title: Single Cell Epigenome Profiling of Cardiac Non-myocyte

summary: The mammalian heart is composed of a variety types of cells that can be roughly categorized into cardiomyocytes and non-myocytes. Instead of being bystanders of cardiac function, cardiac non-myocytes provide critical structural, mechanical and electrophysiological support to the working myocardium. However, the precise cellular identity and molecular features of the non-myocytes at single cell level remain elusive. Depiction of epigenetic landscape with transcriptomic signatures using the latest single cell multi-omics has the potential to unravel the molecular programs of cardiac non-myocytes underlying their cellular diversity. To characterize the molecular and cellular features of cardiac non-myocytes populations in the adult murine heart at single cell level. We applied single cell Assay for Transposase Aaccessible Chromatin using sequencing (scATAC-seq) in combination with high-throughput single cell RNA-seq (scRNA-seq) to map the epigenetic landscape and gene expression program of cardiac non-myocytes from adult murine heart. Through integrated dual-omics data analysis, we categorize the cardiac non-myocytes into 4 defined populations including endothelial cells, fibroblast, pericytes and immune cells with distinct chromatin accessibility patterns. Cis- and trans-regulatory factors for each cell type were identified.  In particular, unbiased sub-clustering and functional annotation of the cardiac fibroblast (FB), indicated the heterogeneity and functionality of FB subtypes associated with cellular response, cytoskeleton organization and immune regulation. We further validated the expression and function of novel markers in major FB sub-populations and experimentally determined the distribution of the FB sub-populations in healthy and injured murine heart. In summary, we comprehensively characterized the non-myocyte cellular identity at the single-cell level and defined FB subpopulations by their functional states.

overall_design: Single-cell ATAC-seq profiles of cardiac non-myocytes from mice aged at 10-12 weeks were generated by 10x Genomics Chromium System.

first: Li

last: Wang

last: Qian


title: Temporal, spatial, and genetic constraints contribute to the patterning and penetrance of murine Neurofibromatosis-1 optic glioma

status: Public on Apr 21 2021

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

country: USA

institute: Washington University in St Louis

type: Expression profiling by high throughput sequencing

summary: Contributing factors to pediatric glioma formation

overall_design: TVZ neuroglial progenitor cells (NPCs) were analyzed over the course of mouse brain development. FACS-isolated progenitors were assessed for functional and molecular differences. The impact of different germline Nf1 mutations on TVZ NPC properties was analyzed using genetically engineered mice.

first: Nicole

middle: M

last: Brossie

first: Sharanya

last: Thondapu

first: Olivia

last: Cobb

middle: H


title: RNA sequencing analysis  of MED1-overexpression induced transcription changes in HER2+ mammary tumors

city: Cincinnati

first: Xiaoting

last: Zhang

state: OH

address: 3125 Eden Ave

department: Cancer Biology

institute: university of Cincinnati

summary:
The goal of this study is to reveals MED1-overexpression induced gene expression changes in HER2+ breast cancers
Total RNA from paired mouse MMTV-HER2 and MMTV-HER2/MMTV-MED1 mammary tumors were prepared using RNA easy mini kit for RNA-Seq analysis the gene expression changes.

overall_design: mRNA profiles of the mammary tumors from MMTV-HER2 control and MMTV-HER2/MMTV-MED1 mice were generated by RNA sequencing, in double, using Illumina HiSeq 2000

first: Yongguang

last: Yang

first: Zhenhua

last: Luo


title: Transcriptional profiling of control versus PAF depleted mouse lung cancer cell lines

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

summary: RNA-Seq analyses of shCtrl (control group) and shPAF (experimental group) KrasG12D; Trp53 knockout (KO)-derived mouse lung cancer cell lines.

overall_design: KrasG12D;Trp53 KO-derived mouse lung cancer (KP) cell lines were stably transduced with lentiviruses encoding shGFP (control) or shPAF (PAF depletion). Two biological replicates (n=2) were used for RNA extraction and RNA-Seq. KP mouse lung cancer cell lines were established from the lung tumors isolated from Ad-Cre-infected Kras LSL-G12D/+;Trp53 floxed/floxed (KP) mice.

first: Moon

last: Kim

first: Jae-II


title: Transcriptional profiling of control versus PAF depleted human lung cancer cell line (H1792)

summary: RNA-Seq analyses of shCtrl (control group) and shPAF (experimental group) H1792 cell lines

overall_design: H1792 (NCI-H1792) cell lines were stably transduced with lentiviruses encoding shGFP (control) or shPAF (PAF depletion). Two biological replicates (n=2) were used for RNA extraction and RNA-Seq.

middle: J


title: Gene expression analysis of human pluripotent stem cells maintained on several laminin-E8 scaffolds.

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

summary: To identify which gene expressions were affected by the different LM-E8  scaffolds, we performed transcriptome analysis using microarrays.

overall_design: Total RNAs were extracted from PSCs mainteined on several laminin-E8 scaffolds and analyzed on Agilent microarrays.

first: Akinori

last: Yuzuriha

first: Sou

last: Nakamura

first: Masato

last: Nakagawa

first: Takuya

last: Yamamoto


title: Profiling tissue-specific modulation of gene expression in response to insulin signalling in Drosophila

city: Cologne

first: Linda

last: Partridge

address: Joseph-Stelzmann-Straße 9B

department: Partridge

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary:
We investigated tissue-specific regulation of gene expression in a long lived Drosophila IIS mutant (dilp2-3,5) compared to its control (wDah).
The longevity of dilp2-3,5 mutants only occurs in the presence of the endosymbiotic bacteria Wolbachia. We therefore use flies (10 day old) in the presence (wDah and dilp2-3,5) or absence (wDahT and dilp2-3,5T)
of Wolbachia to identify the changes in gene expression that could potentially be causal for longevity.  We quantified gene expression for all experimental groups, concurrently on the level of the proteome and the transcriptome and in four key tissues: brain, gut, fat body, and muscle. Transcriptome quantification was carried out on three biological replicates per experimental group. Corresponding proteome quantification was carried out on five biological replicates per experimental group, and published on PRIDE (accession number PXD011589).

overall_design: Tissue-specific mRNA profiles (fat, gut, brain, thorax) of long-lived dilp2-3,5 insulin mutant flies and three control groups (wDah, wDahT, dilp2-3,5T) were generated by single-end, total RNA Illumina sequencing (HiSeq2500)

first: Luke

last: Tain

first: Robert

last: Sehlke


title: Small RNA seq in epididymis of wild type and Alkbh3-/- mice

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA). The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

overall_design: Examination of small RNA difference in epididymis between wild type and Alkbh3-/- mice

first: Hongsheng

last: Wang

first: Guanzheng

first: Bin

last: Shen


title: Small RNA seq in ALKBH3 stable over expresion and control HeLa cells

summary: Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50 nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA). The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

overall_design: Examination of small RNA difference in ALKBH3 stable over expresion and control HeLa cells


title: scRNA-seq of P2 and P7 mouse cochlea and utricle

status: Public on Apr 20 2021

city: Baltimore

first: Seth

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Cell types in the cochlea and utricle were identified using scRNA-seq of each tissue.

overall_design: Examination of expression patterns of genes expressed in day 2 and day 7 mouse cochlea and utricle

first: Beatrice

last: Milon

first: Ronna

last: Hertzano

middle: A


title: A comparison of the gene expression between the lens and body without eyes of larval zebrafish

city: Hongo, Bunkyo-ku

first: Hideaki

last: Morishita

state: Tokyo

department: Department of Biochemistry and Molecular Biology

institute: The University of Tokyo

summary: The lens of the eye is consisted of lens fiber cells that undergo large-scale organelle degradation during terminal differentiation. To understand the molecular mechanism of large-scale organelle degradation, we compared the gene expression profiles between the lens and body without eyes of larval zebrafish using a microarray analysis.

overall_design: Gene expression was measured using lenses (191 lenses) and bodies without eyes (20 bodies) taken from wild-type zebrafish at 10 days post fertilization.

first: Noboru

last: Mizushima


title: HIV-exposed seronegative sex workers express high levels of regulatory T cells, low levels of T cell activation and an intact ectocervical tissue microenvironment

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary: Immunological correlates of natural resistance to HIV have been identified in HIV-exposed seronegative (HESN) individuals. The cervicovaginal epithelium has not been studied for such correlates despite constituting an important barrier against sexual HIV transmission. To fill this gap in knowledge, we collected samples of blood and genital mucosa from Kenyan HESN sex workers (n=29) and controls (n=33). The samples were analyzed by several methods including tissue-based RNA sequencing. A significantly higher relative proportion of regulatory T cells and lower proportion of activated cervical T cells were found in the HESN group compared with the controls. However, they had comparable tissue RNA transcriptional profiles. In conclusion, the identification of an increased proportion of regulatory T cells in blood, a lower proportion of activated cervical T cells, and an intact ectocervical microenvironment in HESN individuals add new data to current knowledge about natural resistance to sexual transmission of HIV.

overall_design:
In this study we compared the gene expression between a group of HIV-exposed seronegative (HESN) women and a group of new negatives (NN), acting as control group. The groups consisted of n = 28 samples each. The RNA was extracted from ectocervical biopsies.

