-KO mutant were sequenced twice.


title: A novel neural stem cell-derived immunocompetent mouse model of glioblastoma for preclinical studies (RNA-Seq)

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

summary: Glioblastomas are the most lethal tumors affecting the central nervous system in adults. Simple and inexpensive syngeneic in vivo models that closely mirror human glioblastoma, including interactions between tumor and immune cells, are urgently needed for deciphering glioma biology and developing more effective treatments. Here, we generated mouse glioblastoma cell lines by repeated in-vivo passaging of neural stem cells and tumor tissue of a neural stem cell-specific Pten/p53 double-knockout genetic mouse model. Transcriptome and genome analyses of the cell lines revealed molecular heterogeneity comparable to that observed in human glioblastoma. Upon orthotopic transplantation into syngeneic hosts they formed high-grade gliomas that faithfully recapitulated the histopathological characteristics, invasiveness and infiltration by myeloid cells characteristic of human glioblastoma. These features make our cell lines unique and useful tools to study multiple aspects of glioma pathomechanism and test immunotherapies in syngeneic preclinical models.

overall_design: Mouse glioblastoma cell lines were established using a genetically engineered, Tamoxifen-induced Pten/Tp53 double knockout specific to neural stem cells. The first passages of each line were establised by in vitro, stem-cell maintaining culture of cells either isolated from the sub-ventricular zone 2 weeks after induction (tNSC0) or from gross tumour (mGB0). Each line was serially transplanted (following intervening further in vitro expansion) into recipient mice to establish the mGB (mGB0, mGB1, mGB2) and tNSC (tNSC0, tNSC1, tNSC2, tNSC3) lines. Normal neural stem cells (experimental control for all mGB and tNSC samples) and splenocytes (copy number-normal control) were also isolated. in vitro-cultured cells were then analysed using whole exome sequencing (WES) and RNA-seq.

last: Costa

first: Michael

middle: N

last: Fletcher

first: Martin

last: Löwer

first: Peter

last: Angel

first: Heike

last: Peterziel


title: Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary:
"The connection between different tissues is vital for the development and function of all organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of
chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF).
To uncover the molecular identity of attachment cells, we first applied high-throughput bulk and single-cell RNA sequencing to murine humeral attachment cells. The results, which were validated by in situ and single-molecule in situ hybridization, reveal that together with the expression of unique sets of genes, the attachment cells express hundreds of chondrogenic and tenogenic genes. In search for the underlying mechanism, we performed ATAC sequencing and found that attachment cells share a significant fraction of accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis further revealed transcriptional enhancer signatures for the majority of these regions. We then examined a subset of these regions using transgenic mouse enhancer reporter assay. Results verified the shared activity of some of these enhancers, supporting the possibility that the transcriptome of attachment cells is regulated by enhancers with shared activities in tenocytes or chondrocytes. Finally, integrative chromatin and motif analyses, as well as the transcriptome data, indicated that KLFs are regulators of attachment cells. Indeed, blocking the expression of Klf2 and Klf4 in the developing limb mesenchyme led to abnormal differentiation of attachment cells, establishing these factors as key regulators of the fate of these cells. In summary, our findings show how the molecular identity of bi-fated attachment cells enables the formation of the unique transitional tissue that connects tendon to bone. More broadly, we show how mixing the transcriptomes of two cell types through shared enhancers and a dedicated set of transcription factors can lead to the formation of a new cell fate that connects them."

overall_design: Comparative transcriptome analysis of tenocytes, attachment cells and chondrocytes populations, isolated by laser capture microdissection (LCM). ATACseq data were measured from E13.5 tenocytes, attachment cells and chondrocytes  isolated by FACS sorting;attachment cells genetically co-labeled Sox9-CreERT2;Rosa26-tdTomato+;ScxGFP+, tenocytes genetically labeled by ScxGFP+, chondrocytes genetically labeled Col2-CreERT; Rosa26-tdTomato+;ScxGFP-.

