title: The X chromosome gene Kdm6a modulates multiple immune response genes in CD4+ T cells and is disease-promoting in autoimmune disease

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: Multiple sclerosis (MS) is a T-cell mediated autoimmune disease that has a sexually dimorphic pattern in disease susceptibility. Consistent with many autoimmune diseases, females are more susceptible than males to MS. Sexual dimorphisms may be due to differences in sex hormones, sex chromosome genes, or both. Regarding sex chromosome genes, a small percentage of X chromosome genes escape the dosage compensation mechanism of X inactivation and have higher expression in females (XX) compared to males (XY). According to the high throughput analysis, the top sexually dimorphic gene with higher expression in CD4+ T cells from females (vs. males) and from XX mice (vs. XY) was Kdm6a, a histone demethylase and transcription factor on the X chromosome. Deletion of Kdm6a specifically in CD4+ T cells ameliorated clinical disease and reduced neuropathology in the classic CD4+ T cell mediated autoimmune disease, experimental autoimmune encephalomyelitis (EAE). Global transcriptome analysis in CD4+ T cells from EAE mice with a specific deletion of Kdm6a showed upregulation of Th2 and Th1 activation pathways and downregulation of neuroinflammation signaling pathways. Together, this demonstrates that the X escapee Kdm6a regulates multiple immune response genes, providing a mechanism for sex differences in autoimmune disease susceptibility.

overall_design: To determine the influence of differential Kdm6a expression in immune cells, whole transcriptome analysis for CD4+ T cells from WT and cKO mice were performed using RNA-Seq.

first: Noriko

first: Lisa

last: Golden

first: Arthur

middle: P

last: Arnold

first: Rhonda

last: Voskuhl


title: Transcriptome profiling analysis of Mactra veneriformis exposed to BDE-47 by deep sequencing

status: Public on Oct 19 2019

city: Yantai

first: Yan

last: Fang

state: Shandong

address: No. 186 Hongqizhong Road

department: agriculture college

country: China

institute: Ludong university

type: Expression profiling by high throughput sequencing

summary: RNA-seq provided a general overview of the gene expression profiles of the digestive glands of Mactra veneriformis exposed to 2, 2′,4,4′-tetrabromodiphenyl ether (BDE-47, a type of widely used brominated flame retardants).

overall_design: After acclimatization, the animals were then divided randomly into control group and BDE-47 treatment group. In treatment group, the clams were exposed to BDE-47 for 3 days with the nominal concentration of 5μg/L. BDE-47 was first dissolved in DMSO, and then added to aquaria water to achieve a final DMSO concentration of 0.05% v/v. In control group, DMSO was added directly to aquaria water with the final concentration of 0.05% v/v. Three replicates of control and treatment were performed. Each replicate contained 30 clams. During the whole experiment, the water was constantly aerated (dissolved oxygen 7.6–8.2 mg/L; pH 8.1; salinity 31; temperature 16 ± 1°C) and changed daily. The clams were fed 2 h before the water change, and the corresponding concentrations of BDE-47 and DMSO were added after the water change. The digestive gland was sampled after 3 days’ exposure. Digestive glands from 30 clams were dissected and pooled together for RNA extraction.


title: Gene expression data from NK cells sorted for PD-L1 after co-incubation with K562 myeloid leukemia cells

status: Public on Oct 18 2019

city: Houston

first: Stephen

last: Wong

state: TX

address: 6670 Bertener

department: Systems Medicine and Bioengineering Department

country: USA

institute: Houston Methodist Neal Cancer Center

summary: The objective was to determine if there are differences in gene expression in PD-L1+ and PD-L1- NK cells after co-incubation of NK cells with target K562 myeloid leukemia cells.

overall_design: Primary NK cells were sorted to >96% purity CD3-CD56+ from 3 healthy donors. These enriched NK cells from the 3 donors were incubated with K562 myeloid leukemia target cells for 24 hours in order to induce PD-L1 expression. After 24 hours the cells were sorted into PD-L1+ and PD-L1- NK cells, RNA extracted and microarray performed on the 6 samples (3 donors PDL-1+ or PDL-1- after co-incubation). Data on differential gene expression of PD-L1+ and PDL-1- NK cells after co-incubation with leukemia target cells will provide more insight into the function and potential usage of these two populations for leukemia.

first: Jianhua

last: Yu


title: Cell-type specific action of Bcl11b in early T-lineage and group 2 innate lymphoid cell

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The zinc finger transcription factor, Bcl11b, is expressed in T cells and group 2 innate lymphoid cells (ILC2s) among hematopoietic cells.  In early T-lineage cells, Bcl11b directly binds and represses endogenous E protein antagonist, Id2, expression to prevent pro-T cell from adopting an innate-like fate.  In contrast, ILC2s co-express both Bcl11b and Id2.  Here, to address this contradiction, we have directly compared Bcl11b action mechanisms in pro-T cells and ILC2s.  We found that Bcl11b binds to distinctive genomic regions across the genome with cell-type specific motif preferences.  Bcl11b occupies functionally different sites in lineage specific way and controls totally different sets of target genes, while both of cell types use the same distal enhancer region to control timing of Bcl11b activation.  In addition, Bcl11b seems to have cell-type specific post-translational modifications and to organize differential protein complexes.  Therefore, despite pro-T cells and ILC2s share Bcl11b for their optimal development and function, Bcl11b is able to regulate substantially different target genes.

overall_design: ChIP-seq and RNA-seq

first: Maile

last: Romero-Wolf

first: Qi

last: Yang

first: Yasutaka

last: Motomura

first: Yoram

last: Groner

first: Kazuyo

last: Moro

first: Tomoaki

last: Tanaka

first: Ellen

middle: V

last: Rothenberg


title: Transcriptomic studies in the development and ripening of strawberry fruits (Agilent)

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary:
Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over
32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.