>>>Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns.<<<

first: Vilde

last: Kaldhusdal

first: Gabriella

last: Edfeldt


title: Integrin avb5 heterodimer is a specific marker of human pancreatic beta cells

city: Parkville

first: Jacqueline

last: Schiesser

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

summary: The identification of cell surface markers specific to pancreatic beta cells is important for both the study of islet biology and for investigating the pathophysiology of diseases in which this cell type is lost or damaged. Following analysis of publicly available single-cell RNAseq data, we identified specific integrin subunits, integrin av and integrin b5, that were expressed in beta cells. Flow cytometry analysis showed that the vast majority of islet cells expressed some level of both the av and b5 subunits. Using our analysis of single-cell sequencing data as a guide, we isolated populations expressing both subunits from isolated human islets and subjected these to bulk RNAseq analysis. This analysis suggested that the avlob5lo population was enriched for endocrine cell types including alpha, delta and gamma cells, whilst the avhib5hi population was enriched for pericytes and stellate cells . Interestingly, the av+b5neg reference population appeared to be enriched for myeloid cells. This finding was further elaborated using immunofluorescence analysis of histological sections derived from donor human pancreas. Despite the broad expression of specific integrin subunits, we found that expression of integrin avb5 heterodimers was restricted to beta cells and that this complex persisted in islet remnants of some type 1 diabetic individuals from which insulin expression had been lost. This study identifies avb5 heterodimers as a novel cell surface marker of human pancreatic beta cells, a finding that will aid in the identification and characterisation of this important cell type.

overall_design: Isolated human pancreatic islets were stained with antibodies against ITGAV and ITGB5 and sorted by FACS using a BD Influx (BD Biosciences) or BD FACSAria Fusion (BD Biosciences). RNA extraction of FACS purified populations was performed using an Isolate II RNA microkit as directed by the manufacturer (Bioline, BIO-65042).

middle: V


title: MicroRNA expression profiling in a mouse spinal cord injury model [P15 and P90, 12h and 3d]

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

country: United Kingdom

institute: University of East Anglia

summary: Spinal cord injury (SCI) is a devastating condition resulting in permanent and irreversible deficits. Despite regeneration attempts, the neurons fail due to several dysfunctions. A number of studies have already revealed that, following SCI, microRNAs show two opposite kinds of alterations, one detrimental and one protective. However, there is still little evidence of specific microRNAs involved in axon regrowth. The aim of this project is the characterization of microRNA expression changes in sensorimotor cortex and corticospinal motor neurons, whose axons are severed by SCI.

overall_design: miRNA profiling in SCI mouse model (P15 and P90) at different time points (12h and 3 days). Complete transection of the spinal cord was induced at the C5-C6 level in postnatal day 15 C57BL/6J male mice at 12h and 3 days after injury (3 WT vs. 3 SCI) and in adult mice at 12h and 3 days post injury (3 WT vs. 3 SCI per each group). The sensorimotor cortex was dissected, collected for RNA extraction and the HD sRNA library was sequenced.

first: Matilde

last: Ghibaudi

first: Marina

last: Boido

first: Archana

last: Singh

first: Elena

last: Signorino

first: Tamas

last: Dalmay

first: Alessandro

last: Vercelli


title: Transcriptome changes in Huntington's disease with SUMO-1 depletion

city: Jupiter, FL 33458

first: Gogce

middle: Ceren

last: Crynen

state: Florida

address: 130 Scripps Way

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

summary: NOT PROVIDED; REQUESTED

overall_design: Mouse brain striatal total RNA-seq of WT, HD, SUMO-1 KO in HD, and SUMO-1 KO in WT mouse

first: Srinivasa

last: Subramaniam

first: Manish

last: Sharma

first: Uri

middle: N

last: Jarquin


title: Fibroblast growth factor 2 promotes bladder hypertrophy caused by partial bladder outlet obstruction

city: Chongqing

first: Zhenxing

last: Yang

state: Chongqing

address: No.183, Xinqiao main street,

department: Urology

country: China

institute: Army Medical University

summary: The current study aims to investigate molecular alterations and biomarkers associated with partial BOO (PBOO) in rats. RNA-seq analyses were conducted to identify molecular alterations. Rats with PBOO experienced hypertrophy of smooth muscle cells and hyperplasia of interstitial cells during the first 4 weeks after the initiation of obstruction. Four weeks later, rats with PBOO showed activation of the adaptive immune response, cell death and apoptosis. The levels of BDNF and FGF2 in the serum gradually increased in the first four weeks and gradually decreased after week 4. FGF2 levels slightly correlated with prostate volume (R=0.156, P=0.0028) but not with age or BMI in BPH patients. FGF2 is involved in the development of hypertrophy in the PBOO bladder and shows a positive correlation with prostate volume in BPH patients.

overall_design: Bladder mRNA profiles in PBOO rat model of week 4 and week 5

first: Ye

last: Gao

first: Peilin

last: Liu

first: Fan

last: He

first: Xingliang

first: Ronghua

last: Wu

first: Wei

last: Chen

first: Longkun

last: Li


title: Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

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

overall_design: Refer to individual Series


title: Effects of a single dose of psilocybin on behaviour, brain 5-HT2A receptor occupancy and gene expression in the pig

city: Copenhagen

first: Gitte

middle: Moos

last: Knudsen

address: 9 Blegdamsvej

department: Neurobiology Research Unit

country: Denmark

institute: Copenhagen University Hospital, Rigshospitalet

summary: mRNA sequencing of pig prefrontal cortex after treatment with one dose of psilocybin or placebo (saline).

overall_design: Adolescent female Danish slaughter pigs of 20kg were used. A single dose of 0.08mg/kg psilocybin or saline was administered iv while the pig was awake and freely roaming around. Either 1day or 1 week later the pigs were euthanized by iv pentobarbital overdose. N=6/group: Saline 1day; Psilocybin 1day, Saline 1week, Psilocybin 1week

first: Lene

last: Lundgaard Donovan

first: Jens

last: Vilstrup Johansen

first: Shohreh

last: Issazadeh-Navikas

first: Elham

last: Jaberi

first: Hanne

last: Demant Hansen

last: Moos Knudsen


title: Systemic and adipocyte transcriptional and functional metabolic dysregulation in Idiopathic Intracranial Hypertension

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Campus

institute: University of Warwick

summary: We examined the transcriptional profile of subcutaneous adipose tissue in Idiopathic intracranial hypertension (IIH) patients compared to a control cohort matched for gender and BMI

overall_design:
Comparison of subcutaneous adipose tissue in IIH patients compared to a control cohort matched for gender and BMI
For additional sample information (such as gender, BMI), please contact the submitter (Alexandra Sinclair; A.B.Sinclair@bham.ac.uk).

first: Connar

middle: S

last: Westgate

first: Mark

last: Walsh

first: Ildem

last: Akerman

first: Alexandra

last: Sinclair


title: Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification [Array]

summary: Transfer RNA (tRNA) molecules contain a variety of post-transcriptional modifications which are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation, to gene expression control and cellular stress response. Recent evidence show that tsRNAs are also modified, however the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. This modification is catalyzed by the tRNA methyltransferase TRMT2A, but its biological role remains largely unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification, resulting in angiogenin (ANG) dependent tsRNA formation. More specifically, m5U54 hypomodification is followed by ANG overexpression and tRNA cleavage near the anticodon, resulting in accumulation of 5’tRNA-derived stress-induced RNAs (5’tiRNAs), in particular 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tsRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tsRNA formation in mammalian cells. These results establish a link between tRNA demethylation and tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.

overall_design: Gene expression profiles were generated for HeLa cells transfected with a siCTRL (control condition) and HeLa cells transfected with siTRMT2A samples (tested condition) using customized oligonucleotide microarrays (Agilent Technologies). 3 biological replicates of each condition were analyzed. RNA sample preparation, labeling, hybridization, microarray wash, scanning and feature extraction were performed according to the manufacturer’s protocol: “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labeling” version 6.9.1 from Agilent Technologies”. Microarray expression profiles were generated using Agilent’s Feature Extraction software.

first: Marisa

last: Pereira

middle: R


title: Honokiol prevents non-alcoholic steatohepatitis-induced liver cancer via EGFR degradation through the glucocorticoid receptor-MIG6 axis

city: Kamigyo-ku

first: Atsushi

last: Umemura

state: Kyoto

address: Kajii-cho, Kawaramachi-Hirokoji

institute: Kyoto Prefectural University of Medicine

summary: Non-alcoholic steatohepatitis (NASH) has become a serious public health problem associated with metabolic syndrome. The mechanisms by which NASH induces hepatocellular carcinoma (HCC) remain unknown. There are no approved drugs for treating NASH or preventing NASH-induced HCC. We used a genetic mouse model in which HCC was induced via high-fat diet feeding. This mouse model strongly resembles human NASH-induced HCC. The natural product honokiol (HNK) was tested for its preventative effects against NASH progression to HCC. Then, to clarify the mechanisms underlying HCC development, human HCC cells were treated with HNK. We found that epidermal growth factor receptor (EGFR) signaling was hyperactivated in the livers of mice with NASH. Inhibition of EGFR signaling by HNK drastically attenuated HCC development in the mouse model. Mechanistically, HNK accelerated the nuclear translocation of glucocorticoid receptor (GR) and promoted mitogen-inducible gene 6 (MIG6)/ERBB receptor feedback inhibitor 1 (ERRFI1) expression, leading to EGFR degradation and thereby resulting in robust tumor suppression. EGFR degradation or inactivation represents a novel approach for NASH–HCC treatment and prevention, and the GR–MIG6 axis is a newly defined target that can be activated by HNK and related compounds.

overall_design: We analyzed more than 30 mice to examine NASH and NASH-induced liver cancer development with or without honokiol treatment. We chose 6 mice (3 with treatment, 3 without treatment) to perform RNA array analysis. Since EGFR expression was different between the two groups, EGFR signaling was further investigated.


title: Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification [Seq]

overall_design: Human tRF and tiRNAs were sequenced from HeLa cells transfected with a siCTRL (control condition) and HeLa cells transfected with siTRMT2A samples (tested condition). Three biological replicates were tested for each condition. For standard small RNA sequencing, the Illumina NextSeq instrument was used.Prior sequencing, between 1-2 ug of total RNA were purified from each sample. Integrity, quality and quantity of each RNA sample was checked using agarose gel electrophoresis and NanodropTM instrument. Since tRNA derived fragments (tRF & tiRNA) are heavily decorated by RNA modifications that interfere with small RNA-seq library construction, total RNA samples were pre treated with the following: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’adaptor ligation, 5’-OH (hydroxyl group) phosphorylationto 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Sequencing libraries were size-selected for the RNA biotypes to be sequenced using an automated gel cutter.  The libraries were qualified and absolutely quantified using Agilent BioAnalyzer 2100. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type was 50bp singleread. Cytoplasmic tRNA sequences were downloaded from GtRNAdb. Mitochondrial tRNA sequences were predicted with tRNAscan-SE software. To generate the mature tRNA libraries, we removed the predicted intronic sequences (if present) and added an additional 3’-terminal “CCA” to each tRNA. To generate the precursor tRNA libraries, we included 40 nucleotides of flanking genomic sequence on either side of the original tRNA sequence.


