title: Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos

city: BANYULS SUR MER

first: Stephanie

last: Bertrand

address: AVENUE PIERRE FABRE

institute: CNRS/SU UMR7232

summary: We compared the transcriptomes of Amphioxus (Branchiostoma lanceolatum) control and SU5402 treated embryos to define putative FGF signalling pathway target genes during somitogenesis. Embryos were treated with 50µM of SU5402 from 5.5hpf to 8.5hpf, 11.5hpf, and 14.5hpf or from 15hpf to 18hpf, 21hpf, 24hpf. Total RNA was extracted from control and treated embryos.

overall_design: Comparison of transcriptomes between control and SU5402 treated emrbyos at three time points and for treatment at two developmental stages.

first: Hector

last: Escriva

first: Lucie

last: Subirana

first: Celine

last: Keime


title: Transcriptome of c-kit+ cells in rat under stress

status: Public on Jan 01 2020

city: Chicago

first: Peng

last: Ji

state: Illinois

address: 303E,Chicago Avenue, Ward3-240

department: Pathology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: RNA-sequencing analysis of the c-Kit positive cells under stress to identify novel factors or pathways involved in rat stress erythropoiesis.

overall_design: 4 female and 2 male 6-8 week old ACI rats were randomly divided into 2 group, each group has 2 females and 1 male. 100mg/kg PHZ or equal amount of PBS were injected through the peritoneal route. The rats were sacrificed on 36hr after injection and total bone marrow cells were isolated from hind legs of ACI rats. Single cell suspension was made and incubated with biotin-c-kit antibody for 20min on ice. Then the cells were washed with PBS and suspended with streptavidin particles  followed by incubation on ice for an additional 20 minutes. C-kit positive cells were purified using EasySep column free cell isolation system. Then total RNAs were extracted using TRIzol and processed to RNAseq.

first: Jingxin

last: Zhang


title: CRISPR knockout screening data and RNAsequencing in LINE-1(+) RPE cells

city: Baltimore

first: Daniel

last: Ardeljan

address: 733 N Broadway, MRB 432

institute: Johns Hopkins University School of Medicine

summary: CRISPR knockout screens were performed in RPE cells with or without wildtype p53 function to determine the genetic fitness interactions that occur upon induction of LINE-1 protein expression. We also performed RNAseq analysis in wildtype p53 RPE cells expressing LINE-1 or Luciferase control to determine transcriptomic changes that occur upon LINE-1 expression.

overall_design: Fitness screens are carried out with the Brunello knockout library (76,114 sgRNAs) transduced into RPE cells expressing either LINE-1 vs. eGFP (p53 wildtype cells) or expressing LINE-1 vs. Luciferase (p53 knockdown RPE). The screen in wildtype p53 RPE took place for 19 days, and there are 2 independent biological replicates per expression group. The screen in p53-knockdown RPE took place over 27 days, and there are 6 sequencing timepoints in total with 3 biological replicates per experimental group.

first: Jared

middle: P

last: Steranka

first: Zhi

last: Li

first: Martin

middle: S

last: Taylor

first: Chunhong

last: Liu

first: Lindsay

middle: M

last: Payer

first: Jacob

last: Sarnecki

first: Pei-Hsun

last: Wu

first: Ralph

middle: H

last: Hruban

first: Jef

middle: D

last: Boeke

first: David

last: Fenyö

first: Agata

last: Smogorzewska

first: Andrew

middle: J

last: Holland

first: Kathleen

last: Burns


title: Transcriptome analysis reveals new insight into iron homeostasis in Populus tomentosa

city: Beijing

first: Huimin

last: Chen

state: Beijing

address: No. 20 Nanxin Village, Xiangshan, Haidian District, Beijing

department: State Key Laboratory of Systematic and Evolutionary Botany

country: China

institute: Institute of Botany, Chinese Academy of Sciences

summary: Iron (Fe) is an essential micronutrient for the survival and proliferation of plants. Plants have evolved complex mechanisms to maintain Fe homeostasis in response of Fe deficiency conditions. To explore the mechanisms of Populus tomentosa response to Fe deficiency, we evaluated the physiological, biochemical and transcriptome differences of P. tomentosa between Fe-sufficient and Fe-deficient conditions. The results showed that, under Fe-free conditions, the chlorophyll synthesis and photosynthesis pathways in shoots were extremely depressed. The inhibition of these pathways caused chlorosis and reduced shoot growth. Meanwhile, although both two photosynthetic systems (PSI and PSII) were inhibited under Fe limited conditions, PSI is affected more serious and earlier than PSII. In order to maintain Fe homeostasis, several genes involved in Fe regulation network were differentially expressed. At the late period of Fe deficiency response, some genes (BTS, bHLH38/39 and PYE) in PYE regulatory network were up-regulated in roots, while some root-specific ethylene-dependent FIT regulatory genes (EIN3, ERF and FIT) were down-regulated. Moreover, FRO2 was induced in P. tomentosa roots to reduce more Fe3+, which is similar with other strategy I plants. It is interest that we found another Fe2+ transporter gene (NRAMP1) was induced, instead of the well-known Fe2+ transporter gene (IRT1) for strategy I plants, to promote Fe2+ absorption at the Fe deficiency late stage.

overall_design: The roots and shoots of two group plants (Fe-sufficient  and Fe-deficient  Populus tomentosa) were collected for RNA-seq, in triplicate, using Illumina Hiseq2500.

first: Hui

first: Yan


title: Progerin-induced transcriptional changes in Huntington's disease human pluripotent stem cells-derived neurons

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Identification of transcriptional changes in Huntington's disease (HD) and normal (WT) human embryonic stem cells (hESC)- and induced pluripotent stem cells(iPSC)-derived striatal GABAergic neruons.

overall_design: RNA-seq (High-throughput Eukaryotic Digital Gene Expression (DGE)) of HD and WT human ESCs- and iPSCs-derived striatal GABAergic neurons, with and without progerin.

first: Dorit

last: Cohen-Carmon

first: Vitaly

last: Lerner

first: Malka

last: Nissim-Rafinia

first: Yosef

last: Yarom

first: Eran

last: Meshorer


title: Analysis of downstream genes associated with JMJD2A silencing in MKN45 cells.

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

country: Japan

institute: Tokushima University

summary: JMJD2A is involved in the regulation of cell proliferation and overexpressed in some cancers, but it remains largely unknown about its interaction with the other genes.

overall_design: Four data (Sample 1-4) from JMJD2A siRNA and four (Sample 5-8) from Random siRNA in MKN45 cells using whole human genome microarray (8 x 60 K; Agilent)

first: Tadahiko

last: Nakagawa


title: Effect of D2O on S. pombe gene expression

city: Copenhagen

first: Rasmus

last: Hartmann-Petersen

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: RNA sequencing of total RNA purified from wild type S. pombe cells after 0, 5 and 24 hours culture in YES containing 100% D2O (deuterium oxide).

overall_design: Condition S0: Total RNA was purified and sequenced from wild type S. pombe cells in exponential phase cultured in YES (H2O). Condition S5: Total RNA was purified and sequenced from wild type S. pombe cells in exponential phase cultured for 5 hours in YES (D2O). Condition S24: Total RNA was purified and sequenced from wild type S. pombe cells in exponential phase cultured for 24 hours in YES (D2O). 4 independent samples for each conditon (1-4).

first: Jens

middle: V

last: Johansen


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [RNA-Seq mouse]

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. Seemingly complex patterns of enhancer-gene connections in this dataset can largely be explained by a simple quantitative Activity-by-Contact (ABC) model, in which the effect of a candidate enhancer on a target gene is predicted by the intrinsic activity of the enhancer multiplied by the contact frequency between the enhancer and promoter. This ABC score can identify regulatory enhancer-gene connections and predict their quantitative effects from DNase-Seq, H3K27ac ChIP-seq, and Hi-C measurements. The ABC model can explain even complex regulatory phenomena including the ability of an enhancer to “skip” over one gene to regulate a more distant one. Our approach provides a foundation for dissecting mechanisms of enhancer-gene regulation and predicting enhancer-gene connections across cell types.

overall_design: We developed a genetic approach based on classical cis-trans tests to distinguish between (i) primary effects on the expression of nearby genes resulting from direct local functions of an enhancer and (ii) secondary effects on nearby genes resulting from indirect downstream consequences of one of the cis targets influencing another gene in the region. We generated clonal cell lines carrying heterozygous genetic modifications at enhancer loci and compared the expression of nearby genes within 1 megabase on the cis and trans alleles (i.e., on the modified and unmodified homologous chromosomes) in the same cells. Changes in neighboring gene expression that involve only the cis allele likely result from local functions, while changes that involve both the cis and trans alleles likely result as downstream effects of non-local functions. We performed genetic modifications in 129/Castaneus F1 hybrid mouse embryonic stem cells (mESCs) that contain ~1 polymorphic site every 140 basepairs (bp), enabling us to distinguish the two alleles using RNA sequencing, and we checked for consistency between knockouts on each genetic background to control for potential haplotype-specific effects. We initially characterized allele-specific gene expression using RNA sequencing combined with hybrid selection.

first: Charles

last: Fulco

first: Joseph

last: Nasser

first: Thouis

last: Jones

first: Glen

last: Munson

first: Drew

middle: T

last: Bergman

first: Vidya

last: Subramanian

first: Sharon

middle: R

last: Grossman

first: Rockwell

last: Anyoha

first: Tejal

last: Patwardhan

first: Tung

last: Nguyen

first: Michael

last: Kane

first: Benjamin

last: Doughty

first: Elizabeth

last: Perez

first: Neva

middle: C

last: Durand

first: Elena

middle: K

last: Stamenova

first: Erez

middle: L

last: Aiden

first: Eric

last: Lander


title: The epigenetic landscapes of histone modifications on HSV-1 genome in human THP-1 cells [RNA-seq]

