title: Large-scale transcriptomic analyses reveal a global co-expression network of cellulase and xylanase genes in filamentous fungi

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: A global co-expression network of cellulase and xylanase genes was identified in P. oxalicum, their transcriptional levels depended on the induction of carbon sources and induction time.

overall_design:
To explore the co-expression of cellulase and xylanase genes under induction conditions and different time points
Relevant sequences in process data have been uploaded in GSE80076.

first: Cheng-Xi

first: Shuai

last: Zhao


title: Next Generation Sequencing of 12 human platelet's miRNA for Alzheimer's disease study

status: Public on Apr 24 2020

city: Yuseing-gu

first: JaeWoong

last: Min

state: Daejeon

address: 17 Techno 4-ro

country: South Korea

institute: Biorchestra

type: Non-coding RNA profiling by high throughput sequencing

summary: We obtained miRNA expression information from 12 human platelet samples using the NGS method. The patient group was divided into "Normal Young", "Normal Old" and "Alzheimer's disease". Twenty miRNAs whose expression gradually changed in 3 groups were selected. Among them, miR150-3p and miR150-5p were highly correlated with each other and had a high correlation with the patient's age. In addition, the expression of miR-150-3p and miR-150-5p showed a miRNA-imbalance phenomenon in which the ratio was specifically changed in Alzheimer's disease.

overall_design: 12 human platelet's miRNAs were generated by next generation sequencing, using Illumina NovaSeq 6000 system.

first: Jae-Woong

first: Jin-Hyeob

last: Ryu

first: Hyun-Jeong

last: Cho


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and DAZAP1 Knockout of ESCC Transcriptomes

city: Jinan

first: Yan

last: Zheng

state: Shandong

address: No.440 Jiyan road

department: Shandong Provincial Key Laboratory of Radiation Oncology

country: China

institute: Shandong Cancer Hospital Affiliated to Shandong University

type: Expression profiling by high throughput sequencing

summary: We aimed to detect the mRNA expression levels in KYSE510 cells after transfection with NC RNA or DAZAP1 siRNAs.

overall_design: There were a total of 3 samples examined. We detected the mRNA expression levels in KYSE510 cells transfected with NC RNA, or DAZAP1 siRNAs.

first: Ming

last: Yang

first: Yunsong

last: Chen

last: Lu


title: Heterotypic cell-cell communication regulates multipotency in glandular epithelial stem cells

city: Bruxelles

first: Alessia

last: Centonze

address: Route de Lennik 808

country: Belgium

institute: Université libre de Bruxelles

summary: Glandular epithelia including the mammary gland (MG) and the prostate are composed of basal cells (BC) and luminal cells (LC). Lineage tracing demonstrates that many glandular epithelia initially develop from multipotent basal stem cells (BaSCs) that are replaced in adult life by distinct pool of unipotent stem cells (SCs). However, adult unipotent BaSC can reactivate multipotency and give rise to LCs upon transplantation or oncogene expression, demonstrating the important plasticity of BaSCs in regenerative and pathological conditions, and suggesting that an active mechanism restricts multipotency in BaSCs during physiological conditions. The nature of this mechanism is currently unknown. Here, we assess whether basal and luminal cell-cell communication restricts multipotency in glandular epithelia. To this end, we performed lineage tracing of BCs together with the ablation of LCs in different adult glandular epithelia including MG, prostate, sweat glands and salivary glands and assessed the fate of BaSCs overtime. Interestingly, ablation of LCs reactivated multipotency in unipotent adult BaSCs from multiple epithelia. To understand the molecular mechanisms that controls multipotency in adult BaSCs, we performed population bulk-RNA-seq and single cell RNA-seq of FACS isolated adult mammary epithelial cells after LC ablation. Upon LC ablation, adult BCs activate a hybrid basal and luminal differentiation program before giving rise to LC, reminiscent of the genetic program that regulate multipotency during embryonic development. Different signaling pathways including Notch, Wnt and Egfr were activated in BaSC and their progeny following LC ablation and blocking these pathways inhibited adult BC multipotency. Altogether, our study demonstrates that heterotypic LC and BC communication is essential to maintain lineage fidelity in glandular epithelial SC during homeostasis and uncovers the lineage trajectory and signaling pathways that promote multipotency during tissue repair.

overall_design: Bulk RNAseq of FACS-sorted mammary gland isolated cells.

first: Cedric Blanpain

first: Shuheng

last: Lin

first: Yura

last: Song


title: The influence of recurrent EBV BRLF1 expression on genetic copy number alterations

city: Miaoli

first: Huang

last: Sheng-Yen

address: No.35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

type: Genome variation profiling by genome tiling array

summary: The EBV BRLF1 expression may exert an influence on genome instability. To test this speculation, the long-term experiment of recurrent BRLF1 expression was performed. The NPC cells (TW01-TetER, doxycycline inducible BRLF1 expressing cell line) were used. Experimental samples were derived from different passages of the NPC cells without or with BRLF1 expression. Array CGH (aCGH) was carried out to investigate the copy-number aberrations in response for different frequencies of BRLF1 expression. Compared to P1 as a common reference, a dramatic increase of aberrations was observed in R15 especially on chromosomes 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17 and 21. However, relatively few aberrations were detected in R1. Under long-term cell culture, P15 was not observed obviously changed in terms of aberrations. According to the results, recurrent expression of BRLF1 may be critical in inducing aggravated genome instability in NPC cells.

overall_design: Samples of four sources (P1, P15, R1 and R15) were analyzed. The NPC cells were seeded. After seeding for 24 h, the cells were mock or treated with 50 ng/ml doxycycline for 24 h. After incubation for 24 h, the cells were recovered by replacing with fresh medium and incubated for 24h. The resulting cells were defined as passage 1 (P1) or BRLF1 expression 1 (R1). The procedure was repeated for 15 rounds and the resulting cells were defined as passage 15 (P15) or BRLF1 expression 15 (R15). Genomic DNA from passage 1 (P1) of NPC cells was used as controls. Genomic DNAs extracted from P15, R1 and R15 cells were used as experimental samples and subjected to Cy5-labeling reactions. Genomic DNAs extracted from P1 cells were used as the common reference sample subjected to Cy3-labeling reactions.

first: Sheng-Yen

last: Huang

first: Jen-Yang


title: Genome-Wide DNA Methylation Profiles of Low- and High-Grade Adenoma Reveals Potential Biomarkers for Early Diagnosis of Colorectal Carcinoma

status: Public on Apr 23 2020

city: Beijing

first: Jian

last: Fan

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers1. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450K) to normal (N=20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA).

overall_design: Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Modulation of Wnt and Activin/Nodal supports efficient derivation, cloning and suspension expansion of human pluripotent stem cells

city: Kunming

first: Tianqing

last: Li

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: Kunming University of Science and Technology

summary: Various culture systems have been used to derive and maintain human pluripotent stem cells (hPSCs), but they are inefficient in sustaining cloning and suspension expansion of hPSCs. Through systematically modulating Wnt and Activin/Nodal signaling, we developed a defined medium (termed AIC), which enables efficient cloning and long-term expansion of hPSCs (AIC-hPSCs) through single-cell passage on feeders, matrix or in suspension (25-fold expansion in 4 days) and maintains genomic stability of hPSCs over extensive expansion. Moreover, the AIC medium supports efficient derivation of hPSCs from blastocysts or somatic cells under feeder-free conditions. Compared to conventional-culture hPSCs, AIC-hPSCs have similar gene expression profiles but down-regulated differentiation genes and display higher metabolic activity. The AIC medium shows a good compatibility for suspension expansion of different hPSC lines. Our study provides a robust culture system for derivation, cloning and suspension expansion of high-quality hPSCs that benefits GMP production and processing of therapeutic hPSC products

first: Zongyong

last: Ai


title: Profiling of miRNA in exosomes during Osteoclastogenesis by RNA-seq

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

summary:
Purpose: The goals of this study are to describe the RNA contents in exosomes derived from osteoclasts at different stages and to compare the differences among those exosomes from difference cell stages. The biological function of these ABs are also predicted and evaluated.
Methods: Primary bone marrow cells were isolated and treated with M-CSF (30ng/mL) to generate bone marrow macrophages (BMMs). BMMs were then used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more. RNA profiles of BMM, pOC and mOC were generated by deep sequencing, using Illumina NovaSeq 6000.
Results: After acquiring of clean reads, we used Hisat2 for spliced mapping. We mapped about 40 million sequence reads per sample to the mouse genome (GRCm38). Saturation rate analysis was then performed evaluating the gene coverage rate along with read depth increase. The transcripts mapping to difference functional region of the genome was then analyzed. Circos software was used to map the consistency of samples with mouse genome on a chromosomal level. The quantification of transcript intensity was analyzed using Fragments Per Kilobase of exon modelper Million mapped fragments (FPKM).
Conclusions: Our study represents the first high-throughput deep RNA sequencing data of cell derived exosomes. The biological prediction and analysis also revealed that exosomes derived from osteoclast of different stages have distinct biological role. Followed by low throughput validation and detailed experiments, we identified that pOC derived ABs are more pro-angiogenic while mOC derived ABs are more pro-osteogenic.

overall_design: Exosomes derived from ostoeclast at distinct differentiation stages were isolated and undergo with deep RNA-seq to reveal their inner RNA content.


title: Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

city: Miami

first: Stephen

last: Lee

state: Florida

department: Biochemistry & Molecular Biology

country: USA

institute: University of Miami

summary: mRNA TE and steady-state levels were measured in normoxic, normoxia-acidosis, hypoxia, hypoxia acidosis U87MG from RNA seq of ribosome density fractionation.

overall_design: TE was defined as the ratio of mRNA abundance in the pooled polysomal fraction to that in the free/monosomal fraction for each condition. Steady-state mRNA expression was defined as the aggregate mRNA abundance across all sequenced fractions for a given condition.

first: Nathan

last: Balukoff


title: The effect of knockdown of amphiregulin or SGK3 on global gene expression in letrozole resistant breast cancer cells

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

summary: LET-R cells were reversely transfected with siRNA negative control, AREG siRNA or SGK3 siRNA for 48 h, and then harvested for RNA sequencing.

