title: H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in giant cell tumour of bone [scRNA-Seq and snRNA-Seq]

first: Nada

last: Jabado

overall_design: We performed single-cell RNA-seq sequencing of n=4 H3.3G34W giant cell tumors of the bone and single-nucleus RNA-seq sequencing of N=4 H3.3G34W xenografts: patient-derived cell line that were orthotopically injected into mice tibias.

first: Sima

last: Khazaei

first: Nicolas

last: De Jay

first: Shriya

last: Deshmukh

first: Liam

last: Hendrikse

first: Wajih

last: Jawhar

first: Carol

last: Chen

first: Leonie

last: Mikael

first: Damien

last: Faury

first: Dylan

last: Marchione

first: Joel

last: Lanoix

first: Éric

last: Bonneil

first: Takeaki

last: Ishii

last: Jain

last: Rossokhata

middle: W

first: Benjamin


title: Transcriptome analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage

status: Public on Oct 01 2020

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

country: China

institute: A&F university

type: Expression profiling by high throughput sequencing

summary:
Purpose:Bamboo shoots rapidly lose water and accumulate lignin when stored under room temperature, while low temperature conditioning (LTC, 4℃) can alleviate lignification and reduce weightlessness rate. However, few transcriptional response and profiling datasets are available to explore the LTC mechanism of bamboo shoots.The goal of this study is to provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage by transcriptome analysis.
Methods:Total RNA was extracted using RNAiso Plus (Takara, Japan) according to the protocol, and after quality testing, was used for library construction and transcriptome sequencing by Illumina Novaseq™ 6000. The quality-controlled reads were aligned to the Phyllostachys edulis reference genome (http://gigadb.org/dataset/100498). The edgeR program25 was used for differential expression analyses.
Results: After raw data filtering, a high clean data rate from each sample was achieved, and the assessment result for the clean data by FastQC all demonstrated that our sequencing data was of high quality, full representativeness and validity. Compared with CK, a total of 7,452 DEGs were identified during LT storage. The Pearson’s correlation coefficient (r) and principle component analysis (PCA) results all suggested a high correlation among all samples. The above results suggest an effective LT treatment of postharvest bamboo shoots and a high-quality bioinformatics analysis of our RNA-seq results.
Conclusions: Our study represents the first detailed analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would reveal the essence of ripening and senescence of fruits and vegetables.

overall_design: Shoots mRNA profiles of different time-courses (0d, 2d, 6d and 20d) under LT condition were generated by deep sequencing, in 4 biological repetitions, using Illumina Novaseq™ 6000.

first: Xinchun

last: Lin


title: Profibrotic regulation of FGFR3 signaling in fibroblasts

city: Erlangen

first: Debomita

last: Chakraborty

address: Ulmenweg 18

country: Germany

institute: Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen

summary: We employed dermal fibroblasts isolated from Fgfr3G374Rneo+ mice, which do not express functional Fgfr3 (Fgfr3KO), from Fgfr3G374Rneo- mice with ligand-independent constitutive activation of Fgfr3 (Fgfr3Act) and from wildtype (WT) mice with normal expression of Fgfr3. Total RNA from these murine dermal fibroblasts (passage 4) were extracted and after quality control, were hybridized to the murine genome U74 gene chip. We have identified that Fgfr3 regulates important profibrotic pathways in fibroblasts. Selective upregulation of fibroblast growth factor receptor 3 (FGFR3) and its ligand FGF9 promote fibroblast activation and tissue fibrosis Transcriptome profiling, in silico analysis and functional experiments revealed that FGFR3 synergistically induces multiple profibrotic pathways including Endothelin-, Interleukin-4- and CTGF-signaling in a CREB-dependent manner. Inhibition of FGFR3 signaling by fibroblast-specific knockout of FGFR3 or FGF9 or pharmacological inhibition of FGFR3 inhibited fibroblast activation and attenuated experimental skin fibrosis. We have characterized FGFR3 as an upstream regulator of a network of profibrotic mediators and as a potential target for the treatment of fibrosis.

overall_design:
We used microarrays to detail the global program of gene expression in fibroblasts.
Three conditions, constitutive activation of Fgfr3 and Fgfr3 knockout with wildtype control (n=3 for all groups).

first: Honglin

last: Zhu

first: Jörg

last: Distler


title: H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone [RNA-Seq]

summary: Glycine 34 to tryptophan (G34W) substitutions in H3.3 arise in ~90% of giant cell tumour of bone (GCT). Here, we show H3.3G34W is necessary for tumour formation. Profiling the epigenome, transcriptome and secreted proteome of patient samples and tumour-derived cells CRISPR/Cas9-edited for H3.3G34W shows that H3.3K36me3 loss on mutant H3.3 induces a shift of the repressive H3K27me3 mark from intergenic to genic regions, beyond areas of H3.3 deposition. This promotes the redistribution of antagonistic chromatin marks and aberrant downregulation of contractile myofibroblast-associated genes altering cell fate in mesenchymal progenitors. Single-cell transcriptomics reveals that H3.3G34W stromal cells recapitulate a neoplastic trajectory from an SPP1+ osteoblast progenitor-like population towards an ACTA2+ myofibroblast population, which secretes extracellular matrix ligands predicted to recruit and activate osteoclasts. Our findings suggest that H3.3G34W leads to GCT by sustaining a transformed state in osteoblast-like progenitors which promotes neoplastic growth, pathological recruitment of giant osteoclasts, and bone destruction.

overall_design: We performed RNA-seq sequencing of isogenic unedited H3.3G34W and isogenic clones where the mutant allele was KO or repaired to WT by CRISPR/Cas9 from three patient-derived cell lines.  We sequenced n=7 mutant and n=9 edited replicates from Im-GCT-4072, n=6 mutant and n=6 edited replicates from Im-GCT-3504, and n=6 mutant and n=4 edited recpliates from Im-GCT-6176.

first: Sima

last: Khazaei

first: Nicolas

last: De Jay

first: Shriya

last: Deshmukh

middle: D

last: Hendrikse

middle: C

middle: G

middle: M

first: Siddhant

middle: U

first: Kateryna

first: Tianna

last: Sihota

first: Robert

last: Eveleigh

first: Véronique

last: Lisi

first: Ashot

middle: S

last: Harutyunyan

first: Sungmi

last: Jung

first: Jason

last: Karamchandani

first: Brendan

last: Dickson

middle: E

last: Turcotte

first: Jay

last: Wunder

first: Pierre

last: Thibault

first: Peter

last: Lewis

middle: A

last: Garcia

first: Stephen

last: Mack

first: Michael

last: Taylor

first: Livia

last: Garzia

first: Claudia

middle: L

last: Kleinman


title: Metabolic basis of metamorphic climax in the wood frog, Rana omeimontis

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of Biology

summary: In this study, we compared the metabolic networks in the liver and tail between pro-metamorphic and climax metamorphic (natural and T3-driven) Rana omeimontis tadpoles by a combination of metabolomics and transcriptomics.

overall_design: Comparative transcriptomics of the liver and tail between T3-driven metamorphic and DMSO-treated pro-metamorphic tadpoles

first: Chang

last: Liming

first: Zhu

last: Wei

first: Wang

last: Bin

first: Jiang

last: Jianping

first: Zhao

last: Tian

first: Zhang

last: Meihua

first: Shu

last: Guocheng

first: Liu

last: Jiongyu

last: Lusha

first: Xie

last: Feng

first: Li

last: cheng


title: Strain differences in responsiveness to chronic restraint stress affect remote contextual fear memory and blood transcriptomics

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

summary: Fear memory regulation is thought to be similar between humans and animals, and the role of stress in altering remote memory is little explored. Since individual variation in stress reactivity exists, should stress alter remote memory, invividuals with differing stress-reactivity would affect it to various degree. We evaluate this question using two strains of rats with differing stress-reactivity. The Fisher 344 (F344) strain is known to have active coping style and represent normal stress-reactivity, while the Wistar–Kyoto (WKY) rat shows passive coping strategies and heightened stress-reactivity.  Male animals were exposed contextual fear conditioning (CFC) and four weeks later, chronic restraint stress (CRS) or no stress (NS) was administered for two weeks. Remote memory, immediate stress response to a second CFC, and reinstated fear memory was measured. Both recent and reinstated fear memory were greater in F344s, regardless of the stress status, In contrast, remote memory was attenuated in F344 only, concurring with their increased immediate stress responsive behavior after CRS. To find if this strain-specific response to CRS can be mirrored by transcriptomic changes in the blood, RNA sequencing was carried out.  Overlapping differentially expressed genes (DEGs) between NS vs. CRS in the blood of F344 and WKY suggest a convergence of stress-related molecular mechanisms, independent of stress-reactivity. In contrast,  DEGs unique to the F344 and the WKY stress responses are divergent in their functionality and networks, beyond that of strain differences in their non-stressed state. These unique DEGs than could be implicated as biomarkers stress-reactivity.

overall_design: Taken together, these results suggest that in some individuals, chronic or prolonged stress can attenuate prior fear memory and blood markers for stress-reactivity can be identified, which may be associated with fear memory forgetting.

first: Jeanie

middle: K

last: Meckes

first: Seung

middle: H

last: Jung

first: Patrick

last: Lim

first: Katherine

last: Przybyl

first: Stephanie

last: Wert

first: Sophie

last: Jenz

first: Wendy

last: Luo

last: Gacek

first: Ryan

last: Jankord

first: Candice

last: Hatcher

first: Eva

last: Redei


title: Charting the prostate epigenomic landscape from transformation to progression

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: We generate histone modification and ATAC cistromes in primary prostate cancer human specimens

overall_design: ChIP-seq for H3K27Ac, H3K27me3 and ATAC-seq

last: Freedman

first: Mark

last: Pomerantz


title: ChIP-Seq of UNC-3 in C. elegans

first: Paschalis

last: Kratsios

department: Department of Neurobiology

institute: University of Chicago

summary: We performed ChIP-seq on endogenously tagged UNC-3::GFP fusion proteins in C. elegans

overall_design: Examination of the genome-wide binding profile of a transcription factor

first: Yinan

last: Li


title: Urothelial-to-Neural Lineage Plasticity Drives Progression to Small Cell Bladder Cancer