overall_design: A custom-made oligo microarray (60-mer length) platform (FraGenomics 35k) containing a total of 35234 singletons corresponding to those sequences published in the strawberry genome project (http://www.strawberry.org). For each sequence, 4 different oligos were printed per block and four blocks were printed per data set. We have analyzed two control samples green fruits, and two samples of red fruits

first: Juan

last: Muñoz-Blanco

first: Laura

last: Medina-Puche

middle: J

first: Rosario

last: Blanco-Portales


title: Role of Fragaria FaPRE1 in fruit ripening [FaPRE1-RNAi]

summary:
The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaPRE1, a non-DNA-binding  bHLH transcription factor.
FaPRE1 is a ripening-related transcription factor that regulates genes involved in cell architecture in strawberry fruit receptacles.

overall_design:
A custom-made oligo microarray (60-mer length) platform (FraGenomics 35k) containing a total of 35234 singletons corresponding to those sequences published in the strawberry genome project (http://www.strawberry.org). For each sequence, 4 different oligos were printed per block and four blocks were printed per data set. We have analyzed three control samples fruits agroinjected with the empty vector, a three samples fruits agroinjected with the RNAi construct.

Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated).  Therefore 3 raw data files for  total 6 samples are linked as Series supplementary files and the associated raw data file is indicated in the corresponding sample description field.


title: PRRX1 overexpression in MDA-MB-231 breast cancer cells

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

institute: Instituto de Neurociencias (CSIC-UMH)

summary:
To investigate downstream targets of PRRX1, we used MDA-MB-231 (MDA231) breast cancer cells which express low level of PRRX1 to generate a stable cell line where human PRRX1 was ectopically overexpressed
(MDA231-PRRX1), and performed comparative microarray analyses. Interestingly, we found many miRNAs that were upregulated in MDA231-PRRX1 cells.

overall_design: MDA231 cells were transduced with lentiviral vectors containing PRRX1, GFP and puromycine resistance cassette, and were selected with antibiotics. Pool of stably transduced cells were used for further analyses and microarray.

first: Oscar

middle: H

last: Ocaña


title: A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

type: Methylation profiling by high throughput sequencing

summary:
Background
Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders.

Results
In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes.

Conclusions
The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.

overall_design: Genomic DNA and RNA were extracted from the samples using MasterPure DNA puriﬁcation kit (Epicentre, USA) and RNeasy Micro Kit (Qiagen Ltd, UK), respectively as described by (Athanasio et al. 2016, 2018). EpiGenome Methyl-Seq kit (Epicentre, USA) was used to prepare the WGBS libraries and sequenced (2x80bp) using Illumina NextSeq 500 platform at the Centre for Genomics and Bioinformatics, Indiana University. The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (1x85bp) using Illumina NextSeq 500 platform at the Centre for Genomics and Bioinformatics, Indiana University. The chromatin immunoprecipitation sequencing libraries (ChIP-seq) were prepared using the iDeal-seq kit, H3K4me3 (C15410003-50, 1 ug/reaction), H3K27me3 (C15410195, 1 µg/reaction) antibodies and sequenced using Illumina HiSeq 2500 (1x50 bp) as part of a service provided by Diagenode (Belgium). Daphnia samples (30 mg wet tissue per sample) were homogenised in 1 ml of PBS/1%formaldehyde using Dounce homogenizer. The collected cells were lysed and the nuclei were collected and sonicated to a final size of 80-400 bp. The mentioned antibodies were used to prepare test samples according to the manual for the iDeal ChIP-seq kit. The IP samples and input samples were quantified using the Qubit dsDNA HS kit. Library preparation was performed on the IP and input samples using the MicroPLEX library preparation protocol on 500 pg of DNA. The amplified libraries (13 PCR cycles) were purified using AMPure beads, quantified using the Qubit ds DNA HS kit and analysed on Bioanalyzer. The prepared libraries were then sequenced on HiSeq 2500.

first: Camila

last: Gonçalves Athanàsio

first: Michael

middle: E

last: Pfrender

first: James

middle: B

last: Brown

first: John

middle: K

last: Colbourne

first: Leda

last: Mirbahai


title: The X chromosome gene Kdm6a modulates multiple immune response genes in CD4+ T cells and is disease promoting in autoimmune disease

first: Yuichiro

last: Itoh

overall_design: To determine the influence of differential Kdm6a expression in immune responses, we induced EAE in cKO mice (Kdm6a gene is conditionally knocked out in CD4 cells) and their WT littermate controls. On EAE day 17, lymph node cells were isolated and cultured with autoantigen (MOG35-55) before CD4+ T cell sorting. Whole transcriptome analysis for CD4+ T cells from WT and cKO EAE mice were performed using RNA-Seq.

first: Noriko

first: Lisa

last: Golden

first: Arthur

last: Arnold

first: Rhonda

last: Voskuhl


title: Absolute quantification of proteins and histone modifications in Drosophila embryos reveals stoichiometric relationships in chromatin regulation

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

summary: High-level H3K27me3 domains are required for proper gene repression mediated by Polycomb proteins. Genome-wide profiling of H3K27 methylation during developmental progression and in animals with reduced PRC2 levels illustrates how mass spectrometry-based normalization permits the quantitative analysis of changes in chromatin states.

overall_design: Definition of high-level H3K27me3 domains by genome segmentation, direct comparison of H3K27me3 profiles in 2-4 hr and 14-16 hr wt embryos as well as in 0-6 hr wt and esc mutant embryos.

