title: Epithelial membrane protein 2 (EMP2) regulates hypoxia induced angiogenesis in retinal epithelial cells

city: Los Angeles

state: CA

address: 675 Charles E Young Dr S

department: Ophthalmology

institute: UCLA

summary: Pathologic retinal neovascularization is a potentially blinding consequence seen in many common diseases including diabetic retinopathy, retinopathy of prematurity, and retinal vascular occlusive diseases, among others. The use of therapeutics targeting pro-angiogenesis factors such as vascular endothelial growth factor (VEGF) has proven to be highly effective, however considerable side effects exist and serial anti-VEGF treatment has been shown to decrease effectiveness over time. Characterization of additional regulators of neovascularization is needed to further understand neovascular disease and identify possible new therapeutic targets. This study investigates epithelial membrane protein 2 (EMP2) and its role as a possible modulator of angiogenesis in human retinal pigment epithelium (RPE) under hypoxia. EMP2 is highly expressed in human RPE and RPE cell lines. Adult retinal pigment epithelial cell line-19 (ARPE-19) cells were genetically modified to either overexpress EMP2 (OE) or knock down EMP2 (KD) and expression at the RNA and protein level was evaluated using RNA sequencing and western blot respectively. Protein expression was evaluated under both normoxic conditions and conditions of hypoxic stress with 0.5% O2. EMP2 expression was found to positively correlate with expression of the pro-angiogenesis factors hypoxia inducible factor 1-alpha (HIF-1a) and VEGF for both RNA and protein. EMP2 mediated changes in ARPE-19 cells was also found to alter the secretion of a paracrine factor(s) in conditioned media that can regulate human umbilical vein endothelial cells (HUVEC) endothelial cell migration and capillary tube formation in in vitro functional angiogenesis assays. This study identifies EMP2 as a potentially important mediator of angiogenesis in the human RPE, a tissue involved in abnormal retinal neovascularization in a number of diseases. EMP2 levels positively correlate with those of the potent pro-angiogenesis mediators HIF-1a and VEGF, however the mechanism of this relationship remains to be clarified. This study supports further investigation of EMP2 as a promising novel target for therapeutic treatment of pathologic neovascularization in the retina.

overall_design: mRNA profiles of ARPE-19 cell panel consisting of EMP2 knock down, EMP2 overexpressing, vector control, and WT ARPE-19 cells under hypoxic and normoxic conditions

first: Nina

last: Cherian

first: Ann

last: Chan

first: Alison

last: Chu

first: Madhuri

last: Wadehra

first: Lynn

middle: K

last: Gordon


title: Grapevine line pattern virus and Hop yellow virus; two putative anulaviruses of the same species

status: Public on Jun 03 2020

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

type: Non-coding RNA profiling by high throughput sequencing

summary: Grapevine line pattern virus (GLPV) was described 30 years ago from Hungary, and in the lack of its sequence until now no additional information about its presence was reported. However High-Throughput Sequencing (HTS) applied on dsRNAs extracts recovered from a grapevine plant (accession Baco22A) infected with GLPV Grapevine line pattern virus (GLPV) allowed us to sequence it with different High-Throughput Sequencing (HTS) methods andthe assembleing of the full genome sequence of this virus. The availability of the sequence allowed us to validate the presence of the virus bot with RT-PCR and with Northern blot hybridization. These methods were also used to test its graft and seed transmission. In accordance as it was originally suggested its genome was found to comprise three RNA segments.Its RNA1 (3.160 bp), RNA2 (2.493 bp) and RNA3 (2.529 bp), encode four proteins, denoted 1a (Methyltransferase, helicase), 2a (RNA-dependent RNA Polymerase), 3a (Movement protein, MP) and 3b (Coat protein, CP). GLPV showed the highest amino acid identity (92%–99%) with all domains of Hop yellow virus (HYV), which is a tentative member of the genus Anulavirus of the family Bromoviridae. The phylogenetic trees constructed based on the amino acid sequences of 2a and 3b also confirmed the belongingness of GLPV to the genus Anulavirus, allocating it in one cluster together with the anulaviruses, and close to HYV. The very high sequence identity found between GLPV and HYV leaves no doubt that both are two isolates of the same viral species.

overall_design: one sample from a virus infected grapevine

first: Toufic

last: Elbeaino

first: Emese

last: Demian

first: Levente

last: Kontra

first: Nikoletta

last: Jaksa-Czotter

first: Amani

middle: B

last: Slimen

first: Richard

last: Fabian

first: Janos

last: Lazar

first: Lucie

last: Tamisier

first: Michele

last: Digiaro

first: Sebastien

last: Massart

first: Eva

last: Varallyay


title: Decreased cytotoxic T cells and TCR clonality in organ transplant recipients with squamous cell carcinoma

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

type: Expression profiling by high throughput sequencing

summary: T-cell landscape differences between cutaneous squamous cell carcinoma (cSCC) tumors in immune competent (SCC in IC) and immunocompromised organ transplant recipients (TSCC in OTR) are unclear. We developed an analytical method to define tumor infiltrating lymphocyte (TIL) phenotype in cSCC from immune competent and immune suppressed patients using single-cell TCR sequencing and gene expression data. TSCC exhibits reduced proportions of cytotoxic and naïve TILs and similar numbers of regulatory TILs. Fewer, more heterogeneous TCR clonotypes are observed in TIL from OTR. Most TCR sequences for top ten clonotypes correspond to known antigens, while 24% correspond to putative neoantigens. OTR show increased cSCC events over 12 months possibly due to reduced cytotoxic T-cells. Our novel method of barcoding CD8+ T-cells is the first providing gene expression and TCR sequences in cSCC. Knowledge regarding putative antigens recognized by TCRs with phenotypic function of T-cells bearing those TCRs could facilitate personalized cSCC treatments.

overall_design: CD8+ T cells were obtained from fresh tissue samples via flow cytometry. The sorted cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10-12e3 cells were loaded per channel. Single-cell RNA-Seq libraries were prepared using the following Single Cell 5â€™ Reagent Kits: Chromiumâ„¢ Single Cell 5â€™ Library & Gel Bead Kit, PN-1000006 and Chromium Single Cell VDJ enrichment kit for Human T Cells (PN-100000). Libraries were run on a NovaSeq 6000 SP or S1 flow cell (depending on sample numbers) for both 5â€™ transcriptome data and TCR clonotype determination. We assessed 5 cutaneous squamous cell carcinoma tumors from immunocompetent patients (SCC1-5) and 6 tumors from immunocompromised patients (i.e., organ transplant recipients) (TSCC1-6).

first: John

middle: A

last: Carucci

first: Aristotelis

last: Tsirigos

first: Nicole

last: Doudican


title: New insights into gonadal sex differentiation provided by single cell transcriptomics in the chicken embryo

city: Clayton

first: Craig

middle: Allen

last: Smith

state: Victoria

address: Wellington Road

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary: Gonadal sex differentiation – testis versus ovary formation – is a fundamental process required for reproduction and evolution. Reflecting this importance, the embryonic gonads of vertebrate species comprise the same key cell types; germ cells, supporting cells and interstitial steroidogenic cells. Remarkably, the genetic triggers for gonadal sex differentiation vary across species (the SRY gene in mammals, DMRT1 in birds and some turtles, temperature in many reptiles, AMH and various other genes in fishes). Despite this variation, the cell biology of gonadal development was long thought to be largely conserved. Here, we present a comprehensive analysis of gonadal sex differentiation, using the chicken embryo as a model and considering the entire gonad. We sampled over 30,000 cells across several developmental stages, prior, during and after the onset of gonadal sex differentiation. The data provide several new insights into cell lineage specification during vertebrate gonadogenesis. Combining lineage tracing with single cell transcriptomics, the data show that somatic supporting cells of the embryonic chicken gonad do not derive from the coelomic epithelium, in contrast to other vertebrates studied. Instead, the early somatic precursors cells of the gonads in both sexes derive from a DMRT1+/PAX2+/WNT4+/OSR1+ mesenchymal cell population. In particular, PAX2 marks immigrating mesenchymal cells that give rise to the supporting cell lineage. We find a greater complexity of gonadal cell types than previously thought, including the identification of two distinct sub-populations of Sertoli cells in developing testes, and derivation of embryonic steroidogenic cells from a differentiated supporting cell lineage. We provide significantly improved resolution of gonadal cell types and identify several new gonadal marker genes. Altogether, these results indicate that, just as the genetic trigger for sex differs across vertebrate groups, cell lineage specification in the gonad may also vary substantially.

overall_design: Single cell RNAseq of whole male and female chicken gonads at 4 developmental timepoints.

first: Martin

last: Estermann

first: Sarah

last: Williams

first: Andrew

middle: T

last: Major

first: Claire

middle: E

last: Hirst

first: Zahida

middle: Y

last: Roly

first: Olivier

last: Serralbo

first: Deepak

last: Adhikari

first: David

last: Powell


title: PIM kinase inhibition in HCC xenograft

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Human HCC cell line, MHCC-97L, was subcutaneously injected to BALB/c nude mice. Two weeks post injection, mice were randomised to receive vehicle or PIM447 (60mg/kg) by oral gavage three times a week for two weeks. Total RNA was extracted from the tumor xenograft (Vehicle, n=2; PIM447, n=2) and subjected to RNA sequencing. Expression profiling of the tumors between vehicle control and PIM447 treated groups was compared.

overall_design: Total RNA extracted from tumor xenograft of mice treated with vehicle (n=2) and PIM447 (n=2) were subjected to RNA sequencing profiling.

first: Regina

last: Lo


title: In vitro transcriptomic responses to thioacetamide-S-oxide exposure in human primary hepatocytes, renal tube epithelial, and cardiomyocytes

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury endpoints from in vitro transcriptomics responses at early time points (9 and 24 hours) after to thioacetamide-S-oxide treatment, the toxic metabolite of thioacetamide. Thioacetamide, an organosulfur compound, have been extensively used in animal studies as a hepatotoxin and carcinogen for its ability to cause acute liver damage.

overall_design: We treated three human cell types, primary hepatocytes (vehicle, low (0.50 mM), or high (0.25 mM) dose), renal tube epithelial cells (vehicle, low (0.25 mM), or high (1.00 mM) dose), and cardiomyocytes (vehicle, low (0.25 mM), or high (0.75 mM) dose) with thioacetamide-S-oxide. RNA-seq data were collected 9 and 24 hours after application of vehicle or thioacetamide-S-oxide.

first: Richard

middle: L

last: Printz

first: Shanea

last: Estes

first: Tracy

middle: P

last: O’Brien

first: Masakazu

last: Shiota

first: Anders

last: Wallqvist


title: Mapping Gata2 enhancer-dependent developmental trajectories by single-cell RNA-sequencing

city: Madison

first: Emery

last: Bresnick

state: WI

address: 8457 WIMR 1111 Highland Ave.

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: We compared single-cell transcriptomes of fetal liver myeloid progenitor pools (CMP/GMP pool) from Gata2 -77 enhancer mutant embryos and wildtype littermates.  Gene expression patterns in -77-deficient mice demonstrated loss of erythroid, megakaryocyte and granulocyte progenitors and an increase in monocyte

overall_design: Lineage-Sca1-cKit+CD34+ cells from E14.5 fetal livers of two wild type and two -77-deleted embryos were processed for single-cell RNA sequening using 10x Genomics Chromium platform.

middle: H

first: Sunduz

last: Keles


title: PI3Kβ-Regulated Pericyte Maturation Governs Vascular Remodeling

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary:
Background: Pericytes regulate vessel stabilization and function and their loss is associated with diseases such as diabetic retinopathy or cancer. Despite their physiological importance, pericyte function and molecular regulation during angiogenesis remain poorly understood.

Methods: To decipher the transcriptomic programs of pericytes during angiogenesis, we crossed the Pdgfrb(BAC)-CreERT2 into the RiboTagflox/flox mice. Pericyte morphological changes were assessed in mural cell-specific R26-mTmG reporter mice, in which low doses of tamoxifen allowed labeling of single cell pericytes at high resolution. To study the role of phosphoinositide 3-kinase (PI3K) signaling in pericyte biology during angiogenesis, we used genetic mouse models which allow selective inactivation of PI3Kα and PI3Kβ isoforms and their negative regulator PTEN (phosphate and tensin homologue deleted on chromosome ten, PTEN) in mural cells.

Results: At the onset of angiogenesis, pericytes exhibit molecular traits of cell proliferation and activated PI3K signaling, whereas during vascular remodeling pericytes upregulate genes involved in mature pericyte cell function, together with a remarkable decrease in PI3K signaling. Immature pericytes showed stellate shape and high proliferation, and mature pericytes were quiescent and elongated. Unexpectedly, we demonstrate that the PI3Kβ, but not PI3Kα, regulates pericyte proliferation and maturation during vessel formation. Genetic PI3Kβ inactivation in pericytes triggered early pericyte maturation. Conversely, unleashing PI3K signaling by means of PTEN deletion delayed pericyte maturation. Pericyte maturation was necessary to undergo vessel remodeling during angiogenesis.

Conclusions: Our results identify new molecular and morphological traits associated to pericyte maturation and uncover PI3Kβ activity as a checkpoint to ensure appropriate vessel formation. In turn, our results may open new therapeutic opportunities to regulate angiogenesis in pathological processes through the manipulation of pericyte PI3Kβ activity.

overall_design: Identification of mural cells signatures in two time points (postnatal day 3 and 9) during retinal postnatal angiogenesis.

middle: M

last: Figueiredo

first: Pilar

last: Villacampa

first: Rodrigo

last: Diéguez-Hurtado

first: Juan

middle: J

last: Lozano

first: Piotr

last: Kobialka

middle: R

last: Cortazar

first: Anabel

last: Martinez-Romero

last: Angulo-Urarte

first: Claudio

last: Franco

first: Marc

last: Claret

first: Ralf

last: Adams

first: Arkaitz

last: Carracedo

first: Mariona

last: Graupera


title: Expression profiling of mouse HPC7 cells

city: Parkville

first: Matthew

last: Ritchie

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary: We have expressed mouse Snai1, mutant Snai1 or empty vector in the HPC7 cell line and performed RNA sequencing analysis to identify targets of Snai1 in mouse hematopoietic progenitor cells.

overall_design: HPC7 cells were engineered to express either wildtype Snai1, a mutant version of Snai1 that cannot bind Lsd1 or an empty vector control using retroviral transduction. GFP+ cells were sorted after 1 week in culture and RNA was extracted for RNA sequencing.

first: Catherine

last: Carmichael

first: Jody

last: Haigh


title: An aphid lncRNA is a member of an aphid-specific family that translocate into plant and is a virulence factor

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

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

sample_organism:
Arabidopsis thaliana
Myzus persicae

platform_organism:
Arabidopsis thaliana
Myzus persicae

overall_design: Refer to individual Series


title: An aphid lncRNA is a member of an aphid-specific family that translocate into plant and is a virulence factor [FeedingSite Expt]

summary: This study provides evidence that aphid lncRNAs play a role in regulating aphid-plant interactions and at least one M. persicae lncRNA is a virulence factor

overall_design: RNASeq exeperiment was desined to investigated  genes that are involved in host adaptaion in Myzus percicae

first: Yazhou

last: Chen

first: Gemy

middle: G

last: Kaithakottill

first: Matteo

last: Gravino

first: Sam

last: Mugford

first: Thomas

middle: C

last: Mathers

first: Cock

last: van Oosterhout

first: David

last: Swarbreck

first: Saskia

last: Hogenhout


title: Single cell sequencing of Tomato+ cells in skin from Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

summary: We report single-cell RNA-seq reveals gene signatures associated with skin from adult Prrx1-CreERT;Tomato mice.

overall_design: Tomato+ cells' mRNA profiles of skin from adult Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days were generated by single cell  sequencing

first: Baojie

last: Li


title: Prrx1 labels stromal stem cells that contribute to the homeostasis and damage repair of the connective tissues


title: Single cell sequencing of Tomato+ cells in Inguinal White Fat from Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days

summary: We report single-cell RNA-seq reveals gene signatures associated with Inguinal White Fat from adult Prrx1-CreERT;Tomato mice.

overall_design: Tomato+ cells' mRNA profiles of Inguinal White Fat from adult Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days were generated by single cell  sequencing


title: Single cell sequencing of Tomato+ cells in bones from Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days

summary: We report single-cell RNA-seq reveals gene signatures associated with bones from adult Prrx1-CreERT;Tomato mice.

overall_design: Tomato+ cells' mRNA profiles of bones from adult Prrx1-CreERT;Tomato mice with the treatment of Tamoxifen for 3 days were generated by single cell  sequencing


title: An aphid lncRNA is a member of an aphid-specific family that translocates into plant and is a virulence factor [HostSwap Expt]

overall_design:
RNA-Seq exeperiment was designed to investigate the genes that are involved in host adaptaion in Myzus percicae.

The following gtf files contain manual annotation of Ya gene in
Aphis glycines (A.glycines.Ya.gtf)
Acyrthosiphon pisum(A.pisum.Ya.gtf)
D. noxia (D.noxia.Ya.gtf)
Myzus cerasi (M.cerasi.Ya.gtf)
Rhopalosiphum padi (R.padi.Ya.gtf)
and the 'Ya_aphid.fa' contains cDNA sequence in fasta format for the above gtf files.


title: MCT1 deletion in Saccharomyces cerevisiae

status: Public on Jun 02 2020

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

summary: MCT1 was deleted in Saccharomyces cerevisiae and gene expression was measured over a timecourse.

overall_design: MCT1 was genetically deleted in W303 Saccharomyces cerevisiae and grown in glucose. At 0 hrs, WT and MCT1 deletion cells were collapsed for RNA-seq, and media was supplemented with raffinose instead of glucose. At 3hr and 12 hr, WT and MCT1 deletion cells were harvested.

first: Sara

last: Nowinksi

first: Jared

last: Rutter


title: Distinct hippocampal expression profiles of lncRNAs in obese type 2 diabetes mice exhibiting cognitive impairment

city: Nanning

first: Chunlin

last: Zou

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

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

summary: Cognitive dysfunction has been accepted as a possible complication of type 2 diabetes (T2D), but few studies revealed the potential roles of Long non‑coding RNAs (lncRNAs) in cognitive dysfunction in T2D. The purpose of the current research is to demonstrate the specific expression patterns of lncRNA-mRNA in the hippocampi of T2D db/db mice exhibiting cognitive impairment. In this study, the results from behavioral tests showed that T2D db/db mice displayed short-term and spatial working memory deficits compared to db/m mice. Furthermore, western blot analysis demonstrated that compared with db/m mice, p-GSK3β (ser9) protein levels were markedly elevated in T2D db/db mice (P<0.01). In addition, though not statistically significant, the ratio of p-Tau (Ser396) to Tau 46, α-Synuclein expression and p-GSK3α (ser21) expression were also relatively higher in T2D db/db mice than in db/m mice. The microarray profiling revealed that 75 lncRNAs and 26 mRNAs were obviously dysregulated in T2D db/db mice (>2.0 fold change, P<0.05). GO analysis demonstrated that the differentially expressed mRNAs participated in immune response, extracellular membrane-bounded organelle and extracellular region. KEGG analysis revealed that the differentially expressed mRNAs were mainly involved in one carbon pool by folate, glyoxylate and dicarboxylate metabolism, autophagy, glycine, serine and threonine metabolism and B cell receptor signaling pathway. An lncRNA‑mRNA coexpression network containing 71 lncRNAs and 26 mRNAs was built to investigate the interaction between lncRNA and mRNA. Collectively, these results revealed the differential hippocampal expression profiles of lncRNAs in T2D mice with cognitive dysfunction, and the findings from this study provide new clues for exploring the potential roles of lncRNAs in the pathogenesis of cognitive dysfunction in T2D.

overall_design: Microarray analysis was performed on the hippocampal tissues of 3 db/db and 3 db/m mice.

first: Qianqian

last: Xu

first: Lihui

last: Wang

first: Qiong

last: Song


title: Analysis of Retinoblastoma Transcriptome

city: Mexico City

first: Diana

middle: Emilce

last: Alvarez Suarez

state: Mexico

address: Av cuautemoc 330

department: Unidad de Investigacion Medica Enf. Infecciosas

country: Mexico

institute: hospital de pediatria CMNSXXI

summary:
In this data, we examined Transcriptome detection and expression in 8 samples of Retinoblastoma. We found a central core shared by all samples .
We used exon arrays to find a detected and undetected transcripts and genes in Retinoblastoma and we compared unilateral and bilateral samples.

overall_design: The samples were obtained from the eight enucleated eyes from patients with retinoblastoma with no chemotherapy treatment.Tumors were cultured for a week in the RPMI medium with 12% FBS and the extraction of RNA from the primary cultures was performed with TRIzol protocol.

last: Alvarez-Suarez

first: Martha

middle: V

last: Ponce-Castañeda

first: Hugo

last: Tovar

first: Enrique

last: Hernandez-Lemus


title: The transcriptomic profile of the hippocampal microglia in the irradiated juvenile mouse brain

city: Stockholm

first: Ahmed

last: Osman

address: Solnavägen 30

country: Sweden

institute: Karolinska Institute

summary: Cranial irradiation (IR), an effective tool to treat malignant brain tumors, triggers a chronic pro-inflammatory microglial response, at least in the adult brain. Using bulk RNA sequencing, we show that the microglial response in the juvenile mouse hippocampus is rapid, but returns toward normal within 1 week. The sensome of irradiated hippocampal microglia reveals an immediate response that declines after one day.  Irradiation of the juvenile brain induces a highly ordered temporal progression of the inflammatory and phenotypic microglial genes

overall_design: Mice were irradiated on postnatal-day 21 with radiation dose of 8Gy. Miced were sacrifced at different time points after irradiation (2h, 6h, 1day, and 1wk). After perfusion, the hippocampus was dissected and the micgloa were FACS isolated based on the expression of Cx3cr1 expression. Total RNA was isloated and processed for bulk RNA-Seq. Each time point consisted iof 6 sham control (SH) and 6 irradiated (IR) animals.

first: A

first: J

last: Kele

first: K

last: Blomgren


title: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower [ncRNA-seq]

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: miRNA-sequencing of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower

overall_design: miRNA-sequencing profiles of seeds of high oleic acid L-1-OL-1 were generated by deep sequencing at 7-, 22- and 37 day.

first: Yan

last: Liu

first: Fei

last: Zhou


title: Transcriptional buffering compensates for eIF4E deficiency  2 in mRNA translation in transformed but not normal cells

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

summary: This study examined genome-wide translational and transcriptional regulation by the initiation factor eIF4E.  The goals of the study were to understand how regulation differed between breast cancer and breast normal cells

overall_design: Stable MDA-MB-231 (breast cancer) and HMEC (breast normal) cells were created to inducibly express short-hairpin targeting eIF4E or a scrambled shRNA control upon addition of doxycycline.  Cells were treated with doxycycline for 6 days and polysome gradient fractionation was performed.  Polysome fractions were combined so that poorly expressed mRNA (2-3 ribosomes), moderately translated (4-6 ribosomes), highly translated (>6 ribosomes) mRNAs were analyzed.  Total RNA prior to fractionation was also analyzed as a measure of total mRNA abundance.

first: Robert

last: Schneider

first: Kelly

last: Ruggles


title: C. elegans LPIN-1 moderates lifespan-shortening effects of dietary glucose via maintaining ω-6 polyunsaturated fatty acids

city: Daejeon

first: Seung-Jae

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

summary: A glucose-rich diet shortens lifespan via altering lipid metabolism in many organisms, including Caenorhabditis elegans. However, it remains incompletely understood how glucose and lipid metabolism regulates lifespan. Here, we show that Lipin 1/LPIN-1, a phosphatidic acid phosphatase and a putative transcription co-regulator that mediates glucose-to-triacylglyceride synthesis, prevents the life-shortening effects of glucose-rich diets on C. elegans. We showed that the expression levels of many genes related to lipid metabolism were differentially regulated by lpin-1 RNAi and glucose treatment.

overall_design: The investigation of the changes of gene expression in lpin-1 RNAi-treated animals on control diets or glucose-rich diets

first: Yoonji

last: Jung

first: Sujeong

last: Kwon

first: Seokjin

last: Ham


title: Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human pancreatic islet cell specification

city: Aurora

first: David

last: Lorberbaum

state: CO

address: 1775 Aurora Court

department: Barbara Davis Center for Diabetes

institute: University of Colorado Denver

summary: Retinoic acid (RA) signaling is essential for multiple developmental processes, including appropriate pancreas formation from the foregut endoderm. RA is also required to generate pancreatic progenitors from human pluripotent stem cells. However, the role of RA during the later stages of pancreas development is not well understood. In this study, we generated an inducible system to block RA signaling and demonstrate that disruption of the RA pathway within the Neurog3-expressing endocrine progenitor population is required for appropriate mouse b cell differentiation and repression of critical d cell genes, including Somatostatin. In addition, inhibition of the RA pathway in hESC-derived pancreatic progenitors downstream of NEUROG3 induction impairs INSULIN expression. We further determined that RA-regulation of endocrine cell differentiation is mediated through Wnt pathway components. Together, these data demonstrate the importance of RA signaling in endocrine specification and identify conserved mechanisms by which RA signaling directs endocrine cell fate.

overall_design: e16.5 pancreas RNA-seq from Neurog3:cre alone (n=3) and Neurog3:cre;RARdnfl/fl (n=3)

middle: S

first: Lori

last: Sussel


title: Single-cell profiling of developing mouse lungs

city: Houston

first: Odemaris

middle: Narvaez

last: del Pilar

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary

institute: MD Anderson Cancer Center

summary: Single-cell profiling of wild type lungs was performed to delineate the expression profile of epithelial, endothelial, mesenchymal and immune cells.

overall_design: FACS-purified whole murine lung epithelial, endothelial, mesenchymal, and immune cells were mixed together in similar proportions and processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics).

last: Narvaez del Pilar

first: Jichao

last: Chen


title: Unique microRNA Alterations in Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Ginkgo biloba leaf extract (GBE) is used in traditional Chinese medicine as an herbal supplement for improving memory. Exposure of B6C3F1/N mice to GBE in a 2-year National Toxicology Program (NTP) bioassay resulted in a dose-dependent increase in hepatocellular carcinomas (HCC). To identify key microRNAs that modulate GBE-induced hepatocarcinogenesis, we compared the global miRNA expression profiles in GBE-exposed HCC (GBE-HCC) and spontaneous HCC (SPNT-HCC) with age-matched vehicle control normal livers (CNTL) from B6C3F1/N mice.  The number of differentially altered miRNAs in GBE-HCC and SPNT-HCC were 74 (52 up and 22 down) and 33 (15 up and 18 down), respectively.  Among the uniquely differentially altered miRNAs in GBE-HCC,, miR-31 was selected for functional validation.  A potential miRNA response element (MRE) in the 3’-untranslated regions (3’-UTR) of Cdk1 mRNA was revealed by in silico analysis and confirmed by luciferase assays.  In mouse hepatoma cell line HEPA-1 cells, we demonstrated an inverse correlation between miR-31 and CDK1 protein levels, but no change in Cdk1 mRNA levels, suggesting a post-transcriptional effect.  Additionally, miRNA expression analysis in non-tumor liver samples from the 90-day GBE mouse study demonstrated an upregulation of miRs-411, 300, 127, 134, 409-3p, and 433-3p in GBE-exposed group compared to vehicle control group, indicating that some of these miRNAs could serve as potential biomarkers for GBE exposure or hepatocellular carcinogenesis.  These data increase our understanding of miRNA-mediated epigenetic regulation of GBE-mediated hepatocellular carcinogenesis in B6C3F1/N mice.

overall_design: Upon examination of morphology using H & E slide prepared from counterpart of frozen tissues, a subset of selected frozen samples from GBE-HCC, SPNT-HCC (from vehicle control groups) and age-matched normal livers (CNTL) from vehicle control B6C3F1/N mice from the 2-year NTP bioassay were used for miRNA array analysis (n=5/group).

first: Haruhiro

last: Yamashita

first: Sailesh

last: Surapureddi

first: Ramesh

last: Kovi

first: Sachin

last: Bhusari

first: Thai

last: Ton

first: Keith

last: Shockley

first: Shyamal

middle: D

last: Peddada

first: Kevin

last: Gerrish

first: Cynthia

last: Rider

first: Mark

last: Hoenerhoff

last: Sills

first: Arun

last: Pandiri


title: Epigenetic adaptation prolongs photoreceptor survival during retinal degeneration

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neural degenerative diseases often display a progressive loss of cells at as a stretched exponential ratedistribution. The mechanisms underlying the survival of a subset of clonal cells in a population beyond what is expected by chance alone remains unknown. To gain mechanistic insights underlying prolonged cellular survival, we used Spata7 mutant mice as a model and performed single-cell transcriptomic profiling of retinal tissue along the time course of photoreceptor degeneration. Intriguingly, rod cells that survive beyond the initial rapid cell apoptosis phase progressively acquire a distinct transcriptome profile. In these rod cells, expression of photoreceptor-specific phototransduction pathway genes is downregulated while expression of other retinal cell type-specific marker genes is upregulated. These transcriptomic changes are achieved by direct modulation of the epigenomeetic modifications and changes of the chromatin state at these gene loci, as indicated by immunofluorescence staining and single-cell ATAC-seq. Consistent with this model, when the induction of the repressive epigenetic state is blocked by in vivo histone deacetylase HDAC inhibition, all photoreceptors in the mutant retina undergo rapid degeneration, strongly curtailing the stretched exponential distribution. Altogether, oOur study reveals an intrinsic mechanism by which the neuralon cells progressively adapt to the genetic stress to achieve prolonged survival through epigenomic regulation and chromatin state modulation.

overall_design: To globally characterize the of retinal tissue along the time course of photoreceptor degeneration, we performed single cell RNA sequencing of retinal cells from wild type and Spata7 knockout mutant mice at 1, 3, 6 month. we used Spata7 mutant mice as a model. To globally characterize the of retinal tissue along the time course of photoreceptor degeneration, we performed single cell ATAC sequencing  of retinal cells from 7M wild type and 6M Spata7 knockout mutant mice.

first: Rachayata

last: Dharmat

first: Yumei

first: Rui


title: Transcriptomic analysis of gip1gip2 compared to WT.

city: Strabourg

first: Marie-Edith

last: Chabouté

address: 12, rue du Général Zimmer

country: France

institute: CNRS

overall_design: NGS analysis was performed on 2 populations of gip1gip2, T12 and T34, showing  increased severity in their root growh phenotypes, as described in Goswami et al., 2020. WT, i.e. Ws x Col-0, was used as a control. Three individual replicates were performed.

first: Stefanie

last: Graindorge

first: Guy

last: Houlné


title: ChIP-seq analysis of Eomes in murine NK cells

city: St Louis

first: Todd

middle: A

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

overall_design: NK cells purified from pooled splenocytes from WT mice were expanded in vitro for 4 days with 100ng/mL IL-15. Cells were then harvested and approximately 10e6 cells were used per ChIP experiment. We sought to identify the binding sites of Eomes in murine NK cells.


summary: Gene expression profiling of EomesΔ/Δ and Wild Type Murine NK cells sorted into specific maturaion stages

overall_design: NK cells were isolated from splenocytes harvested from ILC-EomesΔ/Δ (Ncr1-iCreERT2 KI/WT x Rosa26YFPLSL x Eomesfl/fl mice treated with Tamoxifen) and WT mice and sorted into Stage II (CD27+CD11b-), Stage III (CD27+CD11b+), or Stage IV (CD27-CD11b+). We sought to identify genes regulated by Eomes in NK cells at different NK cell maturation stages.


title: IL-12 From Endogenous cDC1, and Not Vaccine DC, Is Required for Th1 Induction

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: In this study, we generated a chimeric situation by injection of different gene-modified BM-DCs into different strains of gene-modified recipient mice. This allowed us to identify the separate functional contributions of injected versus endogenous DCs for Th1 polarization. We identified the cellular source of IL-12p70 production after subcutaneous BM-DC vaccination as endogenous migratory XCR1+ bystander DCs in the skin draining lymph nodes. DC-DC and DCT cell interaction studies revealed a time course of Th0 priming by injected BM-DCs, followed by interactions of BM-DC with the IL-12+ XCR1+ bystander DCs, and finally IL-12+ XCR1+ bystander DC interactions for Th1 induction. Transcriptional profiling of the bystander DCs underscores their Th1 polarization potential. Together, this study shows that DC-vaccination requires the bystander activation of endogenous DCs for Th1 priming. Our data also challenge the general concept of Th1 priming by a single DC providing all signals 1, 2 and 3 to T cells for Th1 polarization.

overall_design: To study the transcriptional changes occurring in the endogenous migratory bystander DCs, we sorted the migratory MHC II high CD11c+ lymph node DC subsets before (naive mice) and 48h after BM-DC injection (bystander activation). Thereby we could compare migratory XCR1+ CD11b- dDCs (cDC1s), CD11b+ XCR1- dDCs (cDC2s), and CD11b- XCR1- DCs (DN) at steady-state and 48h after LPS.BM-DC injection. Also, the appearance of CD11b+ CD64+ Ly6Clow inflammation-induced MoDCs was identified and these cells were also sorted at 48h.

first: DiyaaElDin

last: Ashour

first: Panagiota

last: Arampatzi

first: Konrad

middle: U

last: Förstner

first: Tsuneyasu

last: Kaisho

first: Andreas

last: Beilhack

first: Florian

last: Erhard

first: Manfred

middle: B

last: Lutz


title: A unified model for the function of YTHDF proteins in the regulation of m6A-modified mRNA

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: N6-methyladenosine (m6A) is the most abundant mRNA nucleotide modification and regulates critical aspects of cellular physiology and differentiation. m6A is thought to mediate its effects through a complex network of interactions between different m6A sites and three functionally distinct cytoplasmic YTHDF m6A-binding proteins (DF1, DF2, and DF3). In contrast to the prevailing model, we show that DF proteins bind the same m6A-modified mRNAs, rather than different mRNAs. Furthermore, we find that DF proteins do not induce translation in HeLa cells. Instead, the DF paralogs act redundantly to mediate mRNA degradation and cellular differentiation. The ability of DF proteins to regulate stability and differentiation becomes evident only when all three DF paralogs are simultaneously depleted. Our studies reveal a unified model of m6A function in which all m6A-modified mRNAs are subjected to the combined action of the YTHDF proteins in proportion to the number of m6A sites.

overall_design: We measured transcript stability, translation rate, and transcript expression analysis upon the silencing of each of the YTHDF protein in HeLa cells. Since all three YTHDF proteins show similar sequence, binding proteins, binding sites and intracellular localization, their redundancy was tested by performing transcript stability, translation rate and transcript levels measurement upon the silencing of all three DF proteins as well. At least three replicates were performed for each measurement.

first: Sara

last: Zaccara


title: Genome-wide analysis of transcription and PIF7 DNA binding in response to long days with daily oscillating temperatures in Arabidopsis thaliana

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

summary: This study aimed to characterise the genome-wide PIF7-mediated responses of Arabidopsis thaliana seedlings to long photoperiods with a warm 27°C midday in comparison to long photoperiods at constant 17°C. Transcriptomic responses were observed in Col-0 wild-type and pif7-1 loss-of-function mutants investigate the potential contribution of the transcription factor PIF7 to the warm temperature response under the described conditions. In parallel, ChIP-seq of a PIF7-MYC-expressing line under the same conditions was employed to investigate global DNA binding changes of PIF7 in response to a change in temperature.

overall_design: Please refer to individual samples

first: Martin

last: Balcerowicz


title: SPECIFIC BIOMARKERS ASSOCIATED WITH CHRONIC RENAL LESIONS IN IGA NEPHROPATHY PATIENTS. A MULTICENTER STUDY

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

summary: The histologic diagnosis of idiopathic IgA Nephopathy (IgAN) is based o renal lesions scores. Aim of our study was to identify specific gene expression changes that characterize active renal lesions that may be more responsive to immunosuppressive therapy than chronic lesions.  Total RNA was extracted from archival FFPE renal tissue samples of 55 IgAN patients, 31 non-IgAN patients. IgAN patients were accurately stratified based on the LUMPED classifications. Genome-wide gene expression profiles were generated and Oneway ANOVA with tukeyHSD post hoc testing was used to identify specific transcripts associated with active and chronic renal lesions in IgAN. RT-PCR was used to validate selected transcripts. Immunohistochemistry (IHC) was used to evaluate specific protein expression in biopsy specimens.  Bioinfomatic analysis identified 183 genes with a Fold Change > 1.5 exclusively modulated in IgAN biopsies with active lesions and 162 genes with Fold Change >  1.5 exclusively modulated in IgAN biopsies with chronic lesions. These genes belonged to renal cellular damage and immune system regulatory pathways. To establish the validity of gene expression determined by microarray analysis, we performed RT-PCR on genes that were putatively involved in generating active and chronic lesions that may be involved in activating local inflammatory response and contributing to renal damage. Validated transcripts were also confirmed at protein level with IHC on kidney biopsy specimens.  Transcriptomics on FFPE renal biopsies integrates histomorphologic renal lesions. Our study identifies specific gene expression changes involved in active and chronic lesions at the time of renal biopsy. This novel information may be used for personalized therapy through a system pharmacology approach to identify targeted molecules able to revert aberrant expression networks characterizing active and chronic lesions.

overall_design: Total RNA obtained from renal biopsy of IgAn patients  compared with healthy tissue and on the basis of their classification.

first: Grazia

last: Serino

first: Claudia

last: Curci

first: Sharon

middle: N

last: Cox

first: Francesco

last: Schena


title: Next generation sequencing based transcriptome comparison between wild-type Drosophila and an Alzheimer's disease model

city: Beijing

first: Xianda

last: Hu

address: 218 Anwaixiaoguanbeili St

institute: Beijing Tibetan Hospital, CTRC

summary: Gene expression profiling of wild-type (WT) fruit flies and transgenic flies that express human amyloid precursor protein was performed to investigate how Aβ42 affects the transcriptome of Drosophila.

overall_design: Head tissues from 3-, 10- and 20-day-old male WT and Alzheimer’s disease (AD) Drosophila model were collected for RNA isolation and high-throughput sequencing.


title: RNA-seq of CBD-treated SK-N-BE(2) cells over a time course of 3hr - 24hr with vehicle (ethanol) matched controls at each time point.

status: Public on Jun 01 2020

city: Boulder

first: William

middle: Marland

last: Old

address: 1945 Colorado Ave.

department: MCDB

institute: University of Colorado Boulder

summary: Cannabidiol (CBD) is an FDA approved drug for treatment of drug-intractable forms of pediatric epilepsy. While a unified mechanism of action has yet to emerge from numerous proposed molecular targets of CBD, preclinical studies reveal a pleiotropic pharmacology. Here, we report the application of temporally-resolved multi-omic profiling and biosensor screening to dissect the molecular mechanism of CBD in human neuroblastoma cells. CDB treatment led to a rise in cytosolic calcium and activation of AMPK signaling within 2 hours. Subcellular profiling of proteins, metabolites, and mRNA transcripts identified CBD-dependent activation of cholesterol biosynthesis, transport and storage. We found that CBD incorporates into cellular membranes, alters cholesterol activity, and increases lipid order. We also report CBD-induced apoptosis in multiple human cell lines, which is rescued by statins and potentiated by compounds that disrupt cholesterol trafficking and storage. Our data point to pharmacological interaction of CBD with cholesterol homeostasis pathways, with potential implications in its therapeutic use.

overall_design: mRNA profiles of CBD or vehicle (ethanol, 0.1% v/v)-treated SK-N-BE(2) cells. Four time points (3h, 6h, 12h, and 24h) were profiled at 20µM, with four replicates of CBD treatment and four replicates vehicle treatment at each time point (total of 32 samples).

first: Zachary

last: Poss

first: Steven

last: Guard

first: Jeremy

last: Jacobsen


title: Compound craniosynostosis, intellectual disability and Noonan-like facial dysmorphism associated with 7q32.3-q35 deletion

city: Poznan

first: Ewelina

last: Bukowska-Olech

address: Rokietnicka 8

country: Poland

institute: Univeristy of Medical Sciences

summary: Craniosynostosis (CS) is the premature fusion of the cranial sutures,occurring either in isolated or syndromic form. CS was described in over 180 genetic syndromes that comprise 15-30% of all CS cases. Syndromic CS usually has a monogenic inheritance and originates in most of the patients from mutations within the FGFR1, FGFR2, FGFR3, and TWIST1 genes. Causative alterations in other genes, or rarely copy number variations (CNVs) were also reported. In this paper, we describe a patient with Noonan-like facial dysmorphism accompanied by intellectual disability, and compound CS, involving coronal, sagittal, and squamous sutures. We have shown that the index carried a large and rare heterozygous deletion, which encompassed 12.782 Mb and mapped to a chromosomal region of 7q32.3-q35 (HG38 – chr7:131837067-144607071). The aberration comprised 109 protein-coding genes, including BRAF, that encodes serine/threonine-protein kinase B-Raf, being a part of the RAS/MAPK signaling pathway. The RAS/MAPK pathway plays an essential role in human development, hence its dysregulation not surprisingly results in severe congenital anomalies, such as phenotypically overlapping syndromes termed RASopathies. To our best knowledge, we report here the first CNV causing haploinsufficiency of BRAF, resulting in dysregulation of the RAS/MAPK cascade, and consequently, in the phenotype observed in our patient. To conclude, with this report, we have pointed to the involvement of the RAS/MAPK signaling pathway in CS development. Moreover, we have shown that the molecular analysis based on both DNA and RNA profiling, undoubtedly constitutes a comprehensive diagnostic and research strategy for elucidating a cause of genetic diseases.

overall_design: female control and female patient


title: Recording of DNA binding events during gut commensalism reveals the action of a repurposed Candida albicans regulatory network

city: San Francisco

first: Suzanne

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

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

sample_organism:
Candida albicans
Mus musculus

platform_organism:
Candida albicans
Mus musculus

overall_design: Refer to individual Series


title: Candida albicans sexual regulators control expression of genes important for commensal fitness [RNA-seq]

summary: We found through competitive fitness experiments that transcription factors that control the mating regulatory program of C. albicans also control the ability of this fungus to colonize the gastrointestinal tract of mice as a commensal. To determine the role of these TFs, we performed mRNA-seq on luminal contents of C. albicans-colonized mice to determine overall expression patterns that could be correlated to the fitness phenotypes of the mutants in vivo.

overall_design: Mice were gastrointestinally-colonized with one of seven C. albicans strains, WT (ySN250 or ySN425), hyperfit mutants WOR1-OE GUT, efg1, or efg1wor1, or hypofit mutants wor1 or czf1. After 10 days of colonization, mice were sacrificed and luminal contents isolated from the large intestines. mRNA-seq using standard Illumina kits was performed.

first: Jessica

last: Witchley


title: RNA-seq of in vitro differentiated human abdominal and gluteal adipocyte cell lines following doxycycline induced RSPO3-knockdown

city: Oxford

first: Nellie

middle: Yen

last: Loh

state: OXON

address: OCDEM, Churchill Hospital, Headington

department: Radcliffe Dept of Medicine

institute: University of Oxford

summary: GWAS studies and our own work have identified RSPO3 as a gene modulating human body fat distribution. The GWAS signal at RSPO3 is coincident with an eQTL in mature adipocytes. To assess the effects of RSPO3 on abdominal and gluteal adipocyte biology, we undertook inducible RSPO3-knockdown in in vitro differentiated immortalized human abdominal and gluteal adipocyte cell lines (DFAT cells).

overall_design: Abdominal and gluteal DFAT preadipocyte cells stably transduced with the tet-pLKO-puro-shRSPO3 (tet-shRSPO3) or tet-pLKO-puro-shCON (tet-shCON) lentiviral vectors were differentiated in standard adipogenic media. On day 13 of differentiation, cells were treated with doxycycline (final concentration of 0.05 µg ml-1), or vehicle, in hormone-free basal media for ~48 hours. On day 15, cells were harvested for RNA. Total RNA purification and on-column DNase I-treatment were performed using the RNeasy Mini kit (Qiagen). RNA-seq was performed on samples from three independent experiments. In addition to tet-shCON cells, vehicle-treated cells were used as controls.

middle: Y

first: Constantinos

last: Christodoulides


title: Role of human CYP2B6 in vivo in diet-induced obesity

city: Clemson

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

institute: Clemson University

summary: To investigate the role of human CYP2B6 in vivo under high-fat diet conditions, we compared our  previously developed Cyp2b triple knockout mouse lacking Cyp2b9, Cyp2b10, and Cyp2b13 (via CRISPER/Cas9; Cyp2b-null), to our newly developed humanized-CYP2B6-transgenic (hCYP2B6-Tg) mouse model (on a Cyp2b-null background). hCYP2B6-Tg and Cyp2b-null mice were fed a high-fat diet consisting of 60% fat for 16 weeks. RNA was extracted from the livers of female and male mice from both treatment groups and used for RNA seqencing. RNAseq and in gene ontology (GO) analysis indicate human CYP2B6 is important in protein processing and phosphorylation, hepatic circadian regulation, and lipid metabolism under HFD conditions.Circadian rhythm-associated genes were up-regulated in HFD-fed hCYP2B6-Tg mice compared to Cyp2b-null mice. Circadian regulation plays an important role in liver metabolism and metabolic disease. In addition, female hCYP2B6-Tg mice had several down-regulated genes involved in lipid metabolism compared to Cyp2b-null mice, notably Angptl8 (logFC = -1.24), a critical modulator of lipid metabolism that has been associated with metabolic disease. Genes identified by RNAseq analysis may contribute to the overall healthier metabolic profile of HFD-fed humanized mice compared to Cyp2b-null mice.

overall_design: Use RNA-sequencing to investigate the role of human CYP2B6 in diet-induced obesity on a transcriptomic level, by comparing the livers of Cyp2b-null and hCYP2B6-Tg mice fed a high-fat diet for 16 weeks using Illumina technology.

first: Melissa

middle: M

last: Heintz

first: Rooksana

middle: E

last: Noorai


title: C. albicans white-opaque transcription factor binding recorded in the mammalian gut

state: CA

summary: Candida albicans is a central fungal component of the human gut microbiota and an opportunistic pathogen. Two C. albicans transcription factors, Wor1 and Efg1, control its ability to colonize the mammalian gut. They are also master regulators of an epigenetic switch required for mating. The mammalian gastrointestinal tract is a complex environment difficult to model in vitro. In C. albicans, it is known that environmental signals can dictate the binding targets of these transcription factors. To study the regulation of transcription factors of C. albicans in the GI tract, a Calling card-seq approach was adopted. This technique allowed us to directly record transcription factor binding that occurred in the mammalian gut.

overall_design: C. albicans strains were constructed by tagging transcription factors Efg1, Wor1 and Czf1 with PiggyBac transposase at native loci. These strains were then grown under the conditions described. Transcription factor binding was mapped to the genome using the position of the PiggyBac transposon, which should be reintegrated at sites where the transcription factor-piggyBac transposase fusion protein binds to the genome.


title: Transcriptome analysis

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

institute: Guizhou Normal University

summary: transcriptomic analysis by a high-throughput sequencing platform.

overall_design: Illumina HiSeq 3000.

first: Yan

last: Huiqing


title: DA Methylation patterns in decitabine treated 786-0 cells

city: NASHVILLE

first: Aguirre

last: de Cubas

state: TN

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 786-0 RCC cells treated with decitabine (100nM and 300nM) or DMSO vehicle. The Illumina Infinium HumanMethylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850K CpGs.

overall_design: Bisulfite converted DNA from 6 samples were hybridized to the Illumina Infinium HumanMethylation EPIC BeadChip

first: W

middle: K

last: Rathmell


title: Transcriptome analysis from human epicardial adipose tissue biopsies analyzed according to postoperative atrial fibrillation occurrence after cardiac surgery

city: Lille

first: Sandro

last: Ninni

address: 1 rue du Professeur Calmette

institute: INSERM

summary: Introduction: Post-operative atrial fibrillation (POAF) is a frequent complication after cardiac surgery, but its pathophysiology remains incompletely understood. Considering that epicardial adipose tissue (EAT) is in close vicinity with the atrial myocardium, we hypothesized that a specific pre-operative EAT phenotype would be associated to POAF onset following surgery.  Methods: Patients undergoing cardiac surgery prospectively enrolled in the POMI-AF cohort between February 2016 and June 2017 were studied. EAT samples were collected at the beginning of surgery. Whole-tissue gene expression patterns and the stromal and vascular fraction (SVF) cellular composition were explored. Patients were followed after surgery by continuous ECG to detect POAF onset.  Results: Among the 60 patients included in the cohort, 15 POAF and 15 non-POAF patients were matched based on pre-operative characteristics. Gene set enrichment analysis of transcriptomic data from pre-operative EAT samples revealed 40 enriched biological processes in POAF vs non-POAF patients. Most of these processes were related to cellular immune response. Leukocytes (63±15% of total cells), and more specifically lymphocytes (56±13% of total CD45+ cells), represented the major cell subset in the preoperative EAT SVF, with no quantitative differences between POAF and SR patients (76 [52; 84]% vs 56 [50; 64]%, p=0.22). However, POAF patients presented a significantly higher cytotoxic CD8+/helper CD4+ T lymphocyte ratio than SR patients (respectively, 0.69[0.55; 1.19] vs 0.50 [0.31; 0.54], p=0.03) suggesting a cytotoxic shift prior to surgery.  Conclusion: Epicardial fat from patients who develop POAF displays a specific pre-operative transcriptome signature characteristic of cellular immune response and cytotoxic lymphocyte enrichment.

overall_design: 30 matched samples analyzed (15 POAF vs 15 SR patients)

first: Eloïse

last: Woitrain

first: Augustin

last: Coisne

first: Céline

last: Gheeraert

first: Staniel

last: Ortmans

first: Thomas

last: Modine

first: Mohammad

last: Koussa

first: Francis

last: Juthier

first: André

last: Vincentelli

first: Olivier

last: Molendi-Coste

first: Laurent

last: Pineau

first: Philippe

last: Lefebvre

first: David

last: Dombrowicz

first: Bart

last: Staels

last: Montaigne


title: ADHERENT1 IS A 3-KETOACYL CoA SYNTHASE REQUIRED FOR MAIZE CUTICLE DEVELOPMENT AND ORGAN SEPARATION

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: DAP-seq was used to generate genome-wide DNA:TF interaction maps for ZmMYB94/FDL1

first: Mary

last: Galli


title: DNA Demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells

first: Aguirre

last: de Cubas

summary: Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable element, is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). Aberrant expression of ERVs can activate host antiviral responses, as well as produce neoantigens. ERV expression is repressed by DNA methylation and can be activated by DNA hypomethylating agents. Here, we investigate whether Decitabine, a DNA hypomethylating agent, can activate ERV expression and host antiviral defenses in RCC to potentially enhance response to ICB. Decitabine induced expression of ERV3-2 and ERV4700 in RCC cells lines, which was accompanied by activation of host antiviral defense genes and increased secretion of inflammatory cytokines. We validated this effect in primary human RCC cell lines. Knockout of RIG-I and MDA5 dsRNA sensors attenuated activation of antiviral responses associated with Decitabine treatment, and RIG-I and MDA5 immunoprecipitations showed increased ERV binding in RCC cells treated with Decitabine. Bioinformatic analysis of RNAseq data showed the Decitabine-induced gene signature could be associated with increased CD8 infiltration and response to ICB. Conditioned media from Decitabine treated RCC cells was capable of inducing host anti-viral defense in naïve RCC cells and could modestly improve activation of T-cells from healthy donors. Further, conditioned media from RCC cells treated with Decitabine significantly enhanced T-cell migration. In a small retrospective cohort of metastatic RCC patients treated with single-agent PD-1/PD-L1 blockade, activation of some host antiviral defense genes was significantly higher in responders compared with nonresponders. Thus, modulation of ERV expression by Decitabine to activate host antiviral defenses could represent a novel therapeutic strategy to enhance RCC patient response to immune checkpoint blockade.

overall_design: RNAseq profiles in HKC and 786-0 kidney cells treated with DMSO or Decitabine (100nM or 300nM)\

first: W

last: Rathmell


title: Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1: Experiment 2

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: Shewanella oneidensis MR-1 was grown on electrodes in electrochemical flow cells (EFC), and the transcriptome profiles of electrode-attached MR-1 cells were compared under electrolyte-flow and static (non-flow) conditions. The results revealed that the SO_3096 gene encoding a putative extracytoplasmic function (ECF) sigma factor, as well as genes related to cyclic-di-guanosine monophosphate and flagella synthesis (e.g., SO_3556 and flrC) and c-type cytochrome maturation (dsbD), was significantly up-regulated under the electrolyte-flow condition. Compared to wild-type MR-1 (WT), a deletion mutant of SO_3096 (∆SO_3096) showed an impaired biofilm formation and a decreased current generation in EFC, suggesting that the ECF sigma factor encoded by this gene is involved in the regulation of biofilm formation and current generation under electrolyte-flow conditions. We also compared the transcriptome profiles of WT and ∆SO_3096 grown in EFC, confirming that many genes up-regulated under the electrolyte-flow condition, including dsbD, were down-regulated in ∆SO_3096. Transcription analysis using lacZ as a reporter gene showed that the promoter of dsbD is activated in the presence of SO_3096. Measurement of current generation by a dsbD-deletion mutant revealed that this gene is essential for electron transfer to electrodes. These results suggest that the SO_3096 protein serves as an ECF sigma factor that regulates cellular functions related to electroactive biofilm formation under electrolyte-flow conditions.

overall_design:
AFP-expressing MR-1 grown under a flow condition.  AFP-expressing ∆SO_3096 grown under a flow condition.
Total 8 samples, 4 biological replicates for each sample

first: Ryota

last: Koga

first: Akiho

last: Matsumoto

first: Kazuya

last: Watanabe


title: Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1: Experiment 1

overall_design:
AFP-expressing MR-1 grown under a non-flow condition. AFP-expressing MR-1 grown under a flow condition.
Total 8 samples, 4 biological replicates for each sample


title: Transcriptome analysis of tumor infiltrating NK and T cells in CT26-bearing BALB/C mice

city: Sacramento

first: Robert

middle: J

last: Canter

address: 4645 2nd Ave, Research III, Room 2200D

department: Surgery

institute: University of California, Davis

summary: CT26 tumors were implanted subcutaneously into syngeneic BALB/C mice and allowed to grow for 15-25 days. Tumors were collected, mechanically dissociated, and immune cells enriched using Percoll gradient. Cells were then stained with viability dye, CD45, CD3, and NKp46 to FACS sort for T cells (Live/CD45+/CD3+/NKp46-) and NK cells (Live/CD45+/CD3-/NKp46+). Isolated tumor infiltrating NK and T cells were then processed for RNA sequencing analysis.

overall_design: #1 - Pooled from N=4 mice, #2 - Pooled from N=6 mice

first: Sean

last: Judge

first: Cordelia

last: Dunai

first: Kevin

last: Stoffel

first: William

last: Murphy


title: Single cell RNA-seq activated microglia cells after irradiation (IR)

city: Uppsala

first: Ying

last: Sun

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

institute: Uppsala University

summary: Cranial irradiation (IR), an effective tool to treat malignant brain tumors, triggers a chronic pro-inflammatory microglial response, at least in the adult brain.  Using single cell and bulk RNA sequencing combined with histology, we show that the microglial response in the juvenile mouse hippocampus is rapid, but returns toward normal within 1 week. We found that a single microglial cell simultaneously upregulates transcripts associated with pro- and anti-inflammatory microglial phenotypes. Our results indicate that microglia are involved in the initial stages, but may not be responsible for driving long-term inflammation in the juvenile brain.

overall_design: We performed whole brain irradiation on 108 postnatal day 21 (P21) with a single dose of 8 Gy. Using the LQ model and an α/β ratio of three for late effects in normal brain tissue, an acute exposure of 8 Gy is equivalent to approximately 18 Gy when delivered in repeated 2 Gy fractions, as in a clinical setting. Subsequently, animals were sacrificed at different time points starting from the acute phase after IR (2 h) up to later stages when hippocampal neurogenesis is severely diminished (6 weeks) compared to sham controls (SH). In order to investigate genes were expressed simultaneously in the same MG or whether hippocampal MG populations are phenotypically heterogeneous,we performed single-cell RNA-seq using the droplet-based method (10x Genomics Chromium) on 8,095 MG isolated at 6 h and 1 wk post-IR.

first: Ahmed

last: Osman

first: Klas

last: Blomgren


title: Comparison of multiple passages of VEEV V4020 to VEEV TC-83 at 2 days after intracranial inoculation in BALB/c mice

city: Louisville

first: Dylan

middle: MacGregor

last: Johnson

state: KY

address: 505 S Hancock St., CTRB RM642B

department: Microbiology & Immunology

institute: University of Louisville, School of Medicine

summary: Experimental V4020 is derived from VEEV TC-83, a vaccine with a long track record of use in lab and military personnel at risk. V4020 was generated from an infectious DNA clone, secured genetic stability by employing stabilizing mutation at position 120 in the E2 protein, and by rearrangement of structural genes. In this study, serial passages in brain tissues of mice were performed to compare safety and genetic stability of V4020 and TC-83 experimental vaccines. During five serial passages in brain, less severe clinical manifestations and lower viral load were observed in V4020 mice and all animals survived. In contrast, 13.3% of mice met euthanasia criteria during the passages in TC-83 group. At 2 DPI, RNA-Seq analysis of brain tissues revealed that V4020 mice had lower rates of mutations throughout five passages.   Higher synonymous mutation ratio was observed in the nsP4 (RdRP) gene of TC-83 compared to V4020 mice. At 2 DPI, both viruses induced different expression profiles of host genes involved into neuro-regeneration.  Taken together, these results provide evidence for the improved safety and genetic stability of the experimental V4020 VEEV vaccine in a murine model. While no single nucleotide polymorphisms that have been previously linked to virulence were identified, more neuro-virulence markers were observed in serial passaged TC-83 compared to V4020.  This study suggests a complex polygenic basis for neuro-virulent reversion in VEEV live attenuated vaccines and provides evidence for the advanced safety and genetic stability of V4020.

overall_design: RNA isolated from brain tissue of VEEV V4020 or VEEV TC-83 mice 2 days following intracranial inoculation of five serial passages was sequenced.  Two replicates of each sample were included except for V4020 passage 1, and TC-83 passages 2, 3, 4, and 5 which were each a single sample.

last: Sokoloski

first: Jenny

last: Jokinen

first: Tia

middle: L

last: Pfeffer

first: Yonh-Kyu

last: Chu

last: Adcock

first: Donghoon

last: Chung

first: Irina

last: Tretyakova

first: Peter

last: Pushko

first: Igor

last: Lukashevich


title: The significance of interleukin 2 receptor subunit gamma in the progression of human gastric cancer

city: Taiyuan

first: Deping

last: Wang

address: 56 Xinjiannanlu Rd

institute: ShanXi Medical University

summary: IL2RG is overexpressed in advanced GC and is associated with poor survival. IL2RG may serve as a biomarker of GC progression and prognosis.

overall_design: we used these tissues to identify the differentially expressed genes (DEGs) with RNA-seq and serial bioinformatics analyses including Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, gene expression profiling interactive analysis (GEPIA) and survival analysis.

first: De-Ping

first: Ji-Min

last: Cao


title: Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5’ mRNA stem loop stimulator and enhanced drop-off

city: Cork

first: John

last: Atkins

address: Western GateWay Building, Western Road, UCC, Cork

department: School of Biochemistry and Cell Biology

country: Ireland

institute: UCC

summary: Ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. Ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5’ stem loop.

sample_organism:
Escherichia coli
Tequatrovirus T4

platform_organism:
Escherichia coli
Tequatrovirus T4

overall_design: Ribosome profiling of 'normal' and long protected fragments obtained from T4 infected E.coli or of E.coli with plasmid-borne cassette with the gene 60 sequence

first: Sinéad

last: O’Loughlin

first: Mark

middle: C

last: Capece

first: Mariia

last: Klimova

first: Norma

last: Wills

first: Arthur

last: Coakley

first: Ekaterina

last: Samatova

first: Patrick

last: O’Connor

first: Gary

last: Loughran

first: Jonathan

last: Weissman

first: Pavel

middle: V

last: Baranov

first: Marina

last: Rodnina

first: Joseph

last: Puglisi

middle: F


title: Identification of differential expressed genes after LAMB3 knockdown in colorectal cancer cells

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

summary: We have identified LAMB3 as an oncogene to promote proliferation and metastasis in colorectal cancer. To elucidate the potential mechanism of LAMB3 in colorectal cancer, RNA-seq analysis was performed in LoVo cells to analyze differential expressed genes after LAMB3 knockdown.

overall_design: LoVo cells stably expressing pLKO.1 control shRNA or shLAMB3_1 or shLAMB3_2

first: Z

first: L

last: Cui

first: C

last: Liu


title: The miR396-GRFs Module Mediates Brassinosteroid-Prevented Photooxidative 1 Damage during Seedling De-etiolation in Arabidopsis

city: Qingdao

first: Lingyan

last: Wang

address: No.72 Binhai Road Jimo

institute: Shandong University

summary: The developmental switch from skotomorphogenesis to photomorphogenesis is critical for the survival and growth of plants, but its regulatory mechanism remains unclear. Here, we report that the steroid hormone brassinosteroids (BRs) play crucial roles in the transition from skotomorphogenesis to photomorphogenesis by regulating chlorophyll biosynthesis to promote the greening of etiolated seedlings upon light exposure. Seedlings of BR-deficient mutant det2-1 accumulated excess protochlorophyllide when grown in darkness, resulting in photo-oxidative damage upon exposure to light. Conversely, the gain-of-function mutant bzr1-1D suppressed the protochlorophyllide-accumulated phenotype of det2-1, thereby promoting greening of etiolated seedlings. Genetic analysis indicated that phytochrome-interacting factors (PIFs) were required for BZR1-promoted seedlings greening. Furthermore, we revealed that the GROWTH REGULATING FACTOR 7 (GRF7) and GRF8 were induced by BZR1 and PIF4 to repress the chlorophyll biosynthesis and promote seedling greening. Suppression the functions of GRFs by overexpressing microRNA396a (miR396a) caused the high-accumulated photochlorophyllide in darkness and more serious photobleach upon light exposure. Additionally, BZR1, PIF4 and GRF7 interact with each other and precisely regulate the expression of chlorophyll biosynthetic genes. Our findings revealed an essential role of brassinosteroid in promoting seedling development and survival during the critical initial emergence of seedlings from subterranean darkness to sunlight.

overall_design: The seedlings of wild type Col-0 and 35S:miR396a were grown on ½ MS medium containing 1% sucrose for 4 days in the dark, and treated with or without light for 3 hrs. Total RNA was extracted with Trizaol RNA extraction kit (Transgene), and the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics Institute. The sequence reads were mapped to theArabidopsis genome using HISAT and Bowtie2 software, and differential geneexpression was analyzed using Noiseq software. Differentially expressed genes were defined by a 2-fold expression difference with a possibility >0.8.

first: Mingyi

last: Bai


title: Transcription Factor Tox2 is required for Follicular Helper T Cells differentiation

first: Jinyi

last: Tang

address: Yueyang road 320

institute: IPS

summary: Follicular helper T (Tfh) cells are crucial for formation of B cell germinal center (GC) and long-term production of antigen-specific antibodies. The molecular mechanism underlying Tfh cell differentiation, however, still remains largely unknown. Here, we show that the transcription factor Thymocyte selection-associated high mobility group box family member 2 (Tox2) is important for Tfh cell development. Tox2 deficiency led to impaired Tfh cell differentiation and subsequently reduced GC formation. Consistently, ectopic expression of Tox2 promoted Tfh cell differentiation. Mechanistically, we found that Tox2 regulated the expression of Ascl2, an initiator in driving CXCR5 transcription in Tfh cells; Tox2 deficiency caused the decreased expression of Ascl2. Restoration of Ascl2 expression in Tox2 deficient CD4+ T cells rescued the defect in Tfh cell differentiation. Our study suggests that Tox2 is an important transcription factor for Tfh cell development.

overall_design: WT OT-II or Tox2-/- SMARTA mice were transferred into Ly5.1 mice, followed by LCMV infection. Spleens  were harvested 7 dpi to sort. For RNAseq, We have four samples, wt-Tfh, ko-Tfh,  wt-nonTfh and ko-nonTfh and  2 replicates for Tfh sample.

first: Haikun

first: Xiaoxue

last: Deng


title: RNA metabolic rates profiling in Fragile X neurons

city: Worcester

first: Huan

middle: Raya

last: Shu

state: MA

address: 373 Plantation St

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Fragile X syndrome (FXS) is caused by inactivation of FMR1 gene and loss of its encoded product the RNA binding protein FMRP, which generally represses translation of its target transcripts in the brain. In mouse models of FXS (i.e., Fmr1 knockout animals; Fmr1 KO), deletion of Cpeb1, which encodes a translational activator, mitigates nearly all pathophysiologies associated with the disorder. We have observed that the wide-spread dys-regulation of RNA abundance in Fmr1 KO brain cortex and its rescue to normal levels in Fmr1/Cpeb1 double KO mice were the driver of the observed dys-regulation and rescue of translation as measured by whole transcriptome ribosome occupany in the brain.  We hypothesize that in Fragile X brain there is wide spread dys-regulation at RNA stability level. Here we test this hypothesis by profiling RNA synthesis, processing and degradation rates in Fragile X and wild type neurons, by taking advantage of short 5-EU labeling and computational modeling. We show that, while RNA synthesis and processing rates were barely changed, there is wide-spread evelated RNA degradation rates in the Fragile X neurons, particularly for genes using optimal codons.

overall_design: RNA metabolic labeling coupled to RNA-seq in Fmr1-KO and wild type mouse neurons

middle: R

first: Elisa

last: Donnard

first: Botao

first: Joel

middle: D

last: Richter


title: Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

city: Los Angeles

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

summary: Using a novel multiplexed reporter assay, we characterize promoter activity of hundreds of thousands of DNA sequences spanning the entire E. coli genome. We use this powerful assay to identify promoters throughout the E. coli genome and systematically dissect their regulatory motifs which encode promoter activity using a series of experiments.

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

overall_design: 1) We measure promoter activity of 17,798 reported transcription start sites (TSSs) and find that a majority of reported TSSs are likely due to transcriptional noise, rather than productive transcription. 2) We measure promoter activity of 321,057 DNA fragments spanning both strands of the E. coli genome with 8.5x coverage in rich LB and minimal glucose media. 3) We measure promoter activity of synthesized fragments overlapping promoter regions identified by characterizing genomic fragments. 4) We perform scanning mutagenesis of 2,142 tss-associated promoters and measure promoter activity of all mutagenized variants.

first: Kimberly

last: Insigne

first: Arielle

last: Tripp

first: Marcia

middle: S

last: Brinck

first: Nathan

last: Lubock

first: Chan

last: Tracey

first: Hwangbeom

last: Kim

first: Kosuri

last: Sriram


title: Identification of an ECF sigma factor that facilitates electroactive biofilm formation by Shewanella oneidensis MR-1

first: Atsushi

last: Kouzuma

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

overall_design: Refer to individual Series


title: CRISPR-mediated mutagenesis of RNA editing cis-regulatory elements

city: Stanford

first: Jin

last: Li

address: M341, 300 Pasteur Dr.

department: Genetics

institute: Stanford University

summary: We used CRISPR KI technology to mutagenize the cis-regulatory elements including the editing stem and the editing complementary sequence of three RNA editing substrates-NEIL1, TTYH2, AJUBA. We designed single nucleotide variants, double-nucleotide variants and other mutant isoforms to interrogate the primary sequence and the secondary structures around the endogenous RNA editing sites. Gene specific primers were used to make the NGS library for each locus. The unique mutation of each tested isoform can be used as barcode and RNA editing level can be measured for each isoform from the pooled library. We found that RNA sequence and structure features synergistically determine the editing levels. Several features, such as mutation number, free energy, and probability of active conformation, play an important role in determining editing efficiency. This study systematically investigated the contribution of cis-regulatory elements to ADAR1 RNA editing by combining CRISPR-based saturation mutagenesis and deep sequencing technology.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Examination of the RNA editing level of  three endogenous substrates whose cis-elements have been subject to saturation mutagenesis.

middle: B

first: Tao

last: Sun


title: TRPM5 Negatively Regulates Lipopolysaccharide-Induced Ca2+ Signaling of B Lymphocytes

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Ca2+ signaling cascades are essential for various immune cell functions. As such, most cells have negative regulators of Ca2+ homeostasis that strictly regulate cytosolic Ca2+ concentration, such as Ca2+-activated monovalent cation channels (CAMs). Transient receptor potential melastatin-related 5 channel (TRPM5), a CAM, is expressed in B lymphocytes. However, its functional role in the immune system is poorly understood. Here, we show that TRPM5 negatively modulates Ca2+ influx, thereby regulating lipopolysaccharide (LPS)-induced proliferative and inflammatory responses by B cells. Trpm5-deficient mice exhibited increased Ca2+ influx, enhanced proliferative responses, and increased production of inflammatory cytokines interleukin-6 and CXCL10 in LPS-stimulated B cells. However, Ca2+ chelation reduced LPS-induced cytokine production by Trpm5-deficient B cells. Furthermore, Trpm5-deficient mice showed exacerbation of endotoxic shock with high mortality. Our findings demonstrate the importance of TRPM5-dependent regulatory mechanisms in LPS-induced Ca2+ signaling of splenic B cells.

overall_design: We analyzed gene expression profiles of wild-type and Trpm5-/- MZB cells after stimulation with LPS and anti-IgM antibody by RNA sequencing analysis in duplicates.

first: Taiki

last: Sakaguchi

first: Kiyoshi

last: Takeda


title: SUM159 BrCa Decitabine Gene Expression

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

summary:
Dysregulation of DNA methylation is an established feature of breast cancers. DNA demethylating therapies like decitabine are proposed for the treatment of triple-negative breast cancers (TNBCs) and indicators of response need to be identified. For this purpose, we characterized the effects of decitabine in a panel of 10 breast cancer cell lines and observed a range of sensitivity to decitabine that was not subtype-specific. Knockdown of potential key effectors demonstrated the requirement of deoxycytidine kinase (DCK) for decitabine response in breast cancer cells. In treatment-naive breast tumors, DCK was higher in TNBCs, and DCK levels were sustained or increased post chemotherapy treatment. This suggests that limited DCK levels will not be a barrier to response in TNBC patients treated with decitabine as a second line treatment or in a clinical trial. Methylome analysis revealed that genome-wide, region-specific, tumor suppressor gene-specific methylation, and decitabine-induced demethylation did not predict response to decitabine. Gene set enrichment analysis (GSEA) of transcriptome data demonstrated that decitabine induced genes within apoptosis, cell cycle, stress, and immune pathways in decitabine treated cells. Induced genes included those characterized by the viral mimicry response; however knockdown of key effectors of the pathway did not affect decitabine sensitivity suggesting that breast cancer growth suppression by decitabine is independent of viral mimicry. Finally, taxol-resistant breast cancer cells expressing high levels of multidrug resistance transporter ABCB1 remained sensitive to decitabine, suggesting that the drug could be used as second-line treatment for chemoresistant patients.
We used microarrays to determine genome-wide expression changes induced by DNA de-methylating agent decitabine in breast cancer cell lines

overall_design: 72 hours treated with 1uM decitabine versus NT

first: Margaret

last: Dahn


title: The lncRNA CCAT2 induces chromosomal instability through the BOP1 – Aurora Kinase B axis in cancers

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary: We  explored the role of CCAT2 in inducing chromosomal instability in gastrointestinal cancers.

platform_organism:
Homo sapiens
Mus musculus

overall_design: In the study presented here, ncRNA expression levels in samples from normal gastric tissue adjacent to adenocarcinomas versus cells from ascites of gastric adenocarcinoma were analyzed.

middle: A

first: Mihnea

middle: P

last: Dragomir


city: Daejeon

first: Han-Seop

address: Gwahak-ro

department: Stem Cell Research Laboratory, Immunotherapy Convergence Research Center,

institute: KRIBB

summary:
A comparative microarray analysis revealed common and distinct features between iNKs and PBMC-NKs. 1523 differentially expressed genes exhibited a 2 fold change when P value of 0.05 is adjusted.  1054 genes were up-regulated and 469 genes were down-regulated in iNKs. Gene ontology (GO) analysis of the top significant up-regulated genes in iNKs revealed the enrichment for mitotic cell cycle, showing the characteristics of growth of iNK. A range of genes involved in NK regulatory functions including receptors, cytokines, chemokines, and adhesion molecules were found to be uniquely up-regulated in iNKs.
To evaluate the properties of iNK cells, primary NK cells (PBMC-NKs) and induced NK cells (iNKs) were compared at total gene expression levels.

overall_design: Total RNA were obtained PBMC-NKs and iNK (at day 28) from two different persons and the level of their global gene expression  .

first: Yee Sook

last: Cho


title: Genome-wide Analysis of mRNAs and lncRNAs in Mycoplasma Bovis infected and non-infected bovine mammray gland tissues.

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

summary: Mycoplasma bovis (M. bovis) causes to the diseases such as arthritis, pneumonia, abortion and mastitis causing to great losses in dairy bovine industries. It undertakes significant functions in the regulation of the immune response formed by many RNA type bacteria such as Messenger RNA (mRNAs) and Long noncoding RNA (lncRNAs). mRNA and lncRNA expression profiles still cannot be majorly known in the bovine mammary gland tissues infected with M. bovis. To illuminate this issue, transcription analysis has been conducted regarding mRNA and IncRNAs in the breast tissues belonging to Holstein cattle infected and not infected with M. Bovis. Differently expressed 1310 mRNAs and 57 IncRNAs have been determined in the bovine mammary gland tissues infected and not infected with M. Bovis. In addition; 392 novel lncRNAs have been detected. Also; it has been found that 19 novel lncRNAs are expressed in a different way. It has been revealed in gene ontology analysis that the differently expressed mRNAs and IncRNAs play a significant role in many vital biological pathways such as Metabolic pathways, T cell receptor signaling pathway, TGF-beta signaling pathway, Pathways in cancer, PI3K-Akt signaling pathway, NF-kappa B signaling pathway, mTOR signaling pathway and Apoptosis including the immune response and cancer. When literature review is conducted, it is seen that this study is the first genome wide IncRNA research conducted on the infected bovine mammary gland tissues with M. bovis agent. Our results have provided bovine mammary gland IncRNA and mRNA resource to understand their roles in the regulation of the immune response against the agent of M. Bovis in the bovine mammary gland tissues.

overall_design:
Examination of mRNAs and lncRNA in Mycoplasma bovis infected and non-infected bovine mammary tissues
Grant information (Grant Id: 116O618; Grant title; TÜBITAK; The Scientific and Technological Research Council of Turkey)

last: ÖZDEMİR

first: Serdar

last: ALTUN


title: Peripheral nerve resident macrophages share tissue-specific programming and features of activated microglia

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

country: USA

institute: Washington University School of Medicine

summary: Whereas microglia are recognized as fundamental players in central nervous system (CNS) development and function, much less is known about macrophages of the peripheral nervous system (PNS). Here, by comparing gene expression across neural and conventional tissue-resident macrophages, we identified transcripts that were shared among neural resident macrophages as well as selectively enriched in PNS macrophages. Remarkably, PNS macrophages constitutively expressed genes previously identified to be upregulated by activated microglia during aging,  neurodegeneration, or loss of Sall1. Several microglial activation-associated and PNS macrophage-enriched genes were also expressed in spinal cord microglia at steady state. We further show that PNS macrophages rely on IL-34 for maintenance and arise from both embryonic and hematopoietic precursors, while their expression of activation-associated genes did not differ by ontogeny. Collectively, these data uncover shared and unique features between neural resident macrophages and emphasize the role of nerve environment for shaping PNS macrophage identity.

overall_design: Bulk and single cell RNA-seq experiments on macrophages isolated from peripheral nerves

first: A

last: Yim

first: Peter

last: Wang


title: Ribosome profiling and RNA-seq of Fragile X mouse brain cortex

first: Huan

last: Shu

summary: Fragile X syndrome (FXS) is caused by inactivation of FMR1 gene and loss of its encoded product the RNA binding protein FMRP, which generally represses translation of its target transcripts in the brain. In mouse models of FXS (i.e., Fmr1 knockout animals; Fmr1 KO), deletion of Cpeb1, which encodes a translational activator, mitigates nearly all pathophysiologies associated with the disorder. Here we reveal unexpected wide-spread dys-regulation of RNA abundance in Fmr1 KO brain cortex and its rescue to normal levels in Fmr1/Cpeb1 double KO mice. Alteration and restoration of RNA levels are the dominant molecular events that drive the observed dys-regulation and rescue of translation as measured by whole transcriptome ribosome occupany in the brain. The RNAs down-regulated and rescued in these animal models are highly enriched for FMRP binding targets and have an optimal codon bias that would predict their stability in wild type and possible instability in FMRP knock-out brain. These results leads to a further study to profile RNA metabolism rates in Fragile X neurons.

overall_design:
Ribosome profiling and RNA-seq in brain cortex of WT and Fmr1-KO mice
Please note that differential expression analyses between samples were generated by DEseq2 (RNADEseq_* and RPFDEseq_*) or Xtail (ROXtail_*) as indicated in the corresponding sample description field.

first: Elisa

last: Donnard

first: Botao

last: Liu

first: Joel

last: Richter


title: Splenic Tfh that express SLAM reside in the follicular mantle zone

city: New York City

first: Ramin

last: Herati

state: NY

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

overall_design: Sorted human splenic CD4 T cell subsets

first: E

last: Wherry


title: Single-cell Profiling Reveals the Transcriptional Landscape and Heterogeneity of Human Prostate Cancer-Associated Macrophages

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

institute: Istituto Nazionale Tumori

summary: Macrophages found in the tumor microenvironment (TME) are causally linked with disease development and progression. Different phenotypes of macrophages have been described, including the M1-like pro-inflammatory/anti-tumor phenotype or the M2-like anti-inflammatory/pro-tumor phenotype. Here we present the first single cell transcriptomic analysis on human prostate cancer (PCa)-resident macrophages.

overall_design: Single cell RNA-sequencing was used to chart the transciptomic heterogeneity of CD14+CD11b+ macrophages isolated from the tumorous and non-tumorous side of the prostate of 4 PCa patients with Gleason Score (GS) between 6 and 7. Our analyses revealed the presence of 14 different clusters of cells.

first: Bianca

last: Cioni

first: Mauro

last: Muraro

first: Iris

last: de Rink

first: Judith

last: Vivié

first: Henk

last: van der Poel

first: Wilbert

last: Zwart

first: Andries

last: Bergman


title: Identification of CLDN6 as a novel tumor-promoting gene in gastric cancer

city: Tokushima

first: Kohmoto

last: Tomohiro

address: Kuramoto-cho 3-18-15

institute: Tokushima University

summary: We identified CLDN6 as a novel tumor-promoting gene in gastric cancer (GC). To clarify the mechanism of tumor promoting by CLDN6, we analyzed the transcriptomic difference between control and CLDN6 knockdown GC cells.

overall_design: To investigate the molecular pathways involved by CLDN6-knockdown, the expression levels of mRNAs in CLDN6-knockdown cells were analyzed using microarray

first: Tomohiro

last: Kohmoto

first: Kiyoshi

last: Masuda

first: Issei

last: Imoto


title: Restoration of KMT2C in human colorectal cancer cell lines HCT116 and RKO reinforces genome wide H3K4me1 profiles

city: Uppsala

first: Chatarina

last: Larsson

address: Rudbeck Laboratory

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary: The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types, however the effects of mutations on epigenome organization, gene expression and cell growth are not clear. To study effects of KMT2C expression in CRC cells we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous KMT2C c.8390delA mutant. Chromatin was analysed by ChIP-sequencing using the Diagenode iDeal ChIP-seq kit for Histones and the H3K4me1 specific antibody (Abcam ab8895).

overall_design: DNA from reverse cross-linked chromatin input and H3K4me1 purified chromatin was quantified with the Qubit dsDNA assay kit. 10ng of DNA was used for high throughput sequencing. Parental RKO cells, one RKO KMT2C knock-in cell line, parental HCT116 cells and two HCT116 KMT2C knock-in cell lines were analyzed.

first: Lina

last: Cordeddu

first: Lee

last: Siggens

first: Karl

last: Ekwall


title: Genomic alteration analysis in ovarian cancers

city: PARIS

first: OUMOU

last: GOUNDIAM

address: 26 RUE D'ULM

institute: INSTITUT CURIE

type: Genome variation profiling by genome tiling array

summary:
In order to check if there is a correlation between centrosome alterations and DNA breakpoints or homologous recombination defects (HRD) assesssed by LST genomic signatures, we used Affimetrix cytoscan array and GAP tool as previously described in Goundiam et al, IJC 2015 (PMID:25892415 DOI:10.1002/ijc.29568 )
67 high grade serous ovarian cancers

overall_design: For these samples we checked if there is a correlation between DNA breakpoints or chromosome content (from cytoscan array) and the number of centrosomes defined by immunoflurescence

first: Jean-Phillippe

last: Morretton

first: Aurelie

last: Herbette

first: Pierre

last: Gestraud

first: Geoges

last: Lucottes

first: Philippe

last: La Rosa

first: Oumou

last: Goundiam

first: Renata

last: Basto


title: Transcriptome analysis of BMDM from wild type and Rasgef1b_fl/fl_vav-icre mice treated or not for four hours with R848

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

summary: Despite much progress, the specific role of some the putative intracellular signaling players upstream to inflammatory gene expression activated by Toll-like receptor (TLRs) in the immune response remains unknown. For instance, the TLR-inducible Ras guanine exchange factor member 1b (RasGEF1b) was previously shown to be expressed in activated macrophages, but its specific function is still obscure. To investigate the role of RasGEF1b in TLR-mediated innate immune response, we generated Rasgef1bfl/fl mice for tissue conditional gene deletion . We found that the expression and production of the neutrophil chemoattractant chemokine KC/Cxcl1 was impaired in response to TLRs stimulation of bone marrow derived macrophages (BMDMs) devoid of RasGEF1b. The production of KC/Cxcl1 was also impaired in in vivo models of LPS-induced peritonitis, and R848-induced acute lung injury inflammation. RasGEF1b was not required or sufficient to neither induce nor increase the transcriptional activation of Cxcl1 promoter. In addition, TLR-triggered inflammatory activation of NF-ΚB signaling pathway was unimpaired in macrophages lacking RasGEF1b suggesting a mechanism independent of the NF-B transcription factor. Our data presented herein revealed an important role of RasGEF1b in innate immunity by regulating gene expression, following TLR stimulation.

overall_design: Bone marrow derived macrophages (BMDMs) were collected from wild type and Rasgef1b_fl/fl_vav-icre mice, and were stimulated or not with R848. Transcriptome analysis was performed using a  Mouse Genome 2.1 ST Array Strip (Affymetrix).

first: Aristóbolo

last: Silva

first: Jôsy

last: Hubner

first: Isadora

last: Oliveira

first: Heliana

last: Fernandes

first: Maria

last: Souza

first: Felipe

last: Leão

first: Brener

last: Carvalho

first: Rhaylla

last: Ferreira

first: Kátia

last: Lima

first: Marliete

last: Costa

first: Natália

last: Scaramele

first: Marcia

last: Marinho

first: Ricardo

middle: T

last: Gazzinelli


title: Skeletal muscle transcriptional response to endurance exercise in Il13-deficent mice

city: Boston

first: Nelson

middle: Howard

last: Knudsen

address: 655 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard T. H. Chan School of Public Health

summary: RNA-seq analysis of gastrocnemius of control and Il13-deficient mice after 5-weeks of endurance exercise training.

overall_design: Differential expression of mRNA from gastrocnemius muscle of control (untrained) and 5-weeks endurance trained (trained), wild-type C57Bl6/J (WT) and Il13 knockout (Il13-/-) mice. 4 samples from each groups was analyzed.

middle: H

first: Chih-Hao

last: Lee