first: Shiri

last: Kult

first: Marco

last: Osterwalder

first: Svetalana

last: Markman

first: Dena

last: Leshkowitz

first: Sharon

last: Krief

first: Ronnie

last: Blecher-Gonen

first: Shani

last: Ben-Moshe

first: Lydia

last: Farack

first: Hadas

last: Keren-Shaul

first: Tomer

middle: M

last: Salame

first: Terence

last: Capellini

first: Shalev

last: Itzkovitz

first: Ido

last: Amit

first: Axel

last: Visel

first: Eli

last: Zelzer


title: A novel neural stem cell-derived immunocompetent mouse model of glioblastoma for preclinical studies (WES)

first: Bernhard

last: Radlwimmer

first: Barbara

last: Costa

first: Michael

last: Fletcher

first: Martin

last: Löwer

first: Peter

last: Angel

first: Heike

last: Peterziel


title: Disentangling mTOR signalling from the lifespan extending effect of dietary restriction in progeroid DNA-repair deficient mice

status: Public on Jan 25 2021

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary:
Dietary restriction (DR) and rapamycin, the best-known DR-mimetic, are two intervention that extend health- and lifespan across multiple species. We have recently shown that DR works extremely well in progeroid DNA repair deficient mice and dramatically extend their lifespan by ~200%. We next questioned the applicability of rapamycin in these mouse mutants. Here we show that treatments with rapamycin did significantly lower mTOR-signalling but did not improve the lifespan of DNA repair deficient Ercc1{delta}/- mice.
These data are an extended version of the data in GEO Series GSE77321

overall_design: 24 samples, five groups with biological replicates, analyzed on Affymetrix genechips


title: A novel neural stem cell-derived immunocompetent mouse model of glioblastoma for preclinical studies

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

overall_design: Refer to individual Series


title: Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University


title: Effect of Decitabine on SKM-1 and MDS-L Gene Expression

status: Public on Jan 26 2021

city: Shanghai

first: Zheng

last: Zhang

address: YiShan Road 600

institute: Shanghai Jiao Tong University

summary:
In order to further study the mechanism of decitabine (DAC) on MDS cell lines, 1uM DAC was used to treat SKM-1 and MDS-L cell lines, and the molecular pathway changes regulated by DAC were explored. Genes whose expression changes more than 2.0 times after drug treatment are defined as regulated genes.
Taking the intersection change of the two cell lines, it was found that compared with the control, 541 genes were up-regulated in the intersection of gene changes treated with DAC, and 762 genes were down-regulated. Gene expression profile analysis shows that DAC can significantly affect various cell biological processes, including antiviral response, immune response, inflammatory response and cell apoptosis.

overall_design: Decitabine-induced gene expression in SKM-1 and MDS-L cells was measured after 5 days exposure at dose of 1uM. The same number of cells were treated with DMSO as a control.

first: Feng

last: Xv


title: The chromosomal protein SMCHD1 regulates DNA methylation by antagonizing TET proteins

first: Gerd

last: Pfeifer


title: Ush regulates macrophage-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: The generation and modulation of lineage-specific gene expression programmes that determine proliferation capacity, metabolic profile and cell type-specific activities at each stage of differentiation are crucial for metazoan development. Gene expression programmes are moulded by a complex interplay between sequence-specific transcription factors, cofactors and epigenetic regulators. Here, we study U-shaped (Ush), a genetically defined transcriptional cofactor that cooperates with GATA transcription factors during blood cell differentiation in Drosophila. We use a cell line that is derived from macrophage precursors to comprehensively analyse Ush function at the cellular level. Using genomewide approaches we reveal that Ush binds to thousands of promoters and enhancers that are enriched for GATA sites and that it is a major regulator of transcription. Ush controls the expression of at least three functionally distinct gene classes encoding proteins relevant to different aspects of macrophage differentiation: cell cycle regulators, key metabolic enzymes and proteins enabling macrophage-specific functions. Ush is essential to maintain proliferative capacity and coordinately regulates fatty acid degradation and synthesis. We employ complementary biochemical approaches to characterise the molecular mechanisms of Ush-mediated gene regulation. We uncover the existence of two major Ush isoforms. One of these, Ush-B, uses a short peptide sequence to bind the Nucleosome Remodeling and Deacetylation (NuRD) complex. We demonstrate that this mode of interaction is conserved between vertebrates and invertebrates. Remarkably, Ush-B/NuRD specifically contributes to the repression of macrophage-specific genes demonstrating that Ush isoforms and epigenetic regulators make differential contributions to Ush controlled transcription programmes. Finally, we use genetic methods to define Ush and NuRD function in the developing fly. Ush and NuRD regulate enhancer activity during macrophage differentiation and both cooperate to suppress the formation of lamellocytes. Our findings uncover how a transcriptional cofactor can coordinate distinct cellular activities (proliferation, metabolism and cell type-specific functions) that are relevant for differentiation and maintenance of cell type-specific phenotypes.