title: Itaconate confers tolerance to late NLRP3 inflammasome activation

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Gene expression in LPS-stimulated, LPS-tolerized or non-tolerized WT and Irg1-deficient BMDMs

overall_design: BMDMs were tolerized with LPS or not for 24h, media was washed, cells rested for 1h and then stimulated with LPS for 3h. Alternatively, BMDMs were stimulated for 24h and directly harvested.

first: Monika

last: Bambouskova

first: Lucie

last: Potuckova

first: Tomas

last: Paulenda

first: Martina

last: Kerndl

first: Denis

last: Mogilenko

first: Kate

last: Lizotte

first: Amanda

last: Swain

first: Sebastian

last: Hayes

first: Ryan

middle: D

last: Sheldon

first: Hyeryun

last: Kim

first: Unnati

last: Kapadnis

first: Abigail

middle: E

last: Ellis

first: Christine

last: Isaguirre

first: Samantha

last: Burdess

first: Anwesha

last: Laha

first: Gaya

middle: K

last: Amarasinghe

first: Victor

last: Chubukov

first: Thomas

middle: P

last: Roddy

first: Michael

last: Diamond

first: Russell

last: Jones

first: Donald

last: Simons


title: Global transcriptional response of P. falciparum NF54 early gametocytes treated with the Jumonji histone demethylase inhibitor JIB-04

city: Pretoria

first: Jessica

middle: I

last: Connacher

address: Lynnwood road, Hatfield

country: South Africa

institute: University of Pretoria

summary: Global transcriptomic profiling of JIB-04 treated and untreated control early gametocytes to determine the downstream effects of Jumonji histone demethylase inhibition on development

overall_design: DNA microarrays (Agilent Technologies, USA, (Painter et al., 2013, DOI: 10.1007/978-1-62703-26-7_14) were used to profile global the transcriptomic changes occuring in P. falciparum gametocytes treated with the Jumonji demethylase inhibitor JIB-04.  P. falciparum NF54 gametocytes (1-3% gametocytaemia and 4% haematocrit induced from asexual parasite cultures through a combination glucose starvation and a drop in haematocrit as described previously (Reader et al., 2015, DOI: 10.1186/s12936-1015-0718-z) were treated with 5 µM JIB-04 (Cayman Chemical) on day 2 and day 3 of development and sampled 24 h later with 0.01% (w/v) saponin. RNA was extracted and cDNA synthesised and dye-coupled to Cy5 as previously described (Painter et al., 2013, DOI: 10.1007/978-1-62703-26-7_14). The two treated (Day2_JIB-04 and Day3_JIB-04) and paired untreated samples (Day2_UT and Day3_UT) were each hybridised to an array with an equal quantitiy of Cy3-labeled reference pool cDNA (consisting of untreated and treated NF54 gametocyte samples and mixed 3D7 asexual parasites). Slides were scanned with an Agilent G2600D scanner using methods previously described (Painter et al., 2013, DOI: 10.1007/978-1-62703-26-7_14).

first: Gabrielle

last: Josling

first: Lindsey

last: Orchard

first: Janette

last: Reader

first: Manuel

last: Llinas

first: Lyn-Marié

last: Birkholtz


title: RAMP2-AS1 Regulates Endothelial Homeostasis and Aging

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: The homeostasis of vascular endothelium is crucial for cardiovascular health and endothelial cell (EC) aging and dysfunction could negatively impact vascular function. Leveraging time-series transcriptomic data obtained from endothelial cells (ECs) subjected to physiological pulsatile flow versus pathophysiological oscillatory flow, we performed principal component analysis (PCA) to identify key genes contributing to divergent transcriptional states of ECs under distinct flow patterns. Through bioinformatics analysis, we identified that a long non-coding RNA (lncRNA) RAMP2- AS1 encoded on the antisense of RAMP2, a determinant of endothelial homeostasis and vascular integrity, is a novel regulator essential for EC homeostasis and function. Knockdown of RAMP2-AS1 inhibited EC angiogenesis and promoted EC senescence, as a result of extensive changes of EC transcriptome. Our study demonstrates an integrative approach to quantifying EC aging based on transcriptome changes, which also identified a number of novel regulators, including protein-coding genes and many lncRNAs involved EC functional modulation.

overall_design: Principal component analysis of time-series transcriptome data identified novel regulators, including protein-coding and non-coding genes, for EC biology and vascular aging. RAMP2-AS1 is a key long non-coding RNA regulating EC homeostasis.

first: Chih-Hung

last: Lai

first: Aleysha

middle: T

last: Chen

first: Andrew

middle: B

last: Burns

first: Kiran

last: Sriram

first: Yingjun

last: Luo

first: Xiaofang

last: Tang

first: Sergio

last: Branciamore

last: O’Meally

first: Szu-Ling

last: Chang

first: Po-Hsun

last: Huang

first: John

middle: Y

last: Shyy

first: Shu

last: Chien

middle: C

last: Rockne

first: Zhen


title: H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum

first: Jessica

last: Connacher

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program.  Several interconnected mechanisms governing sexual commitment have been described. However, the processes that drive the subsequent differentiation and development of the gametocyte remain largely unexplored.  Using chromatin immunoprecipitation followed by high-throughput sequencing we map the genome-wide occupancy of H3K36me2 and H3K36me3 during early gametocyte development and describe an association between these histone modifications and the global changes in the transcriptional program driving gametocyte development post-commitment.

overall_design: Investigation of H3K36me2 and H3K36me3 dynamics during early development in P. falciparum gametocytes

first: Gabrielle

last: Josling

first: Lindsey

last: Orchard

last: Reader


title: Comprehensive identification and alternative splicing of microexons in Drosophila

city: Wuhan

first: Shaobo

last: Liang

address: BaYi Road

department: College of life science

institute: Wuhan University

summary: Interrupted exons in the pre-mRNA transcripts are ligated together through RNA splicing, which plays critical roles in the regulation of gene expression. Exons with length ≤30 nt are defined as microexons that are unique in identifications and gene functions. However, due to difficulties in mapping short segments from sequencing reads, microexons especially shorter than 8 nt, have not been well studied in many organisms. Here, we analyzed mRNA-seq data from a variety of Drosophila samples by a new developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. Differentially alternatively spliced (AS) microexons were investigated between the Drosophila tissues (head, body and gonad) and genders. Most of the AS microexons are found in the head, as well as two AS microexons were identified in the sex-determination pathway gene fruitless.

overall_design: Detect transcriptome for different stages and regions of either female or male individuals

first: Ting-Lin

last: Pang

first: Yong-Zhen

last: Xu


title: Transcriptomic Profiling of Stromal Cell-derived Factor-1 and Exendin-4 Treated Periodontal Ligament Stem Cells Undergoing Osteogenic Differentiation by RNA-Seq

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

summary: We aimed to evaluate the detailed biological mechanism of SDF-1 and EX-4 alone or synergistic in regulating PDLSCs differentiation by RNA-sequencing (RNA-seq).

overall_design: PDLSCs from 5 different individuals were cultured in the osteogenic medium (OM) and treated with SDF-1, Ex-4 or SDF-1+Ex-4 at 21 d, respectively; normal PDLSCs treated with OM was served as control. A total of 20 samples were sequenced to analyze the gene expression at the whole genome level at LC Sceiences (Hangzhou, Zhejiang, China) by RNA-seq.

first: Shaohua

last: Ge


title: The ablation of VEGFR-1 signaling promotes pressure overload–induced cardiac dysfunction and sudden death

city: Kuopio

first: Nicholas

last: Downes

address: P.O.Box 1627 (Neulaniementie 2)

department: A.I.Virtanen Institute for Molecular Sciences

country: Finland

institute: UEF

summary: Deletion of VEGFR-1 signaling appears not to have an effect on normal cardiac function but it inhibits the development of early compensatory LVH, which in turn leads to diastolic dysfunction associated with atrial dilatation and increased risk of sudden cardiac death

overall_design: Cardiac mRNA profiles after AngII induced left ventricular hypertrophy in VEGFR-1 tyrosine kinase knockout and littermate control mice

first: Annakaisa

last: Tirronen

middle: L

first: Jenni

last: Huusko

first: Johanna

last: Laakkonen

first: Tomi

last: Tuomainen

first: Pasi

last: Tavi

first: Marja

last: Hedman

first: Seppo

last: Ylä-Herttuala


title: Persistent inflammatory stimulation drives the transition of MSCs to inflammatory CAFs that promote pro-metastatic characteristics in breast cancer cells [I]

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

summary: The pro-inflammatory cytokines tumor necrosis factor α (TNFα) and interleukin 1β (IL-1β) are expressed simultaneously and have tumor-promoting roles in breast cancer. In parallel, mesenchymal stem cells (MSCs) undergo transition at the tumor site to cancer-associated fibroblasts (CAFs), which are generally connected to enhanced tumor progression. Here, we determined the impact of consistent inflammatory stimulation on stromal cell plasticity. MSCs that were persistently stimulated by TNFα+IL-1β (2-3 weeks) gained a CAF-like morphology, accompanied by prominent changes in gene expression, including in stroma/fibroblast-related genes. These CAF-like cells expressed elevated levels of vimentin and fibroblast activation protein (FAP) and demonstrated significantly increased ability to contract collagen gels. Moreover, they have gained the phenotype of inflammatory CAFs, as indicated by reduced expression of α smooth muscle actin (αSMA), increased proliferation and elevated expression of inflammatory genes and proteins, primarily inflammatory chemokines. These inflammatory CAFs released factors that enhanced tumor cell detachment, spreading and migration; the inflammatory CAF-derived factors elevated cancer cell migration by stimulating the chemokine receptors CCR2, CCR5 and CXCR1/2 and Ras-activating receptors, expressed by the cancer cells. Together, these novel findings demonstrate that chronic inflammation, per se, can induce MSC-to-CAF transition, leading to generation of tumor-promoting inflammatory CAFs.

overall_design: To determine transcriptome alterations upon persistent cytokine stimulation, genome-wide expression analysis was performed on MSCs stimulated by TNFα and IL-1β or by vehicle controls, for 14 days.