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

summary: To study the dynamic changes of histone modifications across HSV-1 genome during lytic infection in THP-1 cells. Totally 20 maps of HSV-1 epigenome were generated at 5 different time points after infection, together with their corresponding gene expression profiles.We found that histone modifications were detected on HSV-1 genome soon after infection; all four studied modifications, H3K9me3, H3K27me3, H3K4me3 and H3K27ac, change rapidly along with virus life cycle progression.The transcription repression marks, H3K9me3 and H3K27me3, tended to decrease along with infection process, and the transcription activation mark H3K27ac increased on viral genome, which were aligned with increased expression of viral genes. Moreover, treatment with C646, an inhibitor for H3K27ac transferase p300, inhibited expression of viral genes; and EPZ6438, an inhibitor for H3K27 methyltransferase EZH2, enhanced viral gene expression.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: To study the distribution of histone modifications on HSV-1 genome during lytic stage, as well as their dynamic changes, we used HSV-1 (1×108 / 10 cm dish) to infect THP-1 cells, and collected samples at 1 hr, 2 hr, 4 hr, 8 hr and 24 hr after infection. The cells were then subjected to RNA-Seq and ChIP-Seq with antibodies recognizing H3K27ac, H3K4me3, H3K9me3 and H3K27me3. Two biological replications were performed for each sequencing and data quality control was done before analysis.

first: Chuan

last: Gao

first: Shanbo

last: Tang


title: TLR4 or CD44 deficiency effect on hepatic stellate cells

city: Chuncheon-si

first: Yoon Mee

last: Yang

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Pharmacy

country: South Korea

institute: Kangwon National University

summary: Analysis of hepatic stellate cells isoltaed from wild-type, TLR4-/-, and CD44-/- mice. TLR4 and CD44 are major hyaluronic acid receptors. Results provide insight into the effects of TLR4 and CD44 loss in hepatic stellate cells.

overall_design: Hepatic stellate cell mRNA profiles of wild-type, TLR4-/-, and TLR4-/- mice were generated by deep sequencing, in triplicate, using Illumina-HiSeq2500/4000

first: Yoon

last: Deng

first: Zhenqui

last: Liu

first: Ekihiro

last: Seki


title: Expression data from tomato fruit at three ripening stages (MG Mature Green, Br Breaker, B10 Breaker+10 days) in wild type line (cv Money Maker, MM)  and two transgenic lines LCY1, LCY3 (cv Money Maker, MM).

city: Rome

first: sarah

last: frusciante

address: Via Anguillarese 301

country: Italy

institute: ENEA Italian National Agency for New Technologies, Energy and Sustainable Development

summary:
Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof.
Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.

overall_design: 27 Total samples were analyzed. We generated for each ripening stage (MG Mature Green, Br Breaker, B10 Breaker+10 days) the following comparisons: LCY (LCY1+LCY3)MG>MM_MG; (LCY1+LCY3)Br>MM_Br; (LCY1+LCY3)B10>MM_B10.

first: Gianfranco

last: Diretto

first: Sarah

last: Frusciante

first: Claudia

last: Fabbri

first: Nicolas

last: Schauer

first: Lucas

last: Busta

first: Zhonghua

last: Wang

first: Alessia

last: Fiore

first: Alisdair

last: Fernie

first: Reinhard

last: Jetter

first: Benedetta

last: Mattei

first: James

last: Giovannoni

first: Giovanni

last: Giuliano


title: Transcriptome analysis of ABCB7 overexpressed U87MG glioblastoma cells

city: Seoul

first: Jung Yun

last: Kim

address: 145 Anam-ro, Seungbuk-gu

institute: Korea University

summary: This study investigated the biological function of ABCB7 in U87MG glioblastoma cell line. Many ABC transporters are known contributions to drug resistance and various biological process. However, mitochondrial ABC transporters aren’t known mechanism to control biological process. We identified the potential roles of ATP-binding cassette (ABC) transporter subfamily member 7 (ABCB7), one of the mitochondrial ABC transporters. ABCB7 activates signaling pathway of hypoxia-inducible factor 1 alpha (HIF1α) by hypoxia independent regulation. This signaling pathway regulates the death inhibitory genes and survival related genes. Also, ABCB7 downregulates cell cycle related genes. Our results provide that ABCB7 is essential for the survival of malignant brain tumors.

overall_design: A Glioblastoma cell line, U87MG, was transfected with pCDH-CMV-MCS-EF1-Puro (U87MG-Con) or pCDH-CMV-ABCB7-EF1-Puro (U87MG-ABCB7). Plasmids for ABCB7 expression (NM_004299.6) were purchased from Korea human gene bank (hMU008618). The 3 biological replicate of RNA extracts in these cells was used for transcriptome analysis.

first: Jung

middle: Y

first: Xiong

last: Jin

first: Hyunggee


title: Hyaluronic Acid Synthase-2 (HAS2) overexpression and deficiency effect on hepatic stellate cells

first: Yoon Mee

last: Yang

summary: Analysis of hepatic stellate cells (HSCs) isoltaed from ASMA-HAS2 transgenic and HSC-specific Has2 knockout mice. HAS2 synthesized hyaluronic acid, one of major extracellular matrix. Results provide insight into the role of HAS2 in hepatic stellate cells.

overall_design: Hepatic stellate cell mRNA profiles of ASMA-HAS2 transgenic (Tg) and Has2 f/f Lrat-cre (KO) mice were generated by deep sequencing, in triplicate, using BGISEQ-500

first: Yoon

last: Deng

first: Zhenqui

last: Liu

first: Ekihiro


title: Interleukin-4 restores neurogenic plasticity of the primary human neural stem  cells through  suppression  of  Kynurenic  acid  production  upon Amyloid-beta42 toxicity

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary:
The immune response is an important determinant of the plasticity and neurogenic capacity of neural stem cells (NSCs) upon amyloid-beta42 (Aβ42) toxicity in Alzheimer’s disease (AD). However, the direct effects of individual immuno-modulatory effectors on NSC plasticity remain to be elucidated and are the motivation for reductionist tissue-mimetic culture experiments. Using starPEG-Heparin hydrogel system that provides a defined 3D cell-instructive neuro-microenvironment culture system, sustains high levels of proliferative and neurogenic activity of human NSCs, and recapitulates the fundamental pathological consequences of Amyloid toxicity upon Aβ42 administration, we found that the anti-inflammatory cytokine interleukin-4 (IL4) restores the plasticity and neurogenic capacity of NSCs by suppressing the Aβ42-induced kynurenic acid-producing enzyme kynurenine aminotransferase 2 (KAT2), which we also found to be upregulated in the brains of the AD model, APP/PS1dE9 mouse. Our transcriptome analyses showed that IL4 treatment restores the expression levels of NSC and cortical subtype markers. Thus, our dissective neuro-microenvironment culture revealed IL4-mediated neuroinflammatory crosstalk for human NSC plasticity and predicted a new mechanistic target for therapeutic intervention in AD.
Primary (from Gestation week 21 of human fetus) and induced (adult human fibroblast-derived) neural stem cells are cultured in 2D and 3D. Next generation sequencing is performed at 3 weeks of culture.

overall_design:
pNSC neural stem cells are cultured in  3D. Next generation sequencing is performed at 3 weeks of culture.
For 3D cultures, Abeta42 is mixed with heparin solution at the time the gels are prepared. Cultures are performed for three weeks with frequent media changes. DMSO, KYNA and IL4 were present in the culture medium throughout the culture at the following concentrations: IL4 (10 nM), KYNA (10 uM), DMSO (0.1%). Cultures are performed for three weeks with frequent media changes.

first: Hilal

last: Celikkaya

first: Christos

last: Papadimitriou

first: Mehmet

middle: I

last: Cosacak

first: Andreas

last: Dahl


title: Transcriptional charecterization of the eds4 mutant transcriptome

city: CABA

first: Marcelo

last: Yanovsky

address: Av. Patricias Argentinas

country: Argentina

institute: FIL/IIBBA-CONICET

summary:
The aim of this study was to perform a transcriptional characterization of the Arabidopsis eds4 mutant. To this end two separate experiments were performed:
Experiment 1: comparison of the transcriptional profile (RNA-seq) of eds4 Arabidopsis mutants in contrast to wild type Col-0 accession grown under continuous light conditions.
Experiment 2: Analysis of the distribution of transcripts (RNA-seq) between nucleus and cytoplasm in the eds4 Arabidopsis mutants in comparison to wild type Col-0 plants grown under continuous light conditions.

overall_design: In both experiments eds4 mutant plants were grown together with Col-0 wild type plants for two weeks under continuous white light (50 μmol·m−2·s−1 ) at 22 degrees centigrade.  For the transcriptional profiling of eds4, whole seedling RNA extraction was performed and analyzed using RNA-seq. For the transcript distribution assay whole cell RNA was also extracted in some of the samples and in others nuclei were first purified using fluorescence-activated cell sorting (FACS) in order to obtain nucleus only RNA and later on compare nuclear and cytoplasmic RNA by RNA-seq.

first: M

last: de Leone


title: The NAD kinase OsNADK1 affects the redox and enhances the tolerance to drought in rice

city: Yangling

first: Kunming

last: Chen

state: Shaanxi

address: Xinong Road 22#

department: College of Life Sciences

institute: Northwest A&F University

summary:
NAD(H) and NADP(H) are crucial coenzymes and play important and distinguishable roles in all living organisms. NAD(H) is primarily involved in catabolic reactions, whereas NADP(H) participates in anabolic reactions, such as NADP(H)-dependent reductive anabolic pathways, signal transduction, and defense against oxidative stress. Hence, regulation of the  intracellular balance of NAD(H) and NADP(H) is critical. NAD(H) kinase (NADK) is the key enzyme in the de novo biosynthesis of NADP(H), catalyzing the transfer of a phosphoryl group from ATP to NAD(H), and thus plays an important role in the regulation of intracellular NAD(H)/NADP(H) balance for NADP(H)-based metabolic pathways.
We used microarrays to detail the global programme of gene expression between WT and osnadk1 and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: The youngest fully expanded leaves from 2.5-month-old WT and osnadk1 plants (three replicates each), grown under normal growth (soil moisture, 47.3%) and drought conditions (soil moisture, 8.5%), were used for RNA extraction and hybridization on Affymetrix microarrays. Control: normal growth condition; Drought: drought stress condition.