overall_design: ChIP-Seq of Ush and Mi-2 in S2 Schneider cells. RNA-Seq after Ush (all isoforms), Mi-2 and Ush Isoform B knockdowns.

first: Jonathan

last: Lenz

first: Alexander

last: Brehm


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ChIP-Seq - INTACT]

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute

summary: TATA box-containing promoters are often associated with tissue-specific effector genes, genes that are important for the structure and function of differentiated tissues. The underlying reason for this promoter preference is unclear, in part because tissue-specific genes have not been studied as widely as genes that drive embryonic development. To fill this gap in knowledge, we performed single-cell RNA-seq on differentiated cells derived from the late Drosophila embryo, identified the various tissues and analyzed the relationship between promoter types and gene expression across tissues. Our analysis confirmed the usage of TATA-containing promoters but revealed that tissue-specific effector genes are induced by two distinct promoter types, which have different mechanisms of regulation by RNA polymerase II (Pol II) and different expression characteristics. TATA-enriched promoters are highly tissue-specific and are only occupied by Pol II in the tissue in which they are active; the other promoter type is depleted in TATA motifs and shows high levels of paused Pol II throughout the embryo, even in tissues where the genes are not expressed. Interestingly, the single-cell RNA-seq data revealed that the paused promoters have more robust expression when expressed, but have higher background expression in tissues where these genes are not expressed. TATA genes, on the other hand, have little background expression, but larger variations in expression among the cells that show expression. To explain this difference, we propose that TATA-containing promoters have a higher activation barrier, but preferentially evolve in tissue-specific genes due to their strong activation potential and higher evolvability.

overall_design: ScRNAseq, RNAseq and Tissue Specific ChIP-Seq or ATAC-Seq was performed in Drosphila embryos.

first: Vivekanandan

last: Ramalingam

first: Malini

last: Natarajan

first: Jeff

last: Johnston


title: Nonspecific induction of distinct regulatory T cell states in oncogene-driven hyperproliferative skin

city: Woolloongabba

first: Chenhao

last: Zhou

state: QLD

address: 37 Kent Street

institute: The University of Queensland Frazer Institute

summary: Regulatory T cells (Tregs) recruited to peripheral tissues are associated with chronic diseases such as cancer. Tissue-specific signals and T cell receptor (TCR) specificity are critical to shape Treg phenotype diversity. We examined single-cell transcriptomic and TCR profiles of Tregs in human papillomavirus (HPV) E7-transformed hyperproliferative skin of mice. Tregs without evidence of E7 specificity were enriched in E7 transgenic skin grafts when compared with non-transgenic grafts. E7 transgenic skin grafts contained more Klrg1+ Tregs and Il1r2+ Tregs than non-transgenic grafts. These two Treg states had distinct effector phenotypes but shared a core gene signature with previously described tumour-infiltrating Tregs. Pseudotime trajectory of Tregs predicted phenotypic plasticity of TCR clonotypes, both within skin and between skin and draining lymph nodes. Together, we reveal that oncogene-driven hyperproliferative skin enables induction of nonspecific Tregs despite the presence of non-self antigen and Tregs exist in distinct cell states with unique effector gene signatures.

overall_design: scRNA-seq and scTCR-seq of immune cells sorted from K14E7 and C57BL/6 skin grafts and graft draining lymph nodes from C57BL/6 recipients