first: Linor

last: Rubinstein-Achiasaf

first: Dina

last: Morein

first: Hagar

last: Etzion

first: Yulia

last: Liubomirski

first: Tsipi

last: Meshel

first: Eti

last: Elbaz

first: Orly

last: Dorot

first: Edward

last: Pichinuk

first: Michael

last: Gershovits

first: Miguel

last: Weil

first: Adit

last: Ben-Baruch


title: Persistent inflammatory stimulation drives the transition of MSCs to inflammatory CAFs that promote pro-metastatic characteristics in breast cancer cells [II]

overall_design: To determine transcriptome alterations upon short-term and persistent cytokine stimulation, with each cytokine alone or both of them together, genome-wide expression analysis was performed on MSCs stimulated by TNFα and/or IL-1β or by vehicle controls, for 48 hrs or for 14 days.


title: Persistent inflammatory stimulation drives the transition of MSCs to inflammatory CAFs that promote pro-metastatic characteristics in breast cancer cells


title: Nanopore DNA sequencing in a model of oxidative stress

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

type: Methylation profiling by high throughput sequencing

summary: Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human cell lineHEK 293T, before and after oxidative stress, using long-read nanopore sequencing.

overall_design: Oxidative stress was induced in vitro with hydrogen peroxide (H2O2) alone or in combination with N-acetyl-cysteine (NAC) as a rescue treatment. mtDNA was enriched by sequential gradient centrifugation and, after linearization with BamH1, samples were barcoded and sequenced with a MinION device (ONT).

first: Chloe

last: Goldsmith


title: Transcriptome profiling of 60 human lung cell lines by strand-specific RNA sequencing after rRNA depletion

city: Freiburg im Breisgau

first: Jagriti

last: Pal

state: Baden Wurttemburg

address: Breisacher Str. 115

department: ZTZ

institute: Universitatsklinikum, Freiburg

summary: We performed deep RNA sequencing of 60 human lung cell lines: 50 lung adenocarcinoma cell lines, 7 NSCLC (non small cell lung cancer, non-adenocarcinoma) cell lines, 3 non-transformed lung cell lines. Total RNA was isolated and subjected to rRNA depletion to maintain also non-polyadenylated transcripts. Strand-specific next generation sequencing (NGS) using Illumina HiSeq allowed us to distinguish reads in the sense and antisense direction. The cell lines were sequenced in 2 or 3 replicates. Reads were aligned to the human reference genome GRCh38 using STAR mapper. The expression of 58,096 genes was calculated in terms of FPKM for every sample.

overall_design: Gene expression profiling of NSCLC lung cancer cell line panel

first: Yanhong

last: Lyu

first: Sven

last: Diederichs


title: Nanopore DNA sequencing of a human liver progenitor-like cell line

summary: Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human hepatocyte-like progenitor cell line HepaRG, before and after in vitro differentiation, using long-read nanopore sequencing.

overall_design: HepaRG cell were differentiated in vitro in three independent wells. mtDNA was enriched by sequential gradient centrifugation and, after linearization with BamH1, samples were barcoded and sequenced with a MinION device (ONT).


title: iPSC-derived Human Intestinal Organoids are permissive to SARS-CoV-2 infection

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using a directed differentiation protocol to generate mesenchyme free, regionally patterned intestinal organoids. These organoids were then infected with SARS-CoV-2, and sequencing was performed 1 and 4 days post infection

overall_design: Global transcriptomic analysis of PSC-derived intestinal organoids infected with SARS-CoV-2 omparing 1 and 4 days post infection to matched mock controls in both proximal and distally patterned infestinal organoids. (n=3 per condition)

first: Aditya

last: Mithal

first: Jonathan

last: Lindstrom-Vautrin

first: Gustavo

last: Mostoslavsky


title: RNA Immunoprecipitation(RIP)-seq of Flag-USP39 in ovarian cancer cells

city: jinan

first: Shourong

last: Wang

address: 44 Wenhua Xi Road

institute: Shandong University

summary: High-grade serous ovarian carcinoma is the most lethal type of gynecologic malignancy.Emerging evidences have suggested the vital roles of splicing factor in the human cancers. RNA splicing pathways was found excessive activated in HGSOC. USP39 was one of overexpressed splicing factor in HGSOC. However, the biological function and concrete regulatory mechanism of USP39 in ovarian cancer remain unclear. In this study, we investigate the oncogenic roles of the splicing factor USP39 in HGSOC through facilitated the growth speed and invasion of ovarian cancer cells.Elevated USP39 expression levels, based on immunohistochemistry staining, were associated with poor survival in HGSOC patients. In order to investigate the binding peaks of USP39 in ovarian cancer,we performed RIP-seq in A2780 cells with Flag-USP39 overexpression.

overall_design: The assay was performed in A2780 cells with Flag-USP39 using anti-Flag antibody.10% of total RNA was used as input.

first: Zhaojina

last: Liu


title: Protective microbes alter the transcriptional response of Caenorhabditis elegans nematodes to pathogenic infection

city: Oxford

first: Kayla

last: King

address: 11a Mansfield Road

department: Department of Zoology

institute: University of Oxford

summary: We sequenced the transcriptome of a host (Caenorhabditis elegans) following its interaction with a non-native bacterium (Enterococcus faecalis) that has protective traits against the pathogen, Staphylococcus aureus. We also investigated the impact that the evolutionary history of the protective bacterium has on the transcriptional history of the host. We tested protective bacteria that had either coevolved against the pathogen within C. elegans, or had evolved on its own within C. elegans.

overall_design: We generated the data over two independent experiments, "1" and "2". Within each independent experiment we included all the comparisons and controls required for each question, i.e. no comparisons were made across the independent experiments.  In  experiment 1, we measured the transcriptional response to three E. faecalis treatments and  a control treatment of Escherichia coli OP50, which is widely used as a food source for C. elegans. We included 5 independent biological replicates for each of these treatments. In experiment 2, we measured the transcriptional response to these same three E. faecalis treatments in the presence of S. aureus, along with a treatment where C. elegans were exposed to just S. aureus alone. We also included the control treatment of Escherichia coli OP50. We included 5 independent biological replicates for each of these treatments. Results and the full materials and methods for experiment 1 are included in one manuscript (insert bioRxiv link here when uploaded), and results ad full materials and methods for experiment 2 are included across two manuscripts, (BioRxiv https://doi.org/10.1101/857540 and insert bioRxiv link here when uploaded). All samples were sequenced evenly across 5 units of a flow cell and were delivered in two batches. The first 3 units were delivered together and the 2 remaining units were delivered together, resulting in two sets of files for each sample.

first: Suzanne

middle: A

last: Ford


title: Identification of novel transcription factors that regulate prostate cancer cell metabolism

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

summary: To understand of the impact of KLF5 and NFYA on metabolism in prostate cancer cells

overall_design: LNCaP cells were plated in RPMI 1640 media with no phenol red and with 5% charcoal stripped serum, sodium pyruvate, penicillin and streptomycin. After 48h (to allow adnrogen deprivation), fresh media was added, with 96% ethanol or the synthetic androgen R1881 (10nM concentration). After trypsinization cells were seeded in media with CSS and transfected with a pool of non-targeted control siRNAs or a pool of siRNAs targeted against KLF5 and NFYA

first: Raghavendra

last: Karthik Poluri


title: RNA sequencing (RNA-SEQ) of USP39 knockdown by shRNA in ovarian cancer cells

summary: High-grade serous ovarian carcinoma is the most lethal type of gynecologic malignancy.Emerging evidences have suggested the vital roles of splicing factor in the human cancers. RNA splicing pathways was found excessive activated in HGSOC. USP39 was one of overexpressed splicing factor in HGSOC. However, the biological function and concrete regulatory mechanism of USP39 in ovarian cancer remain unclear. In this study, we investigate the oncogenic roles of the splicing factor USP39 in HGSOC through facilitated the growth speed and invasion of ovarian cancer cells.Elevated USP39 expression levels, based on immunohistochemistry staining, were associated with poor survival in HGSOC patients. In order to investigate the regulatory mechanism of USP39 in ovarian cancer,we performed RNA-seq in A2780 cells with USP39 knock down compared with control in three repeat. HMGA2 was identified as USP39 target gene because of different expression and downregulated splicing efficiency.

overall_design: The assay was performed in A2780 cells with USP39 knock down and control cells on three biological triplicates .


title: Peptide 1018 disrupts swarming and the swarming-associated, anr-mediated metabolic program of Pseudomonas aeruginosa

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Abstract: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen found ubiquitously in the environment. Responsible for considerable human morbidity and mortality, particularly in nosocomial infections and individuals with cystic fibrosis, P. aeruginosa can adapt to surface growth by undergoing swarming motility. In P. aeruginosa, swarming motility is a rapid multicellular movement that occurs on soft surfaces of appropriate viscosity with amino acids as a nitrogen source. Here we tested the small synthetic host defense peptide, innate defense regulator 1018, and found that it inhibited swarming motility at concentrations as low as 0.75 μg/ml, well below the MIC for planktonic cells. A screen of the PA14 transposon insertion mutant library revealed twenty-nine mutants that demonstrated partial tolerance to 1018 under swarming conditions. Two of these mutants, in the genes anr and rhlB (a regulator of anaerobic metabolism and protein involved in rhamnolipid production, respectively), were complemented to restore susceptibility to 1018. RNA-Seq of peptide-treated cells under swarming conditions revealed the dysregulation of 1,190 genes compared to the untreated swarm front, and 67% of these genes were similarly dysregulated at the untreated swarm centre. In contrast, expression of 70 Anr-regulated genes was upregulated by peptide treatment, and 45 genes showed differential or opposite regulation of expression in peptide-treated and swarm centre cells. Many transcriptional regulators required for swarming were dysregulated in peptide-treated cells, indicative of a mechanism by which 1018 may inhibit swarming motility. Overall, this study illustrates a use for peptide 1018 in inhibiting swarming surface motility, an important bacterial adaptation.

overall_design: RNA-Seq of P. aeruginosa inoculated on swarming agar centre and edge cells in the absence or presence of host-defense peptide IDR-1018 (0.75 ug/ml). Thus, three samples with two replicates each.