first: Xiang

last: Wang

first: Cong-Yi

last: Zhou

first: Kun-Ming


title: U1 snRNP regulates chromatin retention of noncoding RNAs

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

summary: RNA subcellular localization often correlates with its function and regulation. For many long noncoding RNAs (lncRNAs) and some isoforms of coding genes, their transcripts are preferentially retained on the chromatin. However, the mechanisms controlling the chromatin retention of lncRNAs and mRNA transcripts remain largely unknown. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. To comprehensively identify the cis-regulatory elements of RNA transcript, here we have developed a high-throughput sequencing-based method named RNA elements for subcellular localization by sequencing (REL-seq). Using this method, we identified RNA sequences contribute to the chromatin retention of several transcripts. By combining REL-seq with random mutagenesis (mutREL-seq), we further narrowed down the key RNA motifs and residues in regulating their subcellular localization at base resolution. Finally, based on the RNA element we identified, we revealed and confirmed U1 snRNA targeting site contributes to RNA chromatin retention.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: All RNA-seq(s) were designed to reveal differentially subcellular localized RNAs of RSLP library targeted genes.

first: Yafei

last: Yin

first: Jinlong

last: Lu

first: Xiaohua

last: Shen


title: A novel hydrogel-based instructive biohybrid 3D culture system for modeling human neural stem cell plasticity, neurogenesis, neurodevelopment, and neurodegeneration

summary: Meaningful models of human neural development and neurodegeneration are extremely important when exploring stem-cell-based regenerative therapies. However, existing 3D cultures fall short of being highly defined, modular, and controllable. Adapting a glycosaminoglycan-based, cell-responsive hydrogel platform, we stimulated primary and induced human neural stem cells (NSCs) to manifest neurogenic plasticity and form extensive neuronal networks in vitro. The 3D cultures exhibited neurotransmitter responsiveness, electrophysiological activity, and tissue-specific extracellular matrix (ECM) deposition. By whole transcriptome sequencing, we identified that 3D cultures express mature neuronal markers, and reflect the in vivo genetic program of mature cortical neurons compared to 2D cultures. Thus, our data suggest that our established 3D hydrogel culture supports the tissue-mimetic maturation of human neurons in an unprecedented manner. We modeled neurodegenerative conditions by treating the cultures with A?42 peptide and observed the known human pathological effects of Alzheimer?s disease including reduced NSC proliferation, impaired neuronal network formation, synaptic loss and failure in ECM deposition as well as elevated Tau hyperphosphorylation and formation of neurofibrillary tangles. We also determined the changes in transcriptomes of primary and induced NSC-derived neurons after A?42, providing a useful resource for further studies. Thus, our hydrogel-based human cortical 3D cell culture is a powerful platform for studying various aspects of neural development and neurodegeneration, as exemplified for A?42 toxicity and neurogenic stem cell plasticity.

overall_design: Primary (from Gestation week 21 of human fetus) and induced (adult human fibroblast-derived) neural stem cells are cultured in 2D and 3D. Next generation sequencing is performed at 3 weeks of culture.


title: Genome-wide maps RNA Polymerase II and Histone H3 of Hydra vulgaris

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hydra have a remarkable ability to regenerate after bisection or dissociation. Thus, Hydra is a unique model for studying the mechanisms underlying stemness and self renewal biology. The regeneration of Hyrda offers unique way to investigate molecular mechanisms leading to the establishment of organizer activity during animal development. Here we have investigated the genome-wide occurrence of RNA Polymearse II and Histone H3 in Hydra vulgaris.

overall_design: Examination of RNA polymearse II and Histone H3 in Hydra vulgaris.

first: Sanjeev

last: Galande


title: Fat_challenge_tests

city: Wageningen

first: Juri

last: Matualatupauw

address: PO Box 17

department: Human Nutrition

country: Netherlands

institute: Wageningen University

summary:
Exploration of new markers that define impaired metabolic flexibility using an acute postprandial challenge test.
Healthy subjects underwent a 4-week high-fat high-calorie diet. High-fat challenges were performed in these subjects before and after the diet and in subjects with the metabolic syndrome.

overall_design: Whole blood gene expression was measured from total blood RNA at fasting and at 120 and 360 min after the high-fat challenges.

first: Jildau

last: Bouwman


title: Single-cyst transcriptome analysis of Drosophila male germline stem cell

status: Public on Dec 31 2019

first: Xin

state: MD

address: 3400 North Charles Street

department: Biology

institute: JHU

summary: To elucidate endogenous gene expression profiles in germ cells at discrete but continuous differentiation stages, we developed a new experimental strategy that we named Transcriptome Analysis using Single Germline Cyst (TASC).

overall_design: Isolate single germ cell cysts at a particular stage during differentiation and perform RNA-seq analysis.

first: Shi

last: Zhen

first: Lim

last: Cindy

first: Tran

last: Vuong

first: Cui

last: Kairong

first: Zhao

last: Keji

first: Chen

last: Xin


title: Glucocorticoids paradoxically facilitate steroid resistance in subsets of T-cell acute lymphoblastic leukemias and normal thymocytes

city: San Francisco

first: Benjamin

last: Huang

address: 1450 3rd Street

institute: University of California San Francisco

summary: Glucocorticoids (GCs) are a central component of therapy for patients with T-cell acute lymphoblastic leukemia (T-ALL) and while resistance to GCs is a strong negative prognostic indicator in T-ALL, mechanisms of GC resistance remain poorly understood. Using diagnostic samples from patients enrolled on the frontline Children’s Oncology Group (COG) T-ALL clinical trial AALL1231, we demonstrate that one-third of primary T-ALLs are resistant to GCs when cultured in the presence of interleukin-7 (IL7), a cytokine that is critical for normal T-cell function and that plays a well-established role in leukemogenesis. We demonstrate that in these T-ALLs and in distinct populations of normal developing thymocytes, GCs paradoxically induce their own resistance by promoting upregulation of IL7 receptor (IL7R) expression. In the presence of IL7, this augments downstream signal transduction resulting in increased STAT5 transcriptional output, which leads to upregulation of the pro-survival protein BCL-2. Taken together, these data demonstrate that IL7 mediates an intrinsic and physiologic mechanism of GC resistance in normal thymocyte development that is retained during leukemogenesis in a subset of T-ALLs and is reversible with targeted inhibition of the IL7R/JAK/STAT5/BCL-2 axis.

overall_design: Transcriptomes of primary human T-cell acute lymphoblastic leukemias were generated by extracting RNA from primary bone marrow specimens and sequenced using Illumina-based methods.

first: Lauren

last: Meyer

first: Kevin

last: Shannon

first: David

last: Teachey

first: Michelle

last: Hermiston


title: Function of Sox2 and Klf4 during SKM reprogramming

first: Sheng

last: Ding

address: 1650 Owens Street

institute: Gladstone Institute for Cardiovascular Disease

summary: Differentiated somatic cells can be reprogrammed into induced pluripotent stem cells by ectopic expression of transcription factors Oct4, Sox2, Klf4, and c-Myc, but the mechanisms are still to be dissected. The stoichiometry of factors influences the efficiency of induced pluripotent stem cells, and previous studies emphasized the requirement of high levels of overexpressed Oct4. In this study, we showed that, with appropriate stoichiometry achieved by polycistronic cassettes, Sox2 and Klf4 were sufficient to initiate and establish pluripotency in differentiated cells efficiently without Oct4 overexpression.

overall_design:
ChIP-seq: We performed the genome-wide analysis for Sox2 and Klf4 binding in day 2 SKM secondary MEFs

RNA-seq: We performed the global gene expression analysis for the EGFP-positive populations from SKM reprogramming MEFs and NPCs.

first: Peng

last: Liu

first: Zhaojun

last: An

first: Jiashun

last: Zheng

first: Chaozeng

last: Si

first: Yang

last: Chen


title: Adipocyte Epigenetic Alterations and Potential Therapeutic Targets in Transgenerationally Inherited Lean and Obese Phenotypes Following Ancestral Exposure to Environmental Toxicants

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: This study examines the transgenerational adipocyte (fat cell) epigenetic alterations in F3 generation obese and lean rats ancestrally exposed to DDT and atrazine. Adipocytes were isolated from the gonadal fat pad of F3 generation 1-year old rats ancestrally exposed to DDT, atrazine, or vehicle control in order to obtain adipocyte DNA for DNA methylation analysis. Observations indicate that there were differential DNA methylated regions (DMRs) in the adipocytes with the lean or obese phenotypes compared to control normal (non-obese or lean) populations. Interestingly, there were epigenetic changes that were distinct when comparing the lean and obese DMRs between the control and exposure lineage groups. DMR gene associations were identified which included common set of genes previously shown to associate with adipocyte pathology. The comparison of epigenetic alterations indicated that there were substantial overlaps between the different treatment lineage groups for both the lean and obese phenotypes. Novel correlated genes and gene pathways associated with DNA methylation were identified, and may aid in the discovery of potential therapeutic targets for metabolic diseases such as obesity.

overall_design: Gestating F0 generation rats were exposed to atrazine, DDT, or control vehicle from days 8-14 of gestation. The F1 generation offspring exposed in utero were bred within the exposure lineage colony to produce the intercross F2 generation and subsequent F3 generation. No sibling or cousin crosses were used in order to prevent inbreeding artifacts. Adipocytes were isolated from the gonadal fat pad of the one-year old F3 generation of rats ancestrally exposed to DDT, atrazine, or vehicle control. Obese and lean phenotypes were defined as an increase or decrease in adipocyte area, body mass index (BMI), and observed abdominal adiposity at dissection. The lean, obese and normal (non-obese or non-lean) animals were separated for analysis. Adipocyte DNA was isolated from individuals and then pooled into 5 pools of 2-5 different individuals per phenotypic group. A genome-wide methylated DNA immunoprecipitation and next generation sequencing (MeDIP-Seq) was performed on the samples in order to investigate differences in DNA methylation within the adipocyte DNA.