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

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

overall_design: Small cell carcinoma (SCC) of the bladder displays a high propensity for distant metastasis and is associated with short survival. We report a comprehensive molecular analysis of 34 cases of SCC and 84 cases of conventional urothelial carcinoma (UC)


title: Identification of TGF-b targets in the cardiac outflow tract by transcriptomic analysis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Purpose: identifying, with RNA-seq, genes targets of Alk5 during the development of the cardiac outflow tract in zebrafish.  Results: we identified several differential expressed genes, with an enrichment in ECM component genes. As a proof of concept, many TGFb known targets also appeared downregulated.

overall_design: Zebrafish embryos were treated with Alk5 inhibitor E-616452 (or DMSO) and hearts were manually extracted at 56 hpf.

first: Giulia

last: Boezio

last: Guenther


title: Urothelial-to-Neural Lineage Plasticity Drives Progression to Small Cell Bladder Cancer [miRNA]

summary: We report a comprehensive molecular analysis of 22 cases of SCC

overall_design: 22 cases of small cell carcinoma profiled using TaqMan® Array Human MicroRNA A Card v2.0 contains 384 TaqMan® MicroRNA Assays enabling accurate quantitation of 377 human microRNAs. The dataset was used to compare with 80 cases of conventional UCs in GSE128277

first: Guoliang

last: Yang

first: Jolanta

last: Bondaruk

first: Ziqiao

last: Wang

first: Sangkyou

last: Lee

first: June

first: Shizhen

last: Zhang

first: Woonyoung

last: Choi

first: Yan

first: Gang

first: Hui

last: Yao

first: Vipulkumar

last: Dadhania

first: Christopher

last: Logothetis

first: Arlene

last: Siefker-Radtke

first: Ashish

last: Kamat

first: Colin

last: Dinney

first: Dan

last: Theodorescu

first: Marek

last: Kimmel

first: Peng

last: Wei

first: Yu

last: Liang

first: Charles

last: Guo

first: John

middle: N

last: Weinstein

middle: J

last: McConkey

first: Bogdan

last: Czerniak


title: Targets of EOMES in mouse CD4+ T cells

city: Freiburg

first: Ekaterina

last: Lupar

address: Stuebeweg 51

department: Department of Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
To gain mechanistic insights into how EOMES regulates CD4+ T-cell differentiation and function, we performed an RNA-seq analysis using Eomes-GFP reporter mice (Eomes+/GFP) to isolate GFP+ (EOMES+) and GFP- (EOMES-) CD4+ T-cells by FACS sorting.
We also sequenced RNA from Eomes-deficient GFP+ and GFP- CD4+ T-cells isolated from EomesΔT/GFP knock-out mice, in which one Eomes allele is disrupted by GFP insertion and the DNA-binding domain of the other allele is deleted in T cells by Lck-driven Cre recombinase.
Hence, we had two populations of GFP+ cells where the EOMES locus was transcribed, one with a transcriptionally active EOMES protein (Eomes+/GFP) and another one with no transcriptionally active EOMES (EomesΔT/GFP), plus the respective GFP-negative controls isolated from the same mice.
A homogeneous population of EOMES-expressing CD4+ T cells were obtained by transferring naïve sorted CD25- CD45RBhigh CD4+ T-cells isolated from Eomes+/GFP reporter or EomesΔT/GFP knock-out donor animals into Rag2-/- mice.
After three weeks of adoptive transfer GFP+ and GFP- CD4+ T-cell populations from these mice were FACS-sorted for transcriptome analysis by RNA sequencing.

overall_design: Altogether we submit 12 samples, representing 4 biological conditions (Het_GFP_neg, Het_GFP_pos, KO_GFP_neg and KO_GFP_pos), 3 replicates each. The most relevant comparisons are (1): Het_GFP_pos vs Het_GFP_neg, which reveals the transcriptional signature of Eomes-expressing CD4 T cells, and (2): Het_GFP_pos vs KO_GFP_pos, which reveals Eomes-dependent genes. GFP positive and negative cells isolated from the same recipient have the same replicate number (e.g., Het replicate 1).

middle: I

first: Ana

last: Izcue


title: Single cell sequencing of dissected mouse mandibular prominence at embryonic day e11.5 and e13.5

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

overall_design: Mouse mandibular prominences were dissected at embryonic day 11.5 and 13.5. Tissue were dissociated into single cell suspension and used for single cell RNA library preparation and sequencing using 10X Genomics platform.

first: Kelsey

last: Elliott


title: Transcriptomic data of established human AT/RT cell lines BT-12.

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

summary:
The multi-subunit ATP-dependent chromatin remodeling complex BAF ('mammalian SWI/SNF complex') regulates DNA accessibility during cell fate transitions and functions as a context-dependent tumor suppressor. SMARCB1, as a one of the component of BAF complex, was first found to be biallelically inactivated in ~98% of all malignant rhabdoid tumors (MRT), aggressive pediatric tumors that can occur cranially or extracranially. To examine the mechanisms through which inactivation of SMARCB1 drives malignant rhabdoid tumorigenesis, we conducted RNAseq studies in BT-12 cells reconstituted with either WT or M4 mutant (an in-frame deletion (185-193D) was identified from tumor patient) SMARCB1. These results indicate that loss of SMARCB1 promotes cell proliferation but also impairs cell adhesion and migration, consistent with the hypothesis that SMARCB1 exerts its tumor suppressive function predominantly by inhibiting proliferation.

We applied the RNA-Seq to provide the transcriptomic profiling of BT-12 cell lines without or with stable expression of SMARCB1.

overall_design: RNA-Seq of BT-12 cell lines have 3 replicates each.

first: Hao

last: Zhou

first: Yan

last: Wang


title: bulk RNA-seq of wild-type, Gli2f/f;Gli3f/f;Wnt1-Cre, and Hand2f/f;Wnt1-Cre mouse e10.5 dissection mandibular prominences

overall_design: Mandibular prominence mRNA profiles of 10.5 wild-type, Gli2f/f;Gli3f/f;Wnt1-Cre, and Hand2f/f;Wnt1-Cre mice were generated by sequencing using Illumina NovaSeq S1 Flow Cell


title: A genome-wide approach to delineate novel MLL4 targets involved in skeletal muscle metabolism

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

summary:
This experiment was conducted to identify novel MLL4 targets in skeletal muscle
Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. Here, we identified the genome-wide MLL4 occupancy in mouse skeletal muscle by ChIP-seq coupled with RNA-seq analysis. Gene ontology analysis revealed that MLL4 controls muscle fiber-type switching. We thus have revealed novel MLL4 targets involved in muscle metabolism.

overall_design: Using genome-wide approach, ChIPseq,  to delineate novel MLL4 targets involved in skeletal muscle metabolism

first: Lin

last: Liu


title: Insights into food intake response in anadromous Coilia nasus through stomach transcriptome analysis

city: Wuxi

first: Fengjiao

last: Ma

state: CHINA

address: No.69 Xuejia, Xuelang Street, Binhu District

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary: To understand the molecular basis underlying the response to food intake, RNA sequencing was utilized to analyze the stomach transcriptome of C. nasus with feeding group (CSI) and non-feeding group (CSN).

overall_design: RNA sequencing was utilized to produce two transcriptomes of stomachs from CSI and CSN. A total of 610,640,864 high-quality clean reads were generated using Illumina sequencing technology and assembled into 63,567 unigenes, of which 20,608 were classified into GO enrichment and 12,303 were found in KEGG pathway. Comparative analysis of the gene expression between feeding and non-feeding fish identified 1,968 differentially expressed genes (P<0.05), including up-regulated 1180 genes and down-regulated 788 genes. Our result showed that apart from satiation was evoked by gastric distention, several of the most relevant appetite genes (such as LepR, PI3K, 5-HTR, NUCB2, SS) were involved in the suppression of food intake, resulting in the termination of feeding. Furthermore, dramatic differences were also observed in the genes encoding key enzymes involved in metabolic pathways such as protein digestion and absorption, TCA cycle pathways, fatty acid synthesis and glycolysis, indicating C. nasus can utilize carbohydrate and lipid of food to provide energy for their life activities and spawning migration. Real time qPCR confirmed the differential expression in selected genes.

first: Kai


title: Transcriptomic profiling of murine Nfe2l2 knockout melanoma cells

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

summary: The role of Nfe2l2 in established murine melanoma cells was studied by analyzing expression profiles of control and Nfe2l2 knockout melanoma cells, generated by CRISPR/Cas9.

overall_design: Gene expression analysis of murine melanoma cells with Nfe2l2 wildtype or Nfe2l2 knockout background (in vitro) and tumors derived from Nfe2l2 wildtype and knockout cells. Sequencing was done with triplicates (cell lines) or with three independent mouse tumors .

first: Christina

last: Jessen

first: Apoorva

last: Baluapuri

first: Svenja

last: Meierjohann


title: Gli3 and Hand2 ChIP-sequencing of developing face and mandibular prominence

summary: Gli3 and Hand2 ChIP-sequencing were done on E11.5 whole face or dissected mandibular prominences

overall_design: ChIP was performed with FLAG antibodies on either E10.5 whole face or E10.5 dissected mandibular prominences  of mice with endogenous FLAG tags in either the Gli3 or Hand2 locus. 1X75bp reads were generated on a NextSeq (Illumina) instrument.

first: Kevin

last: Peterson


title: Exon-activated functional rescue secures neuronal transcript signatures

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

summary: The production of alternative RNA variants contributes to the tissue-specific regulation of gene expression. In the animal nervous system, a shift towards more distal 3’ processing sites generates hundreds of substantially extended messenger RNAs. These neuronal transcript signatures are crucial for nervous system development and function. However, no clear understanding of the mechanism of systematic 3’ extension in neurons has yet been achieved. Here, we report that the highly conserved RNA-binding protein ELAV globally regulates all events of neuronal 3’ end processing by directly binding to the proximal 3’ end of its target RNAs. We uncover an endogenous strategy of functional gene rescue, by which neuronal RNA signatures are safeguarded in a loss-of-function context. When not directly repressed by ELAV, the transcript encoding the ELAV paralogue FNE acquires a mini‑exon, which equips the new FNE protein with the ability to translocate to the nucleus and rescue neuronal 3’ end processing. We propose that exon-activated functional rescue is a widespread mechanism that ensures robustness of processes that are regulated by a hierarchy, rather than by redundancy, of effectors.