first: Jacques

last: Bonnet

first: Julien

last: Gagneur

first: Georg

last: Stricker

first: Muhammed

last: Çelik


title: Transcriptome-wide comparison of stress granules and P-bodies reveals that translation plays a major role in RNA partitioning

status: Public on Oct 17 2019

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

summary: The eukaryotic cytosol contains multiple RNP granules including P-bodies and stress granules. Three different methods have been used to describe the transcriptome of stress granules or P-bodies, but how these methods compare, and how RNA partitioning occurs between P-bodies and stress granules has not been addressed. Herein, we compare the analysis of the stress granule transcriptome based on differential centrifugation, with and without subsequent stress granule immunopurification. We find that while differential centrifugation alone gives a first approximation of the stress granule transcriptome, this methodology contains non-specific transcripts that play a confounding role in the interpretation of results. We also immunopurify and compare the RNAs in stress granules and P-bodies under arsenite stress and compare those results to the P-body transcriptome described under non-stress conditions. We find that the P-body transcriptome is dominated by poorly translated mRNAs under non-stress conditions, but during arsenite stress, when translation is globally repressed, the P-body transcriptome is very similar to the stress granule transcriptome. This suggests that translation is a dominant factor in targeting mRNAs into both P-bodies and stress granules, and during stress, when most mRNAs are untranslated, the composition of P- bodies reflects this broader translation repression.

overall_design: Pellet and cyotplasmic RNA were obtained from U-2 OS cells during arsenite stress and unsetressed conditions.  Biological triplicates were obtained for each sample. Paired-end libraries were prepared for these samples.  We also sequenced the RNAs from P-bodies during arsenite stress conditions in both WT and G3BP ko U-2 OS cells.  This was achieved by adapting a previously reported stress granule purification protocol, using an anti-EDC3 antibody(Khong et al. 2017).  Biological triplicates were obtained for each sample.  Single-end libraries were prepared for these samples.

first: Tyler

last: Matheny

first: Bhalchandra

last: Rao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NCoR1 KD  CD8a+ Dendritic cells with and without CpG stimulation

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

summary:
Purpose: The goals of this study to dissect mechanism by which NCoR1 regulate expression of diiferent genes at transcriptional level in CD8a+ Dendritic cells.
Methods: mRNA expression of  Control(Empty) and knockdown (NCoR1+/−) before and after CpG and pIC activation were generated by deep sequencing, in duplicate, using Illumina NextSeq 500 . The sequence reads that passed quality filters were analyzed at the transcript level with two methods:TopHat followed by Cufflinks.
Results: we mapped raw reads to the mouse genome (build mm10) with TopHat. Differential expression study was carried out using Cufflinks v2.2.1 and list were filtered using fold change cut-off of 2 and q value <0.05.
Conclusions: We found in our study that NCoR1 knock down dendritic cells (DCs) develop tolerogenic behavior upon activation and these cells have the potential to modulate T helper cell differentiation toward Treg phenotype. Here to understand the mechanism of this process we performed NCoR1 ChIP-seq in wild type DCs before and after CpG ligand activation and transcriptome analysis of NCoR1 KD DCs to identify the direct and indirect target genes. We also predicted PU.1 as the recruting factor for NCoR1 in DCs based on motif enrichment and later on validated that by performing PU.1 ChIP-seq in control and NCoR1 KD DCs.

overall_design: Mechanistic role of NCoR1 co-repressor in dendritic cell function

first: Abdul

last: Ahad

first: Shuchi

last: Smita

first: Mathias

last: Stevanin

first: Gyan

last: Mishra

first: Dheerendra

last: Gupta

first: Sebastian

middle: M

last: Waszak

first: Bhawna

first: Hans

last: Acha-Orbea


title: MicroRNA-7a overexpression in VMH restores the sympathoadrenal response to hypoglycemia

city: Salt Lake City

first: Rahul

last: Agrawal

state: UTAH

institute: University of Utah

type: Non-coding RNA profiling by high throughput sequencing

summary: It is proposed that the impaired sympathoadrenal response to hypoglycemia induced by recurrent insulin-induced hypoglycemia (RH) is an adaptive phenomenon induced by specific changes in microRNA expression in the ventromedial hypothalamus (VMH). To test this hypothesis, genome-wide microRNAomic profiling of the VMH by RNA-sequencing was performed in control and RH treated rats. Differential expression analysis identified microRNA-7a-5p and microRNA-665 as potential mediators of this phenomenon. To further test this hypothesis, experiments were conducted consisting of targeted lentiviral-mediated overexpression of microRNA-7a-5p and downregulation of microRNA-665 in the VMH. Hyperinsulinemic hypoglycemic clamp experiments demonstrated that targeted overexpression of microRNA-7a-5p (but not downregulation of microRNA-665) in the VMH of RH rats restored the epinephrine response to hypoglycemia. This restored response to hypoglycemia was associated with a restoration of GABAA receptor gene expression. Finally, a direct interaction of microRNA-7a-5p with 3’-UTR of GABAA receptor α1-subunit (Gabra1) gene was demonstrated in a luciferase assay. These findings indicate that 1) the impaired sympathoadrenal response induced by RH is associated with changes in VMH microRNA expression, and 2) microRNA-7a-5p, possibly via direct downregulation of GABA receptor gene expression, may serve as a mediator of the altered sympathoadrenal response to hypoglycemia.

overall_design: 12 samples were analysed (6 from each group).

first: Simon

last: Fisher


title: ChIP-seq analysis to understand the mechanistic role of NCoR1 as a tolerogenic program suppressor in dendritic cells

summary: We found in our study that NCoR1 knock down dendritic cells (DCs) develop tolerogenic behavior upon activation and these cells have the potential to modulate T helper cell differentiation toward Treg phenotype. Here to understand the mechanism of this process we performed NCoR1 ChIP-seq in wild type DCs before and after CpG ligand activation and transcriptome analysis of NCoR1 KD DCs to identify the direct and indirect target genes. We also predicted PU.1 as the recruting factor for NCoR1 in DCs based on motif enrichment and later on validated that by performing PU.1 ChIP-seq in control and NCoR1 KD DCs.


title: RNAseq Analysis in glioblastoma cells treated with Mepazine

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

country: France

institute: INSERM

summary: Glioblastoma cells were treated with vehicle (DMSO) or mepazine (MPZ, 20 μM, 4 hours) and prepared for RNAseq according to ActiveMotif standard procedure. The list of differentially expressed genes from DESeq2 output was selected based on 10% adjusted p-value level and FDR of 0.1.

