title: Idenfication of microRNAs regulated by TGFβ in breast cancer cells

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

summary: Upon treatment of TGFβ in MCF10DCIS cells, there are 76 up-regulated and 1 down-regulated microRNAs identified

overall_design: In this study, 4 replicates of MCF10DCIS cells were cultured in the presence of recombinant human TGFβ1 or DMSO control for 72 hours. Then, the cells were collected for total RNA extraction. Differential expressed microRNAs were identified using the NanoString nCounter Human v3 miRNA Expression Assay

first: Ngoc

last: Bui

first: Sean

last: Yoda

first: Jiqiang

last: Yao

first: Laura

last: Hall

first: Tania

last: Mesa


title: Caenorhabditis elegans extracellular vesicle

status: Public on Aug 05 2020

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: The nematode Caenorhabditis elegans has evolutionarily conserved EV signaling pathways. In this study, we apply a recently published method for high specificity purification of EVs from C. elegans to carry out target-independent proteomic and RNA analysis of EVs from C. elegans. Our experiments uncovered diverse coding and non-coding RNA transcripts as well as protein cargo types commonly found in human EVs.

overall_design: Extracellular Vesicle small RNAseq -  1 sample

first: Josh

last: Russel

first: Matt

last: Kaeberlein


title: Modelling the developmental spliceosomal craniofacial disorder Burn-McKeown syndrome using induced pluripotent stem cells

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

country: United Kingdom

institute: University of Manchester

type: Expression profiling by high throughput sequencing

summary: The craniofacial developmental disorder Burn-McKeown Syndrome (BMKS) is caused by biallelic variants in the pre-messenger RNA splicing factor gene TXNL4A/DIB1. The majority of affected individuals with BMKS have a 34 base pair deletion in the promoter region of one allele of TXNL4A combined with a loss-of-function variant on the other allele, resulting in reduced TXNL4A expression. However, it is unclear how reduced expression of this ubiquitously expressed spliceosome protein results in craniofacial defects during development. Here we reprogrammed peripheral mononuclear blood cells from a BMKS patient and her unaffected mother into induced pluripotent stem cells (iPSCs) and differentiated the iPSCs into induced neural crest cells (iNCCs), the key cell type required for correct craniofacial development. BMKS patient-derived iPSCs proliferated more slowly than both mother- and unrelated control-derived iPSCs, and RNA-Seq analysis revealed significant differences in gene expression and alternative splicing. Patient iPSCs displayed defective differentiation into iNCCs compared to maternal and unrelated control iPSCs, in particular a delay in undergoing an epithelial-to-mesenchymal transition (EMT). RNA-Seq analysis of differentiated iNCCs revealed widespread gene expression changes and mis-splicing in genes relevant to craniofacial and embryonic development that highlight a dampened response to WNT signalling, the key pathway activated during iNCC differentiation. Furthermore, we identified the mis-splicing of TCF7L2 exon 4, a key gene in the WNT pathway, as a potential cause of the downregulated WNT response in patient cells. Additionally, mis-spliced genes shared common physical properties such as length, splice site strengths and sequence motifs, suggesting that splicing of particular subsets of genes is particularly sensitive to changes in TXNL4A expression. Together, these data provide the first insight into how reduced TXNL4A expression in BMKS patients might compromise splicing and NCC function, resulting in defective craniofacial development in the embryo.

overall_design: 2 clonal colonies of iPSC from affected individual, 2 from unaffected mother, and 1 clonal colony from 2 unrelated control individuals. All samples were technically-repeated 3 times. This format was also repeated for clonal colonies of iNCCs. Total of 32 samples

first: Katherine

middle: A

last: Wood

first: Charlie

middle: F

last: Rowlands

middle: B

first: Steven

last: Woods

first: Julieta

last: O'Flaherty

first: Sofia

last: Dougzou

first: Sue

last: Kimber

first: William

middle: G

last: Newman

first: Raymond

middle: T

last: O'Keefe


title: Investigating the Role of DNp63 in breast cancer

first: Elsa

last: Flores

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study was to characterize the differences in the global binding affinity of DNp63 to different genomic regions and its downstream target genes in human breast xenograft tumors.

overall_design: We performed a ChIP-seq analysis comparing differential bindings of DNp63 and RNA Pol2 among 2 samples: control DCIS tumors and DNp63-knocked down DCIS tumors

first: Ngoc

last: Bui

middle: R


title: Principles of mRNA control by human Pumilio proteins elucidated from global transcriptome stability, in vitro affinity profiling, and integrative data analysis

city: Ann Arbor

first: Peter

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

summary: The human members of the PUF family of proteins, PUM1 and PUM2, are RNA-binding proteins that post-transcriptionally regulate gene expression through binding to a PUM recognition element (PRE) in the 3′ UTR of target mRNAs, promoting RNA decay. Recent RNA-seq experiments in PUM1/2 knockdown conditions have identified hundreds of known and new human PUM targets through measurement of changes in steady state RNA levels. However, steady-state RNA levels do not allow for measurement of changes in RNA stability between conditions and do not allow for the differentiation between the contributions of changes in transcription rates and changes in RNA decay. Here, we identify hundreds of human PUM1/2 targets that have changes in RNA stability following PUM1/2 knockdown. We separate the contributions of changes in transcription rate and RNA stability and find that human PUM proteins almost exclusively modulate RNA abundance through changing RNA stability and not transcription. In addition, we find that the sequence preferences for all possible 8mers are largely similar between PUM1 and PUM2, suggesting that PUM1 and PUM2 recognize similar targets. We identify an ideal PRE “rulebook” by determining key contextual features around PREs, including local AU content, location of a PRE within a 3′ UTR, clustering of PREs, and number of miRNA sites near a PRE, that help differentiate functional PREs from non-functional ones as measured by our decay dataset. Consistent with previously identified functional roles of mammalian PUMs, we find that human PUM1 and PUM2 modulate the decay of genes related to signaling cascades and neuronal function. Finally, we train machine learning models to predict functional regulation of RNA targets by the human PUM proteins and find that contextual features around PREs contribute meaningful information to our models.

overall_design: Bru-seq and BruChase-seq under PUM1 and PUM2 knockdown in HEK293 cells compared non targeting control with 4 replicates. SEQRS analysis of PUM1 and PUM2 homology domains sequence preference over 5 rounds of selection

first: Michael

last: Wolfe

first: Trista

last: Schagat

first: Michelle

last: Paulsen

first: Brian

last: Magnuson

first: Mats

last: Ljungman

first: Daeyoon

last: Park

first: Chi

last: Zhang

first: Zachary

last: Campbell

first: Aaron

middle: C

last: Goldstrohm

middle: L


title: ob/ob mice on pancreatic islet

city: Lausanne

first: Claudiane

last: Guay

state: Vaud

address: Du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

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

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

overall_design: Refer to individual Series


title: Effects of entero-gastro-anastomosis (EGA) surgery in ob/ob mice on pancreatic islet gene expression

summary: Bariatric surgical techniques are known to cause weight loss and diabetes remission to varying degrees in severly obese patients. However, the mechanisms involved in the restoration of beta-cell function remain to be uncovered. In this study, the leptin-deficient ob/ob mouse was used as a model to investigate the effect of EGA bariactric surgery on pancreatic islet gene expression.

overall_design: At 3 months of age, C57Bl6-ob/ob mice were randomized to EGA or sham surgery. Pancreatic islets were isolated 28 days after the surgery. C57Bl/6J mouse islets were used as lean/non-obese control.

first: Chloé

last: Amouyal

first: Romano

last: Regazzi

first: Christophe

last: Magnan

first: Fabrizio

last: Andreelli


title: Effects of entero-gastro-anastomosis (EGA) surgery in ob/ob mice on pancreatic islet miRNA expression

summary: Bariatric surgical techniques are known to cause weight loss and diabetes remission to varying degrees in severly obese patients. However, the mechanisms involved in the restoration of beta-cell function remain to be uncovered. In this study, the leptin-deficient ob/ob mouse was used as a model to investigate the effect of EGA bariactric surgery on pancreatic islet miRNA expression.

overall_design: At 3 months of age, C57Bl6-ob/ob mice were randomized to EGA or sham surgery. Pancreatic islets were isolated 28 days after the surgery.


title: Effects of leptin supplementation on pancreatic islet miRNA expression in ob/ob mice

summary: Ob/ob mice are characterized by a defect in leptin synthesis. In this study, the contribution of leptin deficiency to the deregulation of miRNA expression in ob/ob mice was determined by comparing leptin infused ob/ob mice to saline control.

overall_design: Diabetic ob/ob mice of 3 months of age were treated with leptin (intraperitonealy injection of 350µg per day ) or 0.9% NaCl (Control) during 21 days. Pancreatic islets were isolated at the end of the treatment period.


title: Genome-wide maps of the chromatin and transcription state transition during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like cells (iHep)

status: Public on Aug 06 2020

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2, or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes (iHep cells) in vitro. Then we mapped 2 histone modification marks (H3K9ac and H3K27me3) and 2 states of Pol2 (with phosphorylated serine 5 and phosphorylated both of serine 5 and serine 2) during the conversion event. Besides we performed FAIRE-Seq to explore the chromatin accessbility in the iHep cells.

overall_design: ChIP-Seq for H3K9ac, H3K27me3, and Pol2 (with phosphorylated serine 5 and phosphorylated both of serine 5 and serine 2), and FAIRE-Seq in iHep_4a1 cells (Foxa1/Hnf4alpha), iHep_4a2 cells (Foxa2/Hnf4alpha), iHep_4a3 cells (Foxa3/Hnf4alpha), 3 cells 48 hours after transfection (48hr_4a1, 48hr_4a2, 48hr_4a3). ChIP-Seq for H3K9ac and H3K27me3 in MEF. ChIP-Seq for Pol2 in hepatocyte and a cell 48 hours after transfection of Foxa3 del2 mutant fused with x3 Ty1-tag and Hnf4alpha [iMEF(Day2)_4a3 del2_x3Ty1].

first: Yasuyuki

last: Ohkawa

first: Masao

last: Nagasaki

first: Kenichi

last: Horisawa

first: Kazuko

last: Ueno


title: Protein Kinase 2 (CK2) Controls CD4+ T-cell Effector Function in the Pathogenesis of Colitis

city: New York

first: Wei

last: Yang

state: NY

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

summary: Crohn’s disease (CD) is one of the major forms of inflammatory bowel disease (IBD), characterized by chronic inflammation of the gastrointestinal tract. CD is associated with aberrant Th1 and Th17 responses accompanied by high levels of IFN-g and IL-17, respectively. Protein kinase 2 (CK2) is a highly conserved serine-threonine kinase that is involved in several signal transduction pathways which regulate inflammatory responses. CK2 promotes Th17 cell differentiation and suppresses the generation of Foxp3+ regulatory T cells. The function of CK2 in CD4+ T-cells during the pathogenesis of CD is unknown. We utilized T-cell induced colitis model, transferring CD45RBhi naïve CD4+ T-cells from CK2afl/fl littermate control and CK2afl/fldLck-Cre mice into Rag1-/- mice. We demonstrate that CD4+ T-cells from CK2afl/fldLck-Cre mice fail to induce wasting disease and significant intestinal inflammation, which is associated with decreased IL-17A+, IFN-g+ and double positive IL-17A+ IFN-g+ CD4+ T-cells in the spleen and colon. Further, we determine that CK2a regulates CD4+ T-cell proliferation through a cell-intrinsic manner. CK2a is also important in controlling CD4+ T-cell responses by regulating NFAT2, which is vital for T-cell activation and proliferation. Thus, our data demonstrate that CK2a contributes to the pathogenesis of colitis by promoting CD4+ T-cell proliferation and Th1 and Th17 responses, and that targeting CK2 kinase activity may be a novel therapeutic treatment for CD patients.

overall_design: Colonic CD45+CD3+CD4+ T-cells were sorted from recipient Rag1-/- mice at 6 weeks after transfer. Total RNA was extracted from FACS-sorted CD4+ T-cells using the miRNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocols and submitted to GENEWIZ (South Plainfield, NJ) for RNA sequencing (RNA-seq) and bioinformatics analysis.

first: Hongwei

last: Qin

first: Etty

middle: N

last: Benveniste


title: Human Endogenous Retrovirus-K in Stem Cell Function and Neuronal Differentiation [dataset 2]

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Human endogenous retrovirus (HERV) genes were incorporated into the genome over millions of years but they mostly have inactivating mutations. HERV-K is the most recently incorporated virus. Incidental HERV-K gene expression occurs in a variety of pathological conditions. However, its physiological role is poorly understood. To study the role of HERV-K in development, we monitored its expression and function in pluripotent stem cells and during the process of neuronal differentiation. The expression of HERV-K env was localized to chromosomes 12 and 19. HERV-K Env was expressed on the cell surface of pluripotent stem cells and was critical in maintaining the stemness and adhesion of the cells. Interactions with CD98HC resulted in activation of signaling pathways that regulate stem cells genes. Down regulation of HERV-K env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. HERV-K env expression during neurodevelopment was regulated by DNA methylation. Thus, HERV-K regulation is critical for human embryonic and neurodevelopment.

overall_design: Six samples representing three iPSC lines (NC5, PAU, WTC) transfected with either siRNA designed to target HERV-K Env (Ei) or transfected with negative control siRNA (Nsi).

first: Tongguang

last: Wang

first: Marie

last: Medynets

first: Wenxue

last: Li

first: Yadi

last: Xu

first: Richa

last: Tyagi

first: Kevon

last: Sampson

first: Nasir

last: Malik

first: Joseph

last: Steiner

first: Alina

last: Hadegan

first: Jeffery

last: Kowalak

first: Avindra

last: Nath


title: Human Endogenous Retrovirus-K in Stem Cell Function and Neuronal Differentiation [dataset 1]

summary: Human endogenous retrovirus (HERV) genes were incorporated into the genome over millions of years but they mostly have inactivating mutations. HERV-K is the most recently incorporated virus. Incidental HERV-K gene expression occurs in a variety of pathological conditions. However, its physiological role is poorly understood. To study the role of HERV-K in development, we monitored its expression and function in pluripotent stem cells and during the process of neuronal differentiation. The expression of HERV-K env was localized to chromosomes 12 and 19. HERV-K Env was expressed on the cell surface of pluripotent stem cells and was critical in maintaining the stemness and adhesion of the cells. Interactions with CD98HC resulted in activation of signaling pathways that regulate stem cells genes. Down regulation of HERV-K env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. HERV-K env expression during neurodevelopment was regulated by DNA methylation. Thus HERV-K regulation is critical for human embryonic and neurodevelopment.

overall_design: Seven sample types were included: iPSC (n=3), NSC (n=3), developing neuron (NEUR) at Day 3 (n=3), developing neuron (NEUR) at Day 5 (n=3), developing neuron (NEUR) at Day 7 (n=2), developing neuron (NEUR) at Day 10 (n=3), and mature neuron (n=1).


title: Human Endogenous Retrovirus-K in Stem Cell Function and Neuronal Differentiation


title: Novel circRNA_103758-miRNA-19b-3p-CIT axis is associated with proliferation and migration of bladder cancer via RhoA-ROCK signaling pathway [microarray]

city: Harbin

first: Yang

state: Heilongjiang

address: No. 23 Youzheng Street

country: China

institute: Harbin Medcial University

summary: To determine the circRNA expression profile in BCa and matched non-tumor tissues, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in BCa and matched non-tumor tissues.

overall_design: Bladder tissues from BCa surgery were distributed into two experimental groups: normol tissue group and tumor tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Zan

last: Liu


title: New Splenic B10 Cells Revealed by Single-cell RNA-sequencing Appear in Experimental Autoimmune Encephalomyelitis.

status: Public on Aug 04 2020

first: Shenyue

address: NO.157 Baojian Road

institute: Harbin Medical University

summary: We report the application of single-cell RNA sequencing technology for high-throughput profiling of B cell clustering in spleen of EAE mouse.

overall_design: The mRNA of mouse splenic B cells in single-cell sequencing during the peak period of EAE

first: Siying

last: Qu


title: Airway Progenitor Clone Formation Is Enhanced by Y-27632–Dependent Changes in the Transcriptome

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

summary: The application of conditional reprogramming culture (CRC) methods to nasal airway epithelial cells would allow more wide-spread incorporation of primary airway epithelial culture models into complex lung disease research. In this study, we adapted the CRC method to nasal airway epithelial cells, investigated the growth advantages afforded by this technique over standard culture methods, and determined the cellular and molecular basis of CRC cell culture effects. We found that the CRC method allowed the production of 7.1 × 1010 cells after 4 passages, approximately 379 times more cells than were generated by the standard bronchial epithelial growth media (BEGM) method. These nasal airway epithelial cells expressed normal basal cell markers and could be induced to form a mucociliary epithelium. Progenitor cell frequency was significantly higher using the CRC method in comparison to the standard culture method, and progenitor cell maintenance was dependent on addition of the Rho-kinase inhibitor Y-27632. Whole-transcriptome sequencing analysis demonstrated widespread gene expression changes in Y-27632–treated basal cells. We found that Y-27632 treatment altered expression of genes fundamental to the formation of the basal cell cytoskeleton, cell–cell junctions, and cell–extracellular matrix (ECM) interactions. Importantly, we found that Y-27632 treatment up-regulated expression of unique basal cell intermediate filament and desmosomal genes. Conversely, Y-27632 down-regulated multiple families of protease/antiprotease genes involved in ECM remodeling. We conclude that Y-27632 fundamentally alters cell–cell and cell–ECM interactions, which preserves basal progenitor cells and allows greater cell amplification.

overall_design: Three paired samples of Y-27632 treated and untreated

first: Susan

middle: D

last: Reynolds

first: Cydney

last: Rios

first: Agata

last: Wesolowska-Andersen

first: Yongbin

last: Zhuang

first: Mary

last: Pinter

first: Carrie

last: Happoldt

first: Cynthia

last: Hill

first: Scott

middle: W

last: Lallier

first: Gregory

middle: P

last: Cosgrove

first: George

middle: M

last: Solomon

first: David

last: Nichols

first: Max

last: Seibold


title: Canonical WNT pathway is activated in the airway epithelium in chronic obstructive pulmonary disease

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: We report that the canonical WNT pathway is upregulated in the proximal epithelium of patients with chronic obstructive pulmonary disease. Our data were obtained by using redifferentiated airway epithelium in air/liquid interface, and sequencing the transcriptional activity of components of the WNT signalling pathway

overall_design: Analysis of WNT transcriptional activity in 47 patients (9 non smoker controls, 10 smoker controls, 9 mild COPD patients, 10 moderate COPD patients and 9 severe to very severe COPD patients)

first: François

last: Carlier

first: Sébastien

last: Dupasquier

first: Bruno

last: Detry

first: Marylène

last: Lecocq

first: Charline

last: Biétry--Claudet

first: Yassine

last: Boukala

first: Jean-Luc

last: Gala

first: Caroline

last: Bouzin

first: Stijn

middle: E

last: Verleden

first: Delphine

last: Hoton

first: Sophie

last: Gohy

first: Bertrand

last: Bearzatto

first: Charles

last: Pilette


title: SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS


title: Contribution of brain pericytes in blood-brain barrier formation and maintenance: A transcriptomic study of cocultured human endothelial cells derived from hematopoietic stem cells

city: Lens

first: Maxime

last: Culot

address: Rue Jean Souvraz - SP 18

country: France

institute: Université d'Artois

summary: The formation, maintenance, and repair of the blood-brain barrier (BBB) are critical for central nervous system homeostasis. The interaction of endothelial cells with brain pericytes is known to induce BBB characteristics in brain endothelial cells during embryogenesis and could be used to differentiate human endothelial cells from stem cell source in in vitro BBB models. However, the molecular events involved in BBB maturation are not fully understood.  To this end, human endothelial cells derived from hematopoietic stem cells were cultivated with either primary bovine or cell line-derived human brain pericytes to induce BBB formation. Subsequently, the transcriptomic profiles of solocultured vs. cocultured endothelial cells were analyzed over time by the Massive Analysis of cDNA Ends (MACE) technology. This RNA sequencing method is a 3’-end targeted, tag-based, reduced representation transcriptome profiling technique that can reliably quantify all polyadenylated transcripts including those with low expression. By analyzing the generated transcriptomic profiles, we can explore the molecular processes responsible for the functional changes observed in endothelial cells in coculture with brain pericytes (e.g. barrier tightening, changes in the expression of transporters and receptors).   Our results identified several up- and downregulated genes and signaling pathways that provide a valuable data source to further delineate complex molecular processes that are involved in BBB formation and BBB maintenance. In addition, this data provides a source to identify novel targets for central nervous system drug delivery strategies.

overall_design: 27 samples were analysed by genome-wide gene expression profiling of solo- and cocultured ECs at 0, 24, 48 and 96 hours after putting ECs in coculture (3 biological replicates each consisting of 3 technical replicates) using the MACE method to identify differentially expressed genes upon pericyte introduction.

first: Marjolein

last: Heymans

first: Ricardo

last: Figueiredo

first: Lucie

last: Dehouck

first: David

last: Francisco

first: Yasuteru

last: Sano

first: Fumitaka

last: Shimizu

first: Takashi

last: Kanda

first: Rémy

last: Bruggmann

first: Peter

last: Winter

first: Fabien

last: Gosselet


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice

city: Los Angeles

first: Mengfei

last: Yu

state: CA

address: 2250 Alcazar St

institute: University of Southern California

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived suture transcriptome profiling (RNA-seq) among wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice
Methods: Suture mRNA profiles from one week after induction of seven-month-old wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.
Results: Using an optimized data analysis workflow, we mapped about 70 million sequence reads per sample to the mouse genome ( mm10) and identified 43,644 transcripts in the suture of wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice with Partek E/M workflow.

first: Yang

last: Chai


title: Functions of calcineurin-NFAT signaling pathway in human embryonic stem cells

city: Shang Hai

first: Hao

last: Chen

state: California

address: 320 Yueyang Road

institute: Shanghai institute of nutrition and health, CAS

summary: Calcineurin-NFAT signaling is associated with a wide range of biological processes and diseases. Our previous study showed that this pathway plays a critical role in mouse embryonic stem cell (mESC) differentiation. However, its function in human ESCs (hESCs) remains unclear. Here, we report that expression of PPP3CC, the gene encoding the catalytic subunit of calcineurin, increases along with the process of hESC differentiation, and its knockdown (KD) enhances the self-renewal ability of hESCs with a simultaneous reduction in the expression of differentiation-associated markers regardless of culture conditions. Moreover, we observed that NFATC3 translocates from the cytoplasm to the nucleus when hESCs exit from a self-renewal state. These results indicate that calcineurin-NFAT signaling is activated and required during hESC differentiation. Mechanistically, we also found that in hESCs NFATC3 interacts with JUN， one of AP-1 complex subunit, and co-expression of exogenous NFATC3 and JUN upregulates lineage markers remarkably even under a self-renewal culture condition. Additionally, inhibition of this cascade represses MAPK signaling rapidly, including ERK1/2, JNK and P38. Taken together, this study delineates the importance of the calcineurin-NFATC3/JUN signaling cascade for the pluripotency maintenance of hESCs.

overall_design: There are 9 samples and they are siNT, siPPP3CC and siNFATC3 for 1.5 days as well as for 3 days. Here SHhES8 hESCs were transfected with non-targeting siRNA (siNT) or siRNAs for PPP3CC and NFATC3, after cultured in conditioned medium for 1.5 and 3 days, the RNA was collected for sequencing. The 3-day samples have two replicates.

first: Yanwu

last: Zeng

first: Min

last: Shao


title: Enhancement of Transgene Expression by the b-Catenin Inhibitor iCRT14

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

department: Chemical & Biological Engineering

institute: Villanova University

summary: The innate immune system allows cells to detect intracellular pathogen-associated molecular patterns (PAMPs) like endotoxin or cytosolic DNA and then induce inflammation, transcriptional or translational inhibition, or apoptosis in the infected cell.  This response is an essential host defense mechanism against viruses and bacteria, but it can also significantly inhibit gene therapy treatments because therapeutic plasmid DNA also triggers an innate immune response.  The goal of this study was to enhance transgene expression by inhibiting key components of the innate immune response with small molecule inhibitors (iCRT14, curcumin, Amlexanox, H-151, SC-514, & VX-702).  While each of these inhibitors significantly increased transgene (luciferase) expression by at least 2-fold, the b-catenin/TCF4 inhibitor iCRT14 showed the highest enhancement (16 to 35-fold) in multiple cell lines (PC-3, MCF7, & MB49) at a concentration of 1 mM without significantly decreasing cellular proliferation.  Alternatively, transgene expression was also enhanced 8-fold by inserting a b-catenin/TCF4 binding motif (TCAAAG) downstream of the EF1a promoter.  To further investigate the role of iCRT14 and b-catenin/TCF4 in transgene expression, mRNA-sequencing experiments were conducted to identify host cell genes that were upregulated following transfection and downregulated after the addition of iCRT14.  As expected, transfection with plasmid DNA activated the innate immune response and upregulated hundreds (687) of host cell genes, but inhibition of b-catenin/TCF4 with iCRT14 appears to enhance transgene expression by significantly downregulating 22 of those genes (e.g., PTGS2, PLA1A, et al.).  Altogether, these results show that inhibition of the innate immune response with SMIs like iCRT14 may be an effective way to improve gene therapy treatments.

overall_design: All samples were obtained from PC-3 prostate cancer cells.  3 samples were unmanipulated (controls, C), 3 samples were treated with 1 uM iCRT14 (I), 3 samples were transfected with a polyplex (PEI + pEF-GFP plasmid, P), and 3 samples were transfected and treated with 1 uM iCRT14 (PI) (24 samples total)

first: Elmer

last: Jacob


title: The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms

city: Pittsburgh

first: Jian

last: Cui

address: E1002 Biomedical Science Tower,  200 Lothrop Street

department: Department of Immunology

institute: University of Pittsburgh

summary: Compound Kushen Injection (CKI) is a TCM fomula  has been in use in hospitals in China for over twenty years for the integrated treatment of cancer.There is little evidence based medicine supporting such complex mixture. Because TCM preparations are often combinations of multiple herbs containing hundreds of compounds, they have been difficult to study.  The development of high throughput -omics methods has allowed better characterization of TCM. We have applied high-throughput transcriptome data in two additional cancer cell lines and integrated our differential expression results across cell lines to identify a reduced set of differentially expressed (DE) candidate genes as well as a reproducible set of candidate pathways that are perturbed by CKI. In our results,CKI induced cell-cycle arrest and apoptosis. We identified 363 core candidate genes that were associated with cell cycle, apoptosis, DNA replication/repair and various cancer pathways. Of these, 7 are known to be clinically relevant to cancer diagnosis or therapy and 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes.By identifying a number of promising candidate pathways and genes associated with CKI based on our transcriptome based analysis, we have shown this type of approach is useful for the systematic analysis of molecular changes resulting from complex mixtures of bioactives in the context of cancer therapy.

overall_design: High-depth paired-end RNA-seq from HEPG2 and MDA-MB-231 cell lines. Each sample contains 3 biological replicates.

last: Adelson


title: Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis [Cut&Run ChIP-seq]

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Several different YAP1 gene fusions have been identified in various human cancers. We performed Cut and Run Chip sequencing on human neural stem cells overexpressing either YAP1-MAMLD1, YAP1-FAM118B, YAP1-TFE3, wild type YAP1, wild type MAMLD1, wild type FAM118B, wild type TFE3, or S127/397A-YAP1 (all HA tagged at the N'terminus)

overall_design:
U5 human neural stem cells were transduced with pLJM1-"transgene"-PGK-Puro. 48 hrs post transduction, positive clones were selected by 72 hrs of Puromycin selection. Cells were lysed and gDNA was extracted for Cut and Run experiments 48 hrs after Puromycin selection. Used antibodies: rabbit anti-HA, mouse anti-TEAD4, rabbit Igg, mouse Igg

***Please note that no processed data was provided for the 'wild type FAM118B HA rep1' and 'wild type MAMLD1 HA rep3' samples as no peaks detected using  the SEACR package.  The experiment was carried out twice, which generated inconsistent results both times (i.e. one replicate gives a million peaks, other gives much lesser, or zero peaks). However, all four samples are submitted and included in the records for users who may try to analyze the data.

first: Frank

last: Szulzewsky

first: Eric

last: Holland


title: Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury [ChIP-seq]

city: Boston

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: We profiled Wt1, a key transcription factor, in purified murine podocytes based on ChIP-seq during the time course of podocyte injury by ADR.

overall_design: Genomic binding/occupancy profiling of Wt1 during podocyte injury by high throughput sequencing

first: Jordan

last: Kreidberg

first: Sandrine

last: Ettou


title: Notch and TLR signaling coordinate monocyte cell fate and inflammation

city: Hannover

first: Jaba

last: Gamrekelashvili

address: Carl-Neuberg-Str. 1

department: Nephrology

country: Germany

institute: Medizinische Hochschule Hannover

summary:
We studied the role of Notch2 signaling in Ly6Chi monocyte cell fate during TLR7-induced acute inflammation.
To characterize the gene expression changes involved in monocyte differentiation, we subjected monocyte subsets from peripheral blood of wt and myeloid Notch2 mutant mice after Sham or IMQ treatment to RNA-sequencing and gene expression analysis.
We found that Cell-intrinsic Notch2 and TLR7-Myd88 pathways independently and synergistically promote Ly6Clo patrolling monocyte development from Ly6Chi monocytes under inflammatory conditions. At the same time TLR7 stimulation in the absence of functional Notch2 signaling promotes resident tissue macrophage gene expression signatures in monocytes and ectopic differentiation of Ly6Chi monocytes into macrophages and dendritic cells.
Thus, Notch2 is a master regulator of Ly6Chi monocyte cell fate and inflammation in response to TLR signaling.

overall_design:
Gene expression analysis of wt or Notch2 mutant monocytes after induction of acute inflammation. Four biological replicates for each experimental condition were analysed;

*Hi samples: Ly6Chi (inflammatory) monocytes sorted from the peripheral blood of the sham-treated mice.
*Hi+A samples: Ly6Chi (inflammatory) monocytes sorted from the peripheral blood of IMQ- (Imiquimod, Aldara) treated mice.
*Lo+A samples: Ly6Clo (patroling) monocytes sorted from the peripheral blood of the IMQ- (Imiquimod, Aldara) treated mice.

first: Florian

last: Limbourg


title: Whole-exome and RNA sequencing of pulmonary carcinoid reveals chromosomal rearrangements associated with recurrence (Exome)

city: Bunkyo ku

first: Akihiko

last: Miyanaga

state: Tokyo

address: 1-1-5 Sendagi,

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

institute: Nippon Medical School

summary:
Introduction: The majority of pulmonary carcinoid (PC) tumors can be cured by surgical resection alone, but a significant proportion of patients experience recurrences. PC is insensitive to conventional chemotherapy, and it would be necessary to reveal the molecular mechanisms of metastasis and develop targeted therapeutics.
Methods: We performed the comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients (including 4 patients who developed postsurgical distant metastasis) and the RNA sequencing of primary tumors from 6 PC patients (including 4 patients who developed postsurgical distant metastasis). Exon array-based gene expression analysis was performed in 25 PC.
Results: We identified a total of 139 alterations in 136 genes. MUC6 and SPTA1 were recurrently mutated with the frequency of 21 % (3/14) and 14% (2/14), respectively. The mucin protein family genes including MUC2, MUC4 and MUC6 were mutated in 36% (5/14) in a mutually exclusive manner. The pathway analysis of mutated genes revealed the enrichment of genes involved in the mitogen-activated protein kinase (MAPK) signaling, regulation of actin cytoskeleton and focal adhesion, and transforming growth factor (TGF)-β signaling pathways. RNA sequencing reveals a total of 8 novel fusion transcripts including one derived from chromosomal translocation between the TRIB2 and PRKCE genes. All the 8 fusion genes were detected in primary PC that had developed metastasis after surgical resection. We identified 14 genes (DENND1B, GRID1, CLMN, DENND1B, NRP1, SEL1L3, C5orf13, TNFRSF21, TES, STK39, MTHFD2, OPN3, MET, and HIST1H3C) up-regulated in 5 PC that had relapsed after surgical resection.
Conclusions: In this study we identified novel somatic mutations and chromosomal rearrangements by examining clinically aggressive cases that had developed postsurgical metastasis. It is essential to validate their clinical significance in an independent larger patient cohort.

overall_design: We performed the comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients.

first: Mari

last: Masuda

first: Noriko

last: Motoi

first: Koji

last: Tsuta

first: Yuka

last: Nakamura

first: Nobuhiko

last: Nishijima

first: Shun-ichi

last: Watanabe

first: Hisao

last: Asamura

last: Tsuchida

first: Masahiro

last: Seike

last: Gemma

first: Tesshi

last: Yamada


title: Whole-exome and RNA sequencing of pulmonary carcinoid reveals chromosomal rearrangements associated with recurrence  (Affymetrix)

overall_design: We performed the exon array-based gene expression analysis of primary tumors from 25 pulmonary carcinoid patients.


title: Physiological responses of Saccharopolyspora erythraea towards perturbation of intracellular NADH/NAD+

city: Kongens Lyngby

first: Xiaobo

last: Li

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

summary: Knowledge about effects of cofactor perturbation on cellular metabolism is scarce with respect to Saccharopolyspora erythraea. The water-forming NADH oxidase (NOX) from Streptococcus pneumonia was expressed in S.erythraea E3, an important industrial strain for erythromycin production, at three different levels to investigate effects of intracellular redox status on secondary metabolism. NOX expression reduced the intracellular [NADH]/[NAD+] ratios significantly, although with a strong constitutive promoter NOX function was limited due to the shortage of oxygen. We demonstrated the negative correlation between [NADH]/[NAD+] ratios and biosynthesis of erythromycin in S.erythraea, but a positive correlation between the redox ratios and pigment production as well. We furthermore completed next-generation RNA sequencing of E3 and two NOX-expression strains. The transcription results showed that transfer processes of carbohydrates, DNA and chemical groups were altered resulting in metabolic shifts to supply more NADH for NOX fully functioning. Additionally, redox status affected transcription of several genes by allosteric effects on their transcription initiation. Specifically, transcriptional analysis along with enzymatic assay suggested that redox status influenced biosynthesis of erythromycin indirectly by allosteric effects on biosynthesis of the secondary messenger, c-di-GMP. The present work provides a basis for future cofactor manipulation in S.erythraea for further improvement of erythromycin production.

overall_design: S.erythraea cultivated in the minimal liquid medium was harvested at early exponential phase (4 h). The total RNA were sequenced in duplicate for both the parental strain E3 as well as the engineered strain A2N and R3N.


title: Whole-exome and RNA sequencing of pulmonary carcinoid reveals chromosomal rearrangements associated with recurrence (RNA)

overall_design: We performed the RNA sequencing of primary tumors from 6 PC patients.


title: SUMOylation on plant chromatin controls transcription switches between development and heat response [RNA-Seq]

city: Guangzhou

first: Danlu

last: Han

state: Guangdong

address: No. 55, West of Yat-sen Avenue

department: School of Life Science

institute: South China Normal University

summary: SUMOylation, a post-translational protein modification, is dramatically upregulated and critically involved in heat stress response conservatively among species. Previous studies in Arabidopsis indicated that numerous chromatin associated proteins are SUMOylation substrates and most of heat-enhancing SUMOylation reactions occur in nucleus. However, the global functional connection between gene expression regulation and SUMOylation on chromatin is completely unknown in plant cells. Here we show a genome-wide relationship of chromatin-associated SUMOylation and transcription switches under room temperature, heat stress, and recovering conditions in Arabidopsis. The SUMO-associated chromatin sites, characterized via whole-genome ChIP-seq assays, are generally correlated with active chromatin markers. In response to heat stress, we found chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in the gene bodies. Further RNA-seq analysis supported the role of chromatin-associated SUMOylation in activation of transcription during rapid responses to high temperature. Changing of SUMO signals on chromatin is correlated with upregulation of heat-responsive genes and downregulation of growth-related genes. Disruption of the SUMO ligase gene SIZ1 abolishes SUMO signals on chromatin and attenuates the rapid transcriptional responses to heat stress. Interestingly, the SUMO signal peaks are enriched in DNA elements recognized by distinguished groups of transcription factors under different temperature conditions. Collectively, our data provide evidence that SUMOylation on chromatin regulates transcription switches during development and heat stress response, improving our understanding on the precise roles of SUMOylation in plant cells.

overall_design: Examination of SUMO1/2 modifications in WT and siz1-2 seedlings before and after treating with 37℃ heat shock 30min and recovery room temperature(23℃) 90min

first: Chengwei

last: Yang


title: Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury

first: Peter

last: Park

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

overall_design: Refer to individual Series


title: microRNA profiling in different grading of gastroenteropancreatic neuroendocrine tumors (GEP-NETs)

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and heterogeneous tumors presenting a wide spectrum of different clinical and biological characteristics. In these tumors, the histological evaluation is a crucial element of clinical management. Currently, tumor grading, determined by Ki-67 staining and mitotic counts, is the most reliable predictor of prognosis. This scoring method is time-consuming and a high reproducibility cannot be achieved. Novel approaches are needed to support histological evaluation and prognosis. In this study, starting from a microarray analysis, we defined the miRNAs signature for poorly differentiated NETs (G3) compared to well differentiated NETs (G1 and G2) consisting of 56 deregulated miRNAs. Moreover, we identified 8 miRNAs that were expressed in all GEP-NETs grades but at different level.  Among these miRNAs, we found miR-96-5p that raised its expression levels from grade 1 to grade 3; inversely, its target FOXO1 was decrease from grade 1 to grade 3.   Our results reveal that the miRNAs expression profile of GEP-NET correlates their expression with grading showing a potential advantage of miRNA quantification to aid clinicians in the classification of common GEP-NETs subtypes.

overall_design: Global miRNA expression profiles of 18 GEP-NETs patients divided in 7 G1, 5 G2 and 6 G3 were determined by miRNA microarray.

first: Elisabetta

last: Cavalcanti

first: Vanessa

last: Galleggiante

first: Sergio

last: Coletta

first: Raffaele

last: Armentano


title: Whole-exome and RNA sequencing of pulmonary carcinoid reveals chromosomal rearrangements associated with recurrence

first: Akihiko

last: Miyanaga

type:
Expression profiling by array
Other


title: Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury [RNA-seq]

summary: We profiled total-RNA data in isolated murine podocytes during the time course of podocyte injury by ADR.

overall_design: total RNA during podocyte injury by high throughput sequencing

first: Jordan

last: Kreidberg

first: Sandrine

last: Ettou


title: Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

summary: Transfer RNAs (tRNA) are quintessential in deciphering the genetic code; disseminating nucleic acid triplets into correct amino acid identity. While this decoding function is clear, an emerging theme is that tRNA abundance and functionality can powerfully impact protein production rate, folding, activity, and messenger RNA stability.   Importantly, however, the expression pattern of tRNAs (in even simple systems) is obliquely known. Limited analysis suggests tRNA levels change during proliferation, differentiation, cancer, and neurodegeneration; possibly mediating changes in translation efficiency and mRNA stability. A major limitation for the field has been the ability to subject tRNA pools to high-throughput analysis as they are highly structured, modified, and of high sequence similarity. Here we present Quantitative Mature tRNA sequencing (QuantM-tRNA seq), an easily implemented high-throughput technique to monitor tRNA abundance and sequence variants (possibly due to RNA modifications). With QuantM-tRNA seq we provide a comprehensive analysis of the tRNA transcriptome from distinct mammalian tissues.  We observe dramatic distinctions in isodecoder expression and likely RNA modifications between unique tissues with a particularly strong signature within the central nervous system.  Remarkably, despite dramatic changes in tRNA isodecoder gene expression, the overall anticodon pool of each tRNA family is similar.  These findings suggest that anticodon pools are buffered via an unknown mechanism to achieve uniform decoding throughout the body.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: tRNA sequencing from total RNA of 293 cells in duplicate. In addition, tRNA sequencing from total RNA from the cerebellum, cortex, medulla oblongata, spinal cord, heart, liver, and tibialis of C57BL/6J wild-type mice.

first: Otis

last: Pinkard

first: Sean

last: McFarland

first: Thomas

last: Sweet

first: Jeffery


title: Chromatin-Associated SUMOylation Controls the Transcriptional Switch between Plant Development and Heat Stress Responses

summary: The post-translational protein modiﬁcation known as SUMOylation has conserved roles in the heat stress responses of various species. The functional connection between the global regulation of gene expression and chromatin-associated SUMOylation in plant cells isunknown. Here, we uncovereda genome-wide relationship between chromatin-associated SUMOylation and transcriptional switches in Arabidopsis thaliana grown at room temperature, exposed to heat stress, and exposed to heat stress followed by recovery. The small ubiquitin-like modiﬁer (SUMO)-associated chromatin sites, characterized by whole-genome ChIP-seq, were generally associated with active chromatin markers. In response to heat stress, chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in gene bodies. RNAseqanalysissupportedthe role ofchromatin-associatedSUMOylationin transcriptionalactivation duringrapid responses to high temperature. Changes inSUMO signals on chromatinwere associated with the upregulation ofheat-responsivegenesandthedownregulationofgrowth-relatedgenes.DisruptionoftheSUMOligasegene SIZ1 abolished SUMO signals on chromatin and attenuated rapid transcriptional responses to heat stress. The SUMO signal peaks were enriched in DNA elements recognized by distinct groups of transcription factors under different temperature conditions. These observations provide evidence that chromatin-associated SUMOylation regulates the transcriptional switch between development and heat stress response in plant cells.

overall_design: Chromatin SUMOylation profiling by ChIP-seq and RNA-seq


title: SUMOylation on plant chromatin controls transcription switches between development and heat response [ChIP-Seq]


title: The profile of miRNAs in lung fibroblast-derived extracellular vesicles from idiopathic pulmonary fibrosis (IPF) patients or non-IPF  individuals.

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

summary: Accelerated senescence in lung epithelial cells is known to play a key role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the exact mechanisms underlying the IPF-related epithelial cell phenotype have yet to be elucidated. Increasing evidence supports the concept that extracellular vesicles (EVs), including exosomes and microvesicles, mediate intercellular communication that contributes to diverse aspects of physiology and pathogenesis. Here, we demonstrate that lung fibroblasts (LFs) from IPF patients accelerate epithelial cell senescence via EV-mediated transfer of LF-derived pathogenic cargo to lung epithelial cells. Mechanistically, IPF LF-derived EVs increase mitochondrial reactive oxygen species (mtROS) and associated mitochondrial damage in lung epithelial cells, leading to mtROS-mediated activation of the DNA damage response and subsequent epithelial cell senescence. We show that IPF LF-derived EVs contain elevated levels of miR-23b-3p and miR-494-3p that are responsible for suppressing SIRT3, resulting in the EV-induced phenotypic changes of lung epithelial cells. Furthermore, we observe that miR-23b-3p and miR-494-3p expression increases in lung epithelial cells from IPF patients’ lungs. Finally, the levels of miR-23b-3p and 494-3p found in IPF LF-derived EVs correlate positively with IPF disease severity. These findings reveal that the accelerated epithelial cell mitochondrial damage and senescence observed during IPF pathogenesis are caused by a novel mechanism in which SIRT3 is suppressed by miR-containing EVs derived from IPF fibroblasts.

overall_design: We pooled six of the individual IPF LF-derived EV samples and six of the individual non-IPF LF-derived EV samples. Individual EV sample was isolated from the conditioned media of primary lung fibroblasts by ultratrancefugation. Total RNAs were extracted from these EVs. Microarray analysis was performed using 20ng of the RNAs.

first: Yusuke

last: Yoshioka

first: Yu

last: Fujita

first: Jun

last: Araya

first: Kazuyoshi

last: Kuwano

first: Takahiro

last: Ochiya


title: Single-cell ATAC-Seq of cells recruited to regenerative portions of large skin wounds.

city: Calgary

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Adult mammalian skin wound healing is typically accompanied by a fibrotic scar that impairs normal skin function and regeneration of skin appendages. Interestingly, however, in adult mice, large skin injuries exhibit de novo formation of hair follicles (HFs, a phenomenon termed wound-induced HF neogenesis) in the center of the wound. Our previous analysis provides compelling evidence suggesting that regional epigenetic changes within the mesenchymal cells of the skin may underlie the divergent response to wound healing. To test this directly, we performed single-cell Assay for Transposase-Accessible Chromatin using Sequencing (sc-ATAC-Seq) on cells isolated from the center of large wounds to identify regions of the genome that are becoming differentially accessible within upper (epithelial-interfacing) fibroblasts as they transition to induce new HFs compared to their lower dermal counterparts that adopt a fibrotic phenotype. Together, our data reveals the identity and dynamics of key coding, non-coding, and regulatory regions that underlie a wound responsive fibroblasts' transition to inductive neodermal condensate cells.

overall_design: To capture the epigenetic landscape of large wound center cells in an unbiased fashion, we profiled 1,578 single-cells using scATAC product from 10x Genomics. Next Generation Sequencing was performed at Genome Quebec using the Illumina HiSeq4000 platform.

first: Sarthak

last: Sinha

first: Elodie

last: Labit


title: Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis[RNASeq]

city: Seattle

first: Sonali

last: Arora

state: WA

summary: Several different YAP1 gene fusions have been identified in various human cancers. We performed RNA sequencing on human neural stem cells overexpressing either YAP1-MAMLD1, YAP1-FAM118B, or YAP1-TFE3, as well as on whole tumor lysates from mouse brain tumors generated by intra-cranial expression of either YAP1-MAMLD1, YAP1-FAM118B, or YAP1-TFE3.

overall_design: We performed RNA sequencing on human neural stem cells overexpressing either YAP1-MAMLD1, YAP1-FAM118B, or YAP1-TFE3. U5 huamn neural stem cells were transduced with pLJM1-"transgene"-PGK-Puro. 48 hrs post transduction, positive clones were selected by 72 hrs of Puromycin selection. Total RNA was extracted 48 hrs after Puromycin selection.

first: Frank

last: Szulzewsky

first: Eric

last: Holland


title: Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis [mouse RNA-seq]

overall_design: Tumors were generated by intracranial injection of RCAS viruses expressing either YAP1-MAMLD1-dR3R1, YAP1-FAM118B, or YAP1-TFE3. Tumors were snap frozen and total RNA was extracted.


title: RNA-seq of different genes expression in Hepatocellular Carcinoma cell lines

status: Public on Aug 03 2020

city: Shapingba district, Chongqing

first: Ling

last: Ling

address: NO. 55 South Rd, University town

institute: chongqing university

summary: We report the different genes expression profile of mRNA in HCC cell lines. we constructed three kinds of cell lines, including control/USP39-KO/SIRT7-KO.

overall_design: different genes mRNA profiles of control, USP39-KO and SIRT7-KO HCC cell lines.

first: Zhenghong

last: Lin

last: Dong

first: Le

last: Yu


title: The mRNA profile of human bronchial epithelial cells transfected with miR-23b-3p, miR-145-5p and miR-494-3p

overall_design: Primary human bronchial epithelial cells and BEAS2B cells transfected with miR-23b-3p, miR-145-5p, miR-494-3p mimics or negative control miRNA. After 24 hours transfection, total RNAs were extracted from them. We used Agilent microarray chip (SurePrint G3 Human GE v3).Microarray analysis was performed using 100ng of EV miRNA.


title: Insulin-like growth factor 2 mRNA-binding protein 3 modulates aggressiveness of Ewing sarcoma by regulating the CD164-CXCR4 axis

city: Bologna

first: Katia

last: Scotlandi

address: via di Barbiano 1/10

institute: IRCCS Istituto Ortopedico Rizzoli

summary:
Ewing sarcoma (EWS) is the second most common bone and soft tissue-associated malignancy in children and young adults. It is driven by the fusion oncogene EWS/FLI1 and characterized by rapid growth and early metastasis. We have previously discovered that the mRNA binding protein IGF2BP3 constitutes an important biomarker for EWS as high expression of IGF2BP3 in primary tumors predicts poor prognosis of EWS patients. We additionally demonstrated that IGF2BP3 enhances anchorage-independent growth and migration of Ewing sarcoma cells suggesting that IGF2BP3 might work as molecular driver and predictor of EWS progression.
The aim of this study was to further define the role of IGF2BP3 in EWS progression. We demonstrated that high IGF2BP3 mRNA expression levels correlated with EWS metastasis and disease progression in well-characterized EWS tumor specimens. EWS tumors with high IGF2BP3 levels were characterized by a specific gene signature enriched in chemokine-mediated signaling pathways. We also discovered that IGF2BP3 regulated the expression of CXCR4 through CD164.
We identified for the first time a tumorigenic axis consisting of IGF2BP3/CD164 and CXCR4, which confers migratory advantage to EWS cells, particularly under stress-adaptive conditions.

overall_design: Specimens from 48 primary localized EWS tumors and 51 EWS metastatic lesions were analyzed by quantitative RT-PCR (qRT-PCR) to establish expression levels and correlations between IGF2BP3, CD164 and CXCR4. 50 paraffin-embedded primary localized EWS specimens were mounted as tissue microarrays and processed for immunohistochemical evaluation of IGF2BP3, CD164 and CXCR4 for validation of gene expression results. 6 primary localized EWS specimens characterized by high (3 samples) or low (3 samples) expression of IGF2BP3 were profiled by RNAseq. Enrichment analysis of differentially expressed genes was performed using MetaCore software (GeneGo, Thomson Reuters). CXCR4 expression was investigated in IGF2BP3-depleted or empty vector-transfected EWS cells using RT2 Profiler Cancer Inflammation and Immunity Crosstalk PCR Array, qRT-PCR and western blotting for validation of RNAseq results. CD164 expression was assessed by western blot in stable IGF2BP3 knockdown EWS cellular models compared to controls while ribo-immunoprecipitation assay and qRT-PCR were used to test IGF2BP3-CD164 interaction. We used confocal microscopy analysis to asses colocalization between CD164 and CXCR4 in response to CXCL12 stimulation. Cell migration in response to CXCL12 stimulation was investigated after treatment with anti-CD164 siRNA or controls and in stable IGF2BP3 knockdown EWS cellular models in hypoxic and normal conditions to asses functional relevance of IGF2BP3/CD164/CXCR4 axis.

first: Caterina

last: Mancarella

first: Giulia

last: Caldoni

first: Irene

last: Ribolsi

first: Alessandro

last: Parra

first: MariaCristina

last: Manara

first: Arthur

last: Mercurio

first: Andrea

last: Morrione


title: Transcriptional portrait of M. bovis BCG during in vitro biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment.

first: Eliza

last: Peterson

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: By RNA-seq analysis, we monitored the early steps of biofilm production in BCG, to distinguish intercellular aggregation from attachment to a surface, and found a number of genes being differentially expressed at these stages.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: We analyzed samples of BCG grown in Sauton medium, at 24 h, 7 days, and 10 days postinoculation in 25cm2 flasks, individually. The experiment was repeated once, so we had a total of 6 samples analyzed by RNASeq.

first: Mario

last: Flores-Valdez


title: Circuit and molecular architecture of a ventral hippocampal network

first: Mazen

last: Kheirbek

address: 675 Nelson Rising Lane, Room 514D

summary: The ventral hippocampus (vHPC) is a critical hub in networks that process emotional information.  While recent studies have indicated that vHPC projection neurons are functionally dissociable, the basic principles of how the inputs and outputs of the vHPC are organized remain unclear.  Here we used viral and sequencing approaches to define the logic of the extended vHPC circuit.   Through molecular profiling of vHPC projection neurons, we show that vHPC neurons with distinct projection targets differ in their  transcriptional signatures.

overall_design: In this study we determined whether ventral hippocampal (vHPC) neurons that project to one of four target areas, lateral hypothalamus (LH) basomedial amygdala (BMA), medial prefrontal cortex (mPFC), and nucleus accumbens (NAc), differ in terms of the genes they express.  To do so, we used transcriptional profiling methods that accessed translating mRNAs in ventral hippocampal neurons defined by their projection to one of these four targets.  We labeled ventral hippocampal neurons that projected to ateral hypothalamus (LH) basomedial amygdala (BMA), medial prefrontal cortex (mPFC), and nucleus accumbens (NAc), in different cohorts of B6.129S4-Gt(ROSA)26Sortm1(CAG-EGFP/Rpl10a,-birA)Wtp/J (Jackson labs stock #022367) by injection of a retrograde traveling adenoassociated virus expressing Cre recombinase in each of the target areas, then used a translating ribosome affinity purification (TRAP) approach to profile translation in each of these populations  . RNA sequencing (RNAseq) was then performed to identify differentially enriched mRNAs in the distinct vHPC projection neurons . Each sample correspond to 6 hippocampi from each projection pathway, perfomed in duplicate or triplicate.


title: ZEB2 locus regulation in differentiating iPSCs

city: Rotterdam

last: Conidi

address: Dr. Molewaterplein 40

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary: The multi-domain transcription factor ZEB2 controls embryonic and adult cell fate decisions and maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie Mowat-Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of an approximately 3.5 Mb-long gene-desert, lacking any protein-coding gene sequence. Using temporal high-resolution Targeted Chromatin Capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 gene promoter and this gene desert during neural differentiation of induced pluripotent cells (iPSCs), including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site (TSS). Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis regulatory elements (REs) located in ZEB2’s gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of relevant cell types, and the molecular characterization of identified MOWS patients that lack mutations in ZEB2 protein-coding exons.

overall_design: Targeted chromatin capture conformation (T2C) of differentiating human iPSCs

first: Rutger

last: Brouwer


title: HTR3A is correlated with the unfavorable histology and promotes proliferation via ERK phosphorylation in lung adenocarcinoma

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Lung cancer is the leading cause of cancer death around the world. Adenocarcinoma is the most common histological type and has various histologic subtypes: lepidic, acinar, papillary, solid, and invasive mucinous adenocarcinoma. Histologic subtypes are related to invasiveness of tumors; for example, lepidic subtype is less invasive than acinar/papillary subtype. HTR3A is the main subunit of 5-hydroxytryptamine 3 (5-HT3) receptors, which are the only ligand-gated ion channels in 7 families of 5-HT receptors. Though 5-HT3 receptor is expressed mainly throughout the central and peripheral nervous systems, some papers report the effect of 5-HT3 receptors on tumor cells including lung cancer. However, whether HTR3A correlates with histopathological findings such as the histologic subtypes or the distribution in an individual sample remains unclear. Immunohistochemically, we revealed, the higher expression level of HTR3A was detected in acinar, papillary, and solid adenocarcinoma than in lepidic adenocarcinoma; the former was more aggressive subtype than the latter. We also showed the relationship between the expression of HTR3A and Ki-67, widely used as a proliferation marker. Moreover, we generated HTR3A-knockdown lung adenocarcinoma cells and showed that the HTR3A knockdown attenuated proliferation via ERK phosphorylation. Our results demonstrated that HTR3A expression was related to proliferation in lung adenocarcinoma by means of both in vitro and immunohistochemical assays on clinical samples. We showed the therapeutic potential of a 5-HT3 receptor antagonist, tropisetron, for the treatment of lung adenocarcinoma.

overall_design: We divided 30 cases into 2 groups. The first group had 20 cases and was composed of relatively indolent histological subtype, such as lepidic, acinar, and papillary (good-prognosis group). The second group had 10 cases and was composed of relatively aggressive subtype, such as micropapillary and solid (poor-prognosis group). We compared the levels of gene expression profiles between 2 groups.

first: Shinichiro

last: Tahara

first: Eiichi

last: Morii


title: Massive Expansion of Functional Human iPSC-derived Cardiomyocytes by Concomitant Glycogen Synthase Kinase-3 Beta Inhibition and Removal of Cell-Cell Contact

city: Suwon-si

first: Soah

last: Lee

state: Geonggi-do

address: 2066 Seobu-ro, Jangan-gu, 530502

department: Pharmacy

country: South Korea

institute: Sungkyunkwan University

summary: Modulating signaling pathways including Wnt and Hippo can induce cardiomyocyte proliferation in vivo. Applying these signaling modulators to human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in vitro can expand CMs only to modest extent (< 5-fold). Here, we demonstrate massive expansion of hiPSC-CMs in vitro (i.e. 100-250-fold) by glycogen synthase kinase-3β (GSK-3β) inhibition using CHIR99021 and concurrent removal of cell-cell contact. We show GSK-3β inhibition suppresses CM maturation while contact removal prevents CMs from cell cycle exit. Remarkably, contact removal enabled 10-to-25-times greater expansion beyond GSK-3β inhibition alone. Mechanistically, cell cycle re-activation required both LEF/TCF activity and AKT phosphorylation, but it was independent from Yes associated protein (YAP) activity.  Engineered heart tissues from expanded hiPSC-CMs showed the comparable contractility to those from unexpanded hiPSC-CMs, demonstrating uncompromised cellular functionality after expansion. In sum, we uncovered a molecular interplay that enables massive expansion hiPSC-CMs for large-scale drug screening and tissue engineering.

overall_design: 24 hours treatment with various Wnt signaling pathway modulators

first: Jan

last: Buikema

first: Sean

last: Wu


title: Gene expression data from human breast cancer MDA-MB-231 cells treated with siRNAs targeting long non-coding RNA TMPO-AS1

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary:
To examine the role of long non-coding RNA TMPO-AS1 in breast cancer, MDA-MB-231 cells were treated with siRNAs targeting TMPO-AS1 (siTMPO-AS1) or control siRNA (siControl).
3 samples

overall_design: Yuichi,Mitobe

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: The role of long noncoding RNAs during pancreas development

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: LncRNAs are developmentally regulated and highly cell type-specific non-coding RNAs that have emerged as important regulators of cell fate commitment and maintenance. In this study, we dissected the role of lncRNAs in human pancreas development by classifying lncRNAs based on their dynamic regulation, subcellular localization, and engagement with ribosomes during the stepwise differentiation of human embryonic stem cells (hESCs) towards pancreatic fate. We then deleted 10 candidate lncRNAs in hESCs and characterized the knockout phenotypes of pancreatic developmental intermediates, prioritizing dynamically regulated lncRNAs with validated translation potential and proximity to developmental TFs. This small-scale loss-of-function screen revealed that most lncRNAs are dispensable for pancreatic development and the regulation of nearby genes. We identify LINC00261 as the first translated lncRNA involved in human endocrine cell development, and show that it regulates gene expression in pancreatic progenitor cells in trans rather than cis. Through systematic dissection of LINC00261's coding and noncoding functions, we can exclude a role for the produced micropeptides in this process. Instead, we posit that, over the course of pancreatic differentiation, the biological activity of multiple lncRNAs is controlled by a regulatory, translation machinery dependent mechanism that employs ribosome engagement and short open reading frame translation to dose lncRNA activity in the nucleus. It is conceivable that inadequate nuclear LINC00261 dosage during human pancreas development could predispose individuals to developing diabetes.

overall_design: RNA-seq and Ribo-seq analysis of H1 embryonic stem cells differentiated towards the pancreatic endocrine cell fate.

first: Bjoern

last: Gaertner


title: Comparing the Transcriptomes of wild type (WT) oocytes  with Dpagt1-Mutant (MUT), Dpagt1F/FAmhr2-CER/+ (Amcko) and Dpagt1F/FGdf9-CER/+ (GCKO) oocytes by RNA-Seq Analysis

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: The goal of this study is to reveal the globle effect of point mutation of Dpagt1, oocyte-specific deletion of Dpagt1 and granulosa cell-specific deletion of Dpagt1 in mice on gene expression in GV-stage fully-grown oocytes (FGOs) by comparing the corresponding transcriptomes via RNA-Seq Analysis.

overall_design: Dpagt1 missense point mutant mice were produced by  applying the “ENU-induced mutagenesis”-based forward genetic approach and producing an A to G transition of base 209 in exon 3 of Dpagt1, which resulted in the mis-sense mutation of aspartic acid 166 into glycine.Dpagt1oocyte-cKO and granulose-cKO mice were produced by crossing female mice carrying the conditional allele of Dpagt1 with male Tg(Gdf9-icre)5092Coo and Amhr2tm3(cre)Bhr  mice expressing the transgene for Cre recombinase specifically in oocytes and granulosa cells,respectively. Then the oocytes were collected in lysis buffer to release all RNAs, which then were reverse transcribed into first cDNA strands by SuperScript II reverse transcriptase(Invitrogen) and random primers. These cDNAs were amplificated according to Smart-seq2 procedures for construct Illumina sequencing library. 3 replictates of each treatment, with 20 oocyte per  samples, were collected for the experiment. The library was constructed using KAPA Hyper Prep Kit for Illumina (Roche) according to the instruction manual, which includes end repair, dA-tailing, adapter ligation, post-ligation cleanup, library amplification and post-amplification cleanup. The libraries were sequenced on an Illumina HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).


title: NONO gene expression profile in breast cancer cell

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

institute: ChuangAng University

summary: NONO is one of RNA Binding protein. To investigate the role of NONO in breast cancer cells (TNBC), we carried out microarray.

overall_design: NONO was silenced in Hs578T and BT20 cell (shCon=3, shNONO=3)

first: Yun-Yong

last: Park


title: Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos

status: Public on Aug 02 2020

city: Pasadena

first: Theodora

last: Koromila

address: 1200 E Califonia Blvd

institute: California Institute of Technology

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

overall_design: Refer to individual Series


title: ATRA enhances differentiation from human induced pluripotent stem cells into esophageal epithelium

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: We developed a method for the differentiation of hiPSCs into esophageal epithelium cells.

overall_design: Comparison of the effciency of the esophageal differentiation from iPSCs in the presence or absence of ATRA

first: Yasufumi

last: Koterazawa

first: Takashi

last: Aoi


title: New insights of Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

summary: The transcriptome profiles of the model plant Arabidopsis thaliana have been extensively studied and charcaterised under different developmental and physiological conditions. However, most of these “RNA-sequencing” datasets have been generated using the sequencing of reverse-transcribed cDNAs from mRNAs that have a relatively short read length. Here, we performed direct RNA sequencing using the latest Oxford Nanopore Technology (ONT) with unusual read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been under-estimated. The ONT direct RNA sequencing technology identified transcript isoforms at a vegetative (14 day old seedlings, stage 1.04) and a reproductive stage (stage 6.00-6)  when 10% of the flowers had opened. In-house software called TrackCluster was used to determine alternative transcription initiation (ATI), possible alternative polyadenylation (APA), poly(A) length, alternative splicing (AS), and fusion transcripts. Tombo software was used to detect RNA base modifications. More than 38,500 novel transcript isoforms were identified, including six categories of fusion-transcripts which may result from differential RNA processing mechanisms. Fusion-transcripts are prone to mis-assembly by sequencing with short reads using next-generation-sequencing (NGS). These new transcript isoforms provide important additions to the annotated Arabidopsis genome. The power of ONT in detecting RNA modifications was demonstrated by characterisation of the modifications between mobile mRNAs and total mRNAs. The mobile mRNAs were enriched in m5C modifications, which is consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary, ONT direct RNA sequencing greatly enhances the identification of novel RNA transcript isoforms and RNA base modifications.

overall_design: Arabidopsis thaliana col-0 seeds were surface sterilized with 50% commercial bleach and 0.01% Triton X-100 for 10 minutes, then washed 5 times with sterilized H2O. The sterilized seeds were sown on ½ MS plate with 1% sucrose and 0.6% Agar (sigma, cat#: A1296). Stratification at 4ºC for 48 hours, then placed in a growth chamber with 16h light/8h dark for 14 days. The 14-day seedlings were harvested (two biological replicates, each with one gram) for RNA extraction. Some seedlings were transplanted into soil for floral buds, the soil-based Arabidopsis seedlings were also treated with photoperiod of 16h light/8h dark. After another three-week growing, floral buds from plants equals to principal growth stage 6.0 to 6.1 were harvested, and they were immediately immersed in a foil boat full of liquid nitrogen in a relative larger liquid nitrogen container. Two Harvested biological replicates were frozen at -80degree freezer till RNA isolation. Total RNAs from Arabidopsis seedlings and floral buds were isolated with Trizol according to manufacturer’s instruction. The extracted total RNAs were then treated with Dnase I (NEB CAT#:M0303). The treated total RNAs were extracted with acidic phenol (125:24:1, pH4.5, ThermoFisher cat#: AM9720) and precipitated with LiCl. The purified RNAs were subjected to mRNA isolation with Dynabeads mRNA purification kit (ThermoFisher cat#: 61006), around 0.9ug mRNAs for each library were used with Nanopore direct RNA sequencing kit (SQK-RNA002). The prepared libraries were loaded onto R9.4.1 flowcells, and sequencing was performed in MinION sequencing machine. Each library was run for 48 hours.

first: Shoudong

last: Zhang

first: Zhongying

last: Zhao

first: Hon-Ming

last: Lam


title: Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos (ChIP-seq, ATAC-seq)

summary: Pioneer factors such as Zelda initiate zygotic transcription within Drosophila early embryos, but whether other factors also support this dynamic patterning process is unclear. Odd-paired (Opa) is a zinc-finger transcription factor expressed during cellularization, shown to act as timing factor to control pair-rule to segmental patterning transition along the anterior-posterior (AP) axis. We found Opa regulates expression through an enhancer active along the dorso-ventral axis (sog_Distal), specifically, to support its late embryonic expression. Opa chromatin immunoprecipitation identified occupancy at this enhancer sequence as well widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences accessibility and has both common as well as distinct target sequences. opa mutants also exhibit DV and AP patterning changes suggesting Opa acts broadly. This study suggests Opa is a late-acting, pioneer factor whose action follows Zelda to herald in a second wave of zygotic gene expression. NIH Grants R35GM118146 and R03HD097535 to A.S.

overall_design:
Genome binding and accessibility profiling by high throughput sequencing:
1. Genome-wide mapping of Opa in 3h and 4h collections of wild-type Drosophila melanogaster embryos, cycles 13-14early and cycle 14mid-gastrulation,  respectively.
2. Genome-wide data from mid nc14 Drosophila single-embryo Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) provide insight into wt versus Opa (sh opa) and Zld (sh zld) dynamics. The raw fastq data (50bp single-end) for Opa ChIP-seq libraries, and for wt, Zld-mutant and Opa-mutant ATAC-seq libraries were generated from the Illumina HiSeq2500 platform.

first: Fan

last: Gao

first: Angelike

last: Stathopoulos

first: Yasuno

last: Iwasaki

first: Peter

last: Gergen


title: Opa is a late-acting, pioneer factor that coordinates with Zelda to broadly regulate gene expression in early embryos (ATAC-seq, RNA-seq)

summary:
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression
contributor: Theodora Koromila (ATAC-seq-RNA-seq)
contributor: Fan Gao (Bioinformatic analysis)
contributor: Angelike Stathopoulos (PI)
contributor: Peng He (Bioinformatic analysis)

overall_design: 1. Genome-wide data from mid nc14B and nc14D Drosophila single-embryo Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) provide insight into wt versus Opa (sh opa and UAS-opa). ATAC-seq libraries were generated from the Illumina HiSeq2500 platform. HOMER (version 4.7, parameters: -localSize 50000 -minDist 50 -size 150 -fragLength 0) (Heinz et al. 2010) was used to call ATAC peaks. 2. Following total RNA isolation from control and sh_opa single embryos at nc14D, RNA was quality controlled and quantified using a Bioanalyzer. Differential expression analysis was performed using Cuffdiff module of Cufflinks with default parameters, and FPKM.

first: Peng

last: He


title: miR-573 rescues endothelial dysfunction during dengue infection under PPARγ regulation

city: singapore

first: justin

last: chu

state: SINGAPORE

address: 5 science drive 2

department: microbiology and immunology

country: Singapore

institute: national university of singapore

summary: We report that DENV2 infection of HUVEC results in differential regulation of miRNA expression. We have used the Illumina HI Seq technoogy to study the miRNA expression levels. We further elucidated the role of miR-573 in regulating endothelial permeability during DENV2 infection.

overall_design: Analysis of miRNA expression patterns in mock-infected and DENV2-infected HUVEC cells

first: Shefali

last: Banerjee

first: Justin

last: Chu


title: 5-Formylcytosine Landscapes of Human Preimplantation Embryos at Single-cell Resolution

city: Guangzhou

first: Lin

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: The epigenetic regulation containing DNA methylation and chromatin accessibility have been extensively explored in human preimplantation development. However, the dynamic of demethylation in this crucial process remains largely unknown. In this study, we use CLEVER-seq to quantify the DNA 5-formylcytosine (5fC) level of human early embryos. The distribution of 5fC exhibits genomic region preference and are enriched in L1 and ERVK, subfamily of repeat element. Unlike in mice, the paired pronuclei presents inconsistent 5fC level although the male pronuclei experiences stronger demethylation. And the centre of 5fC shows less accessible genome especially in proximal region. Collectively, our work offers new insight into the understanding of the complex demethylation in early human embryo development.

overall_design:
In total, we sequenced 130 euploid single cell without copy number viriation (CNV) . The sampling stages covered sperm, oocyte, the first polarbody, tow-cell, four-cell, eight-cell, morula, inner cell mess, trophoectoderm and hESC. The synthesized model DNA contain 5fC modification was spiked in each sample to quantify the efficiency of malononitrile labelling. The average conversion rate was 79.6% in total 130 samples. With ~5× sequencing depth of each single-cell sample, the average clean reads of each sample is 116.8 million with 74.6% averaged mapping rate. 24,830 to 45,398 5fCpG sites were identified from merged same stage samples.

The raw data have been deposited in GSA for Human (https://bigd.big.ac.cn/gsa-human/) under accession HRA000194 due to privacy concerns.

first: Yun

first: Fuchou

last: Tang


title: Single cell RNA-sequencing Identification of Novel Cell-specific Expression of Lung Disease-related Genes in the Human Small Airway Epithelium

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
The human small airway epithelium (SAE) plays a central role in the early events in the pathogenesis of most chronic inherited and acquired lung disorders. Little is known about the molecular phenotypes of the specific cell populations comprising the SAE, and the contribution of specific cell populations to the pathogenesis of human disease.
There was cell type-specific expression of the genes relevant to the pathogenesis of the inherited pulmonary disorders, genes associated with risk of chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), and (non-mutated) driver genes for lung cancers. Some unexpected observations included high expression of CFTR (cystic fibrosis) and SCNN1A and B (bronchiectasis) in ionocytes, DTNBP1 (Hermansky-Pudlak syndrome) in mast cells, FAM13A (COPD) in neuroendocrine cells, RIN3 (COPD) in mast cells, NSPA1L (IPF) in neuroendocrine cells and a variety of lung cancer-related genes expressed in different cell types that, if mutated, become driver genes. Cigarette smoking significantly altered the cell-specific transcriptome of the different cell populations. Many of the genes relevant to the hereditary and acquired disorders exhibited cell-specific modulation by cigarette smoking, including MUC5B (IPF) down-regulation specifically in intermediate, club and mucus-producing cells and SFTPB (surfactant deficiency) up-regulation in ionocytes.

overall_design: Three healthy nonsmokers and three asymptomatic smokers were assessed using approved clinical protocols by Weill Cornell Medical College Institutional Review Board and the small airway epithelium (10th-12th generations of bronchi) were collected by bronchoscopic brushing.  Single cell capture and Drop-seq single-cell RNA-sequencing was performed for 11702 single-cell samples.  Using unbiased clustering on the single cell transcriptome from nonsmokers, 11 distinct cell populations were identified in the SAE brushed samples, including major (basal, intermediate, club, ciliated and mucous-producing cells) and rare epithelial cells (neuroendocrine cells, ionocytes), and immune/inflammatory cells (T cells, mast and antigen-presenting cells). We evaluated the effect of smoking on the 11 distinct nonsmoker cell populations and genes associated with lung disorders.

first: Wu-Lin

last: Zuo

first: Mahboubeh

last: Rostami

first: Sushila

last: Shenoy

first: Michelle

last: LeBlanc

first: Jacqueline

last: Salit

last: Struclovici-Barel

first: Sarah

last: O’Beirne

first: Robert

last: Kaner

first: Philip

last: Leopold

first: Jason

last: Mezey

first: Matthew

last: Thomas

first: Juergen

last: Schymeinsky

first: Karsten

last: Quast

first: Suda

last: Visvanathan

first: Jay

middle: S

last: Fine

first: Ronald

last: Crystal


title: MeDIP sequencing for human samples

status: Public on Aug 01 2020

city: Zhengzhou

first: Weihua

last: Gong

state: Henan

address: ZZ

institute: Zhengzhou University

summary: We report a high-throughput analysis of human breast cancer cells using methylated DNA immunoprecipitation-sequencing.in this study to reveal the difference in methylation between breast cancer drug-resistant cells and sensitive cells. A total of 55076 differentially methylated genes (DMGs) were detected, including 21061 hypermethylated DMGs and 34015 hypomethylated DMGs. Moreover, Gene Ontology (GO) analysis and KEGG pathway analysis reveal the function and pathway of screening genes. These results indicate that DNA methylation may be involved in regulating the occurrence and development of breast cancer.

overall_design: Examination of the whole-gene DNA methylation profile in breast cancer drug-resistant cells MCF-7 / Taxol and sensitive cells MCF-7

first: Ying

last: Shi

first: Xiangrong

first: Xin

last: Zhao


title: Transcriptomics analysis of neurogenesis by striatal astrocytes upon Rbpj-K deletion

city: Stockholm

first: Jens

middle: Peter

last: Magnusson

address: Alfred Nobels Allé 8

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: We achieved local recombination of striatal astrocytes and silenced Notch signalling activity through Rbpj-K depletion. Recombined astrocytes and neural progenitors generated from the striaral glia were FAC sorted and their molecular profile investigated in a scRNAseq experiment performed 5 wpi.

overall_design: Astrocytes and their neurogenic progeny isolated from striata of mice homozygous for the floxed Rbpj gene and subjected to local injection of AAV-Gfap-Cre

first: Margherita

last: Zamboni

first: Jonas

last: Frisen


title: Gene expression profiling in mice with the depletion of prolyl hydroxylase domain proteins in endothelial cells

city: Houston

first: Xinchun

last: Pi

state: Texas

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

summary: To evaluate gene expression changes in response to prolyl hydroxylase domain protein 2 and 3 (PHD2/3) depletion in endothelial cells, we performed mRNA-sequencing analysis with heart samples isolated from PHD2/3 endothelial knockout mice and their littermate control wild type mice.

overall_design: Whole hearts were collected from the PHD2/3 endothelial knockout mice and their littermate control wild type mice at P12.

first: Cristian

last: Coarfa


title: Growth inhibition and transcriptional effects of ribavirin in lymphoma

city: Ciudad de México

first: Alfredo

last: Hidalgo-Miranda

state: CDMX

address: Periferico Sur #4809

department: Cancer Genomic

country: Mexico

institute: INMEGEN

summary:
The cutaneous T-cell lymphoma Hut78 was treated with ribavirin for 120 h, and the gene expression of the treated cells was compared with respect to the expression of the cells without treatment.
We evaluated the effect of treatment with ribavirin upon gene expression in a cutaneous T-cell lymphoma model, Hut78. Ribavirin treatment decreased approximately 90% of the viability of Hut78 cells. A complete genomic analysis of transcriptomic status after treatment with ribavirin of cutaneous T cell lymphoma Hut78 revealed an impact on the overall expression of transcripts.

overall_design: We analyzed expression profile of the Hut78 cell line after treatment with ribavirin versus cells without treatment, using the Affymetrix Human Transcriptome Array 2.0 platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: G

last: Domínguez-Gómez

first: D

last: Cortes-Pedroza

first: J

last: Díaz-Chávez

first: Lucia

last: Taja-Chayeb

first: M

last: Sanchez-Dueñas

first: Fredy

middle: O

last: Beltrán-Anaya

first: Alberto

last: Cedro-Tanda

first: A

last: Schcolnik-Cabrera

last: Chávez-Blanco

last: Gonzalez-Fierro

first: C

last: Trejo-Becerril

first: E

last: Peréz-Cárdenas

last: Dueñas-Gonzalez


title: Regulated expression and function of the GABAB receptor in human pancreatic beta cell line and islets

city: Paris

first: Latif

last: Rachdi

address: 123 bvd Port-Royal

institute: Institut Cochin - Bat. Cassini

summary: G protein-coupled receptors (GPCRs) are seven transmembrane signaling molecules that are involved in a wide variety of physiological processes. They constitute a large protein family of receptors with almost 300 members detected in human pancreatic islet preparations. However, the functional role of these receptors in pancreatic islets is unknown in most cases. We generated a new stable human beta cell line from neonatal pancreas. This cell line, named ECN90 expresses both subunits (GABBR1 and GABBR2) of the metabotropic GABAB receptor compared to human islet. In ECN90 cells, baclofen, a specific GABAB receptor agonist, inhibits cAMP signaling causing decreased expression of beta cell-specific genes such as MAFA and PCSK1, and reduced insulin secretion. We next demonstrated that in primary human islets, GABBR2 mRNA expression is strongly induced under cAMP signaling, while GABBR1 mRNA is constitutively expressed. We also found that induction and activation of the GABAB receptor in human islets modulates insulin secretion.

overall_design: mRNA profiles of ECN90 and EndoC-βH1 cells

last: RACHDI

first: Raphael

last: SCHARFMANN

first: Juliette

last: HAMROUNE

first: Severine

last: PECHBERTY


title: Distinct waves from the hemogenic endothelium give rise to layered Lymphoid Tissue Inducer cell ontogeny

city: Marseille

first: Serge

middle: Alexander

last: van de Pavert

address: 163 Av de Luminy, case 906

department: CIML

institute: Inserm

summary:
LTi cells are part of the ILC family and essential for the formation of secondary lymph nodes within the embryo. This data set contains the analysis of lymphoid tissue (LTi) cell ontogeny, studied by expression profile analysis with RNA bulk sequencing and single cell sequencing of the fetal liver vs. embryonic periphery at embryonic stages E13.5 an E14.5. They indicate a proliferating precursor population mainly in the fetal liver, while the embryonic periphery harbors the definitive lineage.

This SuperSeries is composed of the SubSeries listed below.


title: Transcriptome profiling of inflammatory monocytes and macrophages in breast cancer bone metastasis

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

country: United Kingdom

institute: Queen's Medical Research Institute

summary: Macrophages play a critical role in promoting bone metastasis growth. Microarray was used for determining the transcriptional change of macrophages and their progenitor inflammatory monocytes during bone metastasis progression.

overall_design: We  sorted bone marrow macrophages (Macs) and Ly6C+ inflammatory monocytes (IMs) from mice bearing MetBo2 bone metastasis  and  from healthy bone marrow.  Labeling and hybridization were done in Einstein Microarray Facility using Affymetrix MoGene 2.0 st chips. A total of 19 samples (10 healthy and 9 bone metastasis, 4-5 replicates for each cell type) was profiled.

first: Binzhi

last: Qian

first: Jeffery

last: Pollard


title: Distinct waves from the hemogenic endothelium give rise to layered Lymphoid Tissue Inducer cell ontogeny [scRNA-seq]

summary: LTi cells are part of the ILC family and essential for the formation of secondary lymph nodes within the embryo. This data set contains the analysis of lymphoid tissue (LTi) cell ontogeny, studied by expression profile analysis with RNA single cell sequencing of the fetal liver vs. embryonic periphery at embryonic stages E13.5 an E14.5. They indicate a proliferating precursor population mainly in the fetal liver, while the embryonic periphery harbors the definitive lineage.

overall_design: Ontogeny of lympoid tissue (LTi) cells studied by mRNA expression analysis with single cells sequencing of the fetal liver vs. embryonic periphery at E13.5 and E14.5

first: Milesa

last: Simic

first: Lionel

last: Spinelli


title: Transcriptional profiling of vTreg53 TCR transgenic Regulatory T (Treg) cells stimulated by agonist peptide

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We reported transcriptional characterization of vTreg53 TCR transgenic Treg cells from splenic/lymph nodes and visceral adipose tissue (VAT) stimulated by agonsit peptide fat1562. We identified that peptide immunization is associated with TCR activation and that the VAT Treg transcriptome is largely maintained in the presence of antigen stimulation

overall_design: Treg cells from pooled spleen and lymph nodes of vTreg53 TCR transgenic mice were transferred into CD45.1 B6 mice. Six weeks later, the recipient mice were immunized subcutaneously with CFA/Fat1562, followed by a boost with IFA/Fat1562 intraperitoneally one week later. The clonotype+ Tregs from the spleen/lymph nodes and VAT of recipient mice were double sorted and processed for RNA-seq

first: Chaoran

last: Li

first: Christophe

last: Benoist

first: Diane

last: Mathis