first: Zewen

last: Tuong

first: Samuel

middle: W

last: Lukowski

first: Janin

last: Chandra

first: Ian

middle: H

last: Frazer


title: Expression data in Abdominal Aortic Aneurysms

city: Calgary

first: Jacob

last: Kennard

state: CA-AB

address: 2500 university drive

department: Chemical Engineering

country: Canada

institute: University of Calgary

summary:
Current clinical practice for the assessment of abdominal aortic aneurysms (AAA) is based on vessel diameter and does not account for the multifactorial, heterogeneous remodeling that results in the regional weakening of the aortic wall leading to aortic growth and rupture. This study was conducted to determine correlation between a novel non-invasive surrogate measure of regional aortic weakening and the results from invasive analyses performed on corresponding ex vivo aortic samples. Tissue samples were evaluated to classify local wall weakening and likelihood of further degeneration based on non-invasive indices. A combined, image-based fluid dynamic and in-vivo strain analysis approach was used to estimate the Regional Aortic Weakness (RAW) index and assess individual aortas of AAA patients prior to elective surgery. Nine patients were treated with complete aortic resection allowing the systematic collection of tissue samples that were used to determine regional aortic mechanics, microstructure and gene expression by means of mechanical testing, microscopy and transcriptomic analyses. The RAW index was significantly higher for samples exhibiting lower mechanical strength (p = 0.035) and samples classified with low elastin content (p = 0.020). Samples with higher RAW index had the greatest number of genes differentially expressed compared to any constitutive metric. High RAW samples showed a decrease in gene expression for elastin and a down-regulation of pathways responsible for cell movement, reorganization of cytoskeleton, and angiogenesis.

Please note that the sample 'characteristisc: strain' represents the in-vivo strain corresponding to each section of aorta, which is measured from dynamic CT images of patient AAA using a proprietary software.

overall_design: Samples were taken from different sections of AAA's during open repair surgeries. After surgery RNA was extracted and hybridized with Affymetrix arrays. We sought to validatea novel AAA stability index, the Relative Aortic Weakening (RAW), and therefore samples chosen for microarray analysis were characterized by either a high or a low RAW.

first: Arianna

last: Forneris

first: Alina

last: Ismaguilova

last: Shepherd

first: Deborah

last: Studer

first: Amy

last: Bromley

first: Randy

last: Moore

first: Elena

middle: S

last: Di Martino

first: Kristina

last: Rinker


title: Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

institute: Radboudumc

summary: In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: RNA-seq performed on 4 samples from iPSC-derived neurons co-cultured with rat astrocytes, and 4 samples from HUVEC, cultured either on microfluidic chip (2 replicates per cell type) or on 24-well plate (2 replicates per cell type)

first: H

last: Middelkamp

first: A

last: Verboven

first: P

middle: C

last: 't Hoen

first: N

last: van der Meer


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [RNA-Seq]

first: Julia

last: Zeitlinger

first: Vivekanandan

last: Ramalingam

first: Malini

last: Natarajan

first: Jeff

last: Johnston


title: Single-cell transcriptomic analysis of human hepatocellular carcinoma

first: Xianbin

last: Su

address: Dongchuan Road 800

department: Shanghai Center for Systems Biomedicine

summary: We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 3200 single cells from 4 human hepatocellular carcinoma (HCC) specimens.

overall_design: We used Fluidigm microfluidic-chip approach to analyze the transcriptomic profiles of single cells from human HCC specimens. For each tumor tissue, 800 single cells were randomly captured and sequenced. A total of 3200 single cells were analyzed from 4 HCC patients.

first: Yi

last: Shi

first: Ze-Guang

last: Han


title: Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Road

department: Microbiology and Immunology

institute: Cornell University

summary: Traditional laboratory model organisms represent a small fraction of the diversity of multicellular life, and findings in any given experimental model often do not translate to other species. Immunology research in non-traditional model organisms presents multiple challenges, many stemming from an incomplete understanding of potentially species-specific immune cell types, frequencies and phenotypes. Identifying and characterizing immune cells in such organisms is frequently limited by the availability of species-reactive immunophenotyping reagents for flow cytometry, and insufficient prior knowledge of cell type-defining markers. Here, we demonstrate the utility of single cell RNA sequencing (scRNA-Seq) to characterize immune cells for which traditional experimental tools are limiting. Specifically, we used scRNA-Seq to comprehensively define the cellular diversity of equine peripheral blood mononuclear cells (PBMCs) from healthy horses across different breeds, ages, and sexes. We identified 30 cell type clusters partitioned into five major populations: Monocytes/Dendritic Cells, B cells, CD3+PRF1+ lymphocytes, CD3+PRF1- lymphocytes, and Basophils. Comparative analyses revealed many analogous cell populations in human PBMC, including transcriptionally heterogeneous monocytes and distinct dendritic cell subsets (cDC1, cDC2, plasmacytoid DC). Unexpectedly, we found that a majority of the equine peripheral B cell compartment is comprised of T-bet+ B cells; an immune cell subpopulation typically associated with chronic infection and inflammation in human and mouse. Taken together, our results demonstrate the potential of scRNA-Seq for cellular analyses in non-traditional model organisms, and form the basis for an immune cell atlas of horse peripheral blood.