overall_design: 2 groups (DMSO versus MPZ) each in triplicates

first: Kathryn

last: Jacobs


title: PTENa/b paradoxically promote carcinogenesis through WDR5-H3K4me3 axis [ChIP-seq 2]

city: shanghai

first: ge

last: mengkai

state: State...

address: shanghai

institute: Shanghai Jiao Tong University School of Medicine (SJTU-SM)

summary: We report that USP9X and FBXW11 selectively regulate the stability of PTENa/b but not PTEN proteins by deubiquitination and ubiquitination respectively. USP9X promotes and FBXW11 suppresses tumorigenesis mediated by PTENa/b. In contrast to the current paradigm for PTEN as a tumor suppressor, PTENa/b promote tumorigenesis of cancer cells in a phosphatase-independent manner. Mechanistically, PTENa/b localized in the nucleus regulate expressions of tumor-promoting genes such as NOTCH3 in the similar way as the H3K4 presenter WDR5. Further, PTENa/b but not PTEN directly interact with WDR5 to promote trimethylation of H3K4 and maintain a tumor-promoting signature.

overall_design: To investigate the influence of H3K4me3 at gene promoters with or without PTENa/b depletion by ChIP seq in SMMC-7721.

first: Shao

last: Shen

first: Cheng

last: Zhang

first: Meng

last: Ge

first: Shuang

middle: S

last: Dong


title: Epithelial HMGB1 delays skin wound healing and drives tumor initiation by priming neutrophils for NET formation

status: Public on Oct 16 2019

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Regenerative responses predispose tissues to tumor formation by largely unknown mechanisms. High-mobility group box 1 (HMGB1) is a danger-associated molecular pattern contributing to inflammatory pathologies. Here, we show that HMGB1 derived from keratinocytes, but not myeloid cells, delays cutaneous wound healing and drives skin tumor formation. In wounds of mice lacking HMGB1 selectively in keratinocytes, a marked reduction in neutrophil extracellular trap (NET) formation is observed. Pharmacological targeting of HMGB1 or NETs prevents skin tumorigenesis and accelerates wound regeneration. HMGB1-dependent NET formation and skin tumorigenesis is orchestrated by the cytokine TNF and requires RIPK1 kinase activity. NETs are present in the microenvironment of keratinocyte-derived tumors in mice and lesional and tumor skin of patients suffering from Recessive Dystrophic Epidermolysis Bullosa (RDEB), a disease in which skin blistering predisposes to tumorigenesis. We conclude that tumorigenicity of the wound microenvironment depends on epithelial-derived HMGB1 regulating NET formation, thereby establishing a mechanism linking reparative inflammation to tumor initiation.

overall_design: Bulk RNA Seq= keratinocytes isolated from InvEE HMGB1 fl/fl and InvEE DKer HMGB1 mice

first: Esther

last: Hoste

first: Christian

last: Maueroder

first: Lisette

last: van Hove

first: Leen

last: Catrysse

first: Hanna-Kaisa

last: Vikkula

first: Bastiaan

last: Maes

first: Dyah

last: Karjosukarso

first: Amanda

last: Goncalves

first: Eef

last: Parthoens

first: Ria

last: Roelandt

first: Wim

last: Declercq

first: Ignacia

last: Fuentes

first: Francis

last: Palisson

first: Sergio

last: Gonzalez

first: Julio

middle: C

last: Salas-Alanis

first: Louis

last: Boon

first: Peter

last: Huebener

first: Klaas

middle: W

last: Mulder

first: Kodi

last: Ravichandran

first: Yvan

last: Saeys

first: Robert

middle: F

last: Schwabe

first: Geert

last: van Loo


title: RNASeq of differentiated and undifferentiated BLaER1 cells

city: Munich

first: Veit

last: Hornung

address: Feodor-Lynen-Straße 25

institute: LMU

summary: We generated RNASeq data to investigate the expression levels of RNases in differentiated and undifferentiated BLaER1 cells.

overall_design: Comparision of gene expression profiling between differentiated and undifferentiated BLaER1.

first: Yiming

last: Cheng


title: Tumour-exposed Tregs from IL33 genetical deficient mice

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Ave

institute: NYU Langone

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

overall_design: Refer to individual Series


title: Generation of Blastocyst-like Structures from Extended Pluripotent Stem Cells (single-cell RNA-Seq)

city: La Jolla

first: Ronghui

last: Li

state: CA

address: 10010 North Torrey Pines Road

department: Gene Expression Lab

institute: Salk Institute for Biological Studies

summary: A single mouse blastomere from until 8-cell embryo can generate an entire blastocyst. Whether blastomere-like extended pluripotent stem cells (EPS cells) retain a similar generative capacity remains unknown. Here, we established a 3D differentiation system that enabled the generation of blastocyst-like structures from EPS cells (EPS-blastoids) through lineage segregation and self-organization. EPS-blastoids resembled blastocysts in morphology and cell lineage allocation. EPS-blastoids formation recapitulated key morphogenetic events during preimplantation and early postimplantation development in vitro. Upon transfer, some EPS-blastoids underwent implantation, induced decidualization, and generated live, albeit disorganized, tissues in utero. Single cell and bulk RNA-sequencing analysis revealed that EPS-blastoids contained all three blastocyst cell lineages and shared transcriptional similarity with natural blastocysts. We also provide proof-of-concept that EPS-blastoids can be generated from somatic cells via cellular reprograming. EPS-blastoids provide a unique platform for studying early embryogenesis, and pave the way to generate viable synthetic embryos using cultured cells.

overall_design: To exaimine the similarity and difference between EPS-blastoids and natural blastocysts (control) on the single cell level

first: Yang

last: Yu

first: Cuiqing

last: Zhong

first: Jun

last: Wu

first: Juan Carlos

last: Izpisua Belmonte


city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

summary:
We have found that macrophage migration inhibitory factor (MIF) is essential for the development of effective immunity to the intestinal helminth Heligmosomoides polygyrus, even following vaccination which induces sterile immunity in wild-type mice.
In the context of a Type 2 infection, MIF plays a critical role in polarizing macrophages into the protective alternatively-activated phenotype, and that STAT3 signaling may make a previously unrecognized contribution to immunity to helminths.

overall_design: Intestinal tissues (duodenum) from wild-type (BALB/c) and MIF deficient mice were compared in the steady state and at two different time points (day 3 and day 7) following infection with the gastrointestinal helminth parasite Heligmosomoides polygyrus.

first: Rick

last: Maizels

first: Kara

last: Filbey


title: Gene expression in Tbr2 lineage neurons in the murine cerebral cortex

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

summary:
During cortical development neurons are generated from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activated cell sorting (FACS) to isolate Tbr2-lineage neurons (GFP+) from mice brain at postnatal day 2 (P2) and determined mRNA expression profiles using microarray (Illumina MouseWG-6 v2).
Role of transcription factor Tbr2 in neurodevelopment.

overall_design: FACS isolated Tbr2-lineage neurons (GFP+) from mouse brain cortex at P2 were used for microarray analysis.

first: Tanay

last: Ghosh


title: PTENa/b paradoxically promote carcinogenesis through WDR5-H3K4me3 axis [RNA-seq 2]

first: ge

last: mengkai

overall_design: RNA sequencing in SMMC-7721 cell lines with or without WDR5 depletion by two independent experiments.

first: Shao

last: Shen

first: Cheng

last: Zhang

first: Meng

last: Ge

first: Shuang

last: Dong


title: Transcriptomic analysis (RNAseq) of tumour-exposed Tregs from IL33 genetical deficient mice

summary: Our purpose was to analyse the transcriptomic profile of Tregs from tumor-draining lymph nodes of melanoma-bearing mice in order to understand the functional difference between WT and il33-/- Tregs

overall_design: Examination of Tregs isolated from WT and IL33-deficient melanoma bearing mice

first: Panayotis

last: Verginis


title: Transposition of native chromatin (ATACseq) of tumour-exposed Tregs from IL33 genetical deficient mice

first: Theodoros

last: Sakellaropoulos

summary: Our purpose was to analyse the chromatin landscape of Tregs from tumor-draining lymph nodes of melanoma-bearing mice in order to understand the functional difference between WT and il33-/- Tregs


title: Analysis of the impact of Fto deficiency in mice on gene expression in the vasculature

city: Charlottesville

first: Brant

last: Isakson

address: MR4 Building 409 Lane Road

institute: University of Virginia School of Medicine

summary: In order to analyze the impact of Fto deficiency on the vasculature, RNA was isolated from thoracic aortae of Fto+/+ and Fto-/- mice.

overall_design: In this microarray analysis,  4 samples from Fto +/+ mice were compared to 4 samples from Fto-/- mice. Only RNA with a RNA integrity number > 8 was used for microarray analysis.

first: Nenja

last: Krüger

first: René

last: Deenen

first: Karl

last: Köhrer

first: Ulrich

last: Rüther


title: Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463]

city: Tampere

first: Sanna-Kaisa

middle: Emilia

last: Harjula

address: Arvo Ylpön katu 34

institute: University of Tampere

summary: Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. In addition, we carried out a medium-scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen, we identified a mutant zebrafish line with impaired resistance to a low-dose M. marinum infection. In this line, the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation.

overall_design: Identification of the up- and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed, four biological replicates in each group.

first: Anni

last: Saralahti

first: Markus

last: Ojanen

first: Tommi

last: Rantapero

first: Meri

middle: I

last: Uusi-Mäkelä

first: Matti

last: Nykter

first: Olli

last: Lohi

first: Mataleena

last: Parikka

first: Mika

last: Rämet


title: Single cell and bulk RNAseq profiles of thymic pro-T cells

city: Pasadena

first: Wen

last: Zhou

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

summary: The single cell and bulk expression profiles of early pro T-cell progenitors from mouse thymus

overall_design: Examination of expression profiles of thymic ETP-DN2 population with bulk RNAseq and single cell RNAseq. 10X: Droplet-based 3′ end massively parallel single-cell RNA sequencing droplets were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics). C1: Microfluidic-based full length mRNA scRNAseq were performed with Single-Cell mRNA Seq IFC 5–10 µm chip, and Smartseq 2 chemistry. Bulk: Bulk RNAseq from FACS sorted early T cell populations were performed. RNAeasy MicroKit (Qiagen) were used to purify the total RNA according to manufacturer’s recommendations. Purified RNA samples have been processed with and without SMART-Seq v4 Ultra Low Input RNA Kit(Takara #634888) for pre-amplification, and Nextera® XT library preparation kits for Illumina sequencing. Samples without pre-amp were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50-51 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.

first: Mary

middle: A

last: Yui

first: Brian

last: Williams

first: Jina

last: Yun

first: Barbara

last: Wold

first: Long

last: Cai

first: Ellen

middle: V

last: Rothenberg


title: Characterization of the immune response to Mycobacterium marinum infection in zebrafish

summary: Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. As expected based on the literature, our results showed the induction of genes coding proteins associated to immune signaling, cell migration and acute phase response indicating  that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans.

overall_design: Identification of the up- and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed, four biological replicates in each group.

middle: J


title: Transcriptome analysis of Arabidopsis thaliana roots in response to high nickel

city: Bratislava

first: Milan

last: Zvarik

address: Mlynska dolina

country: Slovakia

institute: Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava

summary: To gain further insights into a larger number of processes potentially altered by high nickel (Ni), we performed a transcriptional profiling of whole roots of Arabidopsis thaliana accession Columbia-0 (Col-0) exposed to 100 µM nickel, a concentration that induces slight chlorosis and intermediate inhibition of root and shoot growth.

overall_design: Gene expression of whole roots of Arabidopsis thaliana (accession Col) after transferring seven-day-old seedlings were transferred to solid half-strength MS agar media containing no added nickel (control) or 100 µM NiSO4 (+nickel) for 4 days. Four biological replicates were used.

first: Ricardo

middle: H

last: Giehl

last: Zvarík

first: Alexandra

last: Lešková


title: Transcriptomic profiling of naïve and memory phenotype CD8 T cells in Dock2-deficient mice

city: Cambridge

first: Vinay

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

summary: Transcriptomic data linked to our study showing that DOCK2 sets the threshold for entry into the virtual memory CD8+ T cell compartment by negatively regulating tonic TCR triggering

overall_design: RNAseq of naïve and memory phenotype CD8+ T cells in wild-type(B6) and Dock2-deficient mice.


title: Single Cell RNAseq profiles of thymic ETP populations

summary: The single cell profiles of sorted ETP populations with cell hashing antibody barcoding from mouse thymus

overall_design:
Examination of single cell expression profile of sorted populations identified from previous pseudotime analysis. Experiment was performed using droplet-based 3′ end RNA expression profiling using Chromium Single Cell 3′ Reagent Kits v3 according to manufacturer’s protocol (10x Genomics), with the FACS sorted individual sub-populations of ETPs tagged with Totalseq-A hashtags (Biolegend).  The cDNA library was sequenced on Illumina Novaseq for 400 million reads, and tag library on HiSeq4000 for 20 million reads, both in pair-end mode following manufacturer's instructions.
Please note that meta.csv.gz contains assigned sample names of individual cells after demultiplexing


title: Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation [ATAC-seq]

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

summary: Activation of T cells is dependent on organized and timely opening and closing of chromatin. We perform ATAC-seq (subseries 1), ChIP-seq (subseries 2), and RNA-seq (subseries 3) at 5, 24, and 60 h of T cell activation with anti-CD3 and -CD28 antibodies in human primary naïve CD4 T cells. We report that chromatin opening at early time points is established by AP-1 transcription factor and associated with transcriptional enhancer identified as risk loci for multiple immune diseases in human naïve CD4 T cells.

overall_design: Open chromatin analyses during T cell activation in human primary naïve CD4 T cells.

first: Masashi

last: Yukawa


title: Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation [ChIP-seq]

overall_design: Analyses for transcription factor and histone modification during T cell activation in human primary naïve CD4 T cells.


title: Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation.


title: Role of nsd2 in Follicular helper T cells

status: Public on Oct 15 2019

city: Nanjing

first: jingjing

last: chen

address: 101 Longmian Road

institute: Nanjing Medical University

summary: Follicular helper T cell (Tfh) provide essential help for humoral immune response. However, how Tfh differentiation is epigenetically regulated remains incompletely understood. Here we found that H3K36me2 methyltransferase Nsd2 is required for Tfh differentiation. Lack of Nsd2 leads to reduced Tfh generation and germinal center response. Mice with Nsd2 deficiency in T cells have reduced capability of chronic virus control. To understand the molecular mechanism by which Nsd2 regulates Tfh differentiation, RNA-seq analysis of Nsd2 wildtype and knockout Tfh cells were performed.

overall_design: CD4+CXCR5+PD1+ Tfh cells were sorted from wildtype (WT) and CD4Cre+Nsd2fl/fl (KO) mice for RNA-seq analysis to identify the differential expressed genes.

first: xue

last: huilong

first: xiaoming

last: wang


title: Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation.

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin’s ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.

overall_design: Hi-C was performed in control, Caph2KO, AS2LV, AS1LV, AS2LV/LV, SMC2WT/∆ and CAPH2KO-AS2LV cell lines in technical replicates.

first: Robin

first: Elzo

last: de Wit


title: Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: Identification of genes that regulate fiber cycling in Pashmina goat.

first: Nazir

last: Ganai


title: Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation [RNA-seq]

overall_design: Transcriptome analysis during T cell activation in human primary naïve CD4 T cells.


title: Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2 (ChIP-seq)

status: Public on Oct 14 2019

city: Basel

first: Joerg

last: Betschinger

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: Developmental cell fate specification is a unidirectional process that can be reverted in response to injury or experimental reprogramming. Whether differentiation and de-differentiation trajectories intersect mechanistically is unclear. Here, we performed comparative screening in lineage-related mouse naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), and identified the constitutively expressed zinc finger transcription factor (TF) Zfp281 as a bi-directional regulator of cell state interconversion. We showed that subtle chromatin occupancy changes in differentiated cells translate into binding and activation of the histone H3 lysine 9 (H3K9) methyltransferase Ehmt1 and the zinc finger TF Zic2 at enhancers and promoters. Genetic gain and loss of function experiments confirmed a critical role of Ehmt1 and Zic2 downstream of Zfp281 both in driving exit from the ESC state, and in restricting EpiSC reprogramming. Our study reveals that cell type-invariant chromatin association of Zfp281 provides an interaction platform for remodeling the cis-regulatory network underlying cellular plasticity.

overall_design: Mouse embryonic stem and differentiated cell chromatin immunoprecipitation (ChIP) profiles of  Zfp281, H3K27ac, Zic2, H3K9me2 and Bio-Ehmt1 in WT and Zfp281 KO cell lines were generated by deep sequencing, in duplicates, using Illumina HiSeq2500.

first: Daniela

last: Mayer

first: Michael

last: Stadler

first: Melanie

last: Rittirsch

first: Sophie

last: Dessus-Babus

first: Kirsten

last: Jacobeit

first: Eliza

last: Pandini Figueiredo Moreno

first: Tim

last: Roloff

first: Sebastien

last: Smallwood


title: Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2 (RNA-seq)

overall_design: Mouse embryonic stem and differentiated cell mRNA profiles of  wild type (WT), Zfp281 KO, Ehmt1 KO, Zic2 KO and Ehmt1/Zic2 KO cell lines were generated by deep sequencing, in duplicates, using Illumina HiSeq2500.


title: Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2

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

overall_design: Refer to individual Series


title: Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets

status: Public on Oct 12 2019

city: Heidelberg

first: John

last: Mariadason

state: Victoria

address: Austin Health, 145 Studyley Road

department: Gastrointestinal Cancers

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary:
Purpose: Biliary tract cancers (BTCs) carry a very poor prognosis and have no approved targeted therapies. Recent genomic profiling of primary BTCs identified a number of potentially actionable drug targets, however accurate model systems to evaluate these targets are currently lacking. The purpose of this study was to compare the genomic landscape of commonly used BTC cell lines to primary BTCs, and to utilize these models for drug target evaluation.
Design: Twenty BTC cell lines were profiled by RNA-seq analysis.
Results: Transcriptomic profiling of BTC cell lines identified two subtypes, enriched for epithelial and mesenchymal genes respectively, which were also identified in primary BTC.
Conclusions: Cell lines harbor similar genomic alterations to primary BTCs. Integration of cell line and primary cancer data identify novel molecular subsets, and highlight specific molecular vulnerabilities in BTC.

overall_design: 20 biliary tract cancer cell lines were profiled by RNA-seq analysis.

first: David

last: Lau

first: Dmitri

last: Mouradov

first: Wiphawan

last: Wasenang

first: Ian

last: Luk

first: Cameron

last: Scott

last: Williams

first: Yvonne

last: Yeung

first: Temduang

last: Limpaiboon

first: George

last: Iatropoulos

first: Laura

last: Jenkins

first: Camilla

last: Reehorst

first: Fiona

last: Chionh

first: Mehrdad

last: Nikfarjam

first: Daniel

last: Croagh

first: Amardeep

last: Dhillon

first: Andrew

last: Weickhardt

first: Niall

last: Tebbutt

first: Oliver

last: Sieber


title: In Vitro and In Vivo Modulation of Alternative Splicing by the Biguanide Metformin.

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Major physiological changes are governed by alternative splicing of RNA, and its misregulation may lead to specific diseases. With the use of a genome-wide approach, we show here that this splicing step can be modified by medication and demonstrate the effects of the biguanide metformin, on alternative splicing. The mechanism of action involves AMPK activation and downregulation of the RBM3 RNA-binding protein. The effects of metformin treatment were tested on myotonic dystrophy type I (DM1), a multisystemic disease considered to be a spliceopathy. We show that this drug promotes a corrective effect on several splicing defects associated with DM1 in derivatives of human embryonic stem cells carrying the causal mutation of DM1 as well as in primary myoblasts derived from patients. The biological effects of metformin were shown to be compatible with typical therapeutic dosages in a clinical investigation involving diabetic patients. The drug appears to act as a modifier of alternative splicing of a subset of genes and may therefore have novel therapeutic potential for many more diseases besides those directly linked to defective alternative splicing.

overall_design: Gene expression and Alternative splices were examined in three samples of WT human pluripotent stem cells derived mesenchymal stem cells treated or not with 50nM digoxin for 48h.

first: Delphine

last: Laustriat

first: Jacqueline

last: Gide

first: Laetitia

last: Barrault

first: Emilie

last: Chautard

first: Clara

last: Benoit-Pilven

first: Didier

last: Auboeuf

first: Anne

last: Boland

first: Christophe

last: Battail

first: François

last: Artiguenave

first: Jean-François

last: Deleuze

first: Paule

last: Bénit

first: Pierre

last: Rustin

first: Sylvia

last: Franc

first: Guillaume

last: Charpentier

first: Denis

last: Furling

last: Bassez

first: Xavier

last: Nissan

first: Cécile

last: Martinat

first: Marc

last: Peschanski

first: Sandrine

last: Baghdoyan


title: Gene expression in basal progenitors in the cerebral cortex of Tbr2 conditional knockout mice

first: Matthias

last: Groszer

summary:
During cortical development neurons are generated from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activated cell sorting (FACS) to isolate BPs from Tbr2-conditional knockout mice brain at early (E13) and late (E16) stages of cortical neurogenesis and determined mRNA expression profiles using microarray (Illumina MouseWG-6 v2).
Role of transcription factor Tbr2 in basal progenitors during corticogenesis.

overall_design: FACS isolated basal progenitors from Tbr2 conditional knockout mouse brain cortex at E13 and E16 were used for microarray analysis.

first: Tanay

last: Ghosh


title: Therapeutic targeting MDR1 expression by RORγ antagonists resensitizes cross-resistant CRPC to taxane via coordinated induction of cell death programs

city: Sacramento

first: Hongwu

last: Chen

state: California

address: 2nd Ave, UCDMC Res III

department: Biochem & Mol Med

institute: UC Davis

summary: We report here that RORγ, a nuclear receptor family member, unexpectedly mediates MDR1/ABCB1 overexpression. RORγ plays an important role in controlling the functions of subsets of immune cells and has been an attractive target for autoimmune diseases. We found that its small-molecule antagonists are efficacious in re-sensitizing DTX and CTX cross-resistant CRPC cells and tumors to taxanes in both androgen receptor (AR)-positive and -negative models. Our mechanistic analyses revealed that combined treatment with RORγ antagonists and taxane elicited a robust synergy in killing the resistant cells, which involves a coordinated alteration of p53, Myc and E2F-controlled programs critical for both intrinsic and extrinsic apoptosis, survival and cell growth. Our results suggest that targeting RORγ with small-molecule inhibitors is a novel strategy for chemotherapy resensitization in tumors with MDR1 overexpression.

overall_design: A total of 4 samples were analyzed in this study.  The study included one cell line C4-2B-TaxR. C4-2B-TaxR cells were cultured in medium and treated for 48 hours with control vehicle, RORgamma inhibitor SR2211 and/or chemotherapy  drug docetaxel.

first: H

first: Y

last: Wang


title: Neonatal injury increases gut permeability by epigenetically suppressing E-cadherin in adulthood