overall_design: Analysis of alternative polyadenyation using RNA-seq and Clip-seq data

first: Judit

last: Carrasco


title: RNAseq analysis of skeletal muscle transcriptomes from wild type and MLL4SET-MKO mice

summary:
This experiment was conducted to identify mRNA transcripts alteration in skeletal muscle of MLL4SET muscle-specific knockout mice.
Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. Here, we identified the genome-wide MLL4 occupancy in mouse skeletal muscle by ChIP-seq coupled with RNA-seq analysis. Gene ontology analysis revealed that MLL4 controls muscle fiber-type switching. We thus have revealed novel MLL4 targets involved in muscle metabolism.

overall_design: Gastrocnemius muscle mRNA profiles of 8-week-old WT and MLL4SET-MKO mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.


title: Toll-like receptor 3 mediates calcific aortic valve disease via a conserved mechanism of calcification

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

summary: The molecular mechanisms underlying valvular immunaging are not well understood. Toll-like receptors (TLRs) are evolutionary conserved pattern recognition receptors at the interface between innate immunity and tissue repair. Here, we identify TLR3 as a central molecular regulator of calcification in cells exposed to mechanical strain. TLR3 is responsible for the phenotypic switch of valvular interstitial cells (VICs) to bone-forming cells in aortic valves and drives bone formation in vertebrates. Tlr3-/- mice exhibit an osteoporotic phenotype and are protected from CAVD. Moreover, we uncover biglycan (BGN), an extracellular matrix protein released upon mechanical tissue damage, as the first known endogenous TLR3-ligand and provide compelling evidence for receptor-ligand interaction. Our results reveal novel insights in the pathogenesis of CAVD and uncover TLR3 as a potential therapeutic target to prevent cardiovascular calcification and death.

overall_design: Gene expression profiling of human valvular interstitial cells, terated with by Poly (I:C) for 72h or 14d and human osteoblasts

first: Hubert

last: Hackl

first: Johannes

last: Holfeld


title: Copy-Number abberation profiles of glioma patient tissue samples and corresponding xenografted tumor samples as well as cell lines derived there-of

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

type: Genome variation profiling by genome tiling array

summary: Three sample types are available: Primary patient samples after surgery that were flash-frozen and after short-term culture and after subsequent xenotransplantation into Nude rats or Nod/Scid, NSG or Nude mice. As well as longterm cell cultures derived from the xenotransplanted human tumors. Patient samples end with _B, mouse xenotransplanted tumors with_X and cell lines with_C. The preceeding numbers always indicate the patient association, whereas the following number inidcates mouse generation (X), passage number(C) or number of surgical samples (B) taken.

overall_design: 69 Samples

first: Simone

last: Niclou

first: Nathalie

last: Nicot

first: Arnaud

last: Müller

first: Anna

last: Golebiewska

first: Daniel

last: Stieber


title: Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrüch Center

summary:
Glioblastoma is a lethal brain tumor which exhibits heterogeneity and
resistance to therapy. Our understanding of tumor homeostasis is limited by a lack of genetic tools to selectively identify tumor states and fate transitions. Here, we use glioblastoma subtype signatures to construct synthetic genetic tracing cassettes and investigate tumor heterogeneity at cellular and molecular level, in vitro and in vivo. Through synthetic locus control regions, we demonstrated that proneural glioblastoma is a hardwired identity, whereas the mesenchymal glioblastoma is an adaptive and metastable cell state driven by pro-inflammatory and differentiation cues and DNA damage, but not hypoxia. Importantly, we discovered that innate immune cells divert glioblastoma cells to a proneural-to-mesenchymal transition which confers therapeutic resistance. Our synthetic genetic tracing methodology is simple, scalable and widely applicable to study homeostasis in development and diseases. In glioblastoma, the method causally links distinct (micro)environmental, genetic and pharmacological perturbations and mesenchymal commitment.

overall_design:
ChIPseq data set: Genome-wide chromatin landscape of MES- and PN-hGICs-MGT#1in vitro and in vivo
RNAseq data set: Transcriptomic profiling of MES-hGICs-MGT#1 co-culture with human Microglia cells

first: G

first: C

last: Company

first: M

last: Schmitt

first: Y

last: Dramaretska

first: A

last: Göhrig

last: Großmann


title: Epigenome analysis of glioma patient surgical samples and corresponding xenotransplants and cell lines

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of glioma patient surgical samples and corresponding xenotransplants and cell lines. The Illumina Infinium 450k Human DNA methylation Beadchip and the Illumina EPIC Beadchip were used to obtain DNA methylation profiles. Samples include 22 patient surgical samples, 26 xenografted patient tumors, and 6 cell lines derived there-of.

overall_design: Bisulphite converted genomic DNA from 54 samples were hybridised to the Illumina Infium Human methylation Beadchip (8 to the 450k Beadchip and 46 to the EPIC Beadchip)

last: Golebewska


title: Transcriptional response of Pseudomonas aeruginosa PA3 to bacteriophage PaP3 infection

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

institute: Third Military Medical University

summary: Explore the genome-scale phage–host interactions across different developmental infection stages

overall_design: Samples were taken from the PA3 infected with phage PaP3 at six internal time (0,5,10,20,30,80 min). Three independent experiments were performed


title: Distinct 3D Genome Organization in the Two Nuclei of Tetrahymena thermophila

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: Somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila are different in chromosome numbers, sizes, functions and cohesin complex locations. Loss of cohesin complex resulted in genome-wide disappearance of topologically associating domains (TADs) and chromatin loops in mammalian cells. However, the higher-level chromatin organization in Tetrahymena thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, using the Hi-C and HiChIP methods, we reveal that, these two nuclei possess distinct three-dimensional genome structures. In the MAC, each chromosome occupies its own territory and there are no chromatin compartmentalization or chromatin domains. The chromatin loops in MAC are mainly related to chromatin structures rather than transcriptional regulation. The MIC also without chromatin compartmentalization, but with chromatin domains and the domain boundaries are consistent with chromatin breakage sites (CBSs) which indicates that each MIC chromatin domain developed to one MAC chromosome during conjugation. Besides, we found the MIC exhibits unique intra-arm and inter-chromosome interactions at the crescent stage of conjugation, when the MIC undergoes meiotic recombination.

overall_design: Hi-C seq are generated from 1.5, 3, 24 hour post-mixing (hpm) Tetrahymena thermophila cells (B2086 and Cu428): whole Cells, isolated macronuclei and isolated micronuclei. HiChIP-seq are generated from 1.5, 3, 24 hpm Tetrahymena thermophila cells (B2086 with Smc1-HA and Cu428 with Rec8-GFP)

first: Zhengyu

last: Luo

first: Tengfei

last: Hu

first: Xiaoyuan

last: Song


title: Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

overall_design: 4C-seq was performed on HCT116 and SW480  colorectal cancer cells

first: Jie

last: Hong


title: ZFP90 promotes colorectal carcinogenesis and stemness [RNA-seq]

summary: To elucidate whether  ZFP90 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  ZFP90-KO and control Control cell.

overall_design: RNA-seq was performed in HCT116  colorectal cancer cells after ZFP90 knockout


title: ZFP90 promotes colorectal carcinogenesis and stemness [ChIP-seq]

summary: Chip-seq analysis was performed to elucidate whether  ZFP90 plays a role in  colorectal cancer tumorigenesis

overall_design: Chip-seq was performed on HCT116  colorectal cancer cells


title: ZFP90 promotes colorectal carcinogenesis and stemness

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

overall_design: Refer to individual Series


title: Effects of the Co-Administration of MK-801 and Clozapine on MiRNA Expression Profiles in Rats

city: Guangzhou

first: hui

middle: Wen

last: Huang

address: Huang pu da dao West 601

institute: Jinan University

summary:
Background: microRNAs (miRNAs) are small, non-coding RNAs, which can silence the expression of various target genes via binding their mRNAs, thus miRNAs serve and regulate a wide range of crucial functions in the body. However, the miRNAs expression profile after the antipsychotics mediation in schizophrenia is largely unknown.
Methods: Noncompetitive N-methyl-D-aspartic acid (NMDA) receptor antagonists like as MK-801 had been shown to provide a useful animal model to investigate these effects of schizophrenia-like symptoms in rodent animals. In this study, the rat hippocampal miRNA expression profiles were examined after the antipsychotic clozapine (CLO) treated the MK-801-pretreated Sprague Dawley rats. The total RNA samples from their hippocampus of three rat groups were sequenced using next generation sequencing (NGS), then processed bioinformatic analysis.
Results: Successfully, we identified 8 miRNAs’ expressions were significantly different in the MK-801 group comparing the VEH control group. Interestingly, 14 miRNAs were largely changed expression in CLO+MK-80-treated group comparing the MK-801-pretreated group, in which the rno-miR-184 was up-regulated significantly. Subsequently, further analyses suggested these miRNAs could modulate their target genes involving in the regulation of endocytosis, ubiquitin mediated proteolysis and regulation of actin cytoskeleton, which might be involved in the important mechanism of schizophrenia.
Conclusion: Our results suggested the altered miRNA expressions might play an important role in the complex pathophysiology of schizophrenia, and subsequently impacted on brain functions.

overall_design: In our study, we aimed to: 1) compare miRNA expression profiles between MK-801 and VEH control groups and identify differentially expressed miRNAs in two groups, and 2) investigate the effect of one atypical antipsychotic drug (CLO) on hippocampal miRNA expression after CLO treated plus MK-801 with rats. We hypothesize that some miRNAs will be differentially expressed in schizophrenia rats, which will be linked with schizophrenic symptoms.

first: Wen-Hui

first: Xue-Feng

last: Gu

first: Yu-Han

last: Bi

first: Wei

first: Mei-Ling

first: Yu

last: Yang

first: Guo-Qing

last: Wan

first: Nian-Hong

first: Ke-Shen

last: Li


title: Using a xenograft model and RNA-seq to differentiate between the tumour and tumour microenvironment transcriptome