first: Stephanie

middle: E

last: King

first: Eric

last: Nilsson

first: Daniel

last: Beck


title: Chimeric Antigen Receptor-Induced Bcl11b Suppression Propagates Natural Killer-Like Cell Development

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: The transcription factor B Cell CLL/Lymphoma 11B (BCL11B) is indispensable for T lineage development of lymphoid progenitors. Here we show that chimeric antigen receptor (CAR) expression early in ex vivo generated lymphoid progenitors suppresses Bcl11b, leading to suppression of T cell-associated gene expression and acquisition of natural killer (NK) cell-like properties. These results give important insights into differentiation of murine and human lymphoid progenitors driven by synthetic CAR transgene-expression and inform the potential use of ex vivo generated CARiK cells as a broadly applicable product for targeted immunotherapy.

overall_design: Microarray data analysis of sorted human CAR-engineered lymphoid progenitors (h1928z3: n=3; h19delta: n= 5; h1928z3 + hCD19: n= 3) from OP9-DL1 in vitro cultures on day 18. Human CD34+ HSPCs derived from umbilical cord blood samples were engineered with a CD28-based second-generation human CAR targeting human CD19 (h1928z3) or a non-signaling control CAR (h19delta) and pre-differentiated on OP9-DL1 stromal cells in vitro. For CAR stimulation, irradiated CD19+ Daudi cells were added during the culture (h1928z3_stim).

first: M

last: Maluski

middle: G

last: Sauer

first: R


title: The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance

city: Montreal

first: Mario

last: Houde

state: Quebec

address: 2080, rue Saint-Urbain

department: Sciences Biologique

country: Canada

institute: Université du Québec à Montréal

summary:
Abstract
Background
Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speed up functional gene characterization.

Results
We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant’s life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected.

Conclusions
This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.

overall_design: Examination of wheat transcript profiles modification in 4 wheat plant types under well watered condition and drought condition.

first: Arnaud

last: Cheuk

first: Francois

last: Ouellet


title: Intermittent exposure to whole cigarette smoke alters the differentiation of primary small airway epithelial cells in the air-liquid interface culture

city: Biberach

first: Karsten

last: Quast

address: Birkendorfer Str. 65

department: Computational Biology

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: Cigarette smoke (CS) is the leading cause to develop COPD. Therefore, we investigated the pathologic effects of whole CS on the differentiation of primary small airway epithelial cells (SAEC), from three healthy donors and three COPD patients, cultured under ALI (air-liquid interface) conditions. The analysis of the epithelial physiology demonstrated that CS impaired barrier formation and reduced cilia beat activity. Although, COPD-derived ALI cultures preserved some features known from COPD patients, the CS-induced effects were similarly pronounced in ALI cultures from patients compared to healthy controls. A RNA sequencing analysis revealed the deregulation for marker genes for basal cells and secretory cells upon CS exposure. The comparison between gene signatures obtained from our in vitro model (CS vs. air) with a published data set from human epithelial brushes (smoker vs. non-smoker) reveals a high degree of similarity between the deregulated genes and pathways.  ALI culture has been generated utilising cells obtained from 3 COPD and 3 healthy subjects. Subsequently cultures have been treated with CS and air respectively for 33 days. Gene expression profiles were generated using next generation sequencing.

overall_design: ALI culture mRNA profiles of COPD and healthy control subjects. Cells from 3 COPD and 3 healthy control donors have been split into 6 ALI cultures, each, resulting in overall 36 culture wells. Half of the wells per donor have been treated with CS and the other half with air. Expression data were generated using Illumina HiSeq3000.

first: Julia

last: Gindele

first: Jürgen

last: Schymeinsky


title: Establishment and characterization of a porcine B cell lymphoma cell line

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary: Cells from porcine lymphoma tumors in the lymph node and spleen were cultured, cloned, and sequenced using Illumina next generation sequencing and compared to CD21+ or CD3+ splenocytes. Lymphoma clones were identified a B cell lymphomas by gene expression and surface marker presence.

overall_design: Cells from 4 different lymphoma clones from the subileac lymph node, 2 lymphoma clones from the spleen, a CD21+ splenocyte sample to be used as a normal B cell control, and a CD3+ splenocyte sample to be used as a normal T cell control were used for RNA isolation and paired end sequencing on an Illumina HiSeq 2500. Raw data was analyzed at the University of Minnesota Informatics Institute and aligned to the Sus Scrofa11.1 genome. The lymphoma sequences were compared to the B cell and T cell controls separately to determine if they were more similar to B or T cells. Since the lymphoma cells were more similar to B cells, they were then compared against the CD21+ B cell control to identify differentially expressed genes between control B cells and the lymphoma cells.

last: Rahe

last: Murtaugh


title: TMX2 is a key regulator of cellular redox state and its dysfunction causes severe brain developmental abnormalities

city: Rotterdam

first: Maarten

last: Fornerod

address: Dr. Molewaterplein 50

department: Cell Biology

institute: ErasmusMC

summary: The redox state of the neural progenitors regulates physiological processes such as neuronal differentiation, dendritic and axonal growth. The relevance of ER-associated oxidoreductases in these processes is largely unexplored. We describe a severe neurological disorder caused by biallelic loss of function variants in the Thioredoxin (TRX)-Related Transmembrane-2 (TMX2) gene, detected by exome sequencing in ten affected individuals from seven unrelated families presenting with congenital microcephaly, cortical polymicrogyria and other migration disorders. TMX2 encodes one of the five TMX proteins of the Protein Disulfide Isomerase family and is the first to be linked to human brain disease. Our mechanistic studies on protein function show that TMX2 localizes to the ER Mitochondria-Associated-Membranes (MAMs), is involved in posttranslational modification and protein folding and undergoes physical interaction with the MAM associated and ER folding chaperone calnexin and ER calcium pump SERCA2. These interactions are functionally relevant because TMX2-deficient fibroblasts show decreased mitochondrial respiratory reserve capacity and compensatory increased basal glycolytic activity. Intriguingly, under basal conditions TMX2 occurs in both reduced and oxidized monomeric form, while it forms a stable dimer under treatment with hydrogen peroxide, recently recognized as signaling molecule in neural morphogenesis and axonal pathfinding. Exogenous expression of the pathogenic TMX2 variants or of variants with in vitro mutagenized TRX domain induces a constitutive TMX2 polymerization, mimicking increased oxidative state. Altogether these data uncover TMX2 as a sensor in the MAM-regulated redox state and identify it as a key adaptive regulator of neuronal proliferation, migration and organization in the developing brain.

overall_design: RNAseq data of RNA isolated from cultured human fibroblasts of 2 affected individuals vs 4 age and gender matched unaffected individuals.

first: Laura

last: Vandervore

first: Grazia

last: Mancini


title: Hotspot mutations induce metabolic reprogramming and vulnerability to serine deprivation

city: Baltimore

first: William

middle: Brian

last: Dalton

state: Maryland

address: 1650 Orleans St.

department: Oncology

institute: Johns Hopkins University School of Medicine

summary: Cancer-associated mutations in the spliceosome gene create a neomorphic protein that produces aberrant mRNA splicing in hundreds of genes, but the ensuing biologic and therapeutic consequences of this missplicing are not well understood. Here we provide evidence that aberrant splicing by mutant alters the transcriptome, proteome, and metabolome of human cells, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway. We also find that mutant induces vulnerability to deprivation of the nonessential amino acid serine, which is mediated by missplicing-associated downregulation of the serine synthesis pathway enzyme PHGDH. This vulnerability is manifest both in vitro and in vivo, as dietary restriction of serine and glycine in mice is able to inhibit the growth ofMUT xenografts. These findings describe a novel role for mutations in altered energy metabolism, and they offer a new therapeutic strategy againstMUT cancers.

overall_design: Four mutant MCF10A replicates (two from the K700E1 clone and two from K700E2) and four wild type replicates (two from R702R1 and two from TWT1) were compared.

middle: B

first: Ben

middle: O

last: Park


title: The Negative Cofactor 2 complex is a master regulator of drug resistance in Aspergillus fumigatus [RNA-seq]

city: Manchester

first: Michael

last: Bromley

state: Greater Manchester

address: 46 Grafton Street

department: Division of Infection, Immunity, and Respiratory mediciney

country: United Kingdom

institute: The University of Manchester

summary: The Negative cofactor 2 (NCT) complex is an evolutionally conserved heterodimeric transcription factor. In Aspergillus fumigatus, the NCT complex consists of two subunits NctA and NctB. Through a genome-wide screening of a transcription factor null mutant strains, we found that loss of the NCT complex leads to a multi-drug resistance phenotype including the azoles (itraconazole, voriconazole and posaconazole) as well as the salvage therapeutic amphotericin B, and terbinafine. To obtain further insight into the molecular mechanisms driving the azole-resistance in the NCT complex null mutants, we analyzed genome-wide gene expression profiles of the nctA and the nctB null mutants using RNA-seq. Our expression profiling revealed that disruption of the genes lead to upregulation of several ergosterol biosynthetic genes, their transcriptional activators, and the azole efflux pump cdr1B. Taken together, these results suggest that the NCT complex plays a role as a master regulator of drug resistance in A. fumigatus.

overall_design: Genome-wide gene expression profile was investigated in the wild-type, the nctA null, and the nctB null mutant using RNA-seq in the absence and the presence of itraconazole (0.5 mg/mL) with three biological replicates.

first: Takanori

last: Furukawa

first: Jane

last: Gilsenan

first: Paul

last: Bowyer


title: The Negative Cofactor 2 complex is a master regulator of drug resistance in Aspergillus fumigatus

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

overall_design: Refer to individual Series


title: The fungal CCAAT-binding complex and HapX display highly variable but evolutionary conserved synergetic promoter-specific DNA recognition

summary: To sustain iron homeostasis, microorganisms have evolved fine-tuned mechanisms for uptake, storage and detoxification of the essential metal iron. In the human pathogen Aspergillus fumigatus, the fungal-specific bZIP-type transcription factor HapX coordinates adaption to both iron starvation and iron excess and is thereby crucial for virulence. Previous studies indicated that a HapX homodimer interacts with the CCAAT-binding complex (CBC) to cooperatively bind bipartite DNA motifs; however, the significance of the HapX and CBC interaction and the mode of HapX-DNA recognition had not been resolved. In this study, we characterized the genome-wide binding profiles of HapX using the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Our ChIP-seq results, in combination with in vitro surface plasmon resonance analysis, phylogenetic comparison, and genetic analysis, revealed an astonishing plasticity of the CBC:HapX DNA-recognition mode.