first: Lauren

middle: V

last: Wilkinson

first: Shannon

last: Coleman

first: Morgan

last: Alford

first: Catherine

last: Wu

middle: H

first: Bradford

last: Ross

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: Tet2 inactivation enhances the anti-tumor activity of tumor-infiltrating lymphocytes

city: Houston

first: Jianfang

last: Li

address: 2121 W. Holcombe Boulevard

institute: Texas A&M University

summary: Inactivation of tumor infiltrating lymphocytes (TILs) is one of the limiting factors of anti-tumor immunity during tumor onset and progression. Epigenetic abnormalities are regarded as a major culprit contributing to the dysfunction of TILs within tumor microenvironment. In this study, we used a murine model of melanoma to discover that Tet2 inactivation significantly enhances the anti-tumor activity of TILs, with the efficacy comparable to immune checkpoint inhibition imposed by anti-PD-L1 treatment. Single-cell RNA-seq analysis further reveals that Tet2-deficient TILs exhibit effector-like features. Transcriptomic and ATAC-seq analysis further demonstrated that Tet2 deletion reshapes the chromatin accessibility and favors the binding of transcription factors geared toward CD8+ T cell activation. In summary, our study establishes that Tet2 constitutes one of the epigenetic barriers contributing to dysfunction of TILs during anti-tumor immunity, and that Tet2 inactivation could benefit anti-tumor immunity and suppress tumor growth.

overall_design: We collected WT and Tet2KO TILs (with and without anti-PD-L1 treatment) 8 days after adoptive T cell transfer for scRNA-seq analysis. We collected WT and Tet2KO TILs before and 3 days after adoptive T cell transfer for RNA-seq and ATAC-seq analysis.

first: Minjung

first: Shaohai

last: Fang

first: Joanna

last: Zhang

first: Anh

last: Vo

first: Wei

last: Han

first: Hongxiang

last: Zeng

first: Sevinj

last: Isgandarova

first: Margie

last: Moczygemba

first: Weidong

first: Yubin

last: Zhou

first: Deqiang

last: Sun

first: Jia

first: Yun

last: Huang


title: mRNA-seq analysis of superficial zone (SFZ) cells articular cartilage of 5-day-old mice

city: Tokyo

first: Yuji

last: Maenohara

address: 7-3-1, Hongo, Bunkyo-ku

department: Orthopaedic department

institute: University of Tokyo

summary: We compared gene expression profiles of SFZ cells of WT mice and Prg4KO mice using mRNA-seq analysis.

overall_design: gene expression profiles of SFZ cells obtained from WT mice and Prg4KO mice

first: Taku

last: Saito


title: Comparison of the hepatic effects of phenobarbital in chimeric mice containing either rat or human hepatocytes with humanized constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mice (hCAR/hPXR mice) [chimeric humanized liver experiments]

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co., Ltd.

summary: Using a chimeric mouse humanized liver model, we provided evidence that human hepatocytes are refractory to the mitogenic effects of rodent constitutive androstane receptor (CAR) activators. To evaluate the functional reliability of this model, the present study examined mitogenic responses to phenobarbital (PB) in chimeric mice transplanted with rat hepatocytes, since rats are responsive to CAR activators. Treatment with 1000 ppm PB for 7 days significantly increased replicative DNA synthesis (RDS) in rat hepatocytes of the chimeric mice, demonstrating that the transplanted hepatocyte model is functionally reliable for cell proliferation analysis. Treatment of humanized CAR and pregnane X receptor (PXR) mice (hCAR/hPXR mice) with 1000 ppm PB for 7 days significantly increased hepatocyte RDS together with increases in several mitogenic genes. Global gene expression analysis was performed with liver samples from this and from previous studies focusing on PB-induced Wnt/β-catenin signaling, and showed that altered genes in hCAR/hPXR mice clustered most closely with liver tumor samples from a diethylnitrosamine/PB initiation/promotion study than with wild type mice. However, different gene clusters were observed for chimeric mice with human hepatocytes for Wnt/ß-catenin signaling when compared to those of hCAR/hPXR mice, wild type mice and liver tumor samples. The results of this study demonstrate clear differences in the effects of PB on hepatocyte RDS and global gene expression between human hepatocytes of chimeric mice and hCAR/hPXR mice, suggesting that the chimeric mouse model is relevant to humans for studies on the hepatic effects of rodent CAR activators, whereas the hCAR/hPXR mouse is not.

overall_design: Male chimeric mice with human hepatocytes (4-5 animals/dose) were fed diets containing 0 (control), 500 or 1000 ppm PB for 7 days. Liver samples of these animals were used for gene expression analysis.

first: Tomoya

last: Yamada


title: Comparison of the hepatic effects of phenobarbital in chimeric mice containing either rat or human hepatocytes with humanized constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mice (hCAR/hPXR mice) [mouse liver experiments]

overall_design: Male CD-1 mice (4 animals/dose) were fed diets containing 0 (control) or 1500 ppm PB for 7 days. Male hCAR/hPXR mice (7 animals/dose) were fed diets containing 0 (control) or 1000 ppm PB for 7 days. Male C3H/HeNCrlCrlj  mice (3 animals/dose) were fed diets containing 0 (control) or 500 ppm PB for 27 weeks after a single intraperitoneal injection of 90 mg/kg diethylnitrosamine. Liver samples of these animals were used for gene expression analysis.


title: Comparison of the hepatic effects of phenobarbital in chimeric mice containing either rat or human hepatocytes with humanized constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mice (hCAR/hPXR mice) [rat liver experiments]

overall_design: Male chimeric mice with rat hepatocytes, Crl:CD(SD) rats and CAR KO rats (4-7 animals/dose) were fed diets containing 0 (control) or 1000 ppm PB for 7 days. Liver samples of these animals were used for gene expression analysis.


title: Histone modification profiling of T-cell prolymphocytic leukemia through chromatin immunoprecipitation and sequencing

city: ROCHESTER

first: Shulan

last: Tian

state: Minnesota

address: 200 1st street SW

department: Health Science Research

institute: Mayo Clinic

summary: T-cell prolymphocytic leukemia (T-PLL) is a rare disease with rapid clinical course. Whole-exome and whole-genome sequencing have identified structural alterations in T-PLL, including inversion, translocation and copy number variation. Epigenetic alterations are the hallmark of many cancers. However, genome-wide epigenomic profiles have not been reported in T-PLL. In this study, we generated genome-wide maps of regulatory regions in both T-PLL patients and healthy individuals using H3K4me3 and H3K27ac ChIP-seq. We revealed a global alteration of both promoter and enhancer landscape in T-PLL, which supported the role of epigenetic regulation in transcriptional dysregulation of oncogenes and genes involved in DNA damage response and T-cell activation.

overall_design:
ChIP was performed with peripheral blood mononuclear cells (PBMCs) in T-PLL patients and healthy individuals, using anti-H3K27ac antibody (Abcam, Cat. # ab4729) and in-house generated anti-H3K4me3 antibody, as previously described (PMID: 29268714). The internal H3K4me3 antibody was validated by dot blotting with peptide, ChIP-qPCR with known positive and negative targets, and ChIP-seq (PMID: 29268714). PBMCs from T-PLL samples are over 90% leukemic T cells. For the normal, CD3+ enriched PBMCs were selected. ChIP-seq libraries were prepared from about 5 ng ChIP and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI). ChIP enrichment was validated using real-time PCR. Libraries were sequenced from as 2 x 51 bp or 2 x 101 bp on a Illumina HiSeq4000 platform.
----------------------
Authors state that they "will submit raw fastq files to dbGap".

last: Ding

first: Huihuang

last: Yan


title: Rapid intrahepatic and peripheral blood HCV RNA decline and HCV-specific immune response increase during IFN-free DAA therapy in HCV treatment-naïve patients [exp1]

city: Beerse

first: Marianne

last: Tuefferd

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary: Over 12 weeks of treatment with a combination of sofosbuvir, simeprevir and daclatasvir, FNABs from 9 chronically HCV infected patients were profiled longitudinally (baseline, day 2, week 1, end of treatment (EOT) and post-treatment follow-up week 24)

overall_design: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient)

first: Sonya

last: MacParland

first: Vera

last: Cherepanov

first: Sagar

last: Marwah

first: Leen

last: Vijge

first: Mohamed

last: Gamil

first: Maria

last: Beumont

first: Sharon

last: Yoon

first: A

last: Rahman

first: Analiza

last: Aquino

first: Camelia

last: Capraru

first: Mayur

last: Brahmania

first: David

last: Wong

first: Richard

last: Harrigan

first: Harry

last: Janssen

first: Mark

last: Sulkowski

first: Jordan

middle: J

last: Feld


title: FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity

city: Philadelphia

first: Klaus

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

summary: Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced.  This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.

overall_design: WGBS, RRBS, and ChIP seq performed on Foxa1/2 mice depleted in liver development or in adulthood

first: Yitzhak

last: Reizel

first: Ashleigh

last: Morgan

first: Kenneth

middle: S

last: Zaret


title: Rapid intrahepatic and peripheral blood HCV RNA decline and HCV-specific immune response increase during IFN-free DAA therapy in HCV treatment-naïve patients

first: Marianne

last: Tuefferd

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

overall_design: Refer to individual Series


title: Rapid intrahepatic and peripheral blood HCV RNA decline and HCV-specific immune response increase during IFN-free DAA therapy in HCV treatment-naïve patients [exp2]

summary: Over 12 weeks of treatment with a combination of sofosbuvir, simeprevir and daclatasvir, PBMCs from 9 chronically HCV infected patients were profiled longitudinally (baseline, day 2, week 1, end of treatment (EOT) and post-treatment follow-up week 24)

overall_design: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient)

first: Sonya

last: MacParland

first: Vera

last: Cherepanov

first: Sagar

last: Marwah

first: Leen

last: Vijge

first: Mohamed

last: Gamil


title: Sequential progenitor states mark the generation of pancreatic endocrine lineages in mice and humans