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary: In addition to the tumour cells, breast tumours contain other cell types such as fibroblasts, adipocytes, inflammatory and immune cells. Together with the extracellular matrix, these non-tumour cells compose the tumour microenvironment (TME). Complex interactions occur between tumour cells and the TME that can inhibit or stimulate tumour cell growth, metastasis and/or chemoresistance.  While treatment of tumours with chemotherapeutic agents such as Abraxane, leads to apoptosis of tumour cells, it can also have consequences for the cellular makeup and transcriptional profile of the TME and these, like the increased infiltration of macrophages, may have detrimental effects. Transcriptome profiling of whole tumours from mice injected with tumour cell lines and treated with combinations of chemotherapeutic drugs has provided novel insights into pathways affected by different agents and diagnostic signatures. However, differences in the cellular composition of tumours from treated mice can have confounding effects and increase variation in whole tumour transcriptomes. To be able to examine the effects of co-treatment of Abraxane with another drug, we performed RNA-seq on tumours from mice injected with the human breast cancer cell line MDA-MB-231. We then separated reads mapped to the human and mouse genomes in silico, creating tumour and TME transcriptomes for control, Abraxane, drug and combination treated mice.  Separation of the tumour and TME profiles revealed that while in the tumour cells, co-addition of the drug potentiated Abraxane’s inhibitory effect on cell cycle genes and promotional effect on antigen presentation genes, in the TME it inhibited genes involved in the inflammation and migration responses and promoted genes involved in lipid and xenobiotic metabolism.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 4 mice per treatment. 4 treatments. Paired end RNA-seq

first: Abel

last: Tan

first: Tara

last: Boulding

first: Sudha

last: Rao


title: Epigenetic patterns with aging and exercise are associated with indicators of healthspan in humans

city: Boulder

first: Christopher

middle: R

last: Martens

state: CO

address: 354 UCB

department: Integrative Physiology

institute: University of Colorado Boulder

summary: Genome wise DNA methylation profiling of peripheral blood mononuclear cells (PBMCs) obtained from younger sedentary (Y-SED), older sedentary (O-SED) and older aerobically exercise trained (O-Ex) human subjects.  The Illumina 450K methylation beadchip array was used to obtain DNA methylation profiles across approximately 450,000 CpG dinucleotide methylation loci in DNA isolated from PBMCs.  Samples include 12 Y-SED subjects, 15 O-SED subjects and 11 O-Ex subjects.

overall_design: DNA methylation was assessed in peripheral blood mononuclear cells (PBMCs) of 12 young-sedentary (Y-SED), 15 older-sedentary (O-SED) and 11 older exercise trained (O-Ex) individuals using the Illumina HumanMethylation 450K array.

first: Kara

last: Lubieniecki

first: Molly

last: McNamara

first: Adam

middle: D

last: Bohr

first: Matthew

middle: B

last: McQueen

first: Douglas

last: Seals


title: Transcription analysis of different water use efficiency genotypes in soybean leaf

status: Public on Sep 30 2020

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: mRNA sequencing of leaf in the flowering stage was performed to reveals gene regulation in relation to water use efficiency in  soybean

overall_design: mRNA profiles of leaf of different water use efficiency genotypes were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript .

first: Yan

last: Jiang


title: Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response [methylation]

city: Los Angeles

first: Anil

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

institute: University of California, Los Angeles

summary: in vitro genomic analyses of clozapine response. Genome wide DNA methylation profiling was performed across several experimental conditions of clozapine exposure. LCLs were exposed to different concentrations of clozapine (vehicle (DMSO), 1x, 20x, 40x and 60 times clinical concentration) and exposure times were 24h and 96h.

overall_design: Genomic DNA was extracted from LCLs and bisulphite converted and subsequently hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Sera

last: de With

middle: P

first: Roel

last: Ophoff


title: Transcriptome analysis of programmed cell death during allorecognition in Cryphonectria parasitica

city: Ottawa

first: Myron

last: Smith

state: Ontario

address: 1125 Colonel By drive

department: Biology

institute: Carleton University

summary: The underlying molecular mechanisms of programmed cell death (PCD) associated with fungal allorecognition, a form of innate immunity, remain largely unknown. In this study, transcriptome analysis was used to infer mechanisms activated during barrage formation in vic3-incompatible strains of C. parasitica, the chestnut blight fungus. Pronounced differential expression occurred in barraging strains of genes involved in mating pheromone (mf2-1, mf2-2), secondary metabolite production, detoxification (including oxidative stress), apoptosis-related, RNA interference and HET-domain genes. Evidence for secondary metabolite production and reactive oxygen species (ROS) accumulation is supported through UPLC-HRMS analysis and cytological staining, respectively. Differential expression of mating-related genes and HET-domain genes was further examined by RT-qPCR of incompatible interactions involving each of the 6 vegetative incompatibility (vic) loci in C. parasitica and revealed distinct recognition process networks. We infer that vegetative incompatibility in C. parasitica activates defence reactions that involve secondary metabolism, resulting in increased toxicity of the extra- and intracellular environment. Accumulation of ROS (and other potential toxins) may result in detoxification failure and activation of apoptosis, sporulation, and the expression of associated pheromone genes. The incompatible reaction leaves abundant traces of a process-specific metabolome as conidiation is initiated.

overall_design: Identification of genes involved in allorecognition in C. parasitica. Total 15 samples: 5 samples with 3 replicas. Controls: 3 monoculture strains (P74-3, EP155, DZ-66), 1 mix strain sample (P74-3+DZ-66). Experiment: 1 mix strain sample (P74-3+P155).

first: Anatoly

last: Belov

first: Tom

last: Witte

first: David

last: Overy


title: Low read depth whole genome sequencing of mouse Cre-loxP-induced Ewsr1-Atf1 translocation tumors

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

summary: Mice formed tumors either after an Hprt-Cre-initiated translocation between Ewsr1 and Atf1 genes on chromosomes 11 and 15. From tumor genomic DNA, libraries were generated and sequenced on an Ilumina NovaSeq instrument to measure copy number variation.

overall_design: low read depth whole genome sequencing of mouse Cre-loxP-induced Ewsr1-Atf1 translocation tumors for copy number analysis

first: Kevin

last: Jones


title: The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice

city: New York

first: Marc-Werner

last: Dobenecker

state: New York

address: 1230 York Ave, Box 301

institute: The Rockefeller University

summary: Humoral immunity in mammals  relies on the function of two developmentally and functionally distinct B cell subsets - B1 and B2 cells. While B2 cells are responsible for the adaptive response to environmental antigens, B1 cells regulate the production of polyreactive and low affinity antibodies for innate humoral immunity. The molecular mechanism of B cell specification into different subsets is understudied. We identified lysine methyltransferase NSD2 (MMSET/WHSC1) as a critical regulator of B1 cell development. In contrast to its minor impact on B2 cells, deletion of the catalytic domain of NSD2 in primary B cells impairs the generation of B1 lineage. Thus, NSD2, a histone H3 K36 dimethylase, is the first-in-class epigenetic regulator of a B cell lineage in mice.

overall_design: Examination of RNAseq and H3K36me2 in resting splenic B cells from Nsd2loxSET/ loxSET  and VAVcre Nsd2loxSET/ loxSET  or Mb1Cre Nsd2loxSET/ loxSET  mice

first: Jonas

last: Marcello

first: Vyacheslav

last: Yurchenko

first: Alexander

last: Tarakhovsky


title: Effects on imidazoacridinone C-1311 on the transcriptomic profile in prostate cancer cell depending on their AR status.

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

summary: Human prostate cancer cells, LNCaP (AR+) and DU-145 (AR-), were treated with C-1311 to identify the transcriptomic profile and functionally relevant androgen-dependent and independent genes using RNA sequencing.

overall_design: We examined the anti-prostate cancer properties of imidazoacridinone, C-1311. Using RNAseq we showed for the first time that C-1311 is a promising agent that targets the androgen receptor pathway by blocking AR transcriptional activity and has potent efficacy towards prostate cancer cells.

first: Anna

last: Skwarska


title: Cre-loxP-induced Ewsr1-Atf1 translocation tumors


title: Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Adult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positional Hox codes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.

overall_design: RNA-seq and WGBS-seq of EOM and TA muscle satellite cells before and after grafting

first: Brendan

last: Evano

first: Diljeet

last: Gill

first: Irene

last: Hernando-Herraez

first: Glenda

last: Comai

first: Thomas

middle: M

last: Stubbs

first: Pierre-Henri

last: Commere

first: Wolf

last: Reik

first: Shahragim

last: Tajbakhsh


title: Next generation RNA-sequencing of YAP and TAZ knockdowns in mel537 melanoma cells

city: Chicago

first: Yan

last: Li

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) data sets between siScrambled negative control groups and YAP, TAZ, or YAP/TAZ knockdown groups

overall_design: siRNA mediated knockdowns of YAP, TAZ, and YAP/TAZ were performed on mel537 melanoma cell. RNA was collected 2 days post transfection and sequenced, in duplicate, and sequenced with Illumina HiSeq4000 to study the transcriptome profiles difference between different KD genotypes on mel537 melanoma cells.

first: Jason

last: Lui

first: Deborah

last: Lang


title: Human iPSC-derived organoids recapitulate development of the cerebellum.

city: Oxford

first: Samuel

middle: Patrick

last: Nayler

address: Sherrington Building, Parks rd

department: Physiology Anatomy and Genetics

institute: Oxford University

summary: Single-cell profiling of stem cell-derived cerebellar organoids revealed transcriptionally-discrete populations encompassing the major cerebellar neuronal cell types including granule cells, roof plate, choroid plexus, Bergmann glia, Purkinje cells and glutamatergic deep cerebellar nuclei. Cellular identity and maturity were confirmed through comparison to an atlas of developing murine cerebellar cell types.

overall_design: Six organoids, individually hash-tagged split into two hash pools. Hash pool 1 comprises 3 organoids condition A (Matrigel-encapsualted). Hash pool 2 comprises 3 organoids condition B (unencapsulated controls). Each individual biological sample (organoid) is labelled with a distinct Antibody conjugatedHash tag oligonucleotide (HTO) - information in features.csv.

first: Devika

last: Agarwal

first: Fabiola

last: Curion

first: Rory

last: Bowden

first: Esther

last: Becker


title: Gene expression profiles in cows subjected to different stress level as assessed by cortisol in milk

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

summary: To assess how different levels of stress exposure affect gene regulation mechanisms in cattle, we investigated gene expression in 13 Italian Red Pied dairy cows falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine biomarker of stress in dairy cows, measured in 126 animals belonging to the same farm in the framework of the Gen2Phen Italian project. The ‘low-’ and ‘high-cortisol’ groups of animals had MC<370 pg/ml and>810 pg/ml, respectively. To date, 13 animals (6 low- and 7 high-MC) have been sequenced. We detected significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) pathway analyses indicated that these genes were mainly involved in immune regulatory pathways, glucocorticoids metabolism and nervous system functions.

overall_design: Cows were ranked on the basis of cortisol in the milk and the 10 cows with the higher and the 10 cows with the lower concentrations were selected for transcriptome analysis.

first: Silvia

last: Bongiorni

first: Bruno

last: Stefanon

first: Sandy

last: Sgorlon

first: Alessio

last: Valentini

first: Paolo

last: Ajmone Marsan

first: Giovanni

last: Chillemi


title: Next-generation sequencing reveals size-dependent pulmonary impact of thin graphene oxide sheets in mice: towards safe-by-design

city: Stockholm

first: Sourav

middle: Prasanna

last: Mukherjee

address: IMM, Karolinska Institutet

country: Sweden

institute: KI

summary: Safety assessment of graphene-based materials (GBMs) including graphene oxide (GO) is essential for their safe use across many sectors of society. In particular, the link between specific material properties and biological effects needs to be further elucidated. Here we compared the effects of lateral dimensions of GO sheets in acute and chronic pulmonary responses after single intranasal instillation in mice. Micrometre-sized GO (1–30 μm) induced stronger pulmonary inflammation than nanometre-sized GO, despite a reduced translocation to the lungs. Genome-wide RNA sequencing also revealed distinct size dependent effects of GO, in agreement with the histopathological results. Although large GO, but not the smallest GO (10–300 nm), triggered the formation of granulomas that persisted up to 90 days, no pulmonary fibrosis was observed. These results could be partly explained by the pattern of size-independent in situ biotransformation of GO, as evidenced by Raman spectroscopy imaging. Our findings demonstrate that lateral dimensions play a fundamental role in the pulmonary response to GO, and suggest that airborne exposure to micrometer sized GO should be avoided in production plant or applications, such as spray coating or painting, where aerosolised dispersions are likely to occur. These results are important for the development of evidence-based risk assessment, and provide information towards the implementation of a safer-by-design approach for GBM enhanced products and applications, for the benefit of workers and end-users.

overall_design: The aim of the present study was to investigate whether lateral dimensions play a significant role in the pulmonary response to GO at short- and long-term after single exposure in mice. Considering the literature, we hypothesised that micrometre-sized GO sheets would induce a more deleterious pulmonary response than nanometre-sized GO after single intranasal (i.n.) instillation (50 μg/mouse). Six to 8-week old female C57BL/6 mice (Envigo, UK) were allowed to acclimatise for 7 days prior to any experiment. Experiments were carried out using 4-5 animals per group. All GO materials were dispersed in an aqueous solution of 5% (m/v) dextrose in ultrapure water (5% dextrose), at a concentration of 1 mg/mL, about 30 min before administration. MWCNTs were dispersed at the same concentration in an aqueous solution of 0.9% (m/v) sodium chloride supplemented with 0.5% (m/v) bovine serum albumin (BSA), followed by bath sonication for 10 min at 80 W (VWR, UK). Animals were anesthesised by inhalation of 2.5% isoflurane in 100% oxygen flowing at 2 L/min. Mice in experimental groups were instilled with 50 μL of the respective nanomaterial dispersions (i.e., 50 μg/mouse), which were equally distributed in each nostril. The same volume of 5% dextrose solution was given to the control group. During administration, the animals were held in a supine position, tilted to about 60°, in order to effectively introduce the full dose. Mice were observed until full recovery, which occurred within 5 min after instillation. Mice were sacrificed at days 1, 7, or 28 days after exposure by overdose via intraperitoneal injection of 2 mL pentobarbitone. At all considered time points, the lungs were carefully dissected from the large airways and small portions of each lobe were extracted for RNA extraction. Tissue samples were placed in RNAlater (Invitrogen, Thermo Fisher Scientific, UK), and placed immediately on ice. Samples in RNAlater solution were homogenised using a TissueLyser LT (QIAGEN, UK). Homogenised samples were then loaded onto spin cartridges containing silica membranes, for extraction of total RNA performed using a PureLink RNA Mini kit (Invitrogen, Thermo Fisher Scientific, UK) according to the manufacturer’s instructions. Total RNA concentration and purity were calculated by measuring the optical density at 230, 260 and 280 nm, using a Biophotometer Plus spectrophotometer (Eppendorf AG, Germany). RNA quantity and RNA integrity number (RIN) were assessed by Agilent 2200 bioanalyzer. Sample RNA with RIN values below 8 was discarded. The isolated RNA samples were stored at -80°C until RNA sequencing was carried out using HiSeq2500 sequencer.

first: Bengt

last: Fadeel

first: Cyrill

last: Bussy

first: Kostas

last: Kostarelos

first: Jun

last: Wang


title: Genome-wide DNA methylation in cows subjected to different stress level as assessed by cortisol in milk

summary: To assess how different levels of stress exposure affect epigenetic regulation mechanisms in cattle, we investigated genome-wide DNA methylation in 20 Italian Red Pied dairy cows falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine biomarker of stress in dairy cows, measured in 126 animals belonging to the same farm in the framework of the Gen2Phen Italian project. The ‘low-’ and ‘high-cortisol’ groups of animals had MC<370 pg/ml and>810 pg/ml, respectively. Their methylome was analysed by Reduced Representation Bisulfite Sequencing, which provides single-base resolution methylation profiles across the whole genome. To date, 20 animals (10 low- and 10 high-MC) have been sequenced. The two groups showed similar proportion of methylation at CpG sites, while they differed at non-CpG sites. Significant methylation changes were observed in 897 regions and 248 genes. KEGG and Gene Ontology (GO) pathway analyses indicated that these genes were mainly involved in immune regulatory pathways, glucocorticoids metabolism and nervous system functions.  These preliminary results suggest that cortisol secretion in livestock is mediated by epigenetic regulation, provide target biomarkers to assess the effect of stress management procedures and candidate genes for the selection of stress-tolerant animals.

overall_design: Cows were ranked on the basis of cortisol in the milk and the 10 cows with the higher and the 10 cows with the lower concentrations were selected for epigenome analysis


title: Benchmarking single-cell RNA sequencing methods for the Human Cell Atlas

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

summary: This cryopreserved HCA reference sample represents the basis for a systematic comparison of scRNAseq techniques.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: The sample consists of two complex tissues (human PBMC and mouse colon, 80% of the sample content) and three cell lines (10% HEK293-RFP, 10% NIH3T3-GFP, <1% MDCK-Turbo650). The sample preparation aims to be standardized for all methods to allow a comparison of library preparation performance of the sample content.

first: Holger

last: Heyn

last: Rodríguez-Esteban


title: Efficient development of platform cell lines using CRISPR-Cas9 and transcriptomics analysis

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

summary: Antibody-drug conjugates offers many advantages as a drug delivery platform that allows for highly specific targeting of cell types and genes. Ideally, testing the efficacy of these systems requires two cell types to be different only in the gene targeted by the drug, with the rest of the cellular machinery unchanged, in order to minimize other potential differences from obscuring the effects of the drug. In this study, we created multiple variants of U87MG cells with targeted mutation in the TP53 gene using the CRISPR-Cas9 system, and determined that their major transcriptional differences stem from the loss of p53 function. Using the transcriptome data, we predicted which mutant clones would have less divergent phenotypes from the wild type and thereby serve as the best candidates to be used as drug delivery testing platforms. Further in vitro and in vivo assays of cell morphology, proliferation rate and antibody-mediated uptake supported our predictions. Based on the combined analysis results, we successfully selected two best qualifying mutant clones. This study serves as proof-of-principle of the approach and paves the way for extending to additional cell types and target genes.

overall_design: Targeted TP53 knockout of U87MG cells was performed using CRISPR-Cas9 gene editing. 7 clones with mutated TP53 were selected for transcriptomics analysis based on CAGE technology. CAGE libraries of the mutant clones and the wild type were constructed (nAnT-iCAGE protocol) and sequenced on illumina HiSeq 2500 (50 nt single read). Each sample was prepared and sequenced in 3 replicates.

last: Tae-Jun Kwon

first: Satoshi

last: Takizawa

first: Takahiro

last: Arakawa

first: Erik

last: Arner


title: Expression profile of miRNAs from Bovine subjected to heats stress

city: Fort Collins

first: Samuel

middle: Gebremedhn

last: Etay

address: 1683 Campus Delivery

department: Biomedical Sciences

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Analysis of conditioned medium cytokine levels of pancreatic cancer cells after JAG1 RNAi

city: Shanghai

first: Peng

address: 270 Dong An Road

department: Department of Integrative Oncology

institute: Fudan University Shanghai Cancer Center

summary: To identify cytokines secreted by pancreatic cancer cells, we compared the cytokine profiles of conditioned medium from pancreatic cancer cell Su.86.86 treated with or without JAG1 siRNA, using a Human Antibody Arrays 507 (L-507, Raybiotech)

overall_design: Two samples. Su.86.68 cells were transfected with either control or siJAG1 and conditoned medium were harvested. The cytokines level were evaluated using Human Antibody Arrays


title: Expression profile of miRNAs in Extracellular vesicles (EVs) obtained from Bovine granulosa cells subjected to heats stress

summary: The study aimed to uncover the release of miRNAs via EVs and the differential release of these miRNAs from bovine granulosa cells  in response to heat stress

overall_design: We used ovarian follicle samples obtained from local slaughterhouse. Granulosa cells were aspirated from small growing follicles (3-6 mm in diameter) and cultured for 24 hours in DMEM-F12 media + 10% Exosome-depleted FBS at 37OC. Following this, the one group of the cells were subjected to 42OC for 24 hours and the control group were left at 37OC.   The spent culture medi was collected from all experimental groups. Following that, samples were centrifuged at 25000 xg for 30 minutes at 4OC to remove microvesicles. The purified cell culture medium was subjected to EVs isolation. For large scale miRNA profiling, 5ml of purified spent culture media was added with 1 ml of ExoQuick-TC (SBI System Biosciences, Inc.) and mixed very well and incubated over night at 4OC. Samples were centrifuged at 1500 xg to obtain the EVs pellet. After washing the pellet with PBS, EVs were resuspended in 500 µl PBS in -80OC until further use. Total RNA enriched with miRNAs from a total of 6 samples (three biological replicates from each treatment) were used for miRNA deep sequencing anaysis.