overall_design: Examination of genome-wide binding profiles of Venus fluorescence protein with a nulcear localization signal (NLS) derived from the Simian Virus 40 (SV40) large T-antigen in steady-state iron-replete (+Fe) and iron-starvation (-Fe) conditions with two biological replicates.

first: Jeffrey

last: Lau

first: Fabio

last: Gsaller

first: Can

last: Zhao

first: Ian

last: Donaldson

first: Matthias

last: Misslinger

first: Vito

last: Valiante

first: Hubertus

last: Haas

first: Peter

last: Hortschansky


title: The genome-scale binding profile of the CCAAT-binding complex in Aspergillus fumigatus

summary: The CCAAT-binding complex (CBC) is a heterotrimetric transcription factor conserved in all eukaryotes. The CBC specifically interacts with the pentanucleotide motif known as the CCAAT box, which is one of the most ubiquitous cis-acting elements on the eukaryotic promoters. In Aspergillus fumigatus, the CBC consists of three subunits HapB, HapC, and HapE, which are all required for specific binding to the target sequences.  This regulatory complex has been shown to be involved in the regulation of a wide range of cellular processes, including primary and secondary metabolism, iron homeostasis, as well as azole drug resistance and virulence in mammalian hosts. In this study, we investigated the genome-wide binding profile of the CBC using the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). We identified over 1,000 peak regions, which showed more than 5-fold enrichment compared to the input control in steady-state iron-replete (+Fe) and iron-starvation (-Fe) conditions. Bioinformatic analysis of the peak regions revealed the 5’-CSAATVR-3’ sequence as the most enriched nucleotide motif, suggesting that this motif acts as the consensus binding sequence for the CBC in vivo.

overall_design: Examination of genome-wide binding profiles of a C-terminally GFP tagged HapC protein in steady-state iron-replete (+Fe) and iron-starvation (-Fe) conditions with two biological replicates.


title: The Negative Cofactor 2 complex is a master regulator of drug resistance in Aspergillus fumigatus [ChIP-seq]

summary: The Negative cofactor 2 (NCT) complex is an evolutionally conserved heterodimeric transcription factor. In Aspergillus fumigatus, the NCT complex consists of two subunits NctA and NctB. Through a genome-wide screening of a transcription factor null mutant strains, we found that loss of the NCT complex leads to a multi-drug resistance phenotype including the azoles (itraconazole, voriconazole and posaconazole) as well as the salvage therapeutic amphotericin B, and terbinafine. To obtain further insight into the molecular mechanisms driving the azole-resistance in the NCT complex null mutants, we analyzed genome-wide binding profiles of NctA using chromatin-immunoprecipitation sequencing (ChIP-seq). Our ChIP-seq analysis revealed that NCT complex binds the promoters of several ergosterol biosynthetic genes, their transcriptional regulators, and the azole efflux pump cdr1B. Taken together, these results suggest that the NCT complex plays a role as a master regulator of drug resistance in A. fumigatus.

overall_design: Examination of genome-wide binding profiles of a C-terminally S-tagged NctA protein in the absence and the presence of itraconazole (0.5 mg/mL) with two biological replicates.

first: Emma

last: Davis


title: Loss of ER and nuclear envelope-associated neutral sphingomyelinase SMPD4 causes a severe neurodevelopmental disorder with microcephaly and congenital arthrogryposis

first: Maarten

last: Fornerod

summary: Several neurodevelopmental processes including neuronal survival, migration and differentiation are controlled by sphingolipid metabolism. Sphingomyelin is an abundant component of cell membranes. Sphingomyelinases generate ceramide from sphingomyelin as a second messenger in intracellular signaling pathways involved in cell proliferation, differentiation, or apoptosis. While the role of acid sphingomyelinase is well established, the role of neutral sphingomyelinases in human neurodevelopment has remained elusive.  Twenty-five children from ten unrelated families presented with microcephaly with simplified gyral pattern, cerebellar hypoplasia, severe developmental encephalopathy, congenital arthrogryposis, diabetes mellitus and early fetal/-postnatal demise. All probands tested have biallelic loss of function variants in SMPD4, coding for neutral sphingomyelinase-3 (nSMase-3 / SMPD4). Fibroblasts from affected individuals showed morphologic endoplasmic reticulum (ER) cisternae abnormalities and increased autophagy, consistent with a previously suggested function of SMPD4 in the ER. Overexpression of human Myc-tagged SMPD4 in HEK293T cells showed  localization to both the outer nuclear envelope and the ER. Previous studies localized SMPD4 to the outer nuclear membrane. Mass spectrometry of SMPD4-associated proteins detected  peptides belonging to nuclear pore complex proteins. After downregulation of SMPD4 by siRNA, delayed cell cycle progression was observed and primary fibrobalsts from affected individuals were more prone to apoptosis than controls. These data are consistent with former studies in HeLa cells showing mitotic abnormalities after siSMPD4 treatment. This study provides a link between  sphingolipid membrane homeostasis, cell fate and mitotic decisions indicating novel pathway in the pathogenesis of microcephaly.

first: Daphne

last: Smits

middle: M


title: HIF-3α2 overexpression ChIP-seq in Hep3B cells and 1 % hypoxia

city: Oulu

first: Jussi-Pekka

middle: Matteus

last: Tolonen

address: Aapistie 7A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

summary: Hypoxia-inducible factor (HIF), an αβ dimer, is the master regulator of oxygen homeostasis. HIF induces the expression of several hundred genes under hypoxic conditions. Three HIF isoforms differing in the oxygen-sensitive α subunit exist in vertebrates. While HIF-1 and HIF-2 are known transcription activators, HIF-3 has been considered as a negative regulator of the hypoxia response pathway by formation of inactive dimers between the HIF-3α and HIF-1α or HIF-2α subunit. However, the human HIF3A mRNA is subject to complex alternative splicing, which leads to production of both long and short HIF-3α variants. It has been shown recently that the long HIF-3α variants can form αβ dimers that possess transcriptional activation capacity, while the short splice variant inhibits hypoxia-inducible gene expression. Chromatin immunoprecipitation analyses of HIF-3α2 overexpression in Hep3B cells show that HIF-3α2 binding associates with canonical hypoxia response elements (5'-RCGTG-3') in the promoter regions of the erythropoietin (EPO) gene among others. Luciferase reporter assays show that the identified HIF-3α2 chromatin-binding regions are sufficient to promote transcription by HIF-3α2 and HIF-1. Furthermore, HIF-3α2 overexpression and knock-down studies by siRNA targeting the HIF3A gene show that EPO mRNA and protein levels are upregulated and downregulated, respectively. Taken together, the results show that HIF-3α2 is a transcription activator that is directly involved in erythropoietin signaling.

overall_design: 1.6 million Hep3B cells transfected with the V5-tagged HIF-3α2 and wildtype HIF-β overexpression plasmids. ChIP was performed with V5 antibody. Samples were prepared in triplicate and pooled for ChIP. HIF-3α2-associated enrichment is compared to input DNA.

first: Minna

last: Komu

first: Hang-Mao

last: Lee

first: Marjo

last: Malinen

first: Jorma

last: Palvimo

first: Gong-Hong

last: Wei

first: Johanna

last: Myllyharju


title: Gene expression data from THP-1 cells exposed to exosomes from acetaminophen-treated or vehicle-treated hepatocytes or corresponding mock- or medium-controls

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary:
In the present study we examined the effect of hepatocyte-derived exosomes (HDE) on innate immune cells by treating a human monocyte cell line (THP-1 cells) with exosomes collected from the culture medium of acetaminophen (APAP)-treated and untreated primary human hepatocytes and comparing the cytokine response to THP-1 cells treated with mock- and medium-controls.
We profiled the gene expression changes observed in the HDE-exposed monocytes prior to LPS stimulation. Findings from our research suggest that HDE may be essential for maintaining immune homeostasis.

overall_design: Twenty-four THP-1 samples were analyzed representing N=1 per donor-specific treatment from N=5 hepatocyte donors except 1 media-only sample from 1 donor that was > 3 SD away from the mean on a PCA plot suggesting that these samples may also be aberrant and were therefore omitted from analysis. Because the mock-control sample from 1 donor was omitted from the array, the mock-APAP data for this donor was duplicated for the purposes of HDE vs mock analysis.


title: Chip data of OsTMF overexpression plants under cold stress

city: wuhan

first: Yan

last: Xu

state: Hubei

address: No. 1, Shizishan street

institute: Huazhong agricultural university

summary:
OsTMF is a transcription factor and negatively regulates cold tolerance
We used microarray analysis to find differentially expressed genes in OsTMF overexpression (OsTMF-OE) plants compared with the wild-type rice ZH11.

overall_design: Two independent OsTMF-OE lines (OE-24 and OE-29) and ZH11 (two independent biological replicates) at the 4-leaf stage were sampled under normal or cold stress conditions for microarray experiments.

first: Lizhong

last: Xiong


title: A recurrently amplified long noncoding RNA in colorectal cancer regulates p53 protein stability through GRWD1/RPL11/MDM2 axis [RNA-seq]

city: shanghai

first: Xuan

last: Deng

address: No.512 Huashan Road

institute: Huashan Hospital

summary: By integrating genome-wide copy number alteration, RNA-seq and proteomics data from 589 colorectal cancer (CRC) patients, we revealed that chromosome 8q24.21 amplification is negatively correlated with p53 protein stability. Using siRNA and CRISPR activation screening, we pinpointed a novel long noncoding gene (PiHL, P53 inHibiting LncRNA) from 8q24.21 as a p53 negative regulator. PiHL is drastically upregulated in CRC and is an independent predictor of CRC poor prognosis. Further In vitro and In vivo models demonstrate that PiHL is crucial in maintaining cell proliferation and inhibiting cell apoptosis through a p53-depedent manner. Mechanistically, PiHL acts to promote p53 ubiquitination by sequestering RPL11 from MDM2, through enhancing GRWD1 and RPL11 complex formation. We further show that p53 can form a feedback loop with PiHL by directly binding to PiHL promoter and regulating its expression. Our study successfully illustrates how cancer cells hijack the PiHL-p53 axis to promote CRC progression and suggests PiHL as a potential therapeutic target in human CRCs.