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: The pancreatic islet contains multiple hormone+ endocrine lineages (alpha, beta, delta, PP and epsilon cells), but the developmental processes that underlie endocrinogenesis are poorly understood. Here, we generated novel mouse lines and combined them with various genetic tools to enrich all types of hormone+ cells for well-based deep single-cell RNA sequencing (scRNA-seq), and gene coexpression networks were extracted from the generated data for the optimization of high-throughput droplet-based scRNA-seq analyses. These analyses defined an entire endocrinogenesis pathway in which different states of endocrine progenitor (EP) cells sequentially differentiate into specific endocrine lineages in mice. Subpopulations of the EP cells at the final stage (EP4-early and EP4-late) show different potentials for distinct endocrine lineages. epsilon cells and an intermediate cell population were identified as distinct progenitors that independently generate both alpha and PP cells. Single-cell analyses were also performed to delineate the human pancreatic endocrinogenesis process. Although the developmental trajectory of pancreatic lineages is generally conserved between humans and mice, clear interspecies differences, including differences in the proportions of cell types and the regulatory networks associated with the differentiation of specific lineages, have been detected. Our findings support a model in which sequential transient progenitor cell states determine the differentiation of multiple cell lineages and provide a blueprint for directing the generation of pancreatic islets in vitro.

overall_design: The overall goal of this study was to comprehensively delineate the developmental trajectory of pancreatic endocrine cells using single-cell RNA-seq (scRNA-seq) analyses. We performed scRNA-seq on EP cells and hormone+ cells from embryonic day (E) 13.5 to postnatal day (P) 3 mice using the Smart-seq2 method. To enrich low-abundance EP cells and their descendant endocrine lineages from the pancreas, we treated Ngn3-CreER;Rosa-RFP mice with a single tamoxifen pulse for 1 or 2 days, and collected RFP+ cells from E13.5-E18.5 by fluorescence-activated cell sorting (FACS). To enrich low-abundance differentiated ε-, δ-, and PP-cells, we generated fluorescent-labeled knock-in Ghrl-P2A-CFP, Sst-P2A-BFP and Ppy-P2A-mNeptune mouse lines. To obtain an unbiased and comprehensive distribution of EP cells and endocrine lineages, we generated 10x Genomics scRNA-seq datasets of E16.5, E17.5, and E18.5 pancreatic cells that were separately from the dorsal and ventral pancreas.

first: Xin-Xin

last: Yu

first: Wei-Lin

last: Qiu

first: Liu

last: Yang

first: Yan-Chun

last: Wang


title: Single Cell Transcriptome Profiling of Cardiac Non-myocyte

city: Guangzhou

first: Yuchen

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: The mammalian heart is composed of a variety types of cells that can be roughly categorized into cardiomyocytes and non-myocytes. Instead of being bystanders of cardiac function, cardiac non-myocytes provide critical structural, mechanical and electrophysiological support to the working myocardium. However, the precise cellular identity and molecular features of the non-myocytes at single cell level remain elusive. Depiction of epigenetic landscape with transcriptomic signatures using the latest single cell multi-omics has the potential to unravel the molecular programs of cardiac non-myocytes underlying their cellular diversity. To characterize the molecular and cellular features of cardiac non-myocytes populations in the adult murine heart at single cell level. We applied single cell Assay for Transposase Aaccessible Chromatin using sequencing (scATAC-seq) in combination with high-throughput single cell RNA-seq (scRNA-seq) to map the epigenetic landscape and gene expression program of cardiac non-myocytes from adult murine heart. Through integrated dual-omics data analysis, we categorize the cardiac non-myocytes into 4 defined populations including endothelial cells, fibroblast, pericytes and immune cells with distinct chromatin accessibility patterns. Cis- and trans-regulatory factors for each cell type were identified.  In particular, unbiased sub-clustering and functional annotation of the cardiac fibroblast (FB), indicated the heterogeneity and functionality of FB subtypes associated with cellular response, cytoskeleton organization and immune regulation. We further validated the expression and function of novel markers in major FB sub-populations and experimentally determined the distribution of the FB sub-populations in healthy and injured murine heart. In summary, we comprehensively characterized the non-myocyte cellular identity at the single-cell level and defined FB subpopulations by their functional states.

overall_design: Single-cell RNA-seq profiles of cardiac non-myocytes isolated at two 10-12 week old mice were generated by deep sequencing using 10x Genomics Chromium System.

first: Li

last: Qian


title: Next-generation RNA Sequencing and Transcriptome Comparison of Mouse Wild Type and Mesenchymal Tgfbr2 conditional knockout  lungs of E15.5

city: Los Angeles

first: Brendan

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Lung mesenchymal knockout of transforming growth factor, beta receptor II (Tgfbr2) will lead to lung malformation, including impaired lung branching and cystic lesion. In order to understand the underlying mechanisms, total RNA of wild type and mesenchymal Tgfbr2 knockout lungs were isolated and sequenced using the next-generation RNA sequencing technique.

overall_design: Tgfbr2 flox mice were crossed with Tbx4-rtTA/TetO-Cre transgenic mice and received doxycycline treatment from E6.5 to generate the lung mesenchyme-specific and inducible Tgfbr2 conditional knockout (CKO) mice. Lung mRNA profiles of E15.5 fetal wild type and Tgfbr2 conditional mice were then generated by deep sequencing, in triplicate.

first: Wei

last: Shi

first: Yongfeng

last: Luo

first: Matthew

last: Thornton


title: Hippocampal GR and pCREB binding analysis of glucocorticoid enhanced memory formation [ChIP-seq]

status: Public on Apr 19 2021

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

summary:
Aim: We investigated whether glucocorticoid effects on memory are associated with genomic interactions between the GR and pCREB in the hippocampus.
Methods: Adult male rats received 3 minutes of object exploration training or no training either with a 3.0mg.kg post-training corticosterone injection or vehicle injection to study the molecular effects underlying enhanced memory formation. Hippocampi were dissected 45 minutes after injection and snap-frozen. Subsequently, Chromatin ImmunoPrecipitation was performed for GR and pCREB and the ChIP samples were sequenced.

overall_design: Hippocampal genomic binding of GR and pCREB in male rats studying glucocorticoid enhanced memory formation.

first: Lisa

last: van Weert

first: Onno

last: Meijer


title: Large-scale Generation of Functional and Transplantable Hepatocytes and Cholangiocytes from Human Endoderm Stem Cells

summary: The ever-increasing therapeutic and pharmaceutical demand for liver cells calls for systems that enable mass production of hepatic cells. Here we describe a large-scale suspension system that uses human endoderm stem cells (hEnSCs) as precursors to generate functional and transplantable hepatocytes (E-heps) or cholangiocytes (E-chos). hEnSC-derived hepatic populations are characterized by single-cell transcriptomic analyses and compared with hESC-derived counterparts, in-vitro-maintained or -expanded primary hepatocytes and adult cells, which reveals that hepatic differentiation of hEnSCs recapitulates in vivo development and that the heterogeneities of the resultant populations can be manipulated by regulating the EGF and MAPK signaling pathways. Functional assessments demonstrate that E-heps and E-chos possess properties comparable with adult counterparts and that, when transplanted intraperitoneally, encapsulated E-heps were able to rescue rats with acute liver failure. Our study lays the foundation for cell-based therapeutic agents and in vitro applications for liver diseases.

overall_design: Human endoderm stem cells (EnSCs) were expanded and used as precursors for stepwise directed differentiation into hepatoblasts, as well as functionally mature and transplantable hepatocytes (E-heps) or cholangiocytes (E-chos) in a spinner-flask-based large-scale serum-free 3D culture system. Thorough functional assessment of E-heps and E-chos was performed to compare them with the adult cells. Single cell transcriptomic analysis was applied to characterize the EnSC-derived hepatic populations and to compare them with the pluripotent stem cell-derived counterparts, the in vitro maintained or expanded primary hepatocytes and the adult hepatic cells.

first: Sisi

last: Feng

first: Jiaying

last: Wu

first: Xiaogang

last: Deng

first: Hao

last: Yin

first: Luonan

last: Chen

first: Cheng-Ran

first: Xin

last: Cheng


title: Whole brain transcriptome analysis of Shank2 knock-out mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Autism spectrum disorders (ASDs) are thought to involve neurodevelopmental dysregulations that lead to visible symptoms at early stages of life. Many ASD-related mechanisms suggested by animal studies are supported by demonstrated improvement in autistic-like phenotypes in adult animals following experimental reversal of dysregulated mechanisms. However, whether such mechanisms also act at earlier stages to cause autistic-like phenotypes is unclear. Here, we show that early correction of a dysregulated mechanism in young mice prevents manifestation of autistic-like phenotypes in adult mice. Shank2–/– mice, known to display N-methyl-D-aspartate receptor (NMDAR) hypofunction and autistic-like behaviors at post-weaning stages after postnatal day 21 (P21), show the opposite synaptic phenotype–NMDAR hyperfunction–at an earlier pre-weaning stage (~P14). Moreover, this NMDAR hyperfunction at P14 is rapidly shifted to NMDAR hypofunction after weaning (~P24). Chronic suppression of the early NMDAR hyperfunction by the NMDAR antagonist memantine (P7?21) prevents the NMDAR hypofunction and autistic-like behaviors from manifesting at later stages (~P28 and P56). These results suggest that early NMDAR hyperfunction leads to late NMDAR hypofunction and autistic-like behaviors in Shank2–/– mice, and that early correction of NMDAR function has the long-lasting effect of preventing autistic-like phenotypes from developing at later stages.

overall_design: Whole brain transcriptome of 6 P14 WT naïve, 6 P25 WT naïve, 6 P14 Shank2 knock-out naïve, 6 P25 Shank2 knock-out naïve mice.

first: Changuk

last: Chung

first: Hyojin

last: Kang


title: Hippocampal GR/pCREB binding and transciptome analysis of glucocorticoid enhanced memory formation


title: Overexpression of circCUL2 in normal fibroblasts

first: Shangyou

last: Zheng

address: Guangzhou

institute: Guangdong Provincial People's Hospital

summary: We have found through previous experiments that circCUL2 acts as a key regulator of cancer-associated fibroblasts activation. To determine how circCUL2 exert its function, we performed mRNA sequencing of normal fibroblasts (NFs) and circCUL2-transduced NFs. 48 hours after transfection, RNA was isolated and sent for total RNA sequencing. Differential gene expression between circCUL2-overexpression and empty vector revealed enrichment for several inflammation pathways implicating involvement of these pathways in inflammatory cancer-associated fibroblasts activation.