last: Gebremedhn

first: Ahmed

last: Gad

first: Hoda

middle: S

last: Aglan

first: Jozef

last: Laurincik

first: Radek

last: Prochazka

first: Michael

last: Hoelker

first: Dessie

last: Salilew-Wondim

first: Karl

last: Schellander

first: Dawit

last: Tesfaye


title: Expression profile of miRNAs in Bovine granulosa cells subjected to heats stress

summary: The study aimed to uncover differential expression pattern of microRNAs in bovine granulosa cells  subjected to heat stress

overall_design: We used ovarian follicle samples obtained from local slaughterhouse. Granulosa cells were aspirated from small growing follicles (3-6 mm in diameter) and cultured for 24 hours in DMEM-F12 media + 10% Exosome-depleted FBS at 37OC. Following this, the one group of the cells were subjected to 42OC for 24 hours and the control group were left at 37OC.   Cells were harvested 24 hours post-treatment and subjected to microRNA enriched total RNA isolation and used for miRNAs deep sequencing. A total of 6 samples (three biological replicates from each treatment) were used for miRNA deep sequencing anaysis.


title: Differential regulation of transcription in Beta-estrodial treated Osteoblasts

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

summary: We preformed RNA-seq analysis on  untreated ST2 cells and ST2 cells treated with 17ß-estradiol and the Selective Estrogen Receptor Modulators raloxifene and lasofoxifene.

overall_design: Analysis of gene expresssion between treated and untreated ST2 cells.

first: Dustin

last: Schones

first: Baruch

last: Frenkel


title: Role of rice AGO17 in rice development

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

summary: Artificial miRNA mediated knock-down ago17 transgenic lines showed developmentally compromised phenotype in both vegetative and reproductive tissues compared to wild-type control, whereas the overexpression of AGO17 enhanced plant growth and yield. We have performed small RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO17 in rice.

overall_design: We have performed small RNA-seq analysis using mature panicles (Stage 12) of WT, over-expression and knock-down transgenic lines of AGO17. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

middle: V

last: Shivaprasad

first: Chenna

last: Swetha


title: Effect of HIFU on Murine Neuroblastoma Tumors

city: Washington

first: Avinash

last: Eranki

state: DC

address: 111 Michigan Avenue, NW, 6th Floor - SZI

institute: Children's National Medical Center

summary:
This study assess the role of HIFU on genetic change intratumorally post-treatment
Immunotherapy promises unprecedented benefits to cancer patients. However, the majority of cancer types, including high-risk neuroblastoma remain immunologically unresponsive. High intensity focused ultrasound (HIFU) is a non-invasive technique that can mechanically fractionate tumors, transforming immunologically ‘‘cold’’ tumors into responsive ‘‘hot’’ tumors. We treated tumors with HIFU, and assessed systemic immune response using flow-cytometry, ELISA, and gene sequencing. In addition, we combined this treatment with αCTLA-4 and αPD-L1 to study its effect on the immune response and long-term survival. Combining HIFU with αCTLA-4 and αPD-L1 significantly enhances anti-tumor response, improving survival from 0 to 62.5%. HIFU alone causes upregulation of splenic and lymph node NK cells and circulating IL-2, IFN-Ɣ, and DAMPs, whereas immune regulators like CD4+Foxp3+, IL-10, and VEGF-A are significantly reduced. We also report significant abscopal effect following unilateral treatment of mice with large, established bilateral tumors using HIFU and checkpoint inhibitors compared to tumors treated with HIFU or checkpoint inhibitors alone (61.1% survival, p<0.0001). HIFU can effectively induce immune sensitization in a previously unresponsive murine neuroblastoma model, and promises a novel yet efficacious immuno-adjuvant modality to overcome therapeutic resistance.

overall_design: We used microarrays to help assess the role of HIFU-mechanical fracitonation on neuroblastoma tumors. mRNA was analyzed on Affymetrix Mouse Clariom S arrays using standard reagents and following the Affymetrix protocol (Thermofisher Scientific, Waltham, MA).  Poly A controls were spiked into the reactions. Briefly, RNA was converted to cDNA, which was then in vitro transcribed into cRNA that was bead purified. Fifteen µg of purified cRNA was converted into ss-cDNA, which was then fragmented, cleaned, and hybridized (2.3 µg) for 16 hr (45°C) to the arrays.  Hybridization solution was removed and arrays were washed and stained on an Affymetrix Fluidics 450 station and scanned with the Affymetrix GeneChip scanner.

first: Eranki

last: Avinash


title: Gene expression in breast cancer cell with shYTHDF3 [mouse]

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary:
Knocking down YTHDF3 in breast cancer cells resulted in an altered gene expression profile
N6-methyl-adenosine (m6A) is the most prevalent internal chemical modification in eukaryotic messenger RNAs and emerging as a critical mRNA chemical mark that mediates post-transcriptional gene expression regulation. YTHDF3 facilitates translation and decay of m6A-modified mRNAs. However, the role for YTHDF3 protein in breast cancer brain metastasis remain to be elucidated. We found that YTHDF3 is overexpressed in brain metastasis of breast cancer cells. Our study will characterize the expression profiling in YTHDF3 silencing breast cancer cells compared to shControl breast cancers cells. The objectives are to identify expression profiles that are specific to shYTHDF3 breast cancer cell to identify new the signaling pathway of YTHDF3 for brain metastasis of breast cancer cells.

overall_design: 4T1Br cells were transduced with shControl and shYTHDF3 lentivirus and selected by puromycin. The RNAs of tumor cells were extracted and hybridized, and then the gene expression analysis was performed with Affymetrix microarrays.

first: Suyun

last: Huang

first: Guoqiang

last: Chang


title: Gene expression in breast cancer cell with shYTHDF3

overall_design: MDA-MB231Br cells were transduced with shControl and shYTHDF3 lentivirus and selected by puromycin. The RNAs of tumor cells were extracted and hybridized, and then the gene expression analysis was performed with Affymetrix microarrays.


title: Arabidopsis seedlings: wild-type vs. gcn20

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

summary: transcriptional profiling of Arabidopsis seedlings comparing wildtype Col7 with gcn20 mutant

overall_design: two-condition experiment, Col7 vs. gcn20


title: Cold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

summary: Cooling patients to sub-physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature-specific changes to the higher-order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18°C, a temperature synonymous with that experienced by patients undergoing controlled deep-hypothermia during surgery. Cells exposed to 18°C exhibit largely nuclear-restricted transcriptome changes. These include the nuclear accumulation of transcripts of genes of the negative limbs of the core circadian clock, most notably REV-ERBα. This response is accompanied by compaction of higher-order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of negative limb gene proteins that resets the circadian clock. We show that cold-induced upregulation of REV-ERBα is sufficient to trigger this resetting. Our findings uncover principles of the cellular cold-response that must be considered for current and future applications involving therapeutic deep-hypothermia.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: RNA was extracted from nuclear and cytoplasmic subcellular fractions after exposing two different cell lines (AC16 and U2OS cells) to different temperature conditions. For Drosophila melanogaster spiked-in samples, RNA was also extracted from nuclear and cytoplasmic fractions of AC16 cells exposed to different temperature conditions spiked-in with a known ratio of Drosophila melanogaster Schneider 2 cells prior to fractionation. The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit for Ion Torrent (Lexogen). Libraries for full-length RNA-seq were prepared using the Ion Total RNA-seq Kit v2 (ThermoFisher). For this full-length RNA-seq polyadenylated RNAs were first purified from total RNA from each fraction using the NEBNext Poly(A) mRNA Isolation Module. Libraries were loaded onto the Ion Chef System (ThermoFisher) for template preparation and chip loading and the resulting chips were sequenced on the Ion Proton Sequencing System (ThermoFisher). Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19 or to a combined hg19 dm6 genome build for Drosophila melanogaster spiked in samples.

first: Andre

last: Furger


title: YTHDF3 Induces the Translation of m6A-enriched Metastasis-associated Gene Transcripts to Promote Breast Cancer Brain Metastasis [RIP-Seq]

summary: Brain metastasis is a major cause of cancer mortality, but its molecular mechanisms are severely understudied. We found that YTHDF3 overexpression clinically correlates with brain metastases in breast cancer patients and is required for brain metastasis. Silencing YTHDF3 suppressed the brain metastasis of breast cancer cells in vitro and in vivo. Integrated transcriptome and m6A-seq analysis revealed alter expression of selected YTHDF3 target genes, including ST6GALNAC5, GJA1, and EGFR by promoting m6A-dependent translation of these target transcripts. Our work uncovers an essential role of YTHDF3 in controlling the interaction between cancer cells and brain microenvironment, thereby gaining brain metastatic competence.

overall_design: Overall design: anti-YTHDF3 of mRNA from MDA-MB-231Br cells


title: genesorteR: Feature Ranking in Clustered Single Cell Data

city: Aachen

first: Mahmoud

last: Ibrahim

address: Pauwelsstraße 30

department: Faculty of Medicine

institute: RWTH Aachen University

summary: Marker genes identified in single cell experiments are expected to be highly specific to a certain cell type and highly expressed in that cell type. Detecting a gene by differential expression analysis does not necessarily satisfy those two conditions and is typically computationally expensive for large cell numbers. Here we present genesorteR, an R package that ranks features in single cell data in a manner consistent with the expected definition of marker genes in experimental biology research. We benchmark genesorteR using various data sets and show that it is distinctly more accurate in large single cell data sets compared to other methods. genesorteR is orders of magnitude faster than current implementations of differential expression analysis methods, can operate on data containing millions of cells and is applicable to both single cell RNA-Seq and single cell ATAC-Seq data.  genesorteR is available at https://github.com/mahmoudibrahim/genesorteR.

overall_design: K562 cells and HEK293T cells were artificially mixed at a 7:3 ratio before nuclei isolation

first: Rafael

last: Kramann


title: RNA sequencing on A549 lung cancer cell line

city: San Antonio

first: Chun-Lin

last: Lin

address: 7703 Floyd Curl Dr., MC8257, 233 STRF

institute: University of Texas Health Science Center at San Antonio

summary: We report the RNA sequencing on A549 lung cancer line with 40 nM TP-0903 treatment.

overall_design: Investigate potential resistant pathways in lung cancer cell after TP-0903 treatment.


title: RNA sequencing on HT29 colorectal cancer cell line

summary: We report the single cell RNA sequencing on HT29 colorectal cancer line with 100 nM dasatinib treatment after double thymidine block.

overall_design: Investigate potential resistant pathways in colorectal cancer cell after dasatinib treatment.


title: Impact on Glioblastoma U87 Cell Gene Expression of a Carborane Cluster-bearing Amino Acid

city: Rensselaer

first: Sridar

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Treatment with carborane bearing amino acid on U87 cells showed cytostatic effect followed by cell death. We used microarrays to investigate the effect of the carborane bearing amino acid on U87 cell gene expression profile and explore the mechanism.

overall_design: U87 cells with treatment of 1 mM carborane bearing amino acid and U87 cells without treatment were used for RNA extraction and hybridization on Affymetrix microarrays  We performed the treatment 48 h after the cells were cultured to increase the cell population for RNA extraction and the treatments were performed in triplicates to check reproducibility

first: Tianyu

last: He

first: Rabi

middle: A

last: Musah


city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

institute: Hoshi University

overall_design: DNA methylation statuses of 293FT cells with TET depletion and NOC18 treatment were analyzed using Infinium MethylationEPIC.

first: Toshikazu

last: Ushijima


title: HUVEC Gene Expression of Irradiated Human Umbilical Vein Endothelial Cells

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

institute: Institute of Nuclear Medicine & Allied Sciences

summary: Ionizing radiation has become common for diagnostic and therapeutic purpose. Since it affects the cells at genetic level, it becomes necessary to evaluate its affects especially on endothelial cells which comprises the blood vessels and thus contributes in migration of blood cells, nutrients, oxygen etc. Human Umbilical Vein Endothelial Cells (HUVECs) are major model system used in vitro to study the nature and behaviour of endothelial cells.

overall_design: Gene Expression of Human Umbilical Vein Endothelial Cells (HUVECs)  24hrs after irradiation of cells with 6Gy ionising radiation.

first: Swati

last: Gupta


title: Gene Expression of Bone Marrow Endothelial Cells under Radiated and Radioprotective Conditions

summary: Bone Marrow Transplantation (BMT) depends greatly on transendothelial migration of stem cells from bloodstream to bone marrow. Therefore Bone Marrow Endothelial Cells (BMECs) becomes an essential component for successful BMT. Since BMT requires prior radiation therapy therefore it is necessary to study the behaviour of BMEC in irradiated and radiprotective conditions. We have conducted transcriptome profiling of Bone Marrow Endothelial Cells (BMECs) to identify the signalling mechanisms required for transendothelial migration to bone marrow under irradiated and radioprotected conditions.

overall_design: Gene Expression of Bone Marrow Endothelial Cells  24hrs after treatment of cells either with amifostine or 6Gy radiation or both amifostine and radiation.


title: The adult haematopoietic stem cell CpG island methylome is almost entirely recapitulated in progeny cells: Implications for disease

city: Westmead

first: Lawrence

last: Ong

state: NSW

address: 176 Hawkesbury Road

institute: Westmead Institute for Medical Research

summary: Background Differences in immune response between individuals is driven in part by epigenetic factors. To understand the contribution of DNA methylation to these differences, we have investigated the role of haematopoietic stem cell methylation in driving variation in daughter cell differentiation and state. Methods Haematopoietic cells (namely CD34+, CD14+ and CD56+) were isolated from peripheral blood of 11 healthy individuals and subject to modified reduced representation bisulfite sequencing. DNA methylation was profiled and compared at CpG islands. Results DNA methylation state is almost entirely recapitulated between progenitor and progeny haematopoietic cells. Fewer differences in DNA methylation were detected between haematopoietic cells than between haematopoietic cells and buccal mucosa. Cell subset differences in methylation were over-represented near genes important in cell lineage specific maturation and function. Methylation differences between individuals at specific CpG islands were generally small. The CpG islands that varied most between individuals consistently across subsets, were associated with several genes, but were not enriched with regard to specific biological processes. Conclusions Overall, this study suggests that the predominant DNA methylation setting in haematopoietic stem cells is transmitted to progeny cells, with differences between cell subsets and between individuals that are likely to be important in immune cell development and variation in response to pathogens and disease. Our findings provide a plausible mechanism by which genetic and environmental factors may contribute to the development of disease via unfavourable DNA methylation settings.

overall_design: 33 samples (11 individuals, each with 3 cell subsets) were analysed

middle: T

first: Grant

last: Parnell

first: David

last: Booth


title: Gene expression of human hematopoietic stem cells (CD34+) stimulated with native & mutant (244) form of myeloid stem-cell transcription factor PU.1 alone & in combination with myeloid specific cytokines (IL3+GMCSF+Flt2+MCSF+SCF)

summary: Human CD34+ hematopoietic stem cells gives rise to complete blood lineages through the process of hematopoiesis. Here we tried to differentiate a particular lineage i.e myeloid from CD34+ hematopoietic stem cells using a transcription factor PU.1 and its mutated form. Gene expression analysis was performed after treating cells with protein factors and different cytokine combinations. Cells were given six different treatments including control-PU.1 only and PU.1 with cytokines combination; Y244D only and Y244D with cytokines combination and only cytokine combination (IL3, GMCSF, Flt2, MCSF, and SCF). After 5 days of incubation, cells were washed and pellet was preserved in RNAlater (Ambion) to be shipped to Genotypic Technologies Pvt. Ltd. (Bangalore) for microarray analysis.

overall_design: HSC Cells were given six different treatments including control-PU.1 only and PU.1 with cytokines combination; Y244D only and Y244D with cytokines combination and only cytokine combination (IL3, GMCSF, Flt2, MCSF, and SCF). After 5 days of incubation, cells were washed and pellet was preserved in RNAlater (Ambion) to be shipped to Genotypic Technologies Pvt. Ltd. (Bangalore) for microarray analysis.

first: Madhuri

last: Joshi

first: Pallavi


title: Gene expression of Myeloid cells stimulated with cytokines.

summary: THP-1 is a human monocytic cell line derived from an acute monocytic leukemia patient. It is efficiently converted into macrophages using cytokine combinations and or by using chemical compound Phorbol 12-myristate 13-acetate (PMA). Together with performing gene expression analysis on HSC’s we also performed gene expression analysis on THP-1 cells in order to check which genes have been expressed/overexpressed during differentiation into macrophages. Cells were given treatment with cytokines combination (GMCSF, MCSF). After 24 hours of incubation, cells were washed and pellet was preserved in RNAlater (Ambion) to be shipped to Genotypic Technologies Pvt. Ltd. (Bangalore) for microarray analysis. RNA was isolated by Qiagen’s RNeasy mini kit and was reverse transcribed into cDNA. Cy3 labeled cRNA was formed by cDNA by T7 promoter based linear amplification using Agilent’s Quick amp labeling kit and quantified in Nanodrop Spectrophotometer and their integrity was checked by Bioanalyser. .

overall_design: THP-1 cells were treated with cytokines(GMCSF, MCSF) for 24hrs. After 24 hours of incubation, cells were washed and pellet was preserved in RNAlater (Ambion) to be shipped to Genotypic Technologies Pvt. Ltd. (Bangalore) for microarray analysis.


title: Genome-wide disclosure of the Nkx2.2 targets in oligodendrocytes and their progenitor cells suggests several novel target genes

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

summary: The Nkx2.2 transcription factor contributes to regulate the timing of myelination in the CNS. Still, information about the regulon of Nkx2.2 in oligodendrocytes (Ols) and their progenitor cells (OPCs) is restricted to a few genes. Therefore we aimed to identify the entire regulon of Nkx2.2. We performed transcript profiling of postnatal Nkx2.2-/- mice, investigated the expression of selected transcripts in Ol lineage cells after siRNA induced Nkx2.2 knock-down, and identified the genome-wide active Nkx2.2 binding sites in murine OPCs and Ols by use of ChIP-sequencing technique. Thereby we have found 521 genes with active Nkx2.2 binding sites within 10,000 bp of their gene loci that furthermore are differently expressed in absence or lower expression of Nkx2.2. Functionally, the target genes are associated with mitosis, migration stop, protein transport, lipid metabolism, mitochondrial biogenesis, formation of Ca2+ waves, and WNT signalling. Furthermore, motif discovery techniques and tests for overlaps between sequencing reads suggest that MYRF, OLIG2, SOX10, and TCF3 interact or compete with Nkx2.2 in OPCs/Ols. However, the activator versus repressor activity of Nkx2.2 does not seem to depend on the potential interaction with either of the transcription factors. Test for overlaps with sites of specific histone 3 modifications show that the Nkx2.2 binding sites are more frequently associated H3K4me3 and H3K27ac in genes to which Nkx2.2 may act as an activator. This supports previous studies showing that Nkx2.2 acts in a HDAC1 dependent way. Together this provides new insight into how Nkx2.2 contributes to the timing of OPC differentiation and myelination in CNS.

overall_design: Transcript profiling was performed to identify the differently expressed transcripts in CNS tissue of Nkx2.2-/- mice compared to  littermate wild-type mice. Five mice were included in each group.