overall_design: Single cell RNA sequencing of libraries prepared from equine peripheral blood mononuclear cells from 7 subjects

first: Roosheel

last: Patel

first: Joy

last: Tomlinson

first: Thomas

last: Divers

last: Van De Walle

first: Brad

last: Rosenberg


title: Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity [RRBS]

first: Lars

last: Ingerslev

summary: Skeletal muscle can undergo large transcriptional changes in response to environmental stimuli such as diet or exercise in order to adapt to energetic demands. This remodelling has been associated with changes in muscle DNA methylation potentially regulating gene transcription. Despite abundant evidence that environmental stimuli can alter muscle DNA methylation, the mechanisms by which DNA methylation machinery respond to these stimuli and whether these have a physiological impact is still unclear. Therefore, we decided to investigate the importance of de novo DNA methylation on muscle methylation and function. We generated muscle specific DNMT3a knockout mice (mDKO) and investigated the impact of ablating DNMT3a in muscle on muscle DNA methylation, exercise capacity and energy metabolism. Loss of DNMT3a reduced DNA methylation in muscle over multiple genomic contexts and altered the transcription of genes known to be influenced by DNA methylation. However, mDKO mice had a similar exercise capacity and whole-body energy metabolism as WT mice. Similarly, loss of DNMT3a did not alter muscle mitochondrial function or the transcriptional response to exercise however did increase the expression of genes involved in muscle development. These data suggest that DNMT3a does not have a large role in the function of mature muscle although a role in muscle development and differentiation is still likely.

overall_design: Reduced Representation Bisulfite Sequencing (RRBS) of Mus musculus soleus muscle in wild-type (WT) and DNMT3a knockout (KO), before (Bas) 10 minutes (10), 30 minutes (30) and 60 minutes (60) after exercise.

first: Lewin

last: Small

first: Rhianna

last: Laker

middle: R

first: Ann

last: Hansen

first: Brendan

last: Deeney

first: Juleen

last: Zierath

first: Romain

last: Barrès


title: Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity [RNA-seq]

overall_design: Total RNA-seq of Mus musculus soleus muscle in wild-type (WT) and DNMT3a knockout (KO), before (Bas) and 60 minutes after exercise (60).


title: Identification of STAT3 downstream targets involved in chemoradiotherapy resistance

city: Goettingen

first: Andreas

last: Leha

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Goettingen

summary: RNA-Seq data of human colorectal cancer cell line SW837 transfected with siRNA against STAT3 (siSTAT3) or control RNA (siCtrl), untreated or treated with Hyper-IL-6 (Hy-IL-6)

overall_design: STAT3 dependent mRNA profile in a) unstimulated and b) Hy-IL-6 stimulated SW837 cells, each with 6 replicates.

first: Kristin

last: Kördel

first: Melanie

last: Spitzner

first: Marian

last: Grade

first: Jürgen

last: Wienands


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [scRNA-Seq]

first: Julia

last: Zeitlinger

first: Vivekanandan

last: Ramalingam

first: Malini

last: Natarajan

first: Jeff

last: Johnston


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [Mnase-Seq]


title: Identification of key genes potentially related to intervertebral disc degeneration by microarray analysis

status: Public on Jan 22 2021

city: 成都市

first: 一

last: 王

state: 四川省

address: 一环路西一段132号

institute: 四川省骨科医院

summary: Although the pathology of sciatica has been studied extensively, the transcriptional changes in the peripheral blood caused by sciatica have not been characterized.  An Agilent SurePrint G3 human gene expression microarray 8 ╳ 60 K was used to analyse gene expression in whole blood from patients with sciatica compared with healthy volunteers.