overall_design: We examined gene expression changes in siRNA-NC and siRNA-PiHL treated HCT116 cells using RNA sequencing.

first: Ming

last: Guan


title: Knock-down of all HIF3A splice variants under 1 % hypoxia by siRNA targeting a shared region in Hep3B cells

summary:
The human HIF3A gene undergoes extensive alternative splicing resulting in seven known isoforms. The short splice variant, HIF-3alpha4, is an inhibitor of the hypoxia response driven by HIF-1 and HIF-2. The role of the long isoforms remains unclear.
We used cDNA microarray to study the overall impact of HIF3A knock-down by transfecting Hep3B cells with siRNA targeting a region shared by all splice variants under 1 % hypoxia.

overall_design: Hep3B cells were transfected twice either with control siRNA or siRNA targeting human HIF3A. The cells were first incubated 24 h in normoxia and then 24 h in 1 % hypoxia after the second transfection.


title: Expression profiling of MCF7 cells upon Aminoflavone (AF) or Oncrasin1 (Onc1) treatment

city: Solna

first: Sylvain

last: Peuget

state: Stockholm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institute

summary: We used microarrays to detail the global programme of gene expression upon treatment

overall_design: MCF7 cells were treated either with AF or Onc1 respectively during 8h or 16h,  for RNA extraction and hybridization on Affymetrix microarrays.

first: S

first: G

last: Sanz


title: Overexpression of the long Hypoxia inducible factor (HIF)-3a2 splice variant under 1 % hypoxia in Hep3B cells

summary:
The human HIF3A gene undergoes extensive alternative splicing resulting in seven known isoforms. The short splice variant, HIF-3alpha4, is an inhibitor of the hypoxia response driven by HIF-1 and HIF-2. The role of the long isoforms remains unclear.
We used cDNA microarray to study the overall impact of HIF-3a2 overexpression in Hep3B cells under 1 % hypoxia.

overall_design: Hep3B cells were transfected either with the pcDNA3.1/Zeo(-) empty vector or the HIF-3a2 overexpression plasmid with the HIF-beta overexpression plasmid. The cells were first incubated 24 h in normoxia and then 24 h in 1 % hypoxia.


title: Gene expression of peripheral blood leukocytes in athletes

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

summary: Probiotics may alter stress sensitivity by modulating the gut-brain axis. The heat-inactivated, enteric-colonizing Lactobacillus gasseri, CP2305 (paraprobiotic CP2305), has been shown to ameliorate psychological stress-related symptoms. This study was designed to reveal the beneficial effects of paraprobiotic CP2305 on top athletes experiencing physical and mental stresses.

overall_design: Forty-nine male university Ekiden runners were randomly assigned to two groups. These athletes consumed a test beverage containing paraprobiotic CP2305  or placebo daily, for 12 weeks. Before and 12 weeks after beverage consumption, the gene expression profiles in peripheral blood leukocytes were assesed by Agilent microarray (SurePrint G3 Human GE 8×60k).

first: Daisuke

last: Sawada


title: The Long-Form Hypoxia-Inducible Factor 3 Is a Transcription Activator that Regulates Erythropoietin Signaling

first: Jussi-Pekka


title: Transcriptome analyses of luminal-derived basal cells induced by hormones in the mammary gland

city: Shanghai

first: Wenqian

last: Song

address: Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS

summary: We have used RNA-seq to examine RNA differential expression among three populations, normal basal cells, luminal-derived basal cells (LdBCs) and normal luminal cells.

overall_design: Examination of RNA differential expression among three populations of epithelial cells isolated from hormone-treated mammary glands.

first: Yi

middle: A

last: Zeng


title: Effect of Ankrd31 deficiency in mouse testicular transcriptome

city: Dresden

first: Attila

last: Toth

state: Saxony

address: Fiedlerstr. 42

department: Faculty of Medicine

institute: TU Dresden

summary: To test if there is any change in transcriptome in Ankrd31+/+ and Ankrd31-/- mice using  RNA-seq

overall_design: RNA-seq experiments were performed in juvenile (12dpp) testes from 3xAnkrd31+/+ and 3xAnkrd31-/- mice


title: Gene expression changes induced by hypomethylating agent, Azacitidine (AZA) ; IDH1 inhibitor, BAY1436032 (BAY) and combination of BAY and AZA in sorted human (CD45+) cells from bone marrow of IDH1mut Patient derived Xenotransplantation mice model.

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Mutations in the enzymes IDH1 and IDH2 have been identified in a wide variety of tumors like glioma, chondrosarcoma, thyroid cancer, lymphoma, melanoma, and in acute myeloid leukemia. Mutated IDH1/2 produces the metabolite 2-hydroxyglutarate (2HG), which interferes with epigenetic regulation of gene expression, and thus may promote tumorigenesis.  Data for IDH1 inhibitors show that 30-40% of AML patients respond to monotherapy with a median duration of response of 8 months, suggesting that IDH1 inhibitors should be combined with other agents to improve efficacy. BAY 1436032 (BAY) is an oral pan-mutant IDH1 inhibitor currently undergoing phase 1 clinical trials. 5-Azacitidine (AZA) is a hypomethylating agent and can activate key epigenetically silenced pathways in AML cells, leading to an arrest of AML cell proliferation.

overall_design: NSG mice were transplanted with cells from human AML patient carrying IDH1mutation. After 60-70% chimerism, mice were treated either with vehicle, azacitidine (1 mg/kg, s.c., days 1 to 5), BAY1436032 (150 mg/kg, p.o., q.d., 4 weeks) or the simultaneous combination of BAY1436032 and azacitidine. Four weeks after treatment, human CD45+ cells were sorted from mouse bone marrow, from which total RNA was extracted and subjected to microarray analysis.

first: Michael

last: Heuser


title: The mRNA expression analysis of mesenchymal stem cell from psoriasis skin lesion

city: Taiyuan

first: Ruifeng

last: Liu

state: Shanxi

address: No. 1 Dong San Dao Xiang

department: Institute of Dermatology

institute: Taiyuan City Centre Hospital

summary: mRNA sequencing for 6 samples of skin-derived mesenchymal stem cells from either normal skin or psoriasis skin lesion.

overall_design: Examining 2 conditions (normal or psoriasis), each with 3 replicates


title: Glioblastoma multiforme cancer stem cells from different patients exhibit consistent gene expression changes following Hes3 RNA interference

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

summary: Cancer cells are plastic, switching between signaling pathways to regulate growth under different conditions. In the tumor microenvironment this likely helps them evade therapies that target specific pathways. We must identify all possible signaling states and utilize them in drug screening programs to. One such state is characterized by expression of the transcription factor Hes3 and sensitivity to Hes3 knockdown and can be modeled in vitro by the use of defined culture conditions. Here we modeled this state in vitro, characterized it, and used it to identify drugs that target it. We cultured three primary human brain cancer cell lines, each from a different patient, under three different culture conditions (low, medium, and high Hes3 expression) and characterized gene regulation (RNA sequencing) and mechanical phenotype (real-time deformability assay). We also assessed gene expression regulation following Hes3 knockdown in conditions that maintain high Hes3 expression. We then employed a commonly used human brain tumor cell line to screen 1,600 FDA-approved compounds that specifically target the Hes3-high state in two different culture conditions (high and low Hes3). Cells from multiple patients behave similarly when placed under distinct culture conditions, in the assays described. We identified 37 FDA-approved compounds that specifically kill cancer cells in conditions characterized by high but not those characterized by low Hes3 expression. Our work reveals novel, potentially core signaling states in cancer, a strategy to identify treatments against them, and a set of putative drugs for potential repurposing.

overall_design: RNA-seq data from quadruplicate samples of different human glioblastoma multiforme primary cancer stem cell lines grown in defined culture conditions and treated with either Hes3 or scrambled control siRNA.

first: Steven

last: Poser

first: Mathias

last: Lesche

last: Dahl

last: Ge

first: Carlo

last: Cannistraci

first: Barbara

last: Klink

first: Konrad

last: Gruetzmann


title: SFPQ depletion is synthetically lethal with BRAFV600E in colorectal cancer cells I

city: New York

first: Florian

last: Uhlitz

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: Oncoproteins such as the BRAFV600E kinase entrust cancer cells with malignant properties, but they also create unique vulnerabilies. Therapeutic targeting of the BRAFV600E-driven cytoplasmic signaling network has proven ineffective, since patients regularly relapse with reactivation of the targeted signaling pathways. Here, we identified the nuclear protein SFPQ to be synthetically lethal with BRAFV600E in a loss-of-function shRNA screen. SFPQ depletion decreased proliferation and induced apoptosis in BRAFV600E-driven colorectal and melanoma cells, and reduced tumor growth in xenografts. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggered the Chk1-dependent replication checkpoint, resulting in replication stress in the absence of overt DNA damage. Affected cells stalled in S-Phase with hallmark signs of impaired replication factories. Induction of BRAFV600E and concomitant loss of SFPQ sensitized cells to a combination of DNA replication checkpoint inhibitors and chemically induced replication stress, pointing towards future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAFV600E.

overall_design: Caco2 wt shRen (Control shRNA), Caco2 wt shSFPQ and Cacc2 BRAFV600E shControl Caco2 BRAFV600E shSFPQ were treated with doxycycline for 48h to induce an ectopic expression of the the shRNAs and if applicable the BRAF oncogene. The RNA was isolated, depleted of ribosomal RNA and paired-end sequenzed (125 bp).