first: Christina

last: Fenger

first: Mads

last: Thomassen


title: Genomic distribution of Spindlin1, H3K4me3 and H3K9me3 in HEK293 cells

status: Public on Sep 29 2020

city: Beijing

first: Fan

last: Zhao

address: Qinghuayuan

institute: Tsinghua University

summary: We performed colocalization studies of Spindlin1 and H3"K4me3-K9me3" and found two kinds of genome distribution patterns in overlapping peaks. One is that Spindlin1, H3K4me3 and H3K9me3 are distributed with sharp peaks in the promoter regions of some genes in euchromatin, and the other is that Spindlin1 and H3K4me3 coexist with sharp peaks in genome regions where H3K9me3 is widely distributed.

overall_design: Detect genomic distribution pattern of Spindlin1, histone modification H3K4me3 and H3K9me3 in HEK293 cells.

first: Yunan

last: Liu

first: Juntao

last: Gao

first: Michael Q.

last: Zhang

first: Haitao

last: Li


title: YTHDF2 iCLIP in glioblastoma stem cells

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Glioblastoma is a universally lethal cancer driven by glioblastoma stem cells (GSCs). Here, we interrogated N6-methyladenosine (m6A) mRNA modifications in GSCs by methyl RNA-immunoprecipitation followed by sequencing (meRIP-seq) and transcriptome analysis, finding transcripts marked by m6A often upregulated. Interrogating m6A regulators, GSCs displayed preferential expression as well as in vitro and in vivo dependency of the m6A reader, YTHDF2, in contrast to normal neural stem cells (NSCs). While YTHDF2 has been reported to destabilize mRNAs, YTHDF2 stabilized the oncogene transcripts, MYC and VEGFA, in GSCs in an m6A-dependent manner. We identified IGFBP3 as a downstream effector of the YTHDF2-MYC axis in GSCs and IGF1/IGF1R inhibitor, Linsitinib, as preferentially targeting YTHDF2-expressing cells, inhibiting the viability of GSCs without affecting NSCs and impairing in vivo glioblastoma growth. Thus, YTHDF2 links RNA epitranscriptomic modifications and GSC growth, laying the foundation for the YTHDF2-MYC-IGFBP3 axis as a specific and novel therapeutic target in glioblastoma.

overall_design: YTHDF2 iCLIP performed on 2 glioblastoma stem cell lines, and 1 neuronal stem cell line

first: Hui

middle: X

last: Poh

first: Deobrat

last: Dixit

first: Samie

last: Jaffrey

first: Jeremy

middle: N

last: Rich


title: Effects of Spodoptera exigua eggs on gene expression in systemic Nicotiana attenuata leaves

status: Public on Sep 28 2020

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

institute: Freie Universität Berlin

summary: Plants received oviposition by S. exigua (1-2 egg clutches). After 1 day, tissue from the next younger (systemic) leaf, or from the respective leaf position of a control plant without eggs, was harvested for RNA extraction.

overall_design: gene expression profiles of Nicotiana attenuata leaves that are systemic to leaves that received Spodoptera exigua eggs are compared to gene expression profiles of control leaves from plants thet received no oviposition.

first: Sylvia

last: Drok

first: Anke

last: Steppuhn


title: Cell-type specific translational changes in prion diseases

city: Zurich

first: Claudia

last: Scheckel

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

summary: Identification of genome-wide translational changes during prion disease via cell-type specific ribosome profiling.

overall_design: Mice expressing GFP-tagged ribosome  in prion disease relevant cell types were inoculated with non-infectious brain homogenate or prions and sacrificed at different time points during disease progression.

first: Adriano

last: Aguzzi


title: The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells [m6A RIP-seq]

overall_design:
RNA m6A profiling of neural stem cells and patient derived glioblastoma stem cells
Please note that each processed data was generated by comparing meRIP-seq to input sample and is linked to the corresponding *IP sample records.

first: Yang

last: Wang

first: Brian

first: Jing

middle: C


title: Expression data from proliferating and quiescent adult hippocampal neural stem and progenitor cells

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

institute: Institute of Health Carlos III

summary: We have characterized the transcriptome of adult rat hippocampal neural stem and progenitor cell (NSPC) cultures. The NSPCs cultures can be reversibly arrested by the quiescence-promoting signal BMP4. We provide expression data from NSPCs grown as neurospheres for 4 days in vitro in the presence of FGF2 (proliferating NSPCs) or FGF2+BMP4 (quiescent NSPCs) showing that entry into quiescence involves major changes in the transcriptional profile of the cells.

overall_design: 6 RNA samples were analyzed. Total RNA was isolated from proliferating NSPCs cultured in FGF2 and quiescent NSPCs cultured in FGF2+BMP4, 3 biological replicates for each condition.

first: H

last: Mira

first: L

last: García-Corzo


title: The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells

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

overall_design: Refer to individual Series


title: Pre-established chromatin interactions mediate acute transcriptional response to Epo

city: Nashville

first: Andrea

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University


title: SPA regulation of high ambient temperature induced gene expressions in Arabidopsis thaliana.

city: Austin

first: Enamul

last: Huq

state: TX

address: Department of MBS, NHB 2.606, Stop A5000, 100 East 24th St.

institute: The University of Texas at Austin

summary: The mRNA expression profiles of WT and the quadruple spa mutant spaQ were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes was analyzed and compared within 22degC and 28degC.

overall_design: Total twelve 24h 22degC and 28degC treated Arabidopsis samples were used. These include three replicates of following genotypes; Col-0, spaQ. Therefore, three replicates of following genotypes and conditions; Col-0 (22degC), spaQ (22degC0, Col-0 (28degC), spaQ (28degC).

first: Sanghwa

last: Lee

first: Inyup

last: Paik


title: Pre-established chromatin interactions mediate acute transcriptional response to Epo [HiChIP]

summary: Although chromatin architecture has been established in a variety of cell and tissue types, chromatin contacts’ dynamics in response to hormone stimulation has yet to be fully elucidated. Using the unique anemia-inducing strain of the Friend virus (FVA) murine model system, we show that there are transcriptional and epigenetic changes in response to erythropoietin within an invariant chromatin domain organization. There is an acute transcriptional response, as seen by genes with significant differential RNA polymerase II occupancy. Additionally, we find that YY1 is highly dynamic in response to Epo stimulation and these binding locations are not shared with CTCF. Using HiChIP, which combines Hi-C and ChIP methodologies, we identified enhancer-promoter interactions mediated by H3K27ac and YY1, revealing a subset of invariant chromatin loops. Together, these findings offer new insights into Epo-mediated gene regulation through chromatin organization.

overall_design: Examination of chromatin interactions mediated by H3K27ac and YY1 in differentiating erythroid cells

first: Jonathan

middle: D

last: Brown

first: Bryan

middle: J

last: Venters


title: Pre-established chromatin interactions mediate acute transcriptional response to Epo [ChIPexo-seq]

overall_design: Examination of structural proteins (CTCF, YY1) and RNA polymerase II in differentiating erythroid cells


title: Nucleus deformation by microtubules during early steps of hematopoiesis

status: Public on Sep 25 2020

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

summary: Cells from the myeloid and lymphoid lineages fulfill distinct functions with specific shapes and intra-cellular architectures. The role of cytokines in the regulation of HSC differentiation has been intensively studied but our understanding of the potential contribution of inner cell architecture is relatively poor. Here we studied the early commitment of human HSC and identified specific microtubule network rearrangements and nucleus shape changes that accompany cells differentiation toward the myeloid lineage. This work established the role of microtubules in the mechanical regulation of nucleus shape, chromatin architecture and HSC differentiation and open new perspectives in our appreciation of the implication of intra-cellular forces in the early specification of the myeloid lineage.

overall_design: We compared the transcriptome of HSCs differentiated for 3 days in normal culture medium, to the transcriptome of HSCs cultured in the same manner but treated with the dynein inhibitor ciliobrevin D (CILIO) or taxol (TX) between day 2 and day 3.

first: S

last: Biedzinski

last: Faivre

first: B

last: Vianay

first: M

last: Blanchoin

first: J

last: Larghero

last: Théry

last: Brunet


title: Pre-established chromatin interactions mediate acute transcriptional response to Epo [RNA-seq]

overall_design: Examination of gene expression (measured by RNA-seq) in differentiating erythroid cells


title: Single nucleus RNA-Seq is not suitable for detection of microglial activation genes in humans

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: Single nucleus RNA-Seq (snRNA-Seq) is used as an alternative to single cell RNA-Seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-Seq is able to detect cellular state in human tissue. Indeed, snRNA-Seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer’s Disease. Our comparison of microglia from single cells and single nuclei of four human subjects revealed that, while the majority of genes showed similar relative abundances in cells and nuclei, a small population of genes (~1%) was depleted in nuclei compared to whole cells. This population was enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously-identified microglial disease-associated genes. Given the low sensitivity of snRNA-Seq to detect many activation genes, we conclude that snRNA-Seq is not suited to detecting cellular activation in microglia in human disease.

overall_design: Single nucleus and single cell sequencing of cortical tissue from 4 neurosurgical patients.

first: Nicola

last: Thrupp

first: Carlo

last: Sala Frigerio

first: Leen

last: Wolfs

first: Nathan

middle: G

last: Skene

last: Fattorelli

first: Suresh

last: Poovathingal

first: Yannick

last: Fourne

first: Paul

last: Matthews

first: Tom

last: Theys

first: Renzo

last: Mancuso

first: Mark

last: Fiers


title: The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells [RNA-seq]

first: Briana

last: Prager

overall_design: RNA sequencing on 387 and 4121 GSCs transduced with either control (nt) or two independent non-overlapping sgRNAs (g1 and g2)

first: Deobrat

last: Dixit

first: Yang

last: Wang

first: Brian

first: Jing

last: Zhao

first: Jeremy

last: Rich


title: To investigate gene expression changes in neurons lacking cap methyltransferase 1 (CMTR1)

city: Taipei

first: Yi-Shuian

last: Huang

state: Nangang

address: 128 Academia Road, Section 2

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Transcriptomic profiles of control and CMTR1-knockdown neurons.

overall_design: Rat cortical neurons at days in vitro 2 (DIV2) were infected with shCTL or shCM1 lentivirus and harvest at DIV7 for total RNA isolation. Two independent experiments were performed to collect samples for Agilent array analysis.

first: Yen-Lurk

last: Lee