overall_design: RNA-sequencing analysis of global gene expression affected by knockdown of AREG or SGK3

first: Wang

last: Yuanzhong

first: Chen

last: Shiuan


title: Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.

overall_design: Gene expression was profiled in brown adipocytes isolated from wildtype and adipocyte-specific Sel1L-deficient mice after 5h of fasting at either room temperature or 4℃.

first: Zhangsen

last: Zhou

first: Mauricio

last: Torres

first: Haibo

last: Sha

first: Christopher

middle: J

last: Halbrook

first: Françoise

last: Van den Bergh

first: Rachel

middle: B

last: Reinert

first: Tatsuya

last: Yamada

first: Siwen

last: Wang

first: Yingying

last: Luo

first: Allen

last: Hunter

first: Chunqing

first: Thomas

middle: H

last: Sanderson

first: Meilian

last: Liu

first: Aaron

last: Taylor

first: Hiromi

last: Sesaki

first: Costas

middle: A

last: Lyssiotis

first: Jun

last: Wu

first: Sander

last: Kersten

first: Dan

last: Beard

first: Ling

last: Qi


title: mRNA expression analysis of irradiated skin tissues of mice

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

summary: Radioactive materials have been widely used in industry, medicine, science, the military and nuclear facilities, which has significantly increased the potential of large-scale, uncontrolled exposure to radiation. The skin is one of the radiosensitive organ systems and radiation-induced skin injury remains a serious concern after ionizing radiation exposure. This study aims to illustrate the early response (mRNA profiles) of skin tissues following radiation and find targets against radiation-induced skin injury.

overall_design: Male C57 mice (4 weeks old) were irradiated with a single 35-Gy dose at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). After 24 h, skin tissues were collected. Skin tissues from nonirradated skin areas and irradiated areas were collected and subjected to RNA sequencing.

first: Shuyu

last: Zhang


title: Gene expression in the islets of 10 day old, 4 week old and 12 week old Non-Obese Diabetic (NOD) mice vs. healthy, age-matched NOD.B10 control mice

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

summary: Gene expression in the islets of NOD vs. NOD.B10 mice at 10 days, 4 weeks and 12 weeks of age insulitis.

overall_design: Pancreatic islets from 10 day old, 4 week old and 12 week old NOD and NOD.B10 mice were isolated by collagenase digestion and dissolved in 0.5 ml Trizol reagent (Invitrogen). 0.1 ml of chloroform was added.  Samples were shaken vigorously and centrifuged at 12,000xg at 4°C. The clear aqueous phase was combined with an equal volume of 70% ethanol, and bound to a RNeasy micro column (Qiagen). RNA was extracted according to manufacturer’s instructions and RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Reagent Kit (Agilent). Total RNA (300 ng) extracted from the islets of NOD mice were labelled with Cy5 and run individually against a pool of Cy3-labeled total RNA (300 ng) isolated from the islets of age-matched NOD.B10 mice (pool of 6 animals). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays (Agilent Technologies).


title: HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

first: Stephen

last: Lee

summary: mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HuR-specific siRNA pools followed by ribosome density fractionation.

first: J

last: Ho


title: Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

summary: mRNA TE and steady-state levels were measured in U87MG cells subjected to 21% or 1% oxygen followed by ribosome density fractionation.


title: An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: While Chronic Myelogenous Leukemia (CML) is generally well controlled with Imatinib and other kinase inhibitors, blast crisis CML (bcCML) continues to be resistant to current therapies and remains highly lethal. In this study, we identify the double stranded RNA binding protein Stau2 as a as key new dependency of bcCML. To define the impact of Staufen2 in myeloid leukemia, we developed a germline knockout with targeted loss of its RNA binding domains. Genetic deletion of Staufen2 led to a profound decrease in bcCML growth and propagation, and markedly improved overall survival in mouse models. Further, Staufen2  was also expressed and required for growth of primary bcCML as well as de novo AML patient samples, indicating a conserved utilization across human disease. Finally, an integrated computational analysis of eCLIP, RNA-Seq analysis and the functional genomic CRISPR screen identified Staufen2 as a regulator of a remarkable network of broad acting chromatin modifiers, resulting in changes in global histone methylation patterns.

overall_design: The eCLIP study was designed to identify genes bound by Stau2 in myeloid leukemia.

first: Jeevisha

last: Bajaj

first: Michael

last: Hamilton

first: James

last: Scott-Browne

first: Eric

middle: L

last: Van Nostrand

first: Yutaka

last: Shima

first: Kendall

last: Chambers

first: Kyle

last: Spinler

first: Steven

middle: M

last: Blue

first: David

last: Rizzeri

first: Charles

last: Chuah

first: Vivian

last: Oehler

first: Elizabeth

last: Broome

first: Roman

last: Sasik

first: Anjana

last: Rao

first: Tannishtha

last: Reya


title: Characterizing pancreatic β-cell heterogeneity in the streptozotocin model by single-cell transcriptomic analysis

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

institute: Peking University

summary:
Objectives
The streptozotocin (STZ) model is widely used in diabetes research. However, the cellular and molecular states of pancreatic endocrine cells in this model remain unclear. This study explored the molecular characteristics of islet cells treated with STZ and re-evaluated β-cell dysfunction and regeneration in the STZ model.

Methods
We performed single-cell RNA sequencing of pancreatic endocrine cells from STZ-treated mice. High-quality sequencing data from 2,999 cells were used to identify clusters via Louvain clustering analysis. Principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), force-directed layout (FDL), and differential expression analysis were used to define the heterogeneity and transcriptomic changes in islet cells. In addition, qPCR and immunofluorescence staining were used to confirm findings from the sequencing data.

Results
Untreated β-cells were divided into two populations at the transcriptomic level, a large high-Glut2 expression (Glut2high) population and a small low-Glut2 expression (Glut2low) population. At the transcriptomic level, Glut2low β-cells in adult mice did not represent a developmentally immature state, although a fraction of genes associated with β-cell maturation and function were downregulated in Glut2low cells. After a single high-dose STZ treatment, most Glut2high cells were killed, but Glut2low cells survived and over time changed to a distinct cell state. We did not observe conversion of Glut2low to Glut2high β-cells up to 9 months after STZ treatment. In addition, we did not detect transcriptomic changes in the non-β endocrine cells or a direct trans-differentiation pathway from the α-cell lineage to the β-cell lineage in the STZ model.

Conclusions
We identified the heterogeneity of β-cells in both physiological and pathological conditions. However, we did not observe conversion of Glut2low to Glut2high β-cells, transcriptomic changes in the non-β endocrine cells, or direct trans-differentiation from the α-cell lineage to the β-cell lineage in the STZ model. Our results clearly define the states of islet cells treated with STZ and allow us to re-evaluate the STZ model widely used in diabetes studies.

overall_design: To explore the transcriptomic status of individual pancreatic endocrine cells in STZ-treated mice, we isolated cells from STZ-treated mice by fluorescence-activated cell sorting (FACS) and performed single-cell RNA sequencing (scRNA-seq) using a modified STRT-seq (mSTRT-seq) approach. To enrich endocrine cells, RFP+ cells were collected from Ngn3-Cre; Rosa-RFP mice. Mice were treated with a single high dose (200 mg/kg) of STZ and were assessed from day 1 (D6) to month 9 (M9). Additionally, to evaluate the maturation status of β-cells, we performed mSTRT-seq on Ngn3-Cre; Rosa-RFP+ cells from postnatal day (P) 3, P12, and P21 mice.

first: Ye

last: Feng

first: Wei-Lin

last: Qiu

first: Xin-Xin

last: Yu

first: Yu

last: Zhang

first: Mao-Yang

last: He

first: Lin-Chen

last: Li

first: Li

last: Yang

first: Weiyi

last: Franti

first: Junqing

last: Ye

first: Joerg

middle: D

last: Hoeck

first: Cheng-Ran


title: Single Cell RNA-sequencing of mammary gland epithelial cells

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

institute: Université Libre de Bruxelles (ULB)

summary: The mammary gland epithelium is composed of basal cells (BC) and luminal cells (LC). Lineage tracing demonstrates that many glandular epithelia initially develop from multipotent basal stem cells (BaSCs) that are replaced in adult life by distinct pool of unipotent stem cells. However, adult unipotent BaSC can reactivate multipotency and give rise to LCs upon transplantation or oncogene expression, demonstrating the important plasticity of BaSCs in regenerative and pathological conditions, and suggesting that an active mechanism restricts multipotency in BaSCs during physiological conditions. Here, we assess whether basal and luminal cell-cell communication restricts multipotency in glandular epithelia.

overall_design: The purpose of this study was to define, at the single cell level, the transcriptional profile of murine mammary gland epithelial cells upon ablation of luminal cells. Particularly, we identified the enrichment of one intermediate population between basal and luminal cells, that shares genes with both basal and luminal cells. The aim of this study was to better characterize this population and understand the lineage trajectory followed by the basal cell, hybrid and newly formed luminal cells. In this experiment, we used mammary gland epithelial cells FACS sorted based on the negative expression of CD140a, CD45 and CD31 and the positive expression of Tomato, CD29 and EpCAM before and after ablation of luminal cells.

first: Alessia

last: Centonze

first: Shuheng

last: Lin

first: Milan

last: Malfait

first: Alejandro

last: Sifrim

first: Thierry

last: Voet


title: Single cell sequencing of mouse retina

status: Public on Apr 22 2020

city: Dallas

first: Rafael

last: Ufret-Vincenty

state: TX

address: 5323 Harry Hines Blvd, Rm E7.244

department: Ophthalmology

institute: UT Southwestern

summary:
Purpose: The goals of this study are to study the expression of Sfxn3 in C57B/L6 mouse retina and retinal cell types
Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome were generated by high throughput sequencing

overall_design: Mouse retina cells were dissociated from 3-4 month old C57B/L6 mice

first: Chao

last: Xing

first: Bogale

last: Aredo

first: Ashwani

last: Kumar


title: Id1 and Id3 Maintain Steady State Hematopoiesis by Promoting Sinusoidal Endothelial Cell Survival and Regeneration

city: Frederick

first: Brad

middle: LaMar

last: Jakubison

state: MD

address: 1050 Boyles St., Building 539, Room 106

department: Mouse Cancer Genetics

institute: National Cancer Institute

summary: Single cell RNA-Seq was performed on ID1 ID3 null endothelial cells to determine the effects of ID gene loss on endothelial cell maintainence and growth.

overall_design: 20,000 SECs and type H vessels from CDH5-CreER ID1+/+ ID3+/- or  CDH5-CreER ID1-/- ID3-/- mice were sorted using FACs and subjected to single cell RNA-Seq.

first: Stephen

last: Gadomski

first: Jonathan

last: Keller


title: HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

last: Lee

summary: mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HIF-2α-specific or HIF-1α-specific siRNA pools followed by ribosome density fractionation.

first: J

last: Ho


title: Coordination of mRNA and tRNA methylations by TRMT10A

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

summary: The post-transcriptional modification of mRNA and tRNA provides an additional layer of regulatory complexity during gene expression. TRMT10A is a tRNA methyltransferase that installs N1-methylguanosine (m1G), while FTO performs demethylation on N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) in mRNA. We find that this tRNA  methyltransferase TRMT10A interacts with mRNA demethylase FTO (ALKBH9), both in vitro and inside cells. Strikingly, depletion of TRMT10A not only led to decreased m1G in tRNA but also significantly increased m6A levels in mRNA. CLIP-seq results showed that TRMT10A shares a significant overlap of associated mRNAs with FTO, and these mRNAs have accelerated decay rates potentially through the regulation by specific m6A reader. Furthermore, transcripts with increased m6A upon TRMT10A ablation contain an overrepresentation of m1G9-containing tRNAs codons read by tRNAGln(TTG), tRNAArg(CCG),  and tRNAThr(CGT). These findings collectively reveal the presence of coordinated mRNA and tRNA modifications and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.

overall_design: m6A profiling in TRMT10A knockdown and control cells, TRMT10A CLIP-seq and FTO CLIP-seq.

first: Kathy

middle: F

first: R

last: Ontiveros

first: Hui

last: Shen


title: Gene expression profiling of 27 gastric cancer cell lines

city: Seoul

first: Yong-Min

last: Huh

address: 50 Shinchon-ro

institute: Yonsei University

summary: We identified molecular subtypes of 27 gastric cancer cell lines.

overall_design: We obtained gene expression profile from 27 gastric cancer cell lines with four repetitions per cell line by HumanHT-12 v3.0 Expression BeadChip array (Illumina).

first: Jae-Ho

last: Cheong


title: Rathke’s Cleft-Like Cysts Arise From Isl1 Deletion in Murine Pituitary Progenitors

city: Ann Arbor

first: Michelle

last: Brinkmeier

state: MI

address: 1241 Catherine St., 5704 MSII

department: Human Genetics

institute: University of Michigan

summary: The transcription factor ISL1 is expressed in pituitary gland stem cells and the thyrotrope and gonadotrope lineages.  Pituitary-specific Isl1 deletion causes hypopituitarism with increased stem cell apoptosis, reduced differentiation of thyrotropes and gonadotropes, and reduced body size.  Conditional Isl1 deletion causes development of multiple Rathke’s cleft-like cysts, with 100% penetrance.  Foxa1 and Foxj1 are abnormally expressed in the pituitary gland and associated with a ciliogenic gene expression program in the cysts.  We confirmed expression of FOXA1, FOXJ1 and stem cell markers in human Rathke's cleft cyst tissue, but not craniopharyngiomas, which suggests these transcription factors are useful, pathological markers for diagnosis of Rathke's cleft cysts.  These studies support a model whereby expression of ISL1 in pituitary progenitors drives differentiation into thyrotropes and gonadotropes, and without it, activation of FOXA1 and FOXJ1 permits development of an oral epithelial cell fate with mucinous cysts.  This pituitary-specific Isl1 mouse knockout sheds light on the etiology of Rathke's cleft cysts and the role of ISL1 in normal pituitary development.

overall_design: RNAseq on whole pituitary glands with posterior lobe removed, 6 individual control and 6 individual Isl1Prop1KO samples were sequenced.

first: Hironori

last: Bando

first: Adriana

middle: C

last: Camarano

first: Shingo

last: Fujio

first: Koji

last: Yoshimoto

first: Flavio

middle: S

last: de Souza

first: Sally

last: Camper


title: Single cell RNA sequencing analysis of sorted T and B cells following natural primary and secondary DENV infection

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: Viable T cells (CD3+ CD19-) and B cells (CD3- CD19+) were sorted from PBMC samples obtained from 6 individuals experiencing either natural primary or natural secondary DENV infection. Single cell RNA sequencing analysis was performed on 2-3 time points  per subject

overall_design: Single cell RNA sequencing analysis of 2-3 time points from 3 subjects experiencing a natural primary DENV infection and 3 subjects experiencing a natural secondary DENV infection

first: Heather

last: Friberg


title: microRNA profiling of exosomes derived from human pulmonary artery smooth muscle cells under PDGF stimulation

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

institute: Incheon National University

summary: Analysis of exosomal microRNAs secreted by PDGF-stimulated human pulmonary artery smooth muscle cells. Results increase our understanding of exosome-mediated crosstalk between vascular cells under a pathological condition.

overall_design: microRNA expression profiles of exosomes secreted by human pulmonary artery smooth muscle cells after exposure to PDGF-BB by Illumina Hi-seq 2000.


title: Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model

city: Sao Paulo

last: Lichtenstein

state: São Paulo

address: Vital Brazil Ave., 1500

department: CDI - Inovation

country: Brazil

institute: Instituto Butantan

summary: We have investigated Amblyomin-X-treated horse melanomas to better understand its mode of action through transcriptome analysis and also the in vivo model. Amblyomin-X is a Kunitz-type homologous protein that selectively leads to the death of tumor cells via ER stress and apoptosis, currently under investigation as a new drug candidate for cancer treatment. Melanomas are immunogenic tumors, and a better understanding of the immune responses are warranted. Equine melanomas are spontaneous and not aggressive as human melanomas are, and we showed that the in vivo treatment of encapsulated horse melanoma tumors led to a significant tumor size reduction or even the complete disappearance of the tumor mass through intratumoral injections of Amblyomin-X. Transcriptome analysis identified ER and mitochondria-stresses, modulation of the innate immune system, apoptosis, and possibly immunogenic cell death activation. Interactome analysis showed that Amblyomin-X potentially interacts with key elements found in transcriptomics. Taken together, Amblyomin-X modulated the tumor immune microenvironment in different ways, making at least part to induce tumor cell death.

overall_design: This is a time series experiment: control 0h, treatment evolution 6h, 12h. For each time-point, we have 3 animals x 2 tumors = 6 samples. We must discard two samples from 12h, due to low library size.

first: Asif

last: Iqbal

first: Sonia

middle: E

last: Alves de Lima Will

first: Rosemary

middle: V

last: Bosch

first: Carlos

last: DeOcesano-Pereira

first: Mauricio

last: Goldfeder

first: Roger

last: Chammas

last: Madureira Trufen

first: Katia

last: Pereira Morais

first: Jean

middle: G

first: Renato

last: Mendonça Natalino

first: Inacio

last: Junqueira de Azevedo

first: Milton

middle: Y

last: Nishiyama Jr

first: Ursula

last: Oliveira

first: Francisco

middle: I

last: Arruda Alves

first: Jaqueline

last: Araujo

first: Aline

last: Ramos Maia Lobba

first: Ana

last: Chudzinski-Tavassi


title: AMPKβ1/β2 isoform-specific gene expression profile in human induced pluripotent stem cells

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

summary:
AMP-activated protein kinase (AMPK) is a key regulator of energy metabolism that, upon activation, phosphorylates a wide range of substrate proteins in order to restore cellular energy balance. AMPK is a heterotrimeric protein that is composed of three subunits: α, β and γ. The α and β subunits are encoded by two, the γ subunit by three genes that are expressed in a tissue- and species-specific manner. However, neither the mechanisms of how different trimer combinations affect AMPK downstream effects nor the functional properties of single isoforms are completely understood so far. We provide evidence that AMPKβ1- and β2-containing AMPK trimers lead to different gene expression profiles in a model of human induced pluripotent stem cells and thereby differentially affect lineage decision.

The analysis of hiPSCs harboring a gene knockout for AMPK β1 (PRKAB1-/-) and for AMPK β2 (PRKAB2-/-) compared to WT hiPSCs revealed major differences in the gene expression profile in all the cell lines. This suggests an isoform-specific regulation of gene expression.

overall_design: Analysis of WT as well as hiPSCs deficient for the AMPK subunit β1 ot the subunit β2 were analyzed by RNA-Seq. Two knockout clones of each genotype were analyzed, using four individual samples for each group.

first: Nicole

last: Ziegler

first: Dieter

last: Schmoll


title: CASPARIAN STRIP INTEGRITY FACTOR 2 (CIF2) peptide induces SCHENGEN3 (SGN3) receptor-kinase dependent transcriptional changes

city: Lausanne

first: Emanuel

last: Schmid-Siegert

address: UNIL Sorge

country: Switzerland

institute: UNIL

summary: Here we show that the CASPARIAN STRIP INTEGRITY FACTOR 2 peptide induces SCHENGEN3 (SGN3) receptor-kinase dependent transcriptional changes both in short-term (30 min) and long-term (480 min) transcriptional changes in roots of Arabidopsis thaliana. We deposit RNA-seq data of wildtype, sgn3, and cif1,2 with or without the CIF2 peptide treatment. Wildtype and cif1,2 presented large transcriptional changes, while the sgn3 receptor mutant showed almost no difference after the treatment.

overall_design: Examination of transcriptional changes in wildtype, sgn3 and cif1/2 mutants after the CIF2 peptide treatment.

first: Satoshi

last: Fujita

first: Tonni

last: Andersen

first: Niko

last: Geldner


title: Gene expression profiles of miR-100-5p-transfected normal endometrial stromal cells

city: yufu city

first: yoko

last: aoyagi

address: 1-1 Idaigaoka hamasamachi

country: Japan

institute: oita university

summary: Accumulating evidence suggests that microRNAs play definite roles in the pathogenesis of endometriosis. The objective of the study was to determine the role of miR-100-5p, one of the upregulated microRNA in endometriotic cyst stromal cells, in the pathogenesis of endometriosis. Downstream targets of miR-100-5p were identified by compulsory expression of miR-100-5p in normal eutopic endometrial stromal cells (NESCs), a global mRNA microarray technique, and pathways analysis.Compulsory expression of miR-100-5p in NESCs directed the induction of cell motility through SWItch/sucrose non-fermentable (SWI/SNF)-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SMARCD1) supression and matrix metallopeptidase 1 (MMP1) activation.

overall_design: NESCs were transfected with precursor hsa-miR-100-5p (Pre-miRTM miRNA precursor- hsa-miR-100, Ambion, Austin, TX, USA) or negative control precursor miRNA (Pre-miRTM miRNA precursor-negative control #1 Ambion) at a final concentration of 10 nM, using LipofectamineTM RNAiMAX (Invitrogen, Carlsbad, CA, USA). Forty-eight hours after transfection, total RNA from cultured NESCs transfected with precursor hsa-miR-100-5p (n=4) and NESCs transfected with negative control precursor miRNA (n=4) was extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA). Then, the samples were subjected to a gene expression microarray analysis with a commercially available human mRNA microarray (G4851A, SurePrint G3 Human Gene Expression Microarray 8x60K v2, Agilent Technologies, Santa Clara, CA, USA).

first: Takebayashi

last: Kanetoshi

first: Nasu

last: Kaei


title: Transcriptome sequencing in patients with tongue cancer

city: Nantong

first: Liang

last: Han

state: Jiangsu

address: 30.tongyang road

department: 1Department of Head and Neck Surgery

institute: Nantong Tumor Hospital

summary: Tongue cancer is one of the most common cancers, and its molecular etiology and pathogenesis remain unclear. This study aimed to uncover its pathogenesis and search for potential novel diagnostic and therapeutic targets for treating tongue cancer.

overall_design: There are 8 samples overall the experiment. 4 cancer tissues and paired 4 paracancerous.

first: Mingming

last: Tang

first: Wencheng

last: Dai

first: Hao

last: Wu

first: Xinjiang

last: Xu

first: Bin

last: Jiang

first: Yingze

last: Wei

first: Hongyan

last: Qian


title: Transcriptomic Analysis of Inflammatory Responses in Bovine Mammary Epithelial Cells following Stimulation with Escherichia coli and Staphylococcus aureus

city: Sendai

first: Haruki

last: Kitazawa

state: Miyagi

address: 468-1 Aramaki Aza Aoba, Aoba-ku,, Sendai

institute: Tohoku University

summary: Bovine mastitis, an inflammatory reaction of the mammary gland, is commonly caused by Staphylococcus aureus or Escherichia coli infections in high-yielding dairy cows. Immunotranscriptomic responses of bovine mammary epithelial cell (bMEC) are pivotal for the understanding of the defense against invading pathogens, and for the fate of udder inflammation. The intracellular chemotaxic protein Cyclophilin A (CyPA), secreted by bMEC during inflammatory reaction is being considered as a marker for the early diagnosis of mastitis. Taken together, the present study aimed to investigate the microarray-based transcriptome alterations in bMEC after in vitro infection with two S. aureus strains (S. aureus JE2 and S. aureus SA003) or E. coli crude lipopolysaccharide (LPS). In addition, the CyPA-induced expression changes of selected cytokine and chemokines were evaluated by qRT-PCR. Differential expression analysis identified 447, 465 and 520 differentially expressed genes (DEGs) in bMEC after LPS, S. aureus JE2 and S. aureus SA003 stimulation, respectively. LPS-induced DEGs are involved in the activation of cytokine-cytokine receptors interaction, NOD-like receptor signaling, chemokine signaling, interleukin-1 signaling and Toll-like receptor signaling pathway; while S. aureus induced DEGs were involved in the enrichment of neuroactive ligand-receptor interaction, GPCR signaling, cytokine-cytokine receptor interaction, and JAK-STAT pathway. A major differential inflammatory response to LPS and S. aureus treatments was the activation of the chemokine signaling pathway by LPS but not either by S. aureus JE2 or SA003. Unlike the S. aureus strains, LPS stimulation resulted significant upregulation of CCL2, CXCL2, CXCL3, CXCL5, CXCL8, CXCL9, IL1A and IL1B that are known to target mononuclear leukocytes, and could induce systemic inflammation. CyPA stimulation was able to upregulate chemokines (CXCL2, CXCL3, CXCL8, IL1A and IL1B) expression in bMEC indicating its ability to promote inflammation. Several of the LPS-induced DEGs were found to have transcription factor binding sites, and their expressions were also predicted to be regulated by sets of microRNAs. The transcriptional alterations associated with inflammatory response in this study may reflect immunomodulatory mechanisms underlying the interaction of bMEC with E. coli and S. aureus during mastitis.

overall_design: Gene expression changes in bovine mammary epitheial cells (bMEC) was measured after 12 h  of E. coli derived lipopolysaccharides (LPS), Staphylococcus aureus SA003, and Staphylococcus aureus JE2 stimulations, respectively. Single sample was generated in each of three cases along with a non-stimulated control.

first: Aminul

last: Islam

first: Michihiro

last: Takagi

first: Julio

last: Villena

first: Hisashi

last: Aso


title: Urban Particles increased Streptococcus pneumonaie colonization to human middle ear epithelia cells

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

summary: Background: Air-pollutants containing toxic particulate matters (PM) deposit in the respiratory tract and increases microbial infections. However, the mechanism underline is not well understood. In this study, we evaluated the effect of urban particles (UP) on S. pneumoniae in-vitro biofilm formation, colonization on Human middle ear epithelium cells (HMEECs) and in mouse nasal cavity and transition to middle ear and lungs.   Methods: S. pneumoniae in vitro biofilms and planktonic growth was evaluated in metal ion free medium in presence of UP, and biofilms were quantified by CV-microplate assay, cfu counts and resazurin staining. Biofilm structures were analyzed using scanning electron microscope (SEM) and confocal microscopy (CM). Gene expressions of biofilms were evaluated using real time RT-PCR. Effects of UP exposure on S. pneumoniae colonization to HMEECs was evaluated using fluorescent in-situ hybridization (FISH), cell viability was detected by EZcyto kit, apoptosis in HMEECs were evaluated using Annexin-V/PI based cytometry analysis and reactive oxygen species (ROS) production were evaluated using Oxiselect kit. Alteration of HMEECs gene expressions on UP exposure or pneumococci colonization were evaluated using microarray. In vivo colonization of pneumococci in presence of UP and transition to middle ear and lungs were evaluated using intranasal mice colonization model.  Results: UP exposure significantly (*p< 0.05) increased pneumococcal in vitro biofilms and planktonic growth. In presence of UP pneumococci formed organized biofilms with matrix, while in absence of UP bacteria was unable to form biofilms. The luxS, ply, lytA, comA, comB and ciaR genes involved in bacterial pathogenesis, biofilms formation and quorum sensing were up-regulated in pneumococci biofilms grown in presence of UP. The HMEECs viability was significantly (p<0.05) decreased and bacteria colonization was significantly (p<0.05) elevated in co-treatment (UP+S. pneumoniae) in compare to single treatment. Similarly, increased apoptosis and ROS produce were detected in HMEECs treated with UP+ pneumococci. The microarray analysis of HMEECs revealed that the genes involve in apoptosis and cell death, inflammation, immune response were up-regulated in co-treatment, those genes were unchanged or expressed in less fold in single treatments of UP or S. pneumoniae. In vivo study showed increased pneumococcal colonization to nasal cavity in presence of UP and higher transition of bacteria to middle ear and lungs in presence of UP.

overall_design: The HMEECs were maintain and routinely culture in airway epithelial cell growth medium (PromoCell GmbH, Sickingenstr Heidelberg Germany) supplemented with bovine pituitary extract (0.004 mL/mL), epidermal growth factor (10 ng/mL), insulin (5 µg/mL), hydrocortisone (0.5 µg/mL), epinephrine (0.5 µg/mL), triiodo-L-thyronine (6.7 ng/mL), transferrin (10 µg/mL), retinoic Acid (0.1 ng/mL) and 1% fetal bovine serum and 5% CO2. 1× 104 HMEECs were seeded in 96-well plate and incubated at 37°C with 5% CO2 for 24 h. Following incubation cells were washed with PBS and medium was replaced with UP (200 µg/mL) containing medium (antibiotic free medium) and further incubated for 8 h. The HMEECs pre-exposed to UP were infected with S. pneumoniae (MOI 10) for 15 h. To educate the molecular mechanism underline for the elevated toxicity of UP + S. pneumoniae, gene expressions analysis was performed using microarray. Global gene expression of HMEECs treated with UP (200 µg/ml) or S. pneumoniae (MOI 10) or co-treatment (UP + S. pneumoniae) were analyzed using Affymetrix microarray chip. Total RNA of HMEECs was extracted using Trizol reagent (Invitrogen, USA), and RNA quality was assessed by Agilent 2100 bioanalyser (Agilent Technologies, USA), and quantity was determined by ND-1000 spectrophotometer (NanoDrop Technologies, USA). The gene expressions of HMEECs were detected by Affymetrix GeneChip® Human Gene 2.0 ST oligonucleotide arrays by manufacturer’s procedure (http://www.affymetrix.com). The change of gene expressions by 2-fold in treated samples with respect to control sample (untreated) was considered significant. The gene ontology (GO) and KEEG pathway analysis was performed using DAVID (http://david.abcc.ncifcrf.gov/), string and Medline databases (http://www.ncbi.nlm.nih.gov/).

first: Jae-Jun

last: Song

middle: K


title: Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells [4C-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

summary: The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanism controlling its transcription are likely divergent between them. Here we determine how two extragenic CREs that are prominent in secretory epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at -44kb and -35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter. The deletions also greatly reduced promoter interactions with the 5’ TAD boundary. We show substantial recruitment of RNAPII to the -35kb element and identify CEBPβ as a key activating transcription factor for airway expression of CFTR, likely through occupancy at both the CRE and the gene promoter.

overall_design: Analysis of the 3D chromatin architecture at the CFTR locus to determine interaction frequencies between elements which lead to changes in CFTR gene regulatory patterns.

first: Shiy

last: Yin

first: Monali

last: NandyMazumdar


title: Characterization of extraembryonic endoderm-like cells from mouse embryonic fibroblasts induced using chemical alone

city: changchun

first: xia

last: he

address: xinmin street

institute: Key laboratory of pathobiology

summary: We reprogrammed mouse embryonic fibroblasts (MEFs) into extraembryonic endoderm-like cells by small molecule-only. To further reveal its properties, the gene expression profiles of these cells were further analyzed by RNA sequencing.

overall_design: MEFs were used as control group containing three repetitive samples. ciXEN cells at passage 5 and 30 were to set as experimental group 1 and experimental group 2, respectively, including three different batches of cells as duplicate samples

first: Xia

last: He

first: Yulin

last: Li


title: ATAC-seq analysis of K562, MKPL-1, MV4-11, NB4 and U937 leukemia cell lines

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mutations in protein-coding genes are well established as the basis for human cancer, yet it remains elusive how alterations within non-coding genome, a substantial fraction of which contain cis-regulatory elements (CREs), contribute to cancer pathophysiology. Here we developed an integrative approach to systematically identify and characterize non-coding regulatory variants with functional consequences in human hematopoietic malignancies. Combining targeted resequencing of hematopoietic lineage-specific CREs and mutation discovery, and uncovered 1,837 recurrently mutated CREs containing leukemia-associated non-coding variants. By enhanced CRISPR/dCas9-based CRE perturbation screening and functional analyses, we identified 218 variant-associated oncogenic or tumor suppressive CREs in human leukemia. Non-coding variants at KRAS and PER2 enhancers reside in nuclear receptor (NR) binding regions and modulate transcriptional activities in response to NR signaling in situ in leukemia cells. NR binding sites frequently co-localize with non-coding variants across cancer types. Hence, recurrent non-coding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies.

overall_design: ATAC-seq was performed to determine the chromatin accessibility in human leukemia cell lines

first: Kailong

first: Yuannyu

last: Zhang

first: Xin

last: Liu

first: Yuxuan


title: Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

summary: While Chronic Myelogenous Leukemia (CML) is generally well controlled with Imatinib and other kinase inhibitors, blast crisis CML (bcCML) continues to be resistant to current therapies and remains highly lethal. Here we report a genome-wide in vivo CRISPR screen to better define the biological determinants of bcCML establishment and propagation in a physiologic context. This screen identified a large number of new genes and programs critically required for bcCML including those essential for chromatin remodeling, spliceosomal assembly, PLK1 and Myc signaling.

overall_design: We generated lentiviral particles from the Brie library (Addgene #73633) and infected 300 million freshly isolated Cas9-GFP+ Lineage- blast crisis CML (bcCML) stem cells from the spleen of pre-morbid mice at an MOI of 0.25 such that a single cell is infected with only one virus carrying one gRNA. 60 hours post spinfection, an aliquot of cells was collected and represented a pool of infected cells with about 200 cells/guide (Pre-Sel sample). The cells were then selected for 48h in puromycin to enrich for cells carrying gRNAs (Post-Sel sample). 35 million cells were transplanted in sub-lethally irradiated recipients (1 million cells/mouse) to ensure a coverage of >400 cells/guide. The recipient mice were sacrificed 7 days post-transplant, before the onset of full-blown disease. The cells from the spleen of all 35 mice were pooled into one sample (InV) after sorting for equal numbers (~1.1 million cells/mouse) of leukemic cells.


title: RNAseq of circulating CD34+ cells derived from TCIRG1-defective patients

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Transcriptomic profile of CD34+ cells circulating in peripheral blood of TCIRG1-mutated osteopetrotic patients, compared to cord blood and mobilized CD34+ cells

overall_design: Circulating CD34+ cells were isolated from peripheral blood of 6 TCIRG1 osteopetrotic patients, using microbeads. Commercially available cord blood (n=3) and mobilized peripheral blood CD34+ cells (n=3) were used as controls.

first: Valentina

last: Capo

first: Sara

last: Penna

first: Anna

last: Villa

first: Matteo

last: Barcella

first: Paolo

last: Uva

first: Roberto

last: Cusano


title: RNA sequencing of S. Cerevisiae treated with the Vacuolar H+-ATPase inhibitor concanamycin A (concA)

city: Salt Lake City

first: Adam

last: Hughes

state: Utah

address: 15 N Medical Drive East, RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

summary: RNA sequencing results identifying transcript abundance changes that occur after treating budding yeast with V-ATPase inhibitors

overall_design: Wild type BY4741 were treated with the V-ATPase inhibitor concA for 0, 1, 3, or 6 hours in triplicate followed by RNA purification and single read RNA sequencing.

first: Casey

first: Troy

last: Coody

first: Mi-Young

last: Jeong

first: Jordan

middle: A

last: Berg

first: Dennis

middle: R

last: Winge


title: mRNA transcriptome sequencing of colon tissues from Usp25+/+ and Usp25-/- mice treated with 2.5% DSS for 5 five days followed by two-day normal water

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: Female Usp25+/+ and Usp25-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days. The colons were flushed with PBS to clear feces and slit open longitudinally. The distal colon tissues (0.5 cm in length, about 0.5 cm away from the anus) were washed in PBS and homogenized in 2 ml TRIzol (Invitrogen). Total RNAs were prepared and the qualities of RNAs were determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently puriﬁed from 10 ug total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. The first strand cDNA was synthesized with NEBNext® RNA First Strand Synthesis Module. NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first strand cDNA. The resulted double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep Kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 100 bp paired-end reads strategy (Novogene Co. Ltd, Beijing). Quality control of mRNA-seq data was performed by using Fatsqc and low-quality bases were trimmed by Cutadapt. All RNA-seq data were mapped to the mouse genome (mm9) by TopHat (version 2.1.1) and allow maximum 2 mismatch per read. Gene expression level was calculated by Cufflinks with default parameters and normalized by FPKM.

overall_design: Two Usp25+/+ mice and two Usp25-/- mice were used.

first: Xiao-Meng

last: Wang

first: Bo

last: Zhong


title: Exosomes mediate intercellular transference of non-autonomous tolerance to proteasome inhibitors in mixed-lineage leukemia.

city: Charlestown

first: Maolin

last: Ge

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

summary: The interplay between cancer cells and microenvironment can influence treatment response and plays a key role in the emergence of drug resistance. Rapidly acquired resistance prevents proteasome inhibitors (PIs) therapies from achieving stable and complete responses. Investigating the underlying mechanisms and developing effective strategies against PI resistance are highly desired in the clinic. Here we uncovered that PI resistance was reversible in mixed-lineage leukemia (MLL), which consistent with the finding that patients could regain sensitivity to PIs after a drug holiday. Exosomes released from PI-treated cells could transmit PI resistance to sensitive cells via facilitating cell cycle arrest and stemness pathway in MLL cells. Furthermore, TieDIE algorithm integration analysis of transcriptome and proteome datasets identified candidate exosomal proteins, providing potential therapeutic targets for treating refractory MLL.

overall_design: Examination of differential expressive genes in RS4;11 cells under Bortezomib therapeutic stress, or treated with naïve RS4;11-derived exosomes (RS4;11-Nexo) or proteasome inhibitor-treated cells released exosomes (RS4;11-Rexo).

first: Han

last: Liu


title: Integrative analysis of non-coding variants in human leukemia

first: Jian

last: Xu

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

overall_design: Refer to individual Series


title: Analysis of gene expression signatures for primary vitreo retinal lymphoma

city: Bunkyo-ku

first: Ayako

last: Arai

state: Tokyo

address: 1-5-45 Yushima

department: Graduate School of Medical and Dental Sciences

institute: Tokyo Medical and Dental University

summary: In order to determine the subtype and biological characteristics of the tumor cells of PVRL, we performed gene expression profiling analysis using RNA extracted from the vitreous samples upon diagnosis.

overall_design: RNA was extracted from the vitreous fluid and the lymph nodes from PVRL and nodal DLBCL patients, respectively.  One-color microarray-based gene expression analysis was performed.

first: Hiroshi

last: Takase


title: Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells [Omni-ATAC-seq]

first: Ann

last: Harris

overall_design: IDR OMNI-ATAC-seq profiles of open chromatin were generated from 2 independent replicates of libraries for 16HBE14o- cells and Calu3 cells

first: Shiy

last: Yin

first: Jenny

middle: L

last: Kerschner


title: Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells


title: Global Epigenomic and Transcriptomic changes associated with Human Retinal Pigment Epithelial Epithelial-to-Mesenchymal Transition in a Stem Cell-based model of Epiretinal Membrane Formation (ChIP-seq)

city: Stanford

first: Tomek

last: Swigut

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: Epithelial to mesenchymal transition (EMT) is a biological process involved in tissue morphogenesis and disease that causes dramatic changes in cell morphology, migration, proliferation, and gene expression. The retinal pigment epithelium (RPE), which supports the neural retina, can undergo EMT, producing fibrous epiretinal membranes (ERMs) associated with vision-impairing clinical conditions such as macular pucker and proliferative vitreoretinopathy. We found that co-treatment with TGFβ1 and TNFα (TNT) accelerates EMT in adult human RPE stem cell (RPESC)-derived RPE cell cultures. We captured the global epigenomic and transcriptional changes elicited by TNT treatment of RPE and identified putative active enhancers associated with actively transcribed genes, including a set of upregulated transcription factors that are candidate regulators. We found that the vitamin B derivative nicotinamide downregulates these factors, inhibits key transcriptional changes and prevents and partially reverses RPE EMT, revealing potential therapeutic routes to benefit patients with ERM, macular pucker and PVR.

overall_design: ChIPseq of histone modifications from retinal pigmented epithelial cells from two donors, either in control culture condition or treated with TNF-alpha and TGF-beta

first: Sally

last: Temple

first: Timothy

last: Blenkinsop


title: Global Epigenomic and Transcriptomic changes associated with Human Retinal Pigment Epithelial Epithelial-to-Mesenchymal Transition in a Stem Cell-based model of Epiretinal Membrane Formation (RNA-seq)

overall_design: Poly-A enriched RNAseq from retinal pigmented epithelial cells from two donors, either in control culture condition or treated with TNF-alpha and TGF-beta


title: Global Epigenomic and Transcriptomic changes associated with Human Retinal Pigment Epithelial Epithelial-to-Mesenchymal Transition in a Stem Cell-based model of Epiretinal Membrane Formation


title: Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells [ChIP-seq]

overall_design: Examination of H3K27Ac and RNA Polymerase II occupancy in 16HBE14o-, Caco2 and Calu3 cells

first: Monali

last: NandyMazumdar

first: Alekh

last: Paranjapye


title: Targeted resequencing of cis-regulatory elements in human leukemia

summary: Mutations in protein-coding genes are well established as the basis for human cancer, yet it remains elusive how alterations within non-coding genome, a substantial fraction of which contain cis-regulatory elements, contribute to cancer pathophysiology largely due to lack of high throughput assays to assess their functional effects. Here we developed an integrative approach to systematically identify and characterize non-coding regulatory variants in human hematopoietic malignancies by combining targeted resequencing, mutation discovery, CRISPR-based enhancer-selective epigenome editing, and enhancer reporter assays. We identify 4,629 recurrent non-coding alterations and 939 mutation-associated pathogenic enhancers controlling proto-oncogenes or tumor suppressors. Enhancer variants at KRAS and PER2 co-localize with nuclear receptor (NR) binding sites and modulate transcriptional activities in response to NR signaling in leukemia cells. NR binding sites frequently associate with non-coding variants across cancer types. Hence, recurrent non-coding somatic variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies.

overall_design: Targeted resequencing of enhancer elements was performed using Ovation® Target Enrichment System (NuGEN) following the manufacture’s protocols. Target enriched library were purified, quantified, and sequenced on an Illumina NextSeq500 system using the 150bp high output sequencing kit

first: Kailong

last: Li

first: Yuannyu

last: Zhang

first: Xin

first: Yuxuan


title: Evaluating Liquid Biopsies for Methylomic Profiling of Prostate Cancer

city: Dublin 4

first: Antoinette

last: Perry

address: Belfield

country: Ireland

institute: University College Dublin

summary: Liquid biopsies offer significant potential for informing on cancer progression and therapeutic resistance via minimally invasive serial monitoring of genetic alterations.  Although the cancer epigenome is a central driving force in most neoplasia, how well the tumour methylome can be monitored via liquid biopsies is relatively unknown. In this first of its kind study we made a direct comparison of two liquid biopsies: urine and blood, asking how well they represent the tumor methylome. Utilizing the Infinium Methylation EPIC BeadChip, we profiled DNA methylation in tissue, urine sediment and cell-free circulating DNA from four men with advanced stage prostate cancer. We show that both urine and plasma are viable surrogates for tumor tissue biopsies, capturing 78.63 and 62.21% of tumor-specific methylation alterations, respectively. We conclude that urine is an easily accessible and sensitive biofluid for the study of prostate cancer epigenomic alterations.

overall_design: Four patients, each with Tumour, Matched Normal, Urine Sediment and Plasma samples (n=16 total)

first: Romina

last: Silva

first: Bruce

last: Moran

first: Ciara

last: Fahey

first: Tatjana

last: Vlajinic

first: Donal

last: Brennan

first: William

middle: M

last: Gallagher


title: Expression data of glioblastoma cells with Crizotinib acute and chronic treatment vs its own vehicle control

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Gene expression of chronically or acutely Crizotinib treated glioblastoma cells vs vehicle controls

overall_design: U87 glioblastoma cells treated with 2uM Crizotinib vs Control; U87 glioblastoma cells treated with 1uM Crizotinib for 3 weeks vs control cells cultured in same medium without Crizotinib.

first: Yiru

first: Markus

last: Siegelin


title: Transcriptome analysis of RFWD2 overexpression (OE) and control (WT) in Multiple myeloma

status: Public on Apr 25 2020

city: Nanjing

first: Rong

middle: Fang

last: Wei

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in Multpile myeloma cells when RFWD2 overexpressed.

overall_design: Examination  of two cell types with two biological repeats

first: Rongfang

first: Wang

last: Wang


title: Influence of 20E on mosquito gene expression

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: To examine the effects of 20E treatment on mosquito gene expression, treated mosquito cells were examined by RNA-seq to determine the influence of 20E treatment.

overall_design: Mosquito cell lines were exposed to 10% ethanol (control) or 20-hydroxyecdysone (20E) in 10% ethanol. After exposure for 24 hrs, cells were harvested for RNA isolation. Samples were collected from four independent biological experiments.

first: Ryan

last: Smith


title: Effect of Stau2 knockdown on H3K4 methylation in human bcCML cells (K562)

status: Public on Apr 21 2020

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

summary: Evaluating the effect of Stau2 knockdown on H3K4me1, H3K4me2, H3K4me3 in K562 cells

overall_design: ChIP-seq comparative analysis of shControl and shStau2 infected human K562 cells

first: Jeevisha

last: Bajaj

first: Tannishtha

last: Reya


title: Role of mitochondrial fission-related genes in mitochondrial morphology and energy metabolism in mouse embryonic stem cells

city: seoul

first: bong jong

last: seo

address: neung-dong ro

department: Stem cell and regenerative biotechnology

institute: Konkuk university

summary: Here we aimed to investigate the function of mitochondrial fission genes in embryonic stem cells (ESCs). Homozygous knockout ESC lines, namely, Fis1-/- , Mff-/- , and Dnm1l-/- ESCs, were generated using the CRISPR-Cas9 system. After then, we analyzed whole genome expression profile for characterizing cellular responses by incomplete mitochondrial fission.

overall_design: Total RNA samples of e14tg2a, Dnm1l-/-, Fis1-/-, Mff-/- embryonic stem cells were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

first: Bong

last: Seo

first: Jeong

middle: T

last: Do


title: Transcriptomes of small intestinal WT and Tph1-deficient ILC2s

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: RNA sequencing of small intestinal ILC2s sorted from Il7rCre/+ Tph1flox/flox or Il7rCre/+ control mice at steady state

overall_design: ILC2s were sort-purified (Lin- CD45+ CD127+ KLRG1+) from the lamina propria of the small intestine of of naïve Il7rCre/+ Tph1fl/fl and Il7rCre/+  mice at steady state. (Il7rCre/+ n= 4 and Il7rCre/+ Tph1flox/flox n= 3).

first: Anne-Laure

last: Flamar

first: David

last: Artis


title: Nerve injury induced protein 1 (Ninjurin1) deletion effect on peritoneal macrophages

city: Incheon

first: Hyun Jin

last: Jung

address: 317 College of Pharmacy, 191 Hambangmoe-ro,  Yeonsu-gu

institute: Seoul National University

summary: We used microarrays to investigate gene expression from peritoneal macrophages associated with Ninjurin1 expression.

overall_design: Peritoneal macrophages were extracted from C57BL/6 WT and Ninjurin1 KO mice for RNA extraction and hybridization on Affymetrix microarrays. WT (n=3), Ninjurin1 KO (n=3)

first: Hyun

first: Seung

middle: H

last: Oh

first: Je

last: Seong


title: Transcriptomes of mesenteric lymph node WT and Tph1-deficient ILC2s

summary: RNA sequencing of mesenteric natural and inflammatory ILC2s sorted from Il7rCre/+ Tph1flox/flox or Il7rCre/+ control mice-infected with N. brasiliensis

overall_design: ILC2s were sort-purified from mesenteric lymph nodes of Il7rCre/+ Tph1fl/fl and Il7rCre/+ control mice (natural ILC2, nILC2: Lin-  CD45+ KLRG1+ ST2+; inflammatory ILC2, iILC2: Lin-  CD45+ KLRG1+ ST2-) on day 7 after N. brasiliensis infection. (mesLN ILC2INFLAM: Il7rCre/+ n= 4 and Il7rCre/+ Tph1fl/fl n= 4, and mesLN ILC2NAT: Il7rCre/+ n= 4 and Il7rCre/+ Tph1fl/fl n= 4).


title: Lung in neonatal mice: Control vs. transplacental treated with dimethylarsinic acid (DMA)

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

summary: ChIP-seq profiling by Histone H3K9me3 antibody between Control and transplacental treated with 200 ppm dimethylarsinic acid (DMA) for 10 days in lung of neonatal male mice.

overall_design: Male and female 10-week-old CD-1 mice were mated, and given 0 (Control) or 200 ppm DMA for 10 days in the drinking water at the 8 days after mating. After parturition, the offspring were sacrificed on postnatal day 0, and removed lungs. Control and DMA transplacental treatment. 10 control male mice, 10 DMA-treated male mice. Mixed 10 samples from each group.


title: miRNAs in the porcine corpus luteum

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of some reproductive functions in mammals via posttranscriptional gene regulation mechanisms. Importantly, miRNAs have been suggested to be an important regulators of various ovarian functions. Applying custom made multispecies arrays we aimed to analyze expression profile of miRNAs in corpus luteum to answer the question whether miRNAs can be involved in maintenance of luteal function during early pregnancy in pigs.

platform_organism:
Homo sapiens
Sus scrofa
Bos taurus
Mus musculus

overall_design: miRNA expression profiles were analyzed in samples collected from corpus luteum on Day 14 of either estrous cycle or pregnancy. Each group was represented by four samples.

first: Emilia

last: Przygrodzka


title: TBX5 ChIP from the Fetal Heart

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: T-box transcription factors play critical roles in the development and identity of the heart. Tbx5 has been implicated as a regulator of the fast-conducting, ventricular conduction system, while Tbx3 has been implicated as a regulator of the slow-conducting node. We hypothesize TBX5 and TBX3 share common binding sites in cardiomyocytes to positively or negatively regulate transcription, respectively, for cardiac cell identity and conduction. To this end, we performed ChIP-sequencing to identify localization of TBX5 during fetal heart development and have compared it with previously published histone (GEO Series: GSE31039; ENCODE Accessions: ENCSR080GQM, ENCSR000CDL, ENCSR000CDM, ENCSR052CDF, ENCSR345RKE, ENCSR007XTC, ENCSR360ANE, ENCSR000CDK, and ENCSR357OED) and TBX3 ChIP-seq (GSM862695).

overall_design: Hearts were dissected from E14.5 CD-1 mouse embryos. Two biological replicates were generated. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516) at 4°C for >12 hours in a total volume of 200 μL. Libraries from ChIP and input DNA were prepared using NEBNext Ultra DNA Library Prep Kit (E7370S). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Sera-Mag magnetic beads (GE, 6515-2105-050-250). DNA libraries were sequenced using Illumina Hi-seq instruments (single-end 50 base) by the Genomics Core Facility at the University of Chicago.

first: Kohta

last: Ikegami

first: Ozanna

last: Burnicka-Turek

first: Ivan

middle: P

last: Moskowitz


title: Lung in neonatal mice: Control vs transplacental treated with dimethylarsinic acid (DMA)

summary: The gene expression profling between Control and transplacental treated with 200 ppm dimethylarsinic acid (DMA) for 10 days in lung of neonatal male mice.

overall_design: Male and female 10-week-old CD-1 mice were mated, and given 0 (Control) or 200 ppm DMA for 10 days in the drinking water at the 8 days after mating. After parturition, the offspring were sacrificed on postnatal day 0, and removed lungs. Control and DMA transplacental treatment. 6 control male mice, 6 DMA-treated male mice. Mixed 6 samples from each group for each array.


title: MBNL2 knockdown in hypoxic breast cancer cells

city: Frankfurt am Main

first: Kathi

last: Zarnack

address: Max-von-Laue-Str. 15

institute: BMLS - Buchmann Institute for Molecular Life Sciences

summary: The transcriptome-wide response of hypoxic breast cancer cells upon MBNL2 knockdown was analyzed. Differential gene expression and alternative splicing were investigated.

overall_design: 4 samples; 2 conditions: hypoxia control siRNA vs hypoxia MBNL2 siRNA; 2 replicates per condition

first: Julia

middle: E

last: Weigand

first: Sandra

last: Fischer

first: Antonella

last: Di Liddo


title: Glioblastoma Hijacks Microglial Gene Expression to Support Tumor Growth

first: Erik

last: Abels

department: Neurology

summary:
Background
Glioblastomas are the most common and lethal primary brain tumors. Microglia, the resident immune cells of the brain survey their environment and respond to pathogens, toxins, and tumors. Glioblastoma cells communicate with microglia, in part by releasing extracellular vesicles (EVs). Despite the presence of large numbers of microglia in glioblastoma, the tumors continue to grow, and these neuroimmune cells appear incapable of keeping the tumor in check. To understand this process, we analyzed gene expression in microglia interacting with glioblastoma cells.
Methods
We used RNASeq to analyze the expression patterns of genes involved in key microglial function of microglia in mice with glioblastoma. We focused on microglia that had taken up tumor-derived EVs and therefore were within and immediately adjacent to the tumor.
Results
We show that these microglia have downregulated expression of genes involved in sensing tumor cells and tumor-derived danger signals, as well as genes used for tumor killing. In contrast, expression of genes involved in facilitating tumor spread was upregulated. These changes appear to be in part EV-mediated, since intracranial injection of EVs in normal mice led to similar transcriptional changes in microglia. We observed a similar microglial transcriptomic signature when we analyzed datasets from human patients with glioblastoma.
Conclusion
Our data define a MicrogliaGlioblastoma specific phenotype, whereby glioblastomas have hijacked gene expression in the neuroimmune system to favor avoiding tumor sensing, suppressing the immune response, clearing a path for invasion and enhancing tumor propagation. For further exploration we developed an interactive online tool at www.glioma-microglia.com with all expression data and additional functional and pathway information for each gene.

overall_design: mRNA expression of microglia isolated from control and tumor-bearing brain were analyzed by RNAseq, using Illumina Nextseq and MiniSeq.

first: Sybren

last: Maas

first: Lieke

last: Van De Haar

first: Xuan

last: Zhang

first: Srinjoy

last: Sil

first: Joana

last: Guedes

first: Pritha

last: Sen

first: Shilpa

last: Prabhakar

first: Suzanne

last: Hickman

first: Charles

last: Lai

last: Ting

first: Xandra

middle: O

last: Breakefield

first: Marike

last: Broekman

first: Joseph

last: El Khoury


title: Hypoxia response of human cancer cells

first: Kathi

last: Zarnack

summary: The transcriptome-wide response of breast and lung cancer cells to chronic hypoxia was analyzed. Differential gene expression, alternative splicing and circRNA levels were quantified.

overall_design: 4 samples; 2 conditions: normoxia vs. hypoxia (48 h, 0.5% oxygen); 2 replicates per condition

last: Weigand


title: Cortical Foxp2 supports behavioral flexibility and developmental dopamine D1 receptor expression

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: FoxP2 encodes a forkhead box transcription factor required for the development of neural circuits underlying language, vocalization, and motor-skill learning. Recent genetic studies have associated FOXP2 variation with neurodevelopmental disorders (NDDs), and within the cortex, it is coexpressed and interacts with other NDD-associated transcription factors. Cortical Foxp2 is required in mice for proper social interactions, but its role in other NDD-relevant behaviors is unknown. Here, we characterized such behaviors and their potential underlying cellular and molecular mechanisms in cortex-specific Foxp2 conditional knockout mice. These mice showed deficits in reversal learning without increased anxiety or hyperactivity. In contrast, they emitted normal vocalizations save for a decrease in loudness of neonatal calls. These behavioral phenotypes were accompanied by decreases in cortical dopamine D1 receptor (D1R) expression at neonatal and adult stages, while general cortical development remained unaffected. Finally, using single-cell transcriptomics, we identified neonatal D1R-expressing cell types in frontal cortex and found changes in D1R cell type composition and gene expression upon cortical Foxp2 deletion. Together these data support a role for Foxp2 in the development of dopamine-modulated cortical circuits potentially relevant to NDDs.

overall_design: We used fluorescence-activated cell sorting (FACS) followed by single-cell RNA sequencing (scRNA-seq) to genetically profile Drd1a-tdTomato+ or golli-τ-eGFP+ frontal cortical neurons from P7 control and Emx1-Cre Foxp2 conditional knockout (cKO) mice. We compared cell type composition and gene expression profiles between control and cKO mice, using two independent replicates per genotype.

first: Marissa

last: Co

first: Stephanie

last: Hickey

first: Ashwinikumar

last: Kulkarni

first: Matthew

last: Harper


title: Kentucky assay: artificial cigarette smoke odor

status: Public on Apr 20 2020

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odors is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or bourgeonal were subjected to microarray analysis using Clariom S arrays


title: The imbalance of excitatory/inhibitory neuron differentiation in neurodevelopmental disorders with an NR2F1 point mutation

city: Shanghai

first: Ke

last: Zhang

address: No.320 Yueyang Road

institute: SIBCB

summary: Recent studies have revealed an essential role for embryonic cortical development in the pathophysiology of neurodevelopmental disorders, including autism spectrum disorder (ASD). However, the genetic basis and underlying mechanisms remain unclear. Here, we generate mutant human embryonic stem cell lines (Mut hESCs) carrying an NR2F1-R112K mutation that has been identified in a patient with ASD features, and investigate their neurodevelopmental alterations. Mut hESCs overproduce ventral telencephalic neuron progenitors (ventral NPCs) and inhibitory neurons, and underproduce dorsal NPCs and excitatory neurons. These alterations can be mainly attributed to the aberrantly activated Hedgehog signaling pathway. Moreover, the corresponding Nr2f1 point mutant mice display a similar excitatory/inhibitory neuron imbalance and abnormal behaviors. Antagonizing the increased inhibitory synaptic transmission partially alleviates their behavioral deficits. Together, our results suggest that the NR2F1-dependent imbalance of excitatory/inhibitory neuron differentiation caused by the activated Hedgehog pathway is one precursor of neurodevelopmental disorders and may enlighten the therapeutic approaches.

overall_design: WT and Mut human NPCs were subjected into transcriptome analysis with two biological replicates. ChIP-Seq was done by over-expressing an equal amount of pcDNA3.1-WT/Mut-NR2F1-Flag plasmids into WT hESC-derived neuron progenitors with two biological replicates, and the DNA-protein complex was precipitated by Flag beads.


title: Stau2 knockdown in human bcCML cells (K562)"

city: La Jolla

first: Michael

last: Hamilton

institute: UCSD

summary: STAU2 knockdown in human K562 cells

overall_design: RNA-seq comparative analysis of shControl and shSTAU2 infected K562 cells

first: Jeevisha

last: Bajaj

first: Tannishtha

last: Reya


title: Global DNA methylation patterns in primary anaplastic thyroid cancer

city: Lund

first: Kajsa

last: Paulsson

address: Sölvegatan 19

department: Department of Clinical Genetics

country: Sweden

institute: Lund University

summary: Anaplastic thyroid cancer (ATC) is one of the most malignant tumors, with a median survival of only a few months. The tumorigenic processes of this disease has not yet been completely unraveled. Here, we report an DNA methylation analysis of ten primary ATC. ATC displayed a global hypomethylation of the genome but with hypermethylation of promoters and CpG islands. This study shows that aberrant DNA methylation is common in ATC and likely contributes to tumorigenesis in this disease. Future explorations of novel treatments should take this into consideration.

overall_design: Bisulphite converted DNA from the anaplastic thyroid cancer samples (n = 10) and normal thyroid samples (n = 4) were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip  v1.0_B4

first: Naveen

last: Ravi

first: Minjun

last: Yang

first: Nektaria

last: Mylona

first: Johan

last: Wennerberg


title: Cell-intrinsic differences between human tracheal epithelial cells from children and adults [cultured basal cells]

city: London

first: Adam

last: Pennycuick

address: 5 University Street

department: UCL Respiratory

country: United Kingdom

institute: University College London

summary: The airway epithelium is a key protective barrier whose integrity is preserved by the self-renewal and differentiation of basal progenitor cells. Epithelial cells are central to the pathogenesis of multiple chronic lung diseases for which age is a principle risk factor. Children are also less susceptible to SARS-CoV-2 infection, suffer less severe symptoms than adults and have a lower rate of mortality. Few studies have addressed differences between airway epithelial cells in children and adults. Here, we perform bulk RNA sequencing studies in laser-captured whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We find that, while the cellular composition of the paediatric and adult tracheal epithelium is broadly similar, in cell culture, paediatric airway epithelial cells displayed higher colony forming ability, better in vitro growth and outcompeted adult cells in competitive proliferation assays. Although recurring differences between airway epithelial gene expression were seen between samples from children and adults, RNA sequencing showed broad conservation of transcriptional programmes. Genes associated with SARS-CoV-2 infection were not differentially expressed between children and adults, although individuals showed some variability in their expression of viral infection-associated genes. Our results chart important cell intrinsic differences in transcriptional profile and regenerative capacity between tracheal epithelial cells of children and adults.

overall_design: Comparison of airway RNAseq data between adults and children. Three related datasets are presented: fresh airway epithelial cells, fresh sorted basal cells and cultured basal cells. This dataset contains cultured basal cells.

first: Elizabeth

middle: F

last: Maughan

first: Kyren

last: Lazarus


title: Genome-wide temporal expression profiling of the DEGs (differentially expressed genes) in mouse stroke brain

city: Chiba City

first: Atsushi

last: Yamaguchi

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City

department: Dept. Med.

institute: Chiba University

summary: Purpose:  The goal of this study is to examine the DEGs in the ispsi-lateral cerebral cortex of post-stroke brain using RNA-seq compared with control (sham).

overall_design: Examination of DEGs in mouse brains at day 1, 3, 7, 14, and 28 post stroke, compared with control (sham).


title: Kentucky assay: 1-pentanethiol


title: Cell-intrinsic differences between human tracheal epithelial cells from children and adults [FACS-sorted basal cells]

overall_design: Comparison of airway RNAseq data between adults and children. Three related datasets are presented: fresh airway epithelial cells, fresh sorted basal cells and cultured basal cells. This dataset contains FACS-sorted basal cells.


title: Kentucky assay: cigarette smoke


title: Analysis of differentially expressed genes between circZbtb20+/+ and circZbtb20-/- ILC3s or between Nr4a1+/+ and Nr4a1-/- ILC3s

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in  circZbtb20 or Nr4a1 deficient ILC3s

overall_design: Gene expression profiling using LinCD90highCD45low ILC3s isolated from  circZbtb20+/+, circZbtb20-/-, Nr4a1+/+ or Nr4a1-/- mice. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix Mouse Gene2.0 analysis protocol (Affymetrix).

first: Zusen

last: Fan


title: Gene expression profiling in Drosophila larvae in normal and Cmi or Trr depletion backgrounds

city: Maywood

first: Andrew

last: Dingwall

state: IL

address: 2160 S First Avenue

department: Cancer Biology

institute: Loyola University Chicago

summary: RNA seq analyses of gene expression in wild type and Cmi or Trr depletion blue gut and clear gut larvae

overall_design:
Examination of transcriptome efffects of depleting COMPASS complex components Cmi and Trr in whole Drosoplhila larvae. Pools of >20 animals of each genotype were used to extract RNA and dteremine gene expression values.

National Science Foundation Grants MCB1413331 and MCB1716431, entitled "Mechanisms of epigenetic gene regulation by the Drosophila COMPASS-like complex", supported this work.

first: Jeffrey

last: Ng

first: Claudia

middle: B

last: Zraly


title: Genome-wide binding of Cmi in Drosophila

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

summary: Cmi (also known as Lpt) is the PHD finger domain-containing subunit of the Drosophila MLR COMPASS (Cmi-Trr) complex. ChIP-seq analysis of Cmi at different stages of Drosophila development suggests dynamic genome localization of the Cmi/MLR complex on enhancers and promoters during Drosophila development.

overall_design: We used an antibody against Cmi/Lpt (raised against amino acids residues 647-1069) to monitor genome-wide binding of this subunit of the Drosophila MLR complex. ChIPs were performed using either S2 cells or whole animals at larval and prepual stages. Previously published embryo Cmi data were analyzed in parallel.


title: Histone crotonylation and its readers control virulence-related biology of a major human commensal and pathogen.

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

summary: PAT-seq approach was utilised to determine the gene expression  of C. albicans. Biological duplicates of wild type and taf14∆∆ mutant samples were grown to log phase, with or without crotonate treatment (50 mM, 2 h).

overall_design: Analysis of RNA-seq following crotonate treatment in C. albicans

first: Ana

last: Traven

first: Jiyoti

last: Verma

first: Qi

last: Wang

first: Angavai

last: Swaminathan

first: Michael

last: See


title: Whole transcriptome RNAseq analysis of somatic cells in Inhba fetal testes

first: Kate

middle: Ann

last: Loveland

address: 27-31 Wright Street

department: Molecular and Translational Sciences and Centre for Reproductive Health

institute: Monash University and Hudson Institute of Medical Resarch

summary: We performed RNA-seq on testicular somatic cells from fetal activin A-deficient mice (Inhba KO) and wildtype littermates at embryonic ages E13.5 and E15.5. Activin A deficiency predominantly affects the Sertoli cell transcriptome. New candidate targets include Minar1, Sel1l3, Vnn1, Sfrp4, Masp1, Nell1, Tthy1 and Prss12. Importantly, the testosterone (T) biosynthetic enzymes present in fetal Sertoli cells, Hsd17b1 and Hsd17b3, were identified as activin-responsive. Activin-deficient testes contained elevated androstenedione (A4), displayed an Inhba gene dose-dependent A4/T ratio, and contained 11-keto androgens.

overall_design: Whole transcriptome RNAseq performed on embryonic E13.5 and E15.5 Inhba x Oct4 GFP WT and KO testicular somatic cells (germ cells excluded). Cells collected from n=3-4 individual animals/age/genotype

first: Penny

last: Whiley

first: Liza

last: O’Donnell

first: Sarah

middle: C

last: Moody

first: David

last: Handelsman

first: Julia

last: Young

last: Richards

first: Kristian

last: Almstrup

first: Patrick

last: Western


title: HBV-infected Primary Human Hepatocytes and HBV-infected HepG2-NTCP cells treatment by Interferon subtypes

first: Yang

address: Dongan road 131

institute: Fudan University

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

overall_design: Refer to individual Series


title: The Mgs1/WRNIP1 ATPase is required to prevent a recombination salvage pathway at damaged replication forks

city: Milan

first: Dana

last: Branzei

address: Via Adamello 16

institute: IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA damage tolerance (DDT) is crucial for genome integrity maintenance. DDT is mainly carried out by template switch recombination, an error-free mode of overcoming DNA lesions, or translesion DNA synthesis, which is error-prone. Here we investigated the role of Mgs1/WRNIP1 in modulating DDT. Using budding yeast, we found that elimination of Mgs1 in cells lacking Rad5, an essential protein for DDT, activates an alternative mode of DNA damage bypass, driven by recombination, that allows chromosome replication and cell viability under stress conditions that block DNA replication forks. This salvage pathway is RAD52- and RAD59-dependent, requires the DNA polymerase and PCNA-modification at K164, and is enabled by Esc2 and the PCNA-unloader Elg1, being inhibited when Mgs1 is present. We propose that Mgs1 is necessary to prevent a potentially toxic recombination salvage pathway at sites of perturbed replication, which in turn favors Rad5-dependent template switching, thus helping to preserve genome stability.

overall_design: Protein binding profiles by ChIP-on-chip analysis were generated as described (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Alexandra

last: Mayer

first: Chinnu

last: Joseph

first: Alberto

last: Jiménez-Martín

first: Irene

last: Saugar

first: Carl

last: Lehmann

first: Barnabas

last: Szakal

first: José

middle: A

last: Tercero


title: RNA-seq analysis of HBV-infected HepG2-NTCP cells treated by Interferon subtypes

last: Wang

summary: Examination of interferon stimulated genes treated with different kind of interferon subtypes in HBV-infected HepG2-NTCP cells.

overall_design: HBV-infected HepG2-NTCP cells treated with IFN-α2 or IFN-α14 at 5 ng/ml for 6 h or mock treated were subjected to RNA-seq analysis

first: Jieliang

last: Chen

first: Fang

last: Shen

first: Yaming

last: Li

first: Wang

last: Yang

first: Zhenghong

last: Yuan


title: A Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells

city: Rockville

first: David

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

department: Division of Preclinical Innovation

institute: NCATS/NIH

summary: To clarify how smoking leads to heart attacks and stroke, we developed an endothelial cell model (iECs) generated from human induced Pluripotent Stem Cells (iPSC) and evaluated its responses to tobacco smoke. These iECs exhibited a uniform endothelial morphology, expressed markers PECAM1/CD31, VWF/von Willebrand Factor, and CDH5/VE-Cadherin, and exhibited tube formation and Acetyl-LDL uptake comparable to primary endothelial cells (EC). RNA sequencing (RNAseq) revealed a robust correlation coefficient between iECs and EC (R = 0.76), whereas gene responses to smoke were qualitatively nearly identical between iECs and primary ECs (R=0.86). Further analysis of transcriptional responses implicated eighteen transcription factors in regulating responses to smoke treatment, and identified gene sets regulated by each transcription factor, including oxidative stress, DNA damage/repair, ER stress, apoptosis, and cell cycle arrest. Assays for 42 cytokines in HUVEC cells and iECs identified 23 cytokines that responded dynamically to cigarette smoke. These cytokines and cellular stress response pathways describe endothelial responses for lymphocyte attachment, activation of coagulation and complement, lymphocyte growth factors, and inflammation and fibrosis; EC-initiated events that collectively lead to atherosclerosis. Thus, these studies validate the iEC model and identify transcriptional response networks by which ECs respond to tobacco smoke. Our results systematically trace how ECs use these response networks to regulate genes and pathways, and finally cytokine signals to other cells, to initiate the diverse processes that lead to atherosclerosis and cardiovascular disease.

overall_design: All cell lines and conditions were represented by biological triplicates. 36 samples were analyzed. The sample set includes control Fibroblasts, control iPSCs, control and smoke treated human aortic endothelial cells (HAEC), control and smoke treated human carotid artery cells (HCAEC), control and smoke treated human umbilical vein endothelial cells (HUVEC), and control and smoke treated cell derived induced endothelial cell clones (iEC, two clones).

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