overall_design: We recruited 17 patients with sciatica confirmed by magnetic resonance imaging, and 17 healthy volunteers with no clinical evidence of low back pain or sciatica. All patients underwent standard Traditional Chinese Medicine treatment for sciatica according to our medical protocol, including electric acupuncture, massage, moxibustion and Chinese medicine fumigation. Ten millilitres of fasting WB was collected from the left median cubital vein of each participant between 7:00 and 7:30 AM. All WB samples were incubated in a PAXgene Blood RNA tube (BD, USA) for less than 72 h at -20°C and then submitted to Shanghai Bohao Biotechnology Co., Ltd (Shanghai, China) for gene chip hybridization screening. The microarray experiments were performed using an Agilent SurePrint G3 human gene expression microarray 8 ╳ 60 K at Shanghai Biotechnology Co., Ltd (Shanghai, China) following the standard protocol of Agilent Technologies (CA, USA).

first: Yi

last: Wang


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ChIP-Seq]


title: A Murine Model of Lyme Disease Demonstrates That Borrelia Species Colonize the Dura Mater and Induce Inflammation in the Central Nervous System.

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary:
Purpose: Studies on gene expression changes in joint and heart tissues of laboratory mice have provided insights into the localized host responses to Borrelia burgdorferi colonization; however, gene expression changes in the CNS of mice during B. burgdorferi infection remain unclear. Therefore, we took an unbiased approach to examine potential changes in the dura mater as well as the brain cortex and hippocampus at day 7 post-infection using RNA sequencing (RNA-seq).
Methods: Dura mater, brain cortex, and hippocampal mRNA profiles of 6-8 week old C3H/HeN mice infected with B. burgdorferi strain 297 or mock infected (n=4 per group) were generated by paired-end sequencing using the Illumina HiSeq 4000. The sequence reads were aligned using STAR aligner followed by DESeq2 for differential expression analysis. qRT–PCR validation was performed using SYBR Green assays.
Results: In the dura mater, the presence of B. burgdorferi is associated with upregulation of genes consistent with TLR/NF-κB signalling and associated inflammatory cytokines and chemokines in addition to upregulation of interferon stimulated genes. In contrast, the brain parenchyma exhibits mainly an increase in interferon stimulated genes in response to B. burgdorferi infection without an associated cytokine response.
Conclusion: Overall, the findings reported in this study are significant, as the lack of a tractable animal model has hindered our understanding of host-pathogen interactions in the CNS. Our results describe a model system that will allow for future studies evaluating the bacterial, host, and environmental factors that can contribute to the severity of CNS involvement during B. burgdorferi infection, as well as evaluating potential novel prophylactic and therapeutic interventions for this important disease.

overall_design: Dura mater, brain cortex, and hippocampal mRNA profiles of 6-8 week old C3H/HeN mice infected with B. burgdorferi strain 297 or mock infected (n=4 per group) were generated by paired-end sequencing using using the Illumina HiSeq 4000.

first: Timothy

last: Casselli

first: Catherine

middle: A

last: Brissette


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo  [ATAC-Seq - INTACT]

overall_design: ScRNAseq, RNAseq,Tissue Specific ChIP-Seq or Whole embryo ChIP-Seq and ATAC-Seq was performed in Drosphila embryos.


title: Aberrant lncRNA expression profiles in OSCC plasma

city: Beijing

first: Hongcheng

last: Jia

state: Beijing

address: No.8 East Jing Shun Rd, Chaoyang District

department: Stomatology Department

institute: Beijing Ditan Hospital, Capital Medical University

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

summary: Carcinogenesis is a genetic process in which molecular changes occur earlier than histomorphological changes. The key to early detection of oral squamous cell carcinoma (OSCC) is to identify genetic alterations. However, aberrant lncRNA expression profiles in OSCC plasma is still largely unknown. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC plasma compared with paired healthy volunteer plasma. Our data revealed 7473 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 3972 lncRNAs were significantly up-regulated and 3501 lncRNAs were down-regulated in OSCC compared with paired healthy volunteer plasma.

overall_design: Plasma was obtained from 3 healthy adult volunteers and 3 patients with OSCC. LncRNA expression profiles were evaluated by an Agilent Human LncRNA Array v4.0 (8 x 60K, Arraystar).

first: Xuan

first: Zheng

last: Sun


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ATAC-Seq]


title: Two promoter types induce tissue-specific effector genes in the late Drosophila embryo

status: Public on Jan 24 2021


title: DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS

status: Public on Jan 23 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL