title: Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: Canonically, Arabidopsis RNA Polymerase IV (Pol IV) is known to produce heterochromatic small RNAs (typically 23-24 nucleotide in length) that maintain silencing of transposable elements (TEs). In contrast, when TEs are transcriptionally activated and produce Pol II transcripts, these transcripts are degraded into 21-22 nt small RNAs (sRNAs) known to participate in post transcriptional gene silencing. Recently, it was reported that Pol IV can also produce 21-22 nt sRNAs in pollen. We investigated the mechanism of Pol IV dependent 21-22 nt sRNAs and show that this mechanism is not specific to pollen. Additionally, we show that these 21-22 nt sRNAs can participate in RNA-directed DNA methylation, are incorporated into ARGONAUTE 1 (AGO1) and may guide AGO1 to cleave genic mRNAs to regulate their expression.

overall_design:
Examination of total small RNA accumulation in wild-type Columbia and eight mutants.
AGO1 protein was immunoprecipitated and small RNAs incorporated in AGO1 was sequenced in wild-type Columbia and pol IV mutant.
Whole genome methylC-seq was performed for two mutants.

first: Kaushik

last: Panda

first: Andrea

middle: D

last: McCue

first: R


title: Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes

status: Public on Feb 24 2020

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

country: China

institute: Wuhan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Mosquito-borne flaviviruses maintain life cycles in mammals and mosquitoes. RNA interference (RNAi) has been demonstrated as an anti-flavivirus mechanism in mosquitoes; however, whether and how flavivirus induces and antagonizes RNAi-mediated antiviral immunity in mammals remains unknown. Here we showed that NS2A of Dengue virus-2 (DENV2) act as a viral suppressor of RNAi (VSR). When NS2A-mediated RNAi suppression was disabled, the resulting mutant DENV2 induced Dicer-dependent production of abundant DENV2-derived siRNAs in differentiated mammalian cells. Importantly, VSR-disabled DENV2 showed severe replication defects in mosquito and mammalian cells, and mice, which were rescued by the deficiency of RNAi. Moreover, NS2As of multiple flaviviruses act as VSRs in vitro and during viral infection in both organisms. Overall, our findings demonstrate that antiviral RNAi can be induced by flavivirus, while flavivirus uses NS2A as bona fide VSR to evade RNAi in mammals and mosquitoes, highlighting the importance of RNAi in flaviviral vector-host life cycles.

sample_organism:
Aedes aegypti
Homo sapiens

platform_organism:
Aedes aegypti
Homo sapiens

overall_design: Small RNA profile of virus-infected cells.

first: Yang

last: Qiu

first: Yan

middle: P

last: Xu

first: Miao

last: Wang

first: Meng

last: Miao

first: Hui

last: Zhou

first: Jiuyue

first: Jing

last: Kong

first: Da

last: Zhang

first: Rui

middle: T

last: Li

first: Rong

middle: R

last: Guo

first: Xiao

middle: F

first: Jie

last: Cui

first: Cheng

last: Qin

first: Xi


title: Genome-wide analysis of histone 3 lysine K27 acetylation in stem-like breast cancer cells in response to HDAC1/3/7 inhibition.

city: Miami

first: Corrado

last: Caslini

state: FL

address: 1501 NW 10th Avenue

country: USA

institute: University of Miami

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We sought to investigate the effects of HDAC1 and HDAC7 inhibition on genome-wide histone 3 lysine 27 acetylation (H3K27ac) in BPLER cells, a stem-like breast cancer (BrCa) cell model (please search for keyword "BPLER" in GEO to access over 30 associated datasets). Treatment of BPLER cells with MS-275 (Entinostat), a HDAC1 and HDAC3 specific inhibitor, specifically downregulates HDAC7 mRNA and protein. We carried out ChIP-seq analysis in BPLER cells treated with MS-275 and found that HDAC1/3/7 inhibition is associated with a decrease in H3K27ac at transcription start sites (TSS) and super-enhancers (SE) in stem-like BrCa cells. Importantly, these changes in chromatin landscape reduced H3K27ac at many SE-associated oncogenes, including c-MYC, CD44, CDKN1B, SLUG, VDR, SMAD3, VEGFA and XBP1. Our findings suggest that inactivation of HDAC1/3-HDAC7 axis may inhibit SE-associated oncogene expression in cancer stem cells, which can be a promising pathway to target for developing novel BrCa therapies.

overall_design: H3K27ac profiling in stem-like BrCa cells treated with MS-275 (Entinostat).

first: Tan

middle: A

last: Ince


title: Genome-wide analysis of histone 3 lysine K27 acetylation and differential expression analysis in stem-like breast cancer cells in response to HDAC1/3/7 inhibition or knockdown

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The transcriptional landscape of Venezuelan equine encephalitis virus infection

status: Public on Feb 25 2020

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

summary: No vaccines or antivirals are approved against Venezuelan equine encephalitis virus (VEEV) infection in humans. To improve our understanding of VEEV-host interactions, we simultaneously profiled host transcriptome and viral RNA (vRNA) in thousands of single cells during infection of human astrocytes. Host transcription was suppressed, and “superproducer cells” with extreme vRNA abundance and altered transcriptome emerged during the first viral life cycle. Cells with increased structural-to-nonstructural transcript ratio demonstrated upregulation of trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral host factors. Single-cell deep sequencing analysis identified a viral E3 protein mutation altering host gene expression. Lastly, comparison with data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the cellular response to VEEV infection, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.

overall_design: viscRNA-Seq on VEEV infection in U87 cells

first: Zhiyuan

last: Yao

first: Sathish

last: Kumar

first: Nuttada

last: Panpradist

first: Avery

last: Muniz

first: Stephen

last: Quake

first: Shirit

last: Einav


title: Sa MW2 vs SAN2

city: Kagoshima

first: Miki

last: Kawada-Matsuo

address: 8-35-1, Sakuragaoka

department: Graduate school of medical and dental sciences

country: Japan

institute: Kagoshima University

summary: Transcriptional profiling of Staphylococcus aureus comparing MW2 strain with SAN2 strain which was nisin A high resistant strain.

overall_design: One-condition experiment, MW2 vs. SAN2. Biological replicates: 3 control replicates, 3 exposed replicates.

first: Yuichi

last: Oogai


title: Transcriptional network controlled by Candida albicans treated by a gemini quaternary ammonium compound, 1, 5-bis(dodecyl)-1, 1, 3, 5, 5-pentamethyl-3-aza-1, 5-pentanediammonium ditetrafluoroborate (PMT12-BF4)

city: Taipei city

first: Li-Hang

last: Hsu

state: Taiwan (R.O.C)

address: No. 1, Sec. 4, Roosevelt Rd

department: Plant Pathology and Microbiology

country: Taiwan

institute: National Taiwan University

summary: In order to identify genes regulated by PMT12-BF4, we compared the genome-wide expression profile in wild-type strain SC5314 untreated or treated with PMT12-BF4 via RNA sequencing. Results showed that in C. albicans 69 genes were up-regulated and 30 genes were down-regulated in the presence of PMT12-BF4. Up-regulated genes were mostly involved in iron ion-related functions (e.g. RBT5, CFL5, CFL4, FET34, FET31 etc.), and down-regulated genes were largely involved in oxidoreductase activity, vitamin binding and coenzyme binding.

overall_design: Total mRNAs extracted from C. albicans wild-type SC5314 treated or untreated with PMT12-BF4 were analyzed using RNA sequencing.

first: Ying-Lien

last: Chen


title: Impact of aromatase inhibitor treatment on global gene expression and its association with antiproliferative response in ER+ breast cancer in postmenopausal patients

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

summary: Endocrine therapy reduces breast cancer mortality by 40%; but resistance remains a major clinical problem. Identification of gene signatures associated with resistance during endocrine treatment should enable rational therapeutic choices to be made to combat this in individual patients. Here we present an in-depth analysis of global gene-expression that was measured on pairs of core-cut biopsies taken at baseline and at surgery from 254 patients with ER-positive primary breast cancer randomised to receive 2-week’s presurgical AI (n=198) or no presurgical treatment (Control n=56) in the POETIC trial, using changes-in and residual-of the proliferation marker, Ki67 as end-points, to investigate the impact of aromatase inhibitor (AI) therapy on gene expression and identify gene modules representing key biological pathways that relate to early AI-therapy resistance.  Our study revealed a high degree of heterogeneity in adaptive mechanisms after as little as 2-weeks’ AI-therapy, however, all appear to converge on cell cycle regulation. Our data support the evaluation of whether an E2F signatures after short-term exposure to AI may identify those patients most likely to benefit from the early addition of CDK4/6 inhibitors.

overall_design: Processed global gene-expression data includes new samples and Samples from GSE105777. Response was assessed by changes in the proliferation marker, Ki67.

first: Qiong


title: Next Generation Sequencing and differential expression analysis in stem-like vs. non-stem breast cancer cells in response to HDAC1 and HDAC7 knockdown

summary:
Purpose: We performed RNA-seq differential expression analysis after 72h HDAC1 and HDAC7 knockdown in order to evaluate the transcriptional regulation exerted by HDAC1 and HDAC7 in a stem-like (BPLER) vs. non-stem (HMLER) breast cancer (BrCa) cell model (please search for keywords "BPLER" or "HMLER" in GEO to access over 240 associated data sets).
Results: HDAC7 knockdown by a pool of siRNAs resulted in altered expression of nearly three times the genes in BPLER vs. HMLER cells (2545 vs. 763), with the two cell types sharing altered expression of 328 genes.  In stem-like BPLER cells, HDAC7 knockdown caused significant alterations in gene expression (1068 down and 1477 up). Fewer genes, less than half of BPLER, were altered in non-stem HMLER cells (448 down and 315 up), with 199 repressed and 129 activated genes shared between the two cell types. In contrast, 72h HDAC1 knockdown resulted in nearly equal numbers of altered genes in BPLER vs. HMLER cells (3187 vs. 2627), with the two cell types sharing altered expression of 637 genes. Moreover, the number of repressed (1570 vs. 1307) and activated (1617 vs. 1320) gene transcripts was similar in the two cell types In HMLER cells, HDAC7 knockdown resulted in alterations of significantly fewer gene transcripts compared to HDAC1 knockdown (508 vs. 2681), in both repressed (305 vs. 1362) and activated (203 vs. 1319) transcripts.
Conclusions: Cumulatively, these results highlight that HDAC7 regulates nearly three times as many genes in stem-like compared to non-stem BrCa cells. In contrast, HDAC1 regulates equal number of genes in the same cell context, suggesting a predominant association of HDAC7 with the cancer stem cell phenotype.

overall_design: RNA-seq differential expression analysis in stem-like BPLER (triplicate) vs. HMLER (duplicate) cells following HDAC1 and HDAC7 knockdown.


title: Myopalladin promotes muscle growth through modulation of the serum response factor pathway

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

summary: Myopalladin (MYPN) is a striated muscle-specific protein located in the Z-line and I-band of the sarcomere as well as the nucleus. Analysis of MYPN knockout (MKO) mice showed a 48% reduction in myofiber cross-sectional area in MKO mice and a consequent reduction in isometric force generation and power output. Similarly, reduced myotube width was observed in MKO primary myoblast cultures. RNA-Seq studies revealed downregulation of serum response factor (SRF)-target genes in MKO mice, important for muscle growth and differentiation, and further studies revealed that MYPN, like its homologue PALLD, can bind and bundle filamentous actin as well as interact with MRTF-A, both major players in the regulation of the SRF pathway. Consistently, MYPN increased MRTF-A-mediated activation of SRF signaling in myogenic cells, and transduction of MKO myoblasts with constitutive active SRF rescued the reduced myotube width, demonstrating that MYPN promotes skeletal muscle growth through activation of the SRF pathway.

overall_design: Profiling of the transcriptome of tibialis anterior muscle from 2- and 4-week-old MYPN knockout and control mice. Two biological replicates were profiled for each condition and time point.

first: Maria

middle: C

last: Filomena

first: Marie-Louise

last: Bang


title: RNA-seq data from C57BL/6N, cS5Ahi and cS5Alo CD8+ murine T-cells isolated from lymph nodes

city: Vienna

first: Richard

middle: H

last: Moriggl

state: Vienna

address: Veterinaerplatz 1

department: Institute of Animal Breeding and Genetics

country: Austria

institute: University of Veterinary Medicine

summary: Recurrent gain-of-function mutations in the transcription factor STAT5B, but not STAT5A, have been detected in mature T- and NK-cell neoplasms. No targeted therapy exists for these heterogeneous and often aggressive diseases. Also, the bystander or balancer role for STAT5A versus STAT5B is unclear. Given this and the shortage of high-fidelity models for peripheral T-cell lymphomas (PTCL), we investigated here whether graded expression of a gain-of-function STAT5A variant produces tumorous T-cell expansions. To mimic STAT5 activity we expressed a hyperactive STAT5A variant at low or high levels in the hematopoietic system of transgenic mice (termed cS5Alo and cS5Ahi). Only cS5Ahi-mice developed a lethal disease resembling human PTCL with full penetrance, characterized by massive expansion of CD8+ T-cells and by destructive organ-infiltration. Neoplastic cS5Ahi-T-cells were cytokine-hypersensitive, showed cytotoxic features, and revealed activated memory CD8+ T-lymphocyte characteristics. Histopathology analysis and mRNA expression profiles of cS5Ahi tumors revealed close correlation with distinct human PTCL subtypes, similar to the hSTAT5BN642H mouse model expressing the most frequent STAT5B mutation. We found pronounced STAT5 expression and activity in patient samples of different PTCL subsets. Clinical-grade JAK inhibitors or a selective STAT5 SH2 domain inhibitor induced cell death in murine and human PTCL cell lines and Ruxolitinib (JAK1/2) ameliorated the disease in cS5Ahi mice.

overall_design: CD8+  (Magnisort) lymph node cells from 15-week-old C57BL/6N, cS5Ahi and cS5Alo mice. For C57BL/6N, lymph nodes from 2-3 mice had to be pooled for one sample.

first: Barbara

last: Maurer

first: Harini

last: Nivarthi

first: Ha

last: Pham

first: Reinhard

last: Grausenburger

first: Thomas

last: Kolbe

first: Veronika

last: Sexl


title: RNA-sequencing on sorted infiltrating CD8 T cells from vehicle or JHU083, pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) treated MC38 (colon cancer) tumor bearing mice

city: Baltimore

first: Jonathan

middle: D.

last: Powell

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

summary: RNA-sequencing was performed on sorted CD11b-CD11c-B220-CD45+TCRbeta+CD44+CD8+ TIL from vehicle or JHU083 treated MC38 tumor-bearing mice  with or without JHU083, pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) treatment for expression profiling

overall_design: Expression profiling by high throughput sequencing performed on NextSeq 500/550 V2 Systems 75 cycles (1x75bp).

first: Leone

last: Robert


title: RNA sequencing of venom glands and venom gland organoids

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus Cowlesi and Naja Nivea), or tissue (Aspidelaps Lubricus Cowlesi). Bulk RNA sequencing from the snake venom gland, liver and pancreas was performed to construct a de novo transcriptome using Trinity.

sample_organism:
Naja nivea
Aspidelaps lubricus cowlesi

platform_organism:
Naja nivea
Aspidelaps lubricus cowlesi

overall_design: Cells from expanding or differentiating organoids or venom gland tissue were single cell sorted in a 384 well plate before processing. For bulk RNA sequencing, RNA was extracted from organoids or whole tissue using Trizol.

first: Yorick

last: Post

first: Jens

last: Puschhof

first: Harald

middle: M

last: Kerkkamp

first: Julien

last: Slagboom

first: Buys

last: de Barbanson

first: Nienke

last: Wevers

first: Xandor

last: Spijkers

last: Olivier

first: Regina

middle: G

last: van Kleef

first: Taline

last: Kazandijan

first: Stuart

last: Ainsworth

first: Ravian

middle: L

last: Van Ineveld

first: Carmen

last: Iglesias

first: Wiline

last: Van de Wetering

last: Heinz

first: Harry

last: Begthel

first: Jeroen

last: Korving

first: Yotam

middle: E

last: Bar-Ephraim

first: Walter

last: Getreuer

first: Hugo

middle: J

last: Snippert

first: Freek

last: Vonk

first: Remco

last: Westerink

first: Anne

last: Rios

first: Alexander

last: Van Oudenaarden

first: Peter

last: Peters

last: Kool

first: Michael

middle: K

last: Richardson

first: Nicholas

last: Casewell

first: Hans

last: Clevers


title: HOS15 and HDA9 negatively regulate immunity through histone deacetylation on intracellular immune receptor NLR genes in Arabidopsis

status: Public on Feb 23 2020

city: Ithaca

first: Leiyun

last: Yang

state: NY

address: 360 Tower road

department: Plant Biology

institute: Cornell University

summary: We isolated AtHOS15 as a negative regulator of plant immunity from genetic screen. To investigate how HOS15 influences plant immunity, we performed whole genome transcriptome (RNA-seq) analysis of the hos15-4 mutant. A total of 3,512 differentially expressed genes, with 1,870 upregulated and 1,642 downregulated, were found in hos15-4 mutant compared to wile-type Col-0. Gene Ontology analysis showed that genes involved in defense responses including immune receptor NLR genes are highly enriched among upregulated genes.

overall_design: Examination of whole genome transriptome (RNA-seq) in hos15-4 mutant compared to wide-type Col-0. Two-week-old plants growing under constant light at 22C were used for RNA extraction.

first: Jian

last: Hua


title: MicroRNA-7 regulates the plasticity of the enteroendocrine lineage

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

summary: Systematic evaluation of the cell populations of the intestinal crypt confirms the plasticity of the EEC progenitors, and uncovering of a functional role for the evolutionarily consvered miRNA-7 in this context.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Separation of mouse intestinal crypts into subpopulations based on expression of Sox9-EGFP, LgR5, or Prox1. Fruit fly midgut was dissected prior to and at various time point following infection by Ecc15. Single cell RNA-seq of enteroids treated by LNAs.

first: Matt

last: Kanke


title: STAT5BN642H is a driver mutation for T-cell neoplasia (RNA-Seq)

city: Wien

first: Ha T T

last: Pham

address: SCHWARZSPANIERSTR 17

institute: Ludwig Boltzmann Institute for Cancer Research

summary: The most frequent mutation in STAT5B is the Asp642His (N642H) mutation that was found in >90 leukemic/lymphoma patients. The development of novel treatment against STAT5BN642H has been hindered by the unavailability of a suitable model and the lack of the direct causal effect of STAT5BN642H on T-cell neoplasia development. We herein demonstrate that mice expressing human STAT5BN642H in the hematopoietic compartment rapidly develop leukemia/lymphoma. The disease is fully transplantable and characterized by the expansion of CD8+ T-cells. hSTAT5BN642H displays persistent and enhanced tyrosine phosphorylation upon cytokine stimulation. This leads to drastic changes in the gene expression profile accompanied by specific alterations in DNA methylation patterns that result in the acceleration of cell cycle progression. hSTAT5BN642H transcriptional activities in T-cell can be inhibited by inhibition of upstream kinases or transcriptional coregulaters, including JAKs, HDACs and BET Bromodomain containing protein. In particular, treatment with ruxolitinib, a JAK kinase inhibitor dramatically reduced tyrosine phosphorylation of hSTAT5BN642H resulting in decreased organ infiltration in vivo. We conclude that hSTAT5BN642H is sufficient to cause leukemia in vivo and JAK inhibitors are potential therapy for leukemic patients with the hSTAT5BN642H.

overall_design: Total RNA  extracted from wt and hSTAT5B and hSTAT5BN642H (transgenic) CD8+ T-cells (5 biological replicates/sample of WT and hSTAT5BN642H mice, 4 biological repicates/sample of hSTAT5B mice), RNA-seq 50 bp single-end libraries sequenced on  HiSeq 2500 (Illumina), to compare gene expression profiles

first: Ha

first: Reinhard

last: Grausenburger

first: Richard

last: Moriggl


title: GATA2 and progesterone receptor interaction in endometrial stromal cells undergoing decidualization [ChIP-Seq]

status: Public on Feb 22 2020

city: Chicago

first: Serdar

last: Bulun

state: IL

address: 303 E. Superior Street

department: Obstetrics and Gynecology

institute: Northwestern University

summary: The zinc-finger transcription factor GATA2 has been shown to be important for endometrial stromal cell decidualization in early pregnancy in mice and humans. Progesterone and its receptor PGR is also critical during decidualization but its interaction with GATA2 in regulating genes and pathways necessary for decidualization in human endometrium are unclear. Human endometrial stromal cells were isolated from 5 premenopausal women for primary cell culture. The cells underwent in vitro decidualization (IVD) or vehicle (Veh) treatment for 10 days. RNA-sequencing (RNA-seq) was performed to compare gene expression profiles (n=3) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) using an antibody against GATA2 (n=2) was performed to examine binding to target genes in the Veh and IVD cells. A public PGR ChIP-seq dataset (GSE69539) was mined to identify PGR-binding regions in IVD-treated human endometrial cells.

overall_design: Genome-wide GATA2 binding profiling in human endometrial stromal cells with and without IVD treatment using ChIP-Seq

first: Amanda

last: Kohlmeier

first: Christia

last: Sison

first: Matthew

last: Dyson


title: GATA2 and progesterone receptor interaction in endometrial stromal cells undergoing decidualization


title: GATA2 and progesterone receptor interaction in endometrial stromal cells undergoing decidualization [RNA-Seq]

overall_design: Genome-wide transcriptome mapping of human endometrial stromal cells with and without IVD treatment using RNA-Seq


title: Transcriptomes of lung adenocarcinomas

city: kashiwa

first: Eri

last: Sugiyama

address: 6-5-1 kashiwanoha

department: Division of Cancer Immunology

institute: National Cancer Center

summary: We performed RNA-seq using 19 human surgically-resected lung adenocarcinomas to investigate of difference between EGFR-mutated and wild-type lung adenocarcinomas.

overall_design: Examination of 19 lung adenocarcinomas by RNA-seq.

first: Hiroyoshi

last: Nishikawa


title: knockout of EZH2 inhibits the tumorigenicity of human ovarian cancers cells SKOV3 by targeting steroid biosynthesis

city: Beijing

first: Xiao

last: Huo

address: No.1 ShuaiFuYuan,Dongcheng District

department: Department of Obstetrics and Gynecology

country: France

institute: Peking Union Medical College Hospital

summary:
Ovarian cancer has the highest mortality in gynecologic cancers and most patients are diagnosed in advanced stages. EZH2 has been a major tumor markers and effective therapeutic targets for ovarian cancer, which molecular mechanism remain unclear. The present study was investigated the biological effects on EZH2 knock-out SKOV3 cells in vitro and in vivo experiment, and explore the molecular mechanism by integrated analysis of mRNA-seq and CHIP-seq.
 CRISPR/Cas9 system was used to establish the knock-out EZH2 SKOV3 cells. Protein expression was detected by Western blot. The effect of EZH2 in ovarian cancer was detected by MTT assay, wound scratch assay and Transwell assay, apoptosis assay in vitro and xenograft model in vivo. mRNA-seq and CHIP-seq was used to explore the molecular mechanism of biological function of EZH2.

overall_design: mRNA and H3K27me3 profiles of wild type (WT) SKOV3 and SKOV3/sgEZH2 were generated by deep sequencing

first: Hengzi

last: Sun

first: Qiuhong

last: Qian

first: Keng

last: Shen


title: Long Non-coding RNA expression predictive of tumour response in patients treated with preoperative chemoradiotherapy for LARC

city: GuangZhou

first: Bing

last: Zeng

address: Yuan Cun second road

department: Department of Gastroenterology, Hernia and Abdominal Wall Surgery

institute: Sun Yat-sen University

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

summary: Neoadjuvant chemoradiotherapy (CRT) followed by surgery is the standard treatment for locally advanced rectal cancer (LARC).   However, there are no good predictive methods. This study investigated whether specific lncRNA expression is associated with response to CRT. Tissue biopsies were obtained from patients before CRT. LncRNA expression was analyzed using one-color microarrays technique comparing signatures between good respondersand poor responders, as measured by tumour regression grade (TRG).

overall_design: Tissue biopsies were obtained from patients before CRT. A total of 3 good response and 3 poor response both for LncRNA  and gene expression experiments.

first: Yin-ru

last: Li


title: Transcriptome of human neck-derived immortalized white preadipocyte cell lines

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: White adipose tissue is a major site of energy storage and plays a noteworthy role in physiological homeostasis and metabolic disease. Different types of fat have been demonstrated to exhibit distinct metabolic and inflammatory profiles and are differentially associated with disease risk. It is unclear whether these differences are intrinsic to the pre-differentiated stage. We address this challenging question using RNA sequencing on clonally-expanded human white preadipocyte cell lines. We have identified differences in gene expression that are separate from the process of browning and beiging.

overall_design: RNA-seq profiling of clonally-expanded human white preadipocyte cell lines.

first: Alfred

last: Ramirez

first: C

last: Kahn

first: Simon

last: Kasif


title: Gene expression profiling of the intact dermal sheath cup of human hair follicle

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Tsuzuki-ku

institute: Shiseido

summary: The dermal sheath cup is the peribulbar component of the hair follicle dermal sheath, and has hair inductive potential similar to the dermal papilla.   To characterize it in comparison with other mesenchymal follicle tissuesparts, we performed gene expression profiling of intact dermal sheath cups, which were separated from hair follicles by microdissection. Gene expression profiles of the dermal sheath cup, dermal papilla and upper dermal sheath were compared. We identified a dermal sheath cup signature composed of 32 upregulated genes, which included extracellular matrix components and BMP binding mollecules, while dermal papilla signature included a number of dermal papilla signature genes which had already reported. Analyses of upstream regulators showed that TGF- b1 is a putative regulator of these genes. These results suggest some of molecular mechanism that contributes to human dermal sheath cup properties, which could be useful for hair follicle bioengineering.

overall_design: Gene expression profiles of the dermal sheath cup, dermal papilla and upper dermal sheath isolated from 3 individuals were compared.


title: Overexpression of nuclear receptor 5A1 induces  and maintains an intermediate state of conversion  between primed and naive pluripotency

city: Kyoto

first: Hirofumi

last: Suemori

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

institute: Kyoto University

summary: Naive and primed human pluripotent stem cells (hPSCs) have provided useful insights into the regulation of pluripotency. However, the molecular mechanisms regulating naive conversion remain elusive. Here, we report intermediate naive conversion induced by overexpressing nuclear receptor 5A1 (NR5A1) in hPSCs. The cells displayed some naive features, such as clonogenicity, glycogen synthase kinase 3β and mitogen activated protein kinase (MAPK) independence, expression of naive-associated genes, and two activated X chromosomes, but lacked others such as KLF17 expression, transforming growth factor β independence, and imprinted gene demethylation. Notably, NR5A1 negated MAPK activation by fibroblast growth factor 2, leading to cell-autonomous self-renewal independent of MAPK inhibition. These phenotypes may be associated with naive conversion, and were regulated by a DPPA2/4-dependent pathway that activates the selective expression of naive-associated genes. This study increases our understanding of the mechanisms regulating the conversion from primed to naive pluripotency.

overall_design: Transcriptome analysis of parental cells and NR5A1 transfectants cultured under TF, CHIR, or tt2iLGöX conditions

first: Kaori

last: Yamauchi

first: Tatsuhiko

last: Ikeda

first: Mihoko

last: Hosokawa

first: Norio

last: Nakatsuji

first: Eihachiro

last: Kawase

first: Shinichiro

last: Chuma

first: Kouichi

last: Hasegawa


title: Water Deficit Response Differs Between Invasive T. chinensis and T. ramosissima Established in Southern and Northern United States

status: Public on Feb 28 2020

city: Brookings

first: Sharon

last: Clay

state: SD

address: Box 2140C, 1390 College Ave

department: Agronomy, Horticulture and Plant Science

institute: South Dakota State University

summary: Transcriptomic profiling of T. chinensis and T. ramosissima shows responses due to water deficit that are common between the two species and differences that shows their invasiveness originating from southern and northern united states.  Several drought related genes that were up-regulated common in both species and transcription factors unique to T.chinensis and T. ramosissima were also found. Gene Ontology classification shows similar functional categories in both the species. Differences in two species due to water deficit were also illustrated in networks constructed from genes enriched in biological processes and molecular functions.

sample_organism:
Tamarix chinensis
Tamarix ramosissima

platform_organism:
Tamarix chinensis
Tamarix ramosissima

overall_design: Transcriptomic responses of two Tamarix species, T. chinensis and T. ramosissima subjected to water-deficit from New Mexico and Montana

first: Michelle

last: Ohrtmann

first: Padmapriya

last: Swaminathan

first: Anne

last: Fennell

first: Abigail

last: Carinder

first: Anup

last: Deuja


title: Tetrahymena thermophila macronucleus chromosomes originate from chromatin breakage sequence defined TAD-like structures in micronucleus chromosomes

status: Public on Feb 21 2020

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, we examined the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP. Interestingly, we found that the crescent MIC possess specific chromosome interaction pattern. All the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which could help to identify the midpoints of centromeres in the MIC. We found the transcriptionally active MAC chromosomes lack A/B compartments, topologically associating domains (TADs) and chromatin loops. The transcriptionally inert MIC chromosomes also without A/B compartments and chromatin loops, but have TAD-like structures. The boundaries of the TAD-like structures in the MIC were highly consistent with the chromatin breakage sequence (CBS) sites, suggesting that each TAD-like structure of the MIC chromosomes develops into one MAC chromosome during MAC development during conjugation. Overall, we revealed the higher-order chromatin organization in the T. thermophila and found the chromatin structures might play important roles during the development of the MAC chromosomes.

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

first: Zhengyu

last: Luo

first: Tengfei

last: Hu

first: Xiaoyuan

last: Song


title: Epigenomes of Hemin exposed trained monocytes [scATAC-seq]

first: Cristian

last: Ruiz-Moreno

state: Utrecht

address: 25 Heidelberglaan

institute: Prinses Máxima Centrum

summary: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components.  In this study we apply epigenomic, H3K27ac ChIP-seq, analysis to healthy human monocytes exposed to Hemin, a danger-associated signal, and B-glucan, a yeast sugar, in vitro.

overall_design: Mice were treated with Vehicle or Heme i.p.; LSK cells were obtained from the bone marrow one week or 28 days after treatment. scATAC sequencing was performed on LSK cells.

first: Elisa

last: Jentho

first: Boris

last: Novakovic

first: Sebastian

last: Weis

first: Hendrik

last: Stunnenberg


title: Steroid Hormones Regulate Genome-Wide Epigenetic Programming and Gene Transcription in Human Endometrial Cells with Marked Aberrancies in Endometriosis [expression]

city: San Francisco

first: Sahar

last: Houshdaran

state: CA

address: 513 Parnassus Ave HSE1619

department: OB/GYN

institute: UCSF

summary: Gene expression profiling of hormone treated normal and endometriosis stromal fibroblast cells (eSF). We used Affymetrix Human Gene 1.0 ST arrays. Samples include 4 normal of no uterine pathology (NUP), 4 endometriosis stage I, 4 endometriosis stage IV samples, each treated with Estrogen (E2), Progesterone (P4), E2+P4, or vehicle (veh), for a total of 48 samples on the Affymetrix platform.

overall_design: eSF from eutopic endometrial biopsies from women without any pelvic or uterine complications as controls and from women with stage I or stage IV endometriosis were grown in culture and treated with ovarian steroid hormone for 14 days in culture. After treatment, cells were harvested and were tested for changes in gene expression (as well as DNA methylation) to assess how gene expression and regulation is affected.

first: Linda

last: Giudice

first: Kim

last: Vo

first: Ashwini

last: Oke

first: Jennifer

last: Fung

first: Camran

last: Nezhat


title: Steroid Hormones Regulate Genome-Wide Epigenetic Programming and Gene Transcription in Human Endometrial Cells with Marked Aberrancies in Endometriosis

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data of MOLT-4 cells treated with romidepsin and tamoxifen

city: Izumo

first: Yoshio

last: Honma

address: 89-1 Enya

department: Biochemistry

institute: Shimane University

summary: Tamoxifen enhaces romidepsin-induced apoptosis in T-cell malignant cells. We compared gene-expression profile among untreated control, romidepsin-treted,

overall_design: MOLT-4 cells were treated with romidepsin and/or tamoxifen for 24 hours. Total RNA was extracted for hybridization on Affymetrix microarray.  We compared gene-expression profile among untreated control, romidepsin-treted, tamoxifen-treated, and romidepsin plus tamoxifen.

first: Wanitpongpun

last: Chinadol

first: Honma

last: Yoshio

first: Okada

last: Takahiro

first: Suzuki

last: Ritsuro

first: Urano

last: Takashi

first: Suzumiya

last: Junji


title: Purity Independent Subtyping of Tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer (NanoString)

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill

summary:
We assess three major subtype classification schemas in the context of results from two clinical trials and by meta-analysis of publicly available expression data to assess statistical criteria of subtype robustness and overall clinical relevance. We then developed a Single Sample Classifier (SSC) using penalized logistic regression based on the most robust and replicable schema. We demonstrate that a tumor-intrinsic two subtype schema is most robust, replicable, and clinically relevant. We developed purity independent subtyping of tumors (PurIST), a SSC with robust and highly replicable performance on a wide range of platforms and sample types. We show that PurIST subtypes have meaningful associations with patient prognosis and have significant implications for treatment response to FOLIFIRNOX.

Keywords: Expression profiling by array

overall_design: Analysis of gene expression in pancreatic adenocarcinoma (PDAC). For primary PDAC tumors, data include 16 flash frozen (FF), 1 formalin-fixed and paraffin embedded (FFPE) and 16 fine-needle aspiration (FNA) ; for patient derived xenograft (PDX), data include 18 FF and 7 FFPE samples.

first: Jen

last: Yeh

first: Naim

last: Rashid


title: RFX8-mediated Transcriptional Activation of DDX24 Promotes Hepatocellular Carcinoma Via LAMB1/SRC Signaling

city: Zhuhai

first: Tianze

last: Liu

address: 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University


title: Cold tolerance in rice plants is partially controlled by root responses

city: Lajeado

first: Raul

middle: Antonio

last: Sperotto

address: Av. Avelino Talini, 171

department: Biological Sciences and Health Center

country: Brazil

institute: University of Taquari Valley - Univates

summary:
Purpose: Rice (Oryza sativa) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the roots of two rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress during the early vegetative stage.
Results: RNAseq analysis revealed that contrasting genotypes present a completely different molecular response to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes that might contribute to rice cold tolerance, including the ones related with cell wall remodeling (glycosyl hydrolase, cellulose synthase, glycosyl transferase, wall-associated kinase, glycine-rich cell wall structural protein), cytoskeleton and growth (microtubule-associated protein 70, kinesin motor domain containing protein, growth regulating factor protein, auxin-independent growth promoter protein, RopGEF7), signaling (receptor-like protein kinase, Rapid Alkalinization Factor 21)), antioxidant system (glutathione peroxidase, metallothionein), lipid metabolism (fatty acid desaturase and phosphatidylinositol transfer protein), and stress response (Tetratricopeptide Repeat-Containing Protein). On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Even though these two genotypes have a similar genetic background (sister lines), some of these genes can probably be involved with cold tolerance or sensitivity and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

overall_design: Identify and characterize novel genes and metabolic pathways in roots of two indica rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress (10°C for up to 10 days) during the early vegetative stage (three-leaf stage, approximately 30 days).

first: Felipe

last: Ricachenevsky

first: Janette

last: Fett


title: RFX8-mediated Transcriptional Activation of DDX24 Promotes Hepatocellular Carcinoma Via LAMB1/SRC Signaling [RNA-seq]

summary: Hepatocellular carcinoma (HCC) is not only the fifth most prevalent cancer, presenting a major global health problem, but also among the leading causes of cancer-related deaths worldwide as its therapeutic targets are limited. To identify novel therapeutic targets, elucidate its oncogenic activities and molecular mechanism in HCC is urgent. We used R language edgeR package screened the expression profiles of 374 tissue samples obtained from patients with HCC and 50 samples of normal liver tissues obtained from The Cancer Genome Atlas (TCGA) database. Focusing on DDX24, we explored the functional effect and clinical significance of DDX24 in HCC. We provided evidence that DDX24 was a potential pro-tumorigenic gene in HCC. DDX24 knockdown inhibited HCC cell growth in vitro and in vivo. Mechanistically, RFX8 was proved to be DDX24 promoter-binding protein that transcriptionally upregulated DDX24 expression. Furthermore, we found that DDX24 bound to, and increased the stability of, LAMB1 mRNA by RNA immunoprecipitation (RIP) sequencing and RNA sequencing. Survival analysis indicated that HCC patients with high DDX24, RFX8, or LAMB1 expression exhibited poor prognosis. Our results demonstrated that DDX24 promoted HCC via RFX8/DDX24/LAMB1 pathway, which can be exploited as potential therapeutic target against HCC.

overall_design: Hep3B cells were infected with lentilviral vectors (siDDX24-1, siDDX24-2) or a lentilviral vector encoding siNC (the negative control) to establish the DDX24 knockdown stable cell lines used for RNA sequencing.

first: Hairun

last: Gan

first: Simeng

last: He


title: RFX8-mediated Transcriptional Activation of DDX24 Promotes Hepatocellular Carcinoma Via LAMB1/SRC Signaling [RIP-seq]

overall_design: Hep3B cells were used for RNA immunoprecipitation (RIP) sequencing. Fold enrichment of RNAs pulled down by DDX24 antibody was detected by High-throughput Sequencing, and input RNAs were used as the negative control.


title: A single nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Malaria causing parasites belonging to genus Plasmodium have a complex life cycle involving two hosts. Within these hosts parasites continuously shift between multiple morphologically distinct stages each of which has unique abilities to invade and survive in different host cell types. As repeatedly shown by independent studies, transcriptional profile of the parasite alters dramatically between stages which highlights the requirement for rapid and precise control of gene expression in these protozoans. However, genome wide studies revealed that plasmodium lacks orthologues of transcription factors found in other eukaryotes, has undefined promotor regions lacking conserved regulatory elements, has a lot smaller predicted specific TF to total proteome ratio compared to other eukaryotes. Instead, these parasites have been shown to contain a sophisticated histone modification machinery, stage specific control of mRNA decay rates, abundance of anti-sense RNA transcription and multiple epigenetic regulatory mechanisms . All these supporting evidences led to the general conception that plasmodium gene expression is primarily regulated by mechanisms other than TFs.

sample_organism:
Plasmodium berghei
Mus musculus

platform_organism:
Plasmodium berghei
Mus musculus

overall_design: Plasmodium berghei wild type vs. AP2

first: Munir

last: Akkaya

first: Abhisheka

last: Bansal

first: Patrick

middle: W

last: Sheehan

first: Mirna

last: Pena

first: Alvaro

last: Molina-Cruz

first: Lindsey

last: Orchard

first: Clare

last: Cimperman

first: Chen-Feng

last: Qi

first: Takele

last: Yazew

first: Daniel

first: Jeff

last: Skinner

first: Manuel

last: Llinas

first: Louis

last: Miller

first: Susan

last: Pierce


title: Polypyrimidine tract binding proteins are essential for B cell development

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: During B cell development, recombination of immunoglobulin loci is tightly coordinated with the cell cycle to avoid unwanted rearrangements of other genomic locations. Several factors have been identified that suppress proliferation in late-pre-B cells to allow light chain recombination. By comparison, our knowledge of factors limiting proliferation during heavy chain recombination at the pro-B cell stage is very limited. Here we identify an essential role for the RNA-binding protein Polypyrimidine Tract Binding Protein 1 (PTBP1) in B cell development. Absence of PTBP1 and the paralog PTBP2 results in a complete block in development at the pro-B cell stage. PTBP1 promotes the fidelity of the transcriptome in pro-B cells. In particular, PTBP1 controls a cell cycle mRNA regulon, suppresses entry into S-phase and promotes progression into mitosis. Our results highlight the importance of S-phase entry suppression and post-transcriptional gene expression control by PTBP1 in pro-B cells for proper B cell development.

overall_design: mRNAseq libraries were prepared from FrB pro-B cells. FrB pro-B cells were isolated from the bone marrow by flow cytometry and cell sorting of B220+, CD19+, IgD-, IgM-, CD2-, CD25-, CD43high, cKIT+, CD24+ and CD249- cells. Bone marrow cells from 4-6 mice from the same genotype and sex were pooled and depleted of unwanted cells with anti Gr-1-bio (RB6-8C5), CD11b (M1/70), IgD-bio (11-26c.2a), NK1.1-bio, CD3e (145-2C11) and Ter119 biotinylated antibodies and anti-biotin microbeads before cell sorting. Five biological replicates were carried out per genotype. iCLIP libraries were described in Monzon-Casanova, E. et al. The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers. Nat. Immunol. 45, 471 (2018).

first: Elisa

last: Monzón-Casanova

first: Louise

middle: S

last: Matheson

first: Kristina

last: Tabbada

first: Kathi

last: Zarnack

first: Christopher

last: Smith

first: Martin

last: Turner


title: Epigenomes of Hemin exposed trained monocytes

city: Utrecht

first: Cristian

last: Ruiz-Moreno

overall_design: Monocytes from healthy donors were cultured in vitro for 24 hours with media, Hemin or B-glucan.

last: Jentho

first: Boris

last: Novakovic

first: Sebastian

last: Weis


title: Transcriptomic analysis of tumor-infiltrating dendritic cells in mouse subcutaneous tumor models

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: CCR7+ tumor-infiltrating DCs (tDCs) transport tumor antigens from the tumor to the draining lymph node (dLN), and thus play a pivotal role in anti-tumor CD8+ T cell responses. However, the molecular mechanisms that underlie tDC activity remain poorly understood. To elucidate this problem, we investigated the transcriptomic properties of CCR7+ tDCs in mouse subcutaneous tumor models.

overall_design: In the LLC and B16F10 subcutaneous tumor models, tumor-infiltrating lineage-negative (CD3, CD19, NK1.1, Ly-6G, Ter-119)- Ly-6C- MHC class II+ CCR7+ tDCs, lineage- CCR7- MHC class II+ cells and CD326- migratory DCs in the dLN were purified by cell sorting at day 10 or day 14 post-tumor inoculation. Then, we performed transcriptome analysis on these cells by 3’ SAGE-seq.

first: Satoshi

last: Ueha

first: Shungo

last: Deshimaru

first: Haru

last: Ogiwara

first: Makoto

last: Kurachi

first: Jun

last: Abe

first: Shin-ichi

last: Hashimoto

first: Kouji

last: Matsushima


title: ZGLP1 is a determinant for the oogenic fate in mice (ChIP-seq)

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Mammalian sexual reproduction relies on the dichotomy of male and female germ cell development. However, the underlying mechanisms remain unclear. Here, we show that ZGLP1, a conserved transcriptional regulator with GATA-like zinc fingers, determines the oogenic fate in mice. ZGLP1 acts downstream of bone morphogenetic protein (BMP), but not retinoic acid (RA), and is essential for the oogenic program and meiotic entry. ZGLP1 overexpression induces differentiation of in vitro primordial germ cell-like cells (PGCLCs) into fetal oocytes by activating the oogenic programs repressed by Polycomb activities, whereas RA signaling contributes to the oogenic program maturation and PGC program repression. Our findings elucidate the mechanism for mammalian oogenic fate determination, providing a foundation for promoting in vitro gametogenesis and reproductive medicine.

overall_design: 8 V5-ChIP-seq samples in 2 cell types with 2 treatments: c7 PGCLCs (Dox Only)_ChIP, c8 PGCLCs (Dox Only)_ChIP, c8 PGCLCs (Dox Only)_Input, c7 PGCLCs (Dox and RA), c8 PGCLCs (Dox and RA), c8 PGCLCs (Dox and RA)_Input, ESCs (Dox and RA)_ChIP, ESCs (Dox and RA)_Input

first: So

middle: I

last: Nagaoka

first: Fumio

last: Nakaki

first: Hidetaka

last: Miyauchi

first: Yoshiaki

last: Nosaka

first: Hiroshi

last: Ohta

first: Kazuki

last: Kurimoto

first: Katsuhiko

last: Hayashi

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: ZGLP1 is a determinant for the oogenic fate in mice


title: Transcriptomes and Epigenomes of Hemin exposed trained monocytes

first: Cristian

last: Ruiz-Moreno

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomes of Hemin exposed trained monocytes

summary: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components.  In this study we apply RNA-seq analysis to healthy human monocytes exposed to Hemin, a danger-associated signal, and B-glucan, a yeast sugar, in vitro.

first: Elisa

last: Jentho

first: Boris

last: Novakovic

first: Sebastian

last: Weis


title: Transcriptional profile of pyramidal neurons in chronic schizophrenia reveals lamina-specific dysfunction of neuronal immunity

status: Public on Feb 20 2020

city: Toledo

first: Robert

last: McCullumsmith

state: OH

address: 3000 Arlington Ave.

institute: The University of Toledo

summary: While the pathophysiology of schizophrenia has been extensively investigated using homogenized postmortem brain samples, few studies have examined changes in brain samples with techniques that may attribute perturbations to specific cell types. To fill this gap, we performed microarray assays on mRNA isolated from anterior cingulate cortex (ACC) superficial and deep pyramidal neurons from 12 schizophrenia and 12 control subjects using laser capture microdissection. Among all the annotated genes, we identified 134 significantly increased and 130 decreased genes in superficial pyramidal neurons, while 93 significantly increased and 101 decreased genes were found in deep pyramidal neurons, in schizophrenia compared to control subjects. In these differentially expressed genes, we detected lamina-specific changes of 55 and 31 genes in superficial and deep neurons in schizophrenia, respectively. Gene set enrichment analysis (GSEA) was applied to the entire pre-ranked differential expression gene lists to gain a complete pathway analysis throughout all annotated genes. Our analysis revealed over-represented groups of gene sets in schizophrenia, particularly in immunity and synapse related pathways in pyramidal neurons, suggesting the disruption of these pathways plays an important role in schizophrenia. We also detected other pathways previously demonstrated in schizophrenia pathophysiology, including cytokine and chemotaxis, post-synaptic signaling, and glutamatergic synapses. In addition, we observed several novel pathways, including ubiquitin-independent protein catabolic process. We also used a bioinformatics approach to compare our differential expression gene profiles with 51 antipsychotic treatment datasets, demonstrating that our results were not influenced by antipsychotic treatment. Taken together, we found pyramidal neuron-specific changes in neuronal immunity, synaptic dysfunction, and olfactory dysregulation in schizophrenia, providing new insights for the cell-subtype specific pathophysiology of chronic schizophrenia.

first: Xiaojun

last: Wu

first: Rammohan

last: Shukla

first: Khaled

last: Alganem

first: Erica

last: Depasquale

first: James

last: Reigle

first: Micah

last: Simmons

first: Chang-Gyu

last: Hahn

first: Vahram

last: Haroutunian

first: Jarek

last: Meller

last: Meador-Woodruff


title: Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
Purpose: Taurine promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Mouse plasmacytoid dendritic cells were stimulated with R837, together with or without taurine for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Genes in the TLR7-IRF7 pathway were augmented by taurine. As a result, the production of type I IFNs increased upon taurine treatment.

overall_design: MRNA profiles of R837 stimulated and R837 plus taurine treated pDCs were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system


title: Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing [array]

city: New Haven

first: Allison

last: Greaney

state: CT

address: 10 Amistad St

department: Biomedical Engineering

institute: Yale University

summary: Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, we isolated and cultured a population of pharmacologically expanded basal cells (peBC) from rat tracheas. At peak basal marker expression we simultaneously split peBC into four in vitro platforms – organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples were evaluated using single-cell RNA sequencing (scRNAseq) and computational pipelines were developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium was also evaluated by scRNAseq as a control for engineered epithelium. Overall this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.

overall_design: Comparison of three primary rat tracheal epithelial scrapings plated into BEGM or EpiX media and grown for 8 days


title: Pex1-G844D NMRI mouse model of mild Zellweger spectrum disorder: liver gene expression profiles

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: Zellweger spectrum disorders (ZSD) are inborn metabolic diseases cause by genetic alterations in PEX genes leading to peroxisomal biogenesis disorder (PBD). Supportive care is standard since no validated treatment is able to modify the dismal natural history of the disease. Mouse models exist to study ZSD pathophysiology but they are limited by poor survival of the affected pups and breeding restrictions. To overcome these limitations, hypomorphic Pex1 p.G844D allele, equivalent to common mild human PEX1 p.G843D mutation, was backcrossed from C57BL/6N mouse to NMRI background. NMRI ZSD mouse breeding lead autosomal recessive Mendelian inheritance pattern with (median (min-max)) 10 (7-15) pups/mating compared to 4 (2-7) pups/mating in C57BL/6N background (p < 0.0001). We longitudinally phenotyped NMRI ZSD mice at 1, 2, 3 and 6 months of age to render this model suitable for future therapeutic interventions. NMRI ZSD mice exhibited growth retardation despite their higher daily energy intake. Mouse embryonic fibroblasts displayed classical PBD immunofluorescence pattern with peroxisomal mosaicism like milder ZSD patients skin fibroblasts. ZSD mice liver were enlarged and no liver lipid accumulation was detected. Yet, ZSD mouse plasma and liver showed very long-chain fatty acids, oxysterols and C27 bile acids intermediates elevation. Longitudinal study depicted trend to normalization for C26 and phytanic acid as it was shown for some ZSD patients reaching adulthood. ZSD mouse liver glycogen content was drastically reduced and liver RNA-Seq analysis confirmed glycogen metabolism genes downregulation. In conclusion, NMRI ZSD mouse model is suitable for ZSD liver-targeted therapies evaluation.

overall_design: 12 samples, 6 control livers and 6 ZSD livers (2 months)

first: Tanguy

last: Demaret

first: Bertrand

last: Bearzatto

first: Etienne

last: Sokal


title: Silencing KDM3A in MCF7 cells to study expression and alternative splicing

status: Public on Feb 26 2020

city: Jerusalem

first: Maayan

last: Salton

address: Ein-Kerem Canpus

country: Israel

institute: Hebrew University

summary: MCF7 cells were transfected with non-targeting siRNA (siNT) and siKDM3A for 72 h. RNA was extracted, libraries prepared and RNA-seq was conducted.

overall_design: siRNA oligos transfected to MCF7 cells. The siNT samples are taken form our previous study GSE109957.


title: ICE1 ChIP-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using ChIP-Seq to study the ICE1 binding sites

overall_design: Examination of ICE1 binding sites using ChIP-Seq

first: Kai

last: Tang

first: Lun

last: Zhao

first: Chunzhao


title: Global Gene expression changes in cholangiocytes with TGF beta treatment

city: Rochester

first: Shubham

last: Basu

state: Minnesota

address: 200 First St. SW

department: Division of Biomedical Statistics and Informatics

institute: Mayo Clinic

summary: Growth factor, TGF beta can have profound effect on global gene expression changes. Since TGF beta signalling is not well studied in liver epithelia , we decided to do Next gen RNA-seq analysis to look at TGF beta signaling in cholangiocytes

overall_design: Cholangiocyte cell line, H69,  were treated with Vehicle or TGF beta for 16 hours to look at the gene expresson changes induced by TGF beta

first: Sayed

middle: O

last: Aseem

first: Robert

last: Huebert


title: DNA hydroxymethylation profiling of paired parental and therapy resistant cancer cell lines

city: Leuven

first: Diether

last: Lambrechts

address: Herestraat 49

department: Human Genetics

institute: KU Leuven

summary: Genome wide DNA methylation profiling of paired parental and therapy resistant cancer cell lines. Parental cell lines are mostly established cell lines. Resistant cell lines were obtained through long term exposure of the parental cells to gradually increasing doses of cancer therapies. Followig the published TAB-sequencing protocol, the Illumina Infinium 450K or EPIC Human DNA methylation Beadchips were used to obtain DNA hydroxymethylation profiles across approximately 450,000 or 850,000 CpGs from the cells. Samples include 5 parental and 6 derived resistant cell lines.

overall_design: DNA from the 11 samples processed according to the TAB-seq protocol were hybridised to the Illumina Infinium 450K or EPIC Human Methylation Beadchips

first: Eva

last: Galle


title: ATM and PRDM9 Regulate SPO11-bound Recombination Intermediates During Meiosis

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: Meiotic recombination is initiated by genome-wide SPO11-induced double-strand breaks (DSBs) that are processed by MRE11-mediated release of SPO11-bound oligonucleotides (SPO11-oligos). The DSB is then resected and loaded with DMC1/RAD51 filaments that invade homologous chromosome templates. In most mammals, DSB locations (“hotspots”) are determined by the DNA sequence specificity of the PRDM9 DNA binding zinc finger array. Here, we demonstrate the first direct detection of meiotic DSBs in vertebrates by performing END-seq on mouse spermatocytes using low sample input. We find that DMC1 limits both the minimum and maximum length of ssDNA produced at all hotspots, whereas 53BP1, BRCA1 and EXO1 play a surprisingly minimal role in meiotic resection. Through enzymatic modifications to the END-seq protocol that mimic the in vivo processing of SPO11, we identify a novel meiotic recombination intermediate (RI) with SPO11 still bound to the 3’ end via a small stretch of dsDNA (“SPO11-RI”) that is dependent on the presence of PRDM9. We propose that SPO11-RI is generated because chromatin-bound PRDM9 blocks MRE11 from releasing SPO11 via 3’-5’ resection. SPO11-RI is present at all hotspots and correlates with the localization and frequency of crossovers and noncrossovers. In Atm–/– spermatocytes, multiple DSBs at the same hotspot reduces SPO11-RI formation, while unresected DNA-bound SPO11 accumulates because of defective MRE11 initiation. Thus in addition to their global roles in governing SPO11 breakage, ATM and PRDM9 are critical local regulators of mammalian SPO11 processing.

overall_design: END-seq and ChIP-seq data used to study meiotic double strand breaks

first: Jacob

last: Paiano

first: Shintaro

last: Yamada

first: Nicholas

last: Sciascia

first: Elsa

last: Callen

first: Ana

middle: P

last: Cotrim

first: Rajashree

middle: A

last: Deshpande

first: Yaakov

last: Maman

first: Amanda

last: Day

first: Tanya

last: Paull

first: André

last: Nussenzweig


title: Suppressing Proteasome Mediated Processing of Topoisomerase II DNA-Protein Adducts Preserves Genome Integrity

institute: Center for Excellence in Molecular Cell Science

summary: Here, we utilize high-resolution mapping of ETO-induced TOP2 lesions genome-wide (END-seq) (Canela et al., 2016), to examine the impact of proteasome inhibition on the fate of TOP2ccs. We found that once ETO-stabilized TOP2ccs had been proteolytically processed throughout the genome, and a robust DDR had been initiated, the large number of newly generated protein-free DSBs were repaired in a highly error-prone manner, resulting in toxic chromosomal translocations and rearrangements that lead to cell death. Notably, mis-repair of ETO-induced lesions occurred independently of the classical NHEJ or HR pathways. By inhibiting proteasome-mediated degradation of TOP2ccs either through chemical inhibition or by ablation of the ubiquitination of TOP2ccs by RNF4, an intact and enzymatically competent TOP2 was able to re-seal the protein-linked DSBs without invoking a significantly DDR. As a result, cells were protected from genomic instability, which ultimately led to enhanced cell survival after treatment with topoisomerase poisons.

overall_design: END-seq profiles in B-cells treated with etoposide and proteasome inhibitor

first: Dali

last: Zong

first: Yilun

last: Sun

first: Nancy

last: Wong

first: Darawalee

last: Wangsa

first: Sam

last: John

first: Thomas

last: Ried

first: Samuel

last: Bunting

first: Yves

last: Pommier


title: lncRNA expression profiles and lncRNA NR-104098 inhibits AML proliferation and induces differentiation through repressing EZH2 transcription by interacting with E2F1

city: Hefei

first: Yu-bin

last: Feng

address: meishan street 81

institute: anhui medical university

summary: Abundant evidence has illustrated that long non-coding RNA (lncRNA) plays a vital role in the regulation of tumor development and progression. Most lncRNA have been proven to have biological and clinical significance in acute myeloid leukemia (AML), but further studies remain to be needed. In this study, we investigated lncRNA NR-104098 in AML and its specific mechanism. The microarray analysis was performed on NB4 cells. Based on the related analysis results, we identified that lncRNA NR-104098 is a suppressor gene that is significantly upregulated in AML cells. lncRNA NR-104098 could inhibit proliferation and induce differentiation in AML cells in vitro, and also play main role in the mouse xenografts. Mechanically, it was confirmed that lncRNA NR-104098 may effectively inhibit EZH2 transcription by directly binding E2F1 and recruiting E2F1 to EZH2 promoter. In addition, ATPR can significantly increase the expression of lncRNA NR-104098, whereas knocking down NR104098 can inhibit the inhibitory effect of ATPR on the proliferation and induction differentiation of AML cells. Taken together, these results lead to a deeper insight into the mechanism of ATPR induces AML differentiation and inhibits proliferation by inhibiting EZH2 on transcriptional level.

overall_design: We performed three independent experiments and only considered significantly and repeated changes in lncRNA and mRNA as positive results.The experimental groups are control1, control2, control3 VS ATPR1, ATPR2, ATPR3

first: Yubin


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Murine Fibroblast Fibroproliferative Response with TGFβ

first: Edward

middle: B.

last: Leof

state: MN

address: 200 First Street SW

department: Thoracic Disease Research Unit

summary: AKR-2B cells were grown in an anchorage independent system to assess transcriptional profile of the TGFβ-dependent fibroproliferative response.

overall_design: AKR-2B cells were grown in soft agar -/+TGFβ, and colonies isolated and total RNA purified at 2, 4, and 8 days, then sent for NGS of mRNA and mRNA, and analyzed for the differentially increased genes associated with TGFβ stimulation.

middle: B

first: Danielle

last: Hernandez

first: Xueqian

last: Yin


first: Diether

last: Lambrechts

summary: RNA sequencing data of paired parental and therapy resistant cancer cell lines. Parental cell lines are mostly established cell lines. Resistant cell lines were obtained through long term exposure of the parental cells to gradually increasing doses of cancer therapies. Samples include 7 parental and 10 derived resistant cell lines. Our aim was to assess whether the resistant cells had undergone Epithelial to Mesenchymal Transition upon resistance acquisition.

overall_design: RNA from in total 21 samples (7 parental cell lines, 10 derived resistant cell lines) processed according to standard Illumina protocols. Of these 21 samples, 4 samples are replicates.

first: Eva

last: Galle


title: A20 contribution to NF-κB regulation, Ripoptosome formation and TNF-induced cell death

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

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

overall_design: Refer to individual Series


title: A20 contribution to NF-κB regulation, Ripoptosome formation and TNF-induced cell death [human]

summary: A20 is known key regulator of NF-κB activity and inflammatory response, but its role in the control of cell death receptor signaling is not completely understood. Although A20 is widely accepted anti-apoptotic protein, we demonstrate that elevated expression of A20 in both, human and murine keratinocytes results in sensitisation to TNF-induced cell death. We prove that the Ripoptosome formation in A20 overexpressing cells is prerequisite for the TNF-induced cell death execution. We demonstrate that both canonical and non-canonical NF-κB signaling pathways are regulated upon increase of A20 expression. A20 dependent alteration of cIAPs and TRAF1 expressions are involved in the multiple level control of cell death in keratinocytes with elevated A20 expression.

overall_design: The effects of A20 overexpression in tumor necrosis factor (TNF)-induced signalling were investigated in human and murine immortalized keratinocytes. This entry contains the results for the human keratinocytes.

first: Maria

last: Feoktistova

first: Roman

last: Makarov

first: Sihem

last: Brenji

first: Anne

last: Schneider

first: Tom

last: Luedde

first: Amir

last: Yazdi

first: Martin

last: Leverkus

first: Diana

last: Panayotova-Dimitrova


title: A20 contribution to NF-κB regulation, Ripoptosome formation and TNF-induced cell death [mouse]

overall_design: The effects of A20 overexpression in tumor necrosis factor (TNF)-induced signalling were investigated in human and murine immortalized keratinocytes. This entry contains the results for the spontaneously immortalized murine keratinocytes.


title: cholangiocytes treated with TGFbeta

first: Shubham

last: Basu


title: ATAC-seq of cholangiocytes treated with TGFbeta

summary: TGF beta has profound effects on global gene expression changes. To understand the epigenetic changes associated with TGF beta stimulation, we performed ATAC-seq of cholangiocytes to understand the changes in chromatin accessibility associated with TGF beta. We also wanted to determine if H3K9ac played a role in TGF beta induced changes in chromatin accessibility. Therefore, H3K9ac inhibitor CPTH6 was used to treat cells.

overall_design: Cholangiocyte cell line, H69,  were treated with Vehicle or TGF beta in the presence or absence of H3K9ac inhibitor, CPTH6 at 50 uM, for 16 hours to evaluate chromatin accessibility induced by TGF beta

first: Sayed

last: Aseem

first: Robert

middle: C

last: Huebert


title: Physiological responses of Saccharopolyspora erythraea towards perturbation of intracellular ATP

city: Kongens Lyngby

first: Xiaobo

last: Li

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

summary: Saccharopolyspora erythraea is used for industrial-scale production of erythromycin. To explore the physiological role of co-factors in regulation of primary and secondary metabolism of S. erythraea, we initially overexpressed the endogenous F1-ATPase in an erythromycin high-producing strain, E3. The engineered strain is named EA. The F1-ATPase expression resulted in a lower [ATP]/[ADP] ratio, which was accompanied by a dramatic increased production of a reddish pigment and a decreased erythromycin production. Transcriptional analysis revealed that the intracellular [ATP]/[ADP] ratio appeared to exert a global regulation on the metabolism of S.erythraea, and the lower [ATP]/[ADP] ratio induced physiological changes to restore the energy balance, mainly via pathways that tend to produce ATP or NADH. The results also indicated a state of redox stress in the engineered strain, which was correlated to the alteration of electron transport at the branch of the terminal oxidases.

overall_design: mRNA profiles of S.erythraea harvested at early exponential phase and at the end of exponential phase were sequenced in duplicate for both the parental strain E3 and the engineered strain EA.


title: Expression data from human bladder cancer cell line with control or knock down of HP1γ (CBX3)

city: Nanjing

first: Xiaojing

last: Huang

address: Xue Fu Road 12

institute: Model Animal Research Center of Nanjing University

summary:
Cancer development is complicated, it invloves a series of gene expression change. As demonstrated in several reports,  HP1γ is upregulated in some types of cancer, and it is essential for cancer development.We want to further clarify HP1γ function in bladder cancer.
We used microarrays to determine the gene expression profile in bladder cancer cell line T24 with depletion of HP1γ.

overall_design: We knocked down HP1γ expression by shRNA in bladder cancer cell line T24 and named this cell line as sh1 T24. Meanwhile, control T24 cell line is named as shCTL T24. Replicate RNA are obtained from shCTL and sh1 T24, respectively, named shCTL-1, shCTL -2, sh1-1, sh1-2.

first: Jun

last: Yan


title: Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic

city: Newark

first: Shawn

last: Polson

state: DE

department: Center for Bioinformatics and Computational Biology

institute: University of Delaware

summary: MDA-MB-231 (ER-) and T47D (ER+)  breast cancer cells were encapsulated in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa, in the range of bone marrow and healthy mammary tissue, and biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures.

overall_design: Examination of two different peptide compositions, collagen (GFOGER) and laminin (IKVAV), on two breast cancer cell lines MDA-MB-231 (ER-) and T47D (ER+) cultured in three dimensional PEG hydrogels for 3 days.

first: April

middle: M

last: Kloxin

first: Elisa

last: Ovadia


first: Diether

last: Lambrechts

summary: Genome wide DNA methylation profiling of paired parental and therapy resistant cancer cell lines. Parental cell lines are mostly established cell lines. Resistant cell lines were obtained through long term exposure of the parental cells to gradually increasing doses of cancer therapies. The Illumina Infinium 450k and EPIC Human DNA methylation Beadchips were used to obtain DNA methylation profiles across approximately 450,000 or 850,000 CpGs from the cells. Samples include 7 parental and 10 derived resistant cell lines.

overall_design: Bisulphite converted DNA from the 18 samples were hybridised to the Illumina Infinium 450k or EPIC Human Methylation Beadchips

first: Eva

last: Galle


title: Co-inhibition of BET proteins and PI3Kα triggers mitochondrial apoptosis in rhabdomyosarcoma cells

status: Public on Feb 19 2020

city: Cologne

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

country: Germany

institute: University of Cologne, Medical Faculty and University Clinic Cologne

summary: Remodeling transcription by targeting bromodomain and extraterminal (BET) proteins has emerged as promising anticancer strategy. Here, we identify a novel synergistic interaction of the BET inhibitor JQ1 with the PI3Kα-specific inhibitor BYL719 to trigger mitochondrial apoptosis and to suppress tumor growth in models of rhabdomyosarcoma (RMS). RNA-Seq revealed that JQ1/BYL719 co-treatment shifts the overall balance of BCL-2 family gene expression towards apoptosis and upregulates expression of BMF, BCL2L11 (BIM) and PMAIP1 (NOXA) while downregulating BCL2L1 (BCL-xL).

overall_design: RNA expression profiles were generated by RNA-seq in biological triplicates from Rh30 cells treated for 6h with either 1) solvent, 2) 1µM JQ1, 3) 3µM BYL719 or 4) 1µM JQ1 / 3µM BYL719 using HiSeq4000 (Illumina).

first: Cathinka

last: Boedicker

first: Michelle

last: Hussong

first: Michal

middle: R

last: Schweiger

first: Simone

last: Fulda


title: Gene expression signatures of LAPTM5 3'UTR overexpression in B cell lymphoma cells

city: Yangzhou

first: yanqing

last: zhang

address: 136 Jiangyang Road

institute: Yangzhou University

summary: LAPTM5 3’UTR suppresses the growth of B-lymphoma cells. To investigate the underline mechanism, we used the Agilent Whole Mouse Genome Microarray 4×44K to profile the differential expressed genes. Ectopic expression of LAPTM5 3’UTR in B-lymphoma cells 38B9 led to upregulation of 225 genes and downregulation of 350 genes with a 2-fold or greater changes compare with empty vector control cells.

overall_design: The differential expressed genes were measured in 3 LAPTM5 3’UTR overexpression 38B9 cells samples and 3 empty vector control 38B9 cells samples. Three independent cells infection experiments were performed at each time.


title: RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells edited at an immune-response trans-eQTL locus

city: NEW YORK

first: Margot

last: Brandt

address: 101 AVENUE OF THE AMERICAS FL 4

institute: New York Genome Center

summary: In order to investigate the genetic effect of an IRF1-associated immune-response trans-eQTL, we used CRISPR editing to introduce deletions at the top variant rs17622517. Five unedited, three heterozygous and five homozygous clones were isolated and RNA-sequencing was performed with no stimulation, with 90min LPS stimulation and 12h LPS stimulation, with two replicates of each. We find a significant correlation between the genetic perturbation here and CRISPRi perturbation of the variant locus, as well as the trans-eQTL effects, suggesting this variant is the causal variant for the immune-response trans-eQTL.

overall_design: Examination of the effect on immune response of editing an immune-response trans-eQTL variant

first: Tuuli

last: Lappalainen


title: RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells with CRISPRi treatment at an immune enhancer

summary: In order to investigate the role of an IRF1-associated trans-response eQTL in immune response, we utilized CRISPRi to repress either the eQTL variant locus or the promoter of IRF1. Cells were treated with a CRISPRi construct and gRNAs targeting a putative IRF1 enhancer, the IRF1 promoter or GFP (control). RNA-sequencing was performed with no stimulation, with 90min LPS stimulation and 12h LPS stimulation, with two replicates of each for each gRNA condition. We find a correlation in the fold changes of differentially expressed genes in the promoter and enhancer gRNA conditions, suggesting the enhancer is indeed affecting expression of IRF1 and producing a similar effect on the transcriptome.

overall_design: Examination of the effect on immune response of repression of IRF1 and an immune-response eQTL variant locus


title: CircRNA expression profiles of pancreatic tissues from severe acute pancreatitis mice

city: Chengdu

first: Yi

last: Yang

state: 四川

address: NO. 270, Rongdu Avenue

institute: The General Hospital of Western Theater Command

summary: Severe acute pancreatitis (SAP) is the most serious type of pancreatitis with high morbidity and mortality. The underlying mechanism behind SAP pathogenesis is complex and remains elusive.  In the present study, next-generation RNA sequencing was utilized to identify circRNA transcripts in the pancreatic tissues from three SAP mice and three matched normal tissues. Our results discovered that 56 circRNAs were differently expressed in SAP compared with normal control. Our findings may provide novel insights for pathophysiological mechanism of SAP and offer novel targets for SAP.

overall_design: exploring the circRNA profile

first: Hongyu

last: Sun

first: Wen

last: Jiang

last: Wu


title: Ependyma-expressed CCN1 restricts the size of the neural stem cell pool in the adult ventricular-subventricular zone

first: Qin

last: Shen

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

summary: Adult neural stem cells (NSCs) reside in specialized niches, which hold a balanced number of NSCs, their progeny, and other cells. How niche capacity is regulated to contain a specific number of NSCs remains unclear. Here, we show that ependyma-derived matricellular protein CCN1 (cellular communication network factor 1) negatively regulates niche capacity and NSC number in the adult ventricular-subventricular zone (V-SVZ). Adult ependyma-specific deletion of Ccn1 transiently enhanced NSC proliferation and reduced neuronal differentiation in mice, increasing the numbers of NSCs and NSC units. Although proliferation of NSCs and neurogenesis seen in Ccn1 knockout mice eventually returned to normal, the expanded NSC pool was maintained in the V-SVZ until old age. Inhibition of EGFR signaling prevented expansion of the NSC population observed in CCN1 deficient mice. Thus, ependyma-derived CCN1 restricts NSC expansion in the adult brain to maintain the proper niche capacity of the V-SVZ.

overall_design: Mice received tamoxifen treatment to induce recombination, which resulted in GFP expression and Ccn1 gene deletion in the ependymal cells. 2 days after TAM treatment, ependymal cells were purified by FACS from the V-SVZ of Ctrl and Ccn1cKO mice, respectively. Gating was mannually set according to GFP expression level in the ependymal cells relative to wild-type cells. Three samples from each genotype were processed for RNA sequencing and bioinformatical analysis.

first: Jun

first: Wenjia

last: Tian

first: Yang

last: Liu

first: Huanhuan

last: Wang

first: Jiangli

last: Zheng

first: Xin

first: Han

last: Pan

first: Ji

last: Li

first: Junyu

last: Luo

first: Xuerui

first: Lester

middle: F

last: Lau

first: H

middle: T

last: Ghashghaei


title: An autoimmune disease risk variant has a trans master regulatory effect mediated by IRF1 under immune stimulation

first: Margot

state: NY


title: Transcriptome analysis of RGA1 mutant (d1-1) meristem by RNA-seq

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: We applied RNA-seq to 3-month-old rice (Oryza sativa) shoot apical meristem to investigate the effect of RGA1(d1-1) mutation on the meristem initiation using transcriptome of d1 as compared to wild type plant.

overall_design: Two biological replicates of rice shoot apical meristem were dissected out from leaf sheath and then collected from three-month-old WT and d1 plants grown as described above and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using the NucleoSpin RNA Plant kit. After examination of the quality (Bioanalyzer, Agilent) and quantity (NanoDrop 2000, ThermoFisher) of each RNA sample, aliquots of total RNA were submitted to the Genomics Core Facility at Penn State University for cDNA library preparation and next generation sequencing on a Hiseq 2500 (Illumina). Approximately 40 million 150 bp single-end sequencing reads were obtained for each library.

last: Su

first: Hong

last: Ma

first: Sarah

last: Assmann


title: Slc1a3-2A-CreERT2 knock-in mouse to study astrocyte gene expression and calcium signaling

city: Linköping

first: Lech

middle: Tadeusz

last: Kaczmarczyk

address: Campus US

country: Sweden

institute: Linköping University

summary: RNA was obtained by applying a RiboTag procedure to RiboTag mice crossed with Slc1a3-2A-CreERT2 mice driving recombination in mouse brain astroglia.

overall_design: Two brain regions were analyzed: cerebellum, and the remaining cerebrum part. In addition, RiboTag input supernatants were analyzed as reference, to determine the relative RNA enrichement and depletion levels.

first: Walker

last: Jackson


title: miR-4711-5p regulates the cancer stemness and cell cycle progression through direct binding to KLF5, MDM2 and TFDP1 in colon cancer cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: It is important to establish cancer stem cells (CSCs)-targeted therapy for eradication of cancer. In this study, we searched for candidate microRNAs (miRNAs) by in silico analyses, which inhibit a stem cell-related gene Krüppel-like factor 5 (KLF5). After in vitro screening we focused on miR-4711-5p which proved to inhibit cancer stemness and G1-S cell cycle progression. We found by luciferase binding assays that miR-4711-5p directly bound to KLF5, TFDP1 (a heterodimeric partner with E2F family), and MDM2 (one responsible gene for degradation of wild type p53). This miRNA suppressed cell proliferation, migration, and invasion ability in DLD-1 and HCT116 cells as well as the cancer stemness including low reactive oxygen species (ROS) activity, and sphere formation ability. The expressions of stem cell markers, LGR5, CD44v9, and BMI1 also decreased. MiR-4711-5p inhibited the in vivo growth of pre-established DLD-1 xenografts without apparent adverse effect.   RNA sequence Analyses indicated that the transition from G1 phase to S phase in cell cycle was disturbed by miR-4711-5p. We indeed found that miR-4711-5p provoked G1 arrest with increase in CDK inhibitor p27KIP1 and/or p21WAF1/CIP1 and decrease in CDK2, 4, 6 and Cyclin D1 protein expression. These changes could be attributed to direct binding of miR-4711-5p to TFDP1. It is also suggested that down-regulation of MDM2 could permit to accumulate the wild type p53 protein in HCT116, leading to drastic induction of the p21WAF1/CIP1 protein and apoptosis. Our data suggest that miR-4711-5p could be a hopeful next generation treatment for CSC-targeted therapy.

overall_design: RNA-sequencing analyses were performed in two cell lines transfected miR-negative control or miR-4711-5p.

first: Yoshihiro

last: Morimoto

first: Okuzaki

last: Daisuke

first: Hirofumi

last: Yamamoto


title: Transcriptome modifications in the porcine intramuscular adipocytes during differentiation and exogenous stimulation with TNF-alpha and serotonin

status: Public on Feb 27 2020

city: Sendai

first: Haruki

last: Kitazawa

state: Miyagi

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

institute: Tohoku University

summary: Adipocytes are dynamic cells that have critical functions to maintain body energy homeostasis. Function of adipocyte is affected by adipogenic differentiation, and exogenous stimulation of biochemical factors such as serotonin and TNF-. Serotonin (5-hydroxytriptamine, 5-HT) is a biogenic monoamine, which known to be involved in lipid metabolism in adipocytes. The TNF- is a proinflammatory cytokines involved in adipocyte biology. Here we investigated the global transcriptome alterations of porcine intramuscular adipocytes at undifferentiated preadipocyte, differentiated adipocytes state, and adipocytes after stimulation with serotonin and TNF- for 12 h by using Agilent’s Porcine (V2) one-color Gene Expression Microarray 4 × 44. Transcriptome analysis revealed that the expression of 443, 261, and 249 genes were altered after differentiation, and after serotonin and TNF- stimulation, respectively. Differentiation process of adipocytes are found to be involved with expression changes of APP, HNF4A, ESR1, EGR1, SRC, HNF1A, FN1, ALB, STAT3, CBL, CEBPB, AR, FOS, CFTR, PAN2, PTPN6, VDR, PPARG, STAT5A and NCOA3 genes which are enriched in the ‘PPAR signaling pathway’ and ‘insulin resistance pathway’. Dose-dependent serotonin stimulation resulted in a decreased fat accumulation in the adipocytes as well as decreased adipocyte proliferation. Serotonin-induced differentially expressed genes in adipocytes were participated in the significant enrichment of GPCR ligand-binding, Cell chemotaxis, blood coagulation and complement pathways, metabolism of lipid and lipoproteins, regulation of lipid metabolism by PPARA; and lipid digestion, mobilization and transport pathways. TNF-α-induced transcriptional modification follows the similar trend, and alteration of many genes shared between both serotonin- and TNF-α stimulations. Our results provide new insights of transcriptome modifications associated with adipogenesis, and exogenous stimulation of serotonin- and TNF- to the porcine intramuscular adipocytes.

overall_design: Gene expression profiles in porcine undifferetiated preadipocytes, differetiated adipocyte, differetiated adipocytes after 12 h exposure of Serotonin (5-HT), TNF-a to mature adipocytes. Single sample was generated in each of three cases along with a non-stimulated control.

first: Asuka

last: Tada

first: Aminul

last: Islam

first: Julio

last: Villena

first: Hishashi

last: Aso


title: Comparative Toxicological Evaluation of the Insensitive Munition (IM) 1-methyl-3-nitroguanidine versus its UV-Degradation Products in Fathead Minnow

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Abstract: The Army is replacing traditional munitions with insensitive munitions (IM) resistant to accidental detonation.  Although the parent IM compound nitroguanidine (NQ) is generally not acutely toxic at concentrations >1000 mg/L in aquatic exposures, products formed by intensive UV-degradation resulted in of multiple-order of magnitude increase in toxicity.   A methylated congener of NQ, 1-methyl-3-nitroguanidine (MeNQ), is also being assessed for potential use in IM explosive formulations and consequently was here investigated for UV-degradation hazard and bioaccumulation potential. While up to 716 mg/L parent MeNQ caused no significant mortality or effects on growth in in larval P. promelas in 7-d exposures, the same concentration of MeNQ subjected to UV-treatment resulted in 85% mortality.  The UV-treatment degraded only 3.3% of the MeNQ (5,800 mg/L stock, UV-treated for 6h at UV 12x > sunlight), indicating that MeNQ degradation products have potentially high potency.  The parent MeNQ exposure decreased transcriptional expression of genes within the significantly enriched insulin metabolic pathway suggesting antagonism of bioenergetics pathways which compliments observed, although non-significant, decreases in body weights.  Transcriptional expression in the UV-degraded MeNQ exposures resulted in significant enrichment of pathways and functions related to cell cycle, but also erythrocyte function related to O2/CO2 exchange.  These functions likely represent the mechanistic source(s) of increased toxicity observed in the UV-degraded MeNQ exposures, which are distinct from previously observed mechanisms underlying increased UV-degraded NQ toxicity in fish.

overall_design: Subchronic 7-d toxicity test using P. promelas was conducted in accordance with the USEPA (2002).  Larval P. promelas (2-d old within 24-h in age) from a single batch of offspring were acclimated to experimental conditions for 24 h. Each exposure concentration consisted of 5 replicates (250-mL glass beakers containing 10 fish and 200 mL test solution).  The target exposure concentrations for the parent MeNQ and the UV-treated MeNQ exposures were:  0 (control), 7, 22, 67, 200, and 600 mg/L.  The UV-treated MeNQ was exposed for 4 hours in a a fan cooled Rayonet Reactor RPR-1000 (Southern New England Ultraviolet Company) equipped with a carousel and sixteen 14 W UV lamps (SNE Ultraviolet Company k = 300 ± 50 nm) to create a photo-intensity of 0.05 mW cm-2 nm-1 was used for all UV-treatment experiments.  This duration of UV exposure correlated to the UV-content of 96 hours of summertime sunlight in Vicksburg, Mississippi, USA. Experiments with the parent and UV-treated MeNQ was initiated within 3 hours of completion of the UV-treatment, where standard exposure methods were conducted absent of UV-light.

first: Guilherme

last: Lotufo

first: Mark

middle: L

last: Ballentine

first: Lee

last: Moores

first: Alan

middle: J

last: Kennedy

first: Natalie

middle: D

last: Barker

first: Qing

last: Ji

first: Pornsawan

last: Chappell


title: A stem cell-driven lymphoangiogenic switch

city: New York

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Tissues rely on stem cells (SCs) for homeostasis and wound-repair. SCs reside in specialized microenvironments (niches) whose complexities and roles in orchestrating tissue growth are still unfolding. Here, we identify lymphatic capillaries as critical SC niche components. In skin, lymphatics form intimate networks around the SCs of each hair follicle (HF) during their non-regenerative phase, and remodel upon regeneration. Seeking understanding, we unravel a secretome switch within SCs that controls lymphatic behavior. Resting SCs express Angiopoietin-like 7 (Angptl7), promoting lymphatic drainage. Upon activation, SCs trigger an anti-lympho-angiogenic program, transiently sparking lymphatic dilation and dampened drainage. In mammals, this dynamic aria between SCs and lymphatics is essential for coordinating HFSC behavior and hair regeneration: Upon either depleting lymphatics, silencing Angptl7 or super-activating anti-lympho-angiogenesis, SCs precociously proliferate and HF regeneration becomes asynchronous. In unearthing lymphatic capillaries as a hitherto under-appreciated SC-niche element, we’ve learned how SCs coordinate their activity across a tissue.

overall_design: Blood endothelial cells and lymphatic endothelial cells in the mouse back skin at the first telogen were FACS-purified for RNA-seq analysis.

first: Shiri

last: Gur-Cohen

first: Elaine

last: Fuchs