first: Kathleen

last: Klotz-Noack

first: Bertram

last: Klinger

first: Maria

last: Rivera

first: Natalie

last: Bublitz

first: Pamela

last: Riemer

first: Mareen

last: Lüthen

first: Thomas

last: Sell

first: Katharina

last: Kasack

first: Bastian

last: Gastl

first: Sylvia

middle: S

last: Ispasanie

first: Tincy

last: Simon

first: Nicole

last: Janssen

first: Matthias

last: Schwab

first: Johannes

last: Zuber

first: David

last: Horst

first: Nils

last: Blüthgen

first: Reinhold

last: Schäfer

first: Markus

last: Morkel

first: Christine

last: Sers


title: microRNA data involved in T3 treated Japanese flounder (Paralichthys olivaceus)

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

type: Non-coding RNA profiling by high throughput sequencing

summary: After comparing albinism rate, T3 treatment and control larvae of 42 DAH were chosen for next high-throughput sequencing analyses of miRNA. A total of 337 miRNAs were identified via miRNA-seq and 12 miRNAs exhibited significantly differential expression patterns in D42_T3 vs D42_Con (TPM > 10, fold change ≥ 1.5 or ≤ 0.67 and q ≤ 0.05). These differentially expressed miRNAs targeted 3658 putative genes, further enriching 10 GO terms (q < 0.05).

overall_design: Examination of the T3 treated and the  control Paralichtys olivaceus

first: Songlin

last: Chen


title: Transcriptome involved in T3 treated Japanese flounder (Paralichthys olivaceus)

summary: After comparing albinism rate, T3 treatment and control larvae of 42 DAH were chosen for next high-throughput sequencing analyses of mRNA. RNA-seq identified 146 differentially expressed genes (DEGs) in D42_T3 versus D42_Con (|log2Foldchange| > 1 and q < 0.005), including pigmentation related genes such as the receptor tyrosine-protein kinase erbB-3, pro-opiomelanocortin A, melanotransferrin, and the growth-related gene somatotropin. These DEGs were significantly enriched to 15 GO terms and 8 KEGG pathways (q < 0.05), among which, several sugar metabolic pathways were included (glycolysis/gluconeogenesis and the pentose phosphate pathway).

overall_design: Examination of the T3 treated and the  control Paralichtys olivaceus  by RNA-seq


title: Next Generation Sequencing Combined Analysis of DNA Methylome and Transcriptome Reveal Novel Candidate Genes of Neuroprotective with Response to Ischemic Preconditioning

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

summary: Ischemic preconditioning (IPC) is a phenomenon in which a short-term sublethal ischemic exposure induces tolerance to a subsequent lethal ischemic insult; however, the detailed mechanism underlying IPC-induced neuroprotection remains unclear. Here, we applied middle cerebral artery occlusion (MCAO) as a preconditioning ischemic insult mouse model to investigate the molecular mechanism underlying cerebral IPC. RNA-seq and whole-genome bisulfite sequencing (WGB-Seq) were performed to explore the gene expression profile and DNA methylation changes after cerebral IPC treatment. In this study, we identified 636 differentially expressed genes enriched for several pathways that were partially overlapping or interconnected. The involvement of several genes involved in IPC induced neuroprotection were first reported. Genes induced by IPC including Arid5a, Nptx2 and Stc2 were validated with a neuroprotective effect against oxygen-glucose deprivation (OGD)-induced neurotoxicity in vitro. Moreover, Arid5a and Nptx2 were two DMR related genes and showed hypo-methylation in their regulative regions. Thus, our findings provide new insights into IPC signaling pathways and offer a new therapeutic strategy for the treatment of stroke.

overall_design: RNA-seq and whole-genome bisulfite sequencing (WGBS) were performed to explore the gene expression profile and DNA methylation changes after cerebral IPC treatment, in triplicate, using Illumina HiSeq 2000 platform.

first: Menghua

last: Cai


title: Improving drug discovery using image-based multiparametric analysis of the epigenetic landscape

status: Public on Dec 29 2019

city: La Jolla

first: Chen

last: Farhy

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: With the advent of automatic cell imaging and machine learning, high-content phenotypic screening has become the approach of choice for drug discovery due to its ability to extract drug-specific multi-layered data, which could be compared to known profiles. In the field of epigenetics, such screening methods have suffered from a lack of tools sensitive to selective epigenetic perturbations. Here we describe a novel approach, Microscopic Imaging of Epigenetic Landscapes (MIEL), which captures the nuclear staining patterns of epigenetic marks (e.g., acetylated and methylated histones) and employs machine learning to accurately distinguish between such patterns. We validated the fidelity and robustness of the MIEL platform across multiple cells lines and using dose-response curves, to insure the robustness of this approach for high content high throughput drug discovery. Focusing on alternative, non-cytotoxic, glioblastoma treatments, we demonstrated that the MIEL assay can identify epigenetically active drugs and classify them by molecular function. Furthermore, we show MIEL was able to accurately rank candidate drugs by their ability to produce a set of desired epigenetic alterations consistent with increased sensitivity to chemotherapeutic agents or with induction of glioblastoma differentiation.

overall_design: Glioblastoma tumor propagating cells untreated or treated with either fetal bovine serum (10%) or Bmp4 (10ng/ml); 3 replicates each. Glioblastoma tumor propagating cells treated with DMSO or one of the following compounds: Digoxin, Digitoxigenin, Fenbendazole, Mebendazole, Etoposide, Irinoteca, Cytarabine, Trifluridine, SAHA, TSA, Valproic-Acid; one replicate each.

first: Alexey

last: Terskikh


title: Age-related transcriptional modules and TF-miRNA-mRNA interactions in neonatal and infant human thymus [miRNA]

status: Public on Dec 27 2019

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: The human thymus shows a transient involution along the neonatal period and starts a continuous process of decline between the 1st and 2nd years. The immune alterations associated to thymic aging in humans have been extensively investigated, but the genomic mechanisms underlying this process remain largely unknown. Here we conducted a temporal gene co-expression network analysis in the newborn and infant thymic tissue aiming to identify transcriptional modules associated to age.

overall_design: Temporal gene co-expression network analysis and miRNA analysis in the newborn and infant thymic tissue aiming to identify transcriptional modules associated to age.

first: Fernanda

last: Bertonha

first: Silvia

last: Bando

first: Leandro

last: Ferreira

first: Paulo

last: Chaccur

first: Christiana

last: Vinhas

first: Maria

last: Zerbini

first: Madga

last: Carneiro-Sampaio


title: Age-related transcriptional modules and TF-miRNA-mRNA interactions in neonatal and infant human thymus [mRNA]


title: Age-related transcriptional modules and TF-miRNA-mRNA interactions in neonatal and infant human thymus

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

overall_design: Refer to individual Series


title: Paracrine orchestration of intestinal tumorigenesis by a confined mesenchymal niche

status: Public on Dec 21 2019

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street, TAC S-569

department: Department of Immunobiology

institute: Yale University


title: Single cell RNA sequencing analysis of the mouse colonic mesenchyme (Drop-seq)

summary: Single cell RNA sequencing of the mouse colonic mesenchyme. Mesenchymal/lamina propria cells were isolated from the middle and distal colon of wild type mice in two biological replicates. For each biological replicate the colons of n = 2 mice were pooled. The vast majority of intestinal epithelial cells were depleted by Ethylenediaminetetraacetic acid (EDTA) treatment of the tissue samples and mesenchymal/lamina propria cells were isolated after enzymatic treatment with collagenase XI and dispase. Single cell RNA sequencing was performed with the Drop-seq protocol. N =5 Drop-seq collections (samples) were processed in total, two from the first biological replicate and three from the second.

overall_design: Two biological replicates (C1 and C2): one with two Drop-seq collections (samples C1A, C1B) and one with three Drop-seq collections (samples C2A, C2B, C2C)

first: Manolis

last: Roulis


title: Single cell RNA sequencing of intestinal fibroblast-crypt co-cultures in organoid growth media with/without Ptger4/EP4 inhibitor (Drop-seq)

summary: Mouse small intestinal crypts were co-cultured with primary intestinal fibroblasts in Organoid Growth Media (OGM) with/without inhibitor for the prostaglandin E2 receptor Ptger4 (EP4), labeled respectively as “Ptger4-OFF” and “Ptger4-ON” conditions. Crypts co-cultured with fibroblasts in Ptger4-ON conditions (OGM containing DMSO vehicle control) acquired a spheroid morphology. Crypts co-cultured with fibroblasts in Ptger4-OFF conditions (OGM supplemented with Ptger4 inhibitor) developed into budding organoids. Fibroblasts were isolated from the small intestine of wild type mice. For the co-cultures 2 x 10e4 fibroblasts were seeded in 48-well plates overnight. Freshly isolated crypts (n = 500) were suspended in 1:1 Matrigel (Corning, 356231) and IntestiCult Organoid Growth Medium (Stem Cell Technologies, 06005) and added as an overlay on the fibroblasts. Crypts/fibroblasts were co-cultured with IntestiCult Organoid Growth Medium for 4 days. The ONO-AE3-208 Ptger4 (EP4) inhibitor (Cayman, 14522) dissolved in DMSO was added to the co-cultureson days 0 and 2 at a final concentration of 10 uM. DMSO was used as a vehicle control for the untreated co-cultures. On day 4, one pool of six Ptger4-ON co-cultures and one pool of six Ptger4-OFF co-cultures were subjected to the Drop-seq protocol.

overall_design: One pool of n = 6 Ptger4-ON intestinal fibroblast/crypt co-cultures (DMSO vehicle control, spheroid growth) and one pool of n = 6 Ptger4-OFF intestinal fibroblast/crypt co-cultures (ONO-AE3-208 Ptger4 inhibitor, budding organoid growth)


title: Comparative transcriptome analysis of banana (Musa acuminata L. AAA group, cv. Cavendish) leaves and roots in response to low-potassium stress

city: Haikou

first: Min

last: Xu

address: No.58 Renmin Avenue,Haikou, Hainan, China

institute: Hainan University

summary: Potassium (K+) is a crucial macronutrient in high biomass plants, especially in banana.we comparatively studyed the phenotypic traits and transcriptomic profiles of banana leaves and roots between low potassium group (LK) and normal-potassium group (NK). In our study, the K+ content and biomass index of banana seedling were all significantly decreased under the stress of low potassium group. Moreover, thirty differentially expressed genes (DEGs) related to potassium transport and uptake and transcription factors were analyzed deeply. DEGs about ABC transporters, protein kinases and ion transporters were also detected, these genes may play important roles during potassium deficiency. These results provide valuable information about banana response to low potassium conditions.