overall_design: Analyze of differentially expressed genes in circCUL2-overexpression NFs by Next-generation sequencing

first: Chonghui

last: Hu

first: Hongcao

last: Lin


title: Hippocampal transcriptome analysis of glucocorticoid enhanced memory formation [RNA-seq]

summary:
Aim: We investigated whether glucocorticoid effects on memory are associated with genomic interactions between the GR and pCREB in the hippocampus.
Methods: Adult male rats received 3 minutes of object exploration training or no training either with a 3.0mg.kg post-training corticosterone or vehicle injection to study the molecular effects underlying enhanced memory formation. Hippocampi were dissected 3 hours after injection and snap-frozen. Subsequently, total RNA was isolated and send for 100bp paired-end sequencing by BGI.

overall_design: Hippocampal mRNA profiles of male rats studying glucocorticoid enhanced memory formation.


title: Subtype specific analyses reveal Infiltrative Basal Cell Carcinoma are highly interactive with their environment

city: Brisbane

first: Valentine

last: Murigneux

state: QLD

address: 37 Kent St, Woolloongabba

institute: The University of Queensland Diamantina Institute, Faculty of Medicine

summary: Little is known regarding the differences between BCC subtypes, despite clearly distinct phenotypes and clinical outcomes. In particular, what distinguishes the aggressive infiltrative BCC subtype. We determine that infiltrative BCC do not contain an obviously distinct genomic variant profile however show clear molecular signalling differences compared to less aggressive subtypes. RNA sequencing enabled identification of candidate regulators of infiltrative subtype development such as Wnt and Integrin signalling, and suggested that infiltrative BCC have a strong relationship with their surrounding environment. In particular, WISP1 and Periostin gene expression is associated with the infiltrating subtype and represent candidate regulators of subtype differences in human BCC.

overall_design: RNA extraction direct from human tissue used to generate RNA profiles for BCC subtype. BCC subtype indicates majority subtype, classified via histological investigation.

first: Rehan

last: Villani

first: Josue

last: Alexis

first: Seen-Ling

last: Sim

first: Edwige

last: Roy

first: Michael

last: Wagels

first: Nicholas

last: Saunders

first: H

last: Soyer

first: Lynn

last: Fink

first: Kiarash

last: Khosrotehrani


title: EGF-induced Transcriptome Changes in GBM stem-like cells

city: Baltimore

first: Mingyao

last: Ying

state: MD

address: 733 N Broadway

department: Department of Neurology

country: USA

institute: Johns Hopkins School of Medicine

summary: GBM neurosphere line GBM1B were depleted of growth factors for 16 hours followed by EGF stimulation for 4 and 24 hours. RNA-seq was used to identify differentially-expressed (DE) genes after EGF treatment.

overall_design: Total RNA was extracted using the RNeasy kit (Qiagen). 4 µg of total RNA was subjected to library preparation using Illumina TrueSeq RNA Sample Preparation kit v2 (Illumina). Libraries were assessed using an Agilent Bioanalyzer (Agilent Technologies) to confirm that cDNA fragment sizes were between 200 and 500 bp in length. Sequencing was performed using an Illumina HiSeq 2500 platform (Illumina). The raw reads were aligned to reference human genome build hg19 using HISAT2 with default parameters. For each gene, the number of reads aligned to its exons were counted and summarized into gene level counts by StringTie based on the GENCODE hg19 annotation. Normalization between samples was carried out by R package edgeR, which controls sequencing depth and RNA composition effects.

first: John

last: Laterra


title: Genome-wide mRNA profiling of induced Medulloblastoma (iMB) from human iPS cells

summary: We used human induced pluripotent stem cells (iPSCs) to establish tumors recapitulating the histological and transcriptional hallmarks of MYC-driven medulloblastoma (MB). We generated neuronal precursors from human iPSCs. These neuronal precursors were transformed by the MYC oncogene combined with p53 loss-of-function to generate MB xenografts for RNA-seq analysis.

overall_design: Transcriptomic profiling of induced medulloblastoma xenografts from human iPS cells and comparing to clinical medulloblastoma specimens.


title: Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors  [ATAC-seq]

city: BOSTON

first: CHANGHEE

last: LEE

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

summary: The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.

overall_design: We used ATAC-seq to profile the open chromatin regions in early embryonic chick retinal tissue

first: Nicolas

last: Lonfat

first: Su

last: Wang

first: ChangHee

last: Lee

first: Mauricio

last: Garcia

first: Jiho

last: Choi

first: Peter

last: Park

first: Connie

last: Cepko


title: TAZ ChIP-sequencing in GBM cells

summary: ChIP-Sequencing for the transcription factor TAZ (WWTR1) was performed to define genome-wide TAZ binding sites in GBM stem-like cells.

overall_design: Cells after EGF treatment for 4 hours were subjected to TAZ ChIP using the MAGnify ChIP system (Invitrogen) following the manufacturer’s protocol. TAZ-associated DNA was immunoprecipitated using rabbit anti-TAZ antibody (Cell Signaling) and Dynabeads magnetic beads (Invitrogen). ChIP-enriched DNA or input DNA (10 ng each) was subjected to library preparation using a ChIP-Seq DNA Sample Prep kit (Illumina). Sequencing was performed using an Illumina HiSeq 2500 platform.


title: Identification of network hub genes in FUS-dependent amyotrophic lateral sclerosis iPS cell models RNA-seq analysis of NSC-34 mouse motor neuron-like cells

city: Fujisawa

first: MASAHIRO

last: NOGAMI

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company Limited


title: Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors [CUT&RUN]

overall_design: CUT&RUN assay was carried out using antibodies against Otx2, Oc1 and H3K27me3 and IgG control on WT chick E5 retina


title: Next Generation Sequencing of exosomal microRNA derived from MCU downregulated and control MDA-MB-231 cells.

first: Xianchong

last: Zheng

address: No.651, Dongfengdonglu, Yuexiu District

institute: Sun Yat-sen University Cancer Center

summary: To explore the role of the mitochondrial Ca2+ uniporter (MCU) in exosomal microRNA(miRNA) sorting in MDA-MB-231 cells, we isolated miRNA from the exosomes derived from MCU-downregulated and control MDA-MB-231 cells. We then performed Next Generation Sequencing (NGS) and real-time quantitative polymerase chain reaction (qRT-PCR) to find and validate differetial expressed exosomal miRNAs that regulated by MCU.

overall_design: Examination of differential expressed exosomal miRNAs in MCU-downregualted and control MDA-MB-231 cells.

first: Hehai

last: Huang


title: Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors

summary:
The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome expression changes in human gastric epithelial cells co-cultured with Helicobacter pylori lysate of different generations.

status: Public on Apr 18 2021

first: Xiulin

last: Zhang

address: No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing

institute: Capital Medical University

summary: With the colonization of Helicobacter Pylori (H.pylori) in the human stomach, a large amount of Helicobacter Pylori (H.pylori)colonized into the stomach disintegrates and releases a large number plenty of toxic proteins and other bacterial structure components. TollToll-like receptors (TLRs) in gastric epithelial cells which sensitive to the components of bacteria lysate around the microenvironment attach them and activite innate immune and pro-inflammatory response once contact with antigen. The consequences after long-term stimulation of H.pylori lysate in gastric epithelial cells has not been reported . To investigate the effects of H.pylori lysate on TLRs expression and inflammatory cytokines level during long-term stimulation of gastric epithelial cells and clarify the potential mechanismHence, we detected TLRs mRNA level and inflammatory cytokines expression in GES-1 cells co-culture with lysate from 1 to 30 generations. The sensitivity to H.pylori or H.pylori lysate in GES-1 cells were also monitored. We also explored whether LPS was the main factors contributing to this change. Mongolian gerbils were used to replicate H.pylori infection animal model. After transcriptome sequencing，A TLR2/6 heterodimers agonist Pam2CSK4 and a highly selective inhibitor of PI3K LY294002 were used to clarify the TLR6 signaling pathways. In a conclusion, we discovered that the sensitivity of TLRs in human gastric epithelial cells decreased while after long-time co-culture with H.pylori lysate. Human gastric epithelial cells shows tolerance to H.pylori lysate in TLRs and inflammatory cytokines level.  decreased the high level of TLRs and inflammatory cytokines after stimulating GES-1 cells with H.pylori lysate for a short-term. And Tthis process may  works through the TLR6/PI3K/NF-κKB axis.

overall_design: We performed RNA - Seq of wild GES-1 cells, GES-1 cells co-cultured with Helicobacter pylori lysate for 1 generation and GES-1 cells co-cultured with Helicobacter pylori lysate for 30 generations  in triplicate.

first: Changlong

last: Li

first: Zhenwen

last: Chen


title: Chromatin accessibility profiling of primary human T cells

city: San Francisco

first: Ruby

last: Yu

address: 513 Parnassus Ave

institute: UCSF

summary: Genetically-engineered immune cell therapies have been in development for decades and recently have proven effective to treat some types of cancer. CRISPR-based genome editing methods enabling more flexible and targeted sequence integrations than viral transduction have potential to extend the clinical utility of cell therapies. Realization of this potential depends on improved knowledge of how coding and non-coding sites throughout the genome can be modified efficiently and on improved methods to discover novel synthetic DNA sequences that can be introduced at targeted sites to enhance critical immune cell functions. Here, we developed improved rules for non-viral genome targeting in human T cells and a pooled discovery platform to identify synthetic genome modifications that enhance therapeutically-relevant cell functions.  We elucidated the breadth of targetable genomic loci by performing large knockins at 91 different genomic sites in primary human T cells, and demonstrated the power of flexible genome targeting by generating cells with Genetically Engineered Endogenous Proteins (GEEPs) that seamlessly integrate synthetic and endogenous genetic elements to alter signaling input, output, or regulatory control of genes encoding key immune receptors. Motivated by success in introducing synthetic circuits into endogenous sites, we then developed a platform to facilitate discovery of novel multi-gene circuits that reprogram both T cell specificity and function. We knocked-in barcoded pools of large DNA sequences encoding poly-cistronic gene programs. High-throughput pooled screening of targeted knock-ins to the endogenous T cell receptor (TCR) locus revealed a transcriptional regulator and novel protein chimeras that combined with a new TCR specificity to enhance T cell responses in the presence of suppressive conditions in vitro and in vivo. Overall, these pre-clinical studies provide flexible tools to discover complex synthetic gene programs that can be written into targeted genome sites to generate more effective therapeutic cells.

overall_design: ATAC-seq profiling of primary human CD4+ or CD8+ T cells on day of isolation (pre-stimulation, Day -2) or day of nucleofection (48 hours post-stimulation, Day 0), with 6 different biological replicates (6 individual donors) and two technical replicates per sample.

first: Theodore

last: Roth

first: Michelle

last: Nguyen

first: Alexander

last: Marson


title: RNA-seq analysis of NSC-34 mouse motor neuron-like cells treated with Negative Control siRNA#1 (siNC#1), siNC#2, miR-125b-5p mimic, pre-miR-125b and siRNA (-) control

summary: Fused in sarcoma/translated in liposarcoma (FUS) is a causative gene of familial amyotrophic lateral sclerosis (fALS). Mutated FUS causes accumulation of DNA damage and stress granule (SG) formation, etc., thereby motor neuron (MN) death. However, key molecular aetiology of mutated FUS-dependent fALS (fALS-FUS) remains unclear. Here, both regular bioinformatics and Bayesian gene regulatory networks (GRN) analyses were applied to large-scale transcriptome datasets of induced pluripotent stem cell (iPSC)-derived MNs possessing wild-type form of FUS and mutated FUSH517D (FUSH517D MNs). From regular bioinformatics provided DNA damage response (DDR)-related genes were uniformly down-regulated in FUSH517D MNs. Bayesian GRN calculated by Super-Computer identified miR-125b-5p, TIMELESS and PRKDC as "hub genes/miRNA" which influence the GRNs. miR-125b-5p was up-regulated in FUSH517D MNs and negatively correlated with FUS, TIMELESS and miR-125b-5p target mRNAs. Introduction of miR-125b-5p suppressed Fus, Timeless and DDR-related genes in addition to miR-125b-5p targets in expression, and caused DNA damage. Furthermore, knocking-down Timeless expression caused DNA damage. PRKDC was down-regulated in FUSH517D MNs and the cellular model analyses validated DNA damage under impaired DNA-PK activity promoted FUS mis-localization to SGs. Collectively, our strategy with Bayesian GRNs based on the iPSC model would provide the first compelling evidence to elucidate fALS-FUSH517D molecular aetiology.

overall_design:
To explore the specific target mRNA molecules of miR-125b-5p in motor neuron, NSC-34 were treated with siNC#1, siNC#2, miR-125b-5p mimic, pre-miR-125b and siRNA (-) control and standard RNA-seq was performed.
5 samples were analyzed. "siRNA (-)", "siNC#1" and "siNC#2" are control.

first: Masahiro

last: Nogami

first: Takahisa

last: Ogasawara

first: Masato

last: Yano

first: Hideyuki

last: Okano


title: mRNA-seq data for mouse ovarian tumors arising from oviduct with combinations of (Tamoxifen-inducible) inactivation of Brca1, Trp53, Rb1, and Nf1, or Apc and Pten, and normal ovaries and oviducts.

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: We engineered mice to have Ovgp1 promotor-driven expression of a tamoxifen-inducible Cre recombinase (iCre-ERT2), which inactivated the function of combinations of engineered floxed alleles of combinations of tumor suppressor genes in mouse oviducts (Fallopian tube) when mice were treated with tamoxifen. 21 samples were from oviductal tumors from mice with combinations of floxed alleles of Brca1, Trp53, Rb1, and/or Nf1 (BPRN mice), of which we analyzed 19. 6 samples were from oviductal tumors of mice with floxed alleles of Apc and Pten. 4 control samples were from pooled ovaries from BPRN mice that were not tamoxifen treated, and 4 other control samples were similar pools from mouse oviducts. Our goal was to investigate the similarity of these mouse models of ovarian cancer with different subgroups of human ovarian cancer. We provide raw read data, mapped count data for genes and transcripts, several normalizations of the count data, and supplementary files that contain our first analyses, and may be convenient for consumers wanting to investigate details about their favorite genes. The supplementary files are briefly described in our supplementary file Readme_GEOsupplements_s0.txt.

first: Kevin

last: McCool

first: Zach

last: Freeman

first: Yali

last: Zhai

last: Hu

first: Rong

last: Wu

first: Chiajen

last: Liu

first: Scott

last: Tomlins

first: Eric

middle: R

last: Fearon

first: Brian

last: Magnuson

first: Kathleen

last: Cho


title: RNA-seq analysis of NSC-34 mouse motor neuron-like cells treated with Negative Control siRNA#1 (siNC#1), siNC#2, Fus siRNA#1 (siFus#1), siFus#4, siFus#5 and siRNA (-) control

first: MASAHIRO

last: NOGAMI

overall_design:
To evaluate the effect of down-regulating Fus expression levels in motor neuron, NSC-34 were treated with siNC#1, siNC#2, siFus#1, siFus#4, siFus#5 and siRNA (-) control and standard RNA-seq was performed.
6 samples were analyzed. "siRNA (-)", "siNC#1" and "siNC#2" are control.


title: HTA2.0 (human transcriptome array) analysis of control iPSC-derived motor neurons (MN), FUS-H517D-hetero-iPSC-MN, and FUS-H517D-homo-iPSC-MNs

summary:
To assess  RNA regulation in the MN possessing mutated FUS-H517D gene.
Fused in sarcoma/translated in liposarcoma (FUS) is a causative gene of familial amyotrophic lateral sclerosis (fALS). Mutated FUS causes accumulation of DNA damage stress and stress granule (SG) formation, etc., thereby motor neuron (MN) death. However, key molecular etiology of mutated FUS-dependent fALS (fALS-FUS) remains unclear. Here, Bayesian gene regulatory networks (GRN) calculated by Super-Computer with transcriptome data sets of induced pluripotent stem cell (iPSC)-derived MNs possessing mutated FUSH517D (FUSH517D MNs) and FUSWT identified TIMELESS, PRKDC and miR-125b-5p as "hub genes" which influence fALS-FUS GRNs. miR-125b-5p expression up-regulated in FUSH517D MNs, showed opposite correlations against FUS and TIMELESS mRNA levels as well as reported targets of miR-125b-5p. In addition, ectopic introduction of miR-125b-5p could suppress mRNA expression levels of FUS and TIMELESS in the cells. Furthermore, we found TIMELESS and PRKDC among key players of DNA damage stress response (DDR) were down-regulated in FUSH517D MNs and cellular model analysis validated DDR under impaired DNA-PK activity promoted cytosolic FUS mis-localization to SGs. Our GRNs based on iPSC models would reflect fALS-FUS molecular etiology.

overall_design: RNA from each control MN,  FALS-derived MN possessing H517D mutation in hetero and isogenic MN possessing H517D mutation in homo.  One array per biological replicate.

first: Mitsuru

last: Ishikawa


title: Differential mRNA expression analysis of EGFR-TKI-sensitive cells vs. EGFR-TKI-resistant cells

city: Shanghai

first: Zhang

last: Ke-Ren

address: Chongqing South Road, No. 227

institute: Shanghai Jiao Tong University School of Medicine

summary: Epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) resistance remains unknown. We determined gene expression profiling in EGFR-TKI-resistant cells using RNA-seq analysis

overall_design: Transcription profiling of lung cancer cells

first: Liang

last: Zhu

first: Ke-Ren

last: Zhang


title: Epicardial adipose tissue (EAT) miRNA profiles of healthy control and CAD patients

first: Congcong

address: Anzhen Road 2

institute: Beijing Institute of Heart Lung and Vascular Disease

summary: MicroRNAs (miRNAs) are involved in the formation of atherosclerosis. However, the alteration of miRNA profile in epicardial adipose tissue (EAT) during atherosclerosis is still uncovered. In this study, we compared the miRNA expression profiles of EAT from non-coronary atherosclerosis disease (CAD) and CAD patients, and found that 250 miRNAs were differentially expressed in CAD patients, which were associated with metabolism, ECM and inflammation process. Among the top 20 up-regulated miRNAs, we found that the expression levels of miR-200 family members (hsa-miR-200b/c-3p, miR-141-3p and miR-429), which were rich in endothelial cells, were increased in EAT from CAD patients significantly.

overall_design: EAT miRNA profiles of healthy control and CAD patients. 3 healthy control samples and 5 CAD samples were collected from EAT.

first: Fan


title: Reprogramming the spleen into a functioning “liver” in vivo

status: Public on Apr 17 2021

city: Nanjing

first: Chunyan

address: 163 Xianlin Avenue

institute: Nanjing University

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


title: Identification of M3 muscarinic acetylcholine receptor reactive Th17 cells in patients with primary Sjögren’s syndrome

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: Previously M3 muscarinic acetylcholine receptore (M3R) reactive Th1 cells were identified, and here, M3R reactive Th17 cells were identified in peripheral blood of primary Sjögren’s syndrome patients using ELISpot method. To assess TCR repertoire overlap between identified M3R reactive Th17 cells, and salivary gland infiltrating T cells,  we performed high throughput TCR sequencing of those cells from pSS patient.

overall_design: From pSS patient who were detected positive for M3R reactive Th17 cells by ELISpot method, IL-17 producing CD4+ T cells were FACS sorted after stimulating with M3R peptide for 8 days. Salivary gland(SG) was taken at the time of diagnosis, and stored in RNA later solution. Then, we prepared libraries from these CD4+ T cell sample, together with salivary gland sample and performed unbiased high throughput TCR sequencing using an Ion Genestudio S5 next generation sequencer.

first: Hiroyasu

last: Aoki

first: Kouji

last: Matsushima

first: Saori

last: Abe

first: Hiroyuki

last: Takahashi

first: Hiroto

last: Tsuboi

first: Isao

last: Matsumoto

first: Takayuki

last: Sumida