overall_design: RNA-Seq (Quantification) of 60-day treated low potassium group (LK) and normal-potassium group (NK) banana seedlings were generated by deep sequencing, using Illumina HiSeqTM 2000.

first: Can

last: Zeng

first: Rui

last: He

last: Peng

first: Zhen

last: Yan

first: Zhao

last: Qi

last: Xiong

first: Yu

last: Cheng

first: Dong

middle: T

middle: Z

last: Ruan

first: Yin

middle: H

first: Shuang

last: Wei

first: Jun

last: Xie

first: You

middle: Q

last: Xia

first: Hua

last: Tang


title: Expression profile of MDA-MB435 cells

status: Public on Dec 19 2019

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

institute: Hebrew University

summary:
To further analyze the effect of WWOX on metastasis formation, we studied the differential expression of mRNAs using Affymetrix genechip in WWOX- sufficient and deficient metastatic cells.
We set to determine comprehensive molecular and proteomic changes in WWOX –expressing cancer cell lines.

overall_design: We performed mRNA profiling in empty-vector (Ev), WWOX and WWOX-WFPA mutant – expressing in MDA-MB435s cells.

first: Saleh

last: Khawaled

first: Yoav

last: Smith


title: Characterisation of Cap-G binding and its role in post-mitotic neurons in Drosophila

status: Public on Dec 17 2019

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: In order to gain a greater understanding of the role of the condensin subunit Cap-G in post-mitotic neurons, we profiled the binding of Cap-G to chromatin in neurons (at different stages of maturation) and neural stem cells in Drosophila using Targeted DamID. We also performed RNA-seq on larval brains that had Cap-G was knocked-down specifically in neurons.

overall_design: Profiling of Cap-G binding in neurons of Drosophila. Also RNA-seq profiling of Cap-G knockdown larval brains.

middle: D

first: Amira

last: Hassan

first: Gabriel

middle: N

last: Aughey


title: Whole genome expression profiling of triple negative breast tumors in 226 African American women

city: Detroit

first: Kristen

last: Purrington

state: MI

address: 4100 John R St.

institute: Wayne State University

summary: Purpose: Black/African American (AA) women are twice as likely to be diagnosed with triple negative breast cancer (TNBC) compared to whites, an aggressive breast cancer subtype associated with poor prognosis. There are no routinely used targeted clinical therapies for TNBC; thus there is a clear need to identify prognostic markers and potential therapeutic targets.  Methods: We evaluated expression of 27,016 genes in 155 treatment-naïve TN tumors from AA women in Detroit. Associations with survival were evaluated using Cox proportional hazards models adjusting for stage and age at diagnosis, and p-values were corrected using a false discovery rate. Our validation sample consisted of 158 TN tumors (54 AA) from The Cancer Genome Atlas (TCGA). Meta-analyses were performed to obtain summary estimates by combining TCGA and Detroit AA cohort results.  Results: In the Detroit AA cohort, CLCA2 [Hazard ratio (HR)=1.56, 95% confidence interval (CI) 1.31-1.86, nominal p=5.1x10-7, FDR p=0.014], SPIC [HR=1.47, 95%CI 1.26-1.73, nominal p=1.8x10-6, FDR p=0.022], and MIR4311 [HR=1.57, 95% CI 1.31-1.92, nominal p=2.5x10-5, FDR p=0.022] expression were associated with overall survival. Further adjustment for treatment and breast cancer specific survival analysis did not substantially alter effect estimates. Meta-analysis with TCGA data showed that CLCA2 and SPIC were associated with overall survival for TNBC among AA women.  Conclusions: We identified three potential prognostic markers for TNBC in AA women, for which SPIC may be an AA-specific prognostic marker.

overall_design: 226 RNA samples from FFPE triple negative breast tumors. No replicates or control included


title: Single cell RNA sequencing of cells isolated from the intestinal crypts of mice bearing epithelial cell-specific Ptger4 ablation (Drop-seq)

first: Richard

last: Flavell

summary: Crypts isolated from the small intestine of mice bearing epithelial cell-specific ablation of the Ptger4 gene (VillinCrePtger4flox, "V") and normal littermate control mice (Ptger4flox, "F") were dissociated into single cell suspensions and subjected to the Drop-seq protocol. N = 2 mice per genotype were independently processed as biological replicates (V1, V2 and F1, F2). A total of three Drop-seq collections (samples) were processed for each genotype, two from the first biological replicate (V1A, V1B, F1A, F1B) and one from the second biological replicate (V2, F2).

overall_design: A total of three Drop-seq collections (samples) were analyzed per genotype from two biological replicates per genotype

first: Manolis

last: Roulis


title: Gene expression profile of subcutaneous adipose tissue in BMI-discordant monozygotic twin pairs in obesity

status: Public on Dec 13 2019

city: Helsinki

first: Maheswary

last: Muniandy

address: Tukholmankatu 8

institute: University Helsinki

summary:
Background
Subcutaneous adipose tissue (SAT) undergoes major changes in obesity, but little is known about the whole-genome scale patterns of these changes or about their variation between different obesity subgroups. We sought to compare how transcriptomics profiles in SAT differ between monozygotic (MZ) co-twins who are discordant for body mass index (BMI), whether the profiles vary between twin pairs and whether the variation can be linked to clinical characteristics.
Methods
We analyzed the transcriptomics (Affymetrix U133 Plus 2.0) patterns of SAT in young MZ twin pairs (n =26, intrapair difference in BMI>3 kg/m2, aged 23-36), from 10 birth cohorts of adult Finnish twins. The clinical data included measurements of body composition, insulin resistance, lipids, and adipokines.
Results
We found 2108 genes differentially expressed (FDR<0.05) in SAT of the BMI-discordant pairs. Pathway analyses of these genes revealed a significant downregulation of mitochondrial oxidative pathways (p<0.05) and upregulation of inflammation pathways (p<0.05). Hierarchical clustering of heavy/lean twin ratios, representing effects of acquired obesity in the transcriptomics data, revealed three sub-groups with different molecular profiles (FDR<0.05). Analyses comparing these sub-groups showed that, in the heavy co-twins, downregulation of the mitochondrial pathways, especially that of branched chain amino acid (BCAA) degradation was more evident in two last clusters while and upregulation of the inflammatory response was most evident in the last, presumably the unhealthiest cluster. High fasting insulin levels and large adipocyte diameter were the predominant clinical characteristic of the heavy co-twins in this cluster (Bonferroni adjusted p<0.05).
Conclusions
This is the first study in BMI-discordant MZ twin pairs reporting sub-types of obesity based on both SAT gene expression profiles and clinical traits. We conclude that a decrease in mitochondrial BCAA degradation and an increase in inflammation in SAT co-occur and associate with hyperinsulinemia and large adipocyte size in unhealthy obesity.

overall_design: 52 samples made out of 26 twin pairs who are discordant for BMI

first: Kirsi

last: Pietilainen


title: Transcriptomic analysis of Pichia pastoris (Komagataella phaffii) GS115 during heterologous protein production using a high-cell-density fed-batch cultivation strategy

status: Public on Dec 20 2019

city: Kunming

first: Zunxi

last: Huang

state: Yunnan

address: 768 Ju Xian Street

institute: Yunnan Normal University

summary: We investigated gene expression during the bench-scale batch fermentation phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth, and may regulate the AOX1 promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris protein expression, regulation, and secretory mechanisms.

overall_design: Investigate the physiological and metabolic characteristics of Pichia pastoris producing exogenous proteins under high-cell-density culture conditions

first: Chengbo

last: Zhang


title: Single cell RNA-seq analyses of dermis from wound day 18 large skin wounds that healed in a fibrotic or regenerative fashion.

status: Public on Dec 12 2019

first: Denise

last: Gay

address: 550 1st avenue

institute: NYU langone

summary: Human and murine skin wounding commonly result in fibrotic scarring but the murine wounding model Wound Induced Hair Neogenesis (WIHN) can frequently result in a regenerative repair response. Here we show in single cell RNA-seq comparisons of semi-regenerative and fibrotic WIHN wounds, increased expression of phagocytic/lysosomal genes in macrophages associated with predominance of fibrotic myofibroblasts in fibrotic wounds. Investigation revealed that macrophages in the late wound drive fibrosis by phagocytizing dermal Wnt inhibitor SFRP4 to establish persistent Wnt activity. In accordance, phagocytosis abrogation resulted in transient Wnt activity and a more regenerative healing. Phagocytosis of SFRP4 was integrin-mediated and dependent on the interaction of SFRP4 with the EDA splice variant of fibronectin. In the human skin condition Hidradenitis suppurativa, phagocytosis of SFRP4 by macrophages correlated with fibrotic wound repair. These results reveal that macrophages can modulate a key signaling pathway via phagocytosis to alter the skin wound healing fate.

overall_design: These are single analyses of two distinct healing fates (fibrotic or regenerative) in large wounds. 6-8 wounds were combined from each condition for each analysis.


title: Adaptation to industrial stressors through genomic and transcriptional plasticity in a bioethanol producing fission yeast isolate [RNA-seq]

status: Public on Dec 11 2019

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ~100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.

overall_design: RNA-sequencing for Wilmar-A and WIlmar-P cells cultured in rich (YES) medium containing 3% glucose, 3% glycerol + 0.1% glucose (glucose-deficient) or 3% glycerol (glucose-starved) conditions. Additionally, RNA-seq  data from laboratory S> pombe 972h- and WIlmar-P cells cultured in molasses medium.

first: Brendon

last: Monahan