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

summary: Epithelial cell juntion integrity is thought to play an important role in the pathogenesis of inflammatory bowel disease (IBD). Early life stressors are suspected to impact epithelial barrier function later in life. We postulated that based on our previous findings that early life exposure to an inflammatory event could lead to epigegenetic changes mediating an exagerated response to a second inflammatory insult as an adult. In addition, we hypothesized that this increased inflammatory response could be mediated by alterations in miRNA expression impacting essential junction protein E-cadherin.

overall_design: Rat neonates were divided randomly into four groups: 1) vehicle treatment in neontatal and adult stages (Ctl+Ctl); 2) vehicle treatment as neonates followed by inlammatory insult as adults (Ctl+AI); 3) neonatal inflammatory event and then sham treatment as adults (NI+Ctl); and 4) inflammatory insults both as neonates and adults (NI+AI). Trinitrobenzenesulfonic acid (TNBS) administered intraluminally into the colon served as inflammatory insult. Neonatal inflammation (NI) was induced on post-natal day 10 and adult inflammation (AI) was induced 6-8 weeks later. Seven days after the AI, rats were euthanilized. Colonic mucosa/submucosa was isolated, snap-frozen in liquid nitrogen, and pulverized. Total RNA was isolated using miRNeasy Mini Kit (Qiagen) and miRNA microarray was performed (LC Sciences).

first: Kevin

middle: T

last: Kline

first: Haifeng

last: Lian

first: Xiaoying

last: Zhong

first: Xiuju

last: Luo

first: Syed

middle: Z

last: Nayeem

first: John

last: Winston

first: Zingzi

last: Cong

first: Tor

last: Savidge

first: Roderick

last: Dashwood

first: Don

last: Powell

last: LI


title: RNA-Seq analysis of cSCC cells after siRNA-induced gene knockdown of lncRNA PRECSIT

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

institute: University of Turku

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Long non-coding RNAs (lncRNAs) are involved in various biological processes, and their role in cancer progression is emerging. Whole transcriptome analysis of cSCC cell lines (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) revealed overexpression of long intergenic ncRNA (LINC00346) in cSCC cells (GSE66412). We wanted to futher study the RNA expression profile of LINC00346 knockdown cSCC cells. Based on our observations, LINC00346 was named PRECSIT (p53 regulated carcinoma-associated STAT3-activating long intergenic non-protein coding transcript).

overall_design: Total RNAs from negative control and PRECSIT siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina HiSeq3000.

first: Minna

last: Piipponen

first: Veli-Matti

last: Kähäri


title: mRNA Sequencing to identify transcriptional changes in early and late stages of  lung in human Idiopathic Pulmonary Fibrosis

status: Public on Oct 11 2019

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 1 Gilbert street

institute: Yale University

summary: Idiopathic pulmonary fibrosis (IPF) is a specific form of chronic progressive fibrosing interstitial pneumonia leading to progressive dyspnea and finally death.The classic diagnosis of IPF is based on the histological pattern of usual interstitial pneumonia (UIP).we have no information about the molecular events that characterize the progression of IPF in the human lung. Understanding the molecular  changes that characterize the progression of IPF from early, through progressive changes and into end-stage would allow development of therapeutic strategies that address the disease in all of its stages.In this study we applied a systems biology approach to model dynamic molecular changes during the progression of IPF in the human lung by using a unique resource of carefully characterized, differentially affected regions in human lungs.

overall_design: We sampled multiple regions in human lungs collected following lung transplantation for severe IPF and determined the extent of fibrosis using microCT quantitative imaging and tissue histology to classify them as early, progressive, or end-stage fibrosis. We then performed RNA-seq and microRNA profiling to determine gene expression at these selected stages and applied a linear mixed-effects model to identify differentially expressed genes

first: Farida

last: Ahangari

middle: E

last: McDonough

first: Xiting

last: Yan

first: Bart

last: Vanaudenaerde

last: Kaminiski


title: Heterozygous SNORA31 mutations in patients with herpes simplex encephalitis

first: Thomas

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: MIT

summary: Pseudo-seq was used to measure differences in the extent of pseudouridine (Ψ) modification in rRNA from human cell lines with heterozygous, and homozygous disruptions of SNORA31.

overall_design:
CMC treatment of RNA followed by next generation sequencing was used to measure the extent of pseudouridylation at mapped human rRNA Ψ sites.
CMC: carbodiimide N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate

first: Fabien

middle: G

last: Lafaille

first: Jean-Laurent

last: Casanova

first: Wendy

last: Gilbert

first: Shen-Ying

last: Zhang


title: Region-specific Innate Antiviral Responses of the Human Epididymis

city: Cleveland

first: Ann

last: Harris

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

summary: Viral infections of the epididymis are associated with epididymitis, which damages the epithelium and impairs fertility. We showed previously that innate immune response genes were differentially expressed in the corpus and cauda region of the human epididymis in comparison to the caput. Here we investigate the antiviral defense response mechanisms of human epididymis epithelial (HEE) cells. Toll-like receptor (TLR) 3 and retinoic acid-inducible gene I (RIG-I)- like receptors (RLRs) are enriched in HEE cells from the corpus and cauda region. Furthermore, corpus and cauda HEE cells show an enhanced response to antiviral ligands (poly(I:C) and HSV-60), as shown by increased IFN-β mRNA expression and secretion of IFN-β. We also show that paired box 2 (PAX2), which was implicated in regulating antiviral response pathways is required for basal expression of the DNA sensor, Z-DNA binding protein (ZBP1) and type I interferon, in caput but not in cauda cells.

overall_design: mRNA profiles from Caput HEE cells transfected with negative control (NC) or PAX2 siRNA, in triplicate.

first: James

last: Browne


title: Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

summary: APUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis.   Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses.  By combining a range of transient assays, we show here that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunits of the decapping complex suggesting that APUM9-mediated mRNA decay predominantly occurs via the decapping-dependent exonucleolytic pathway.  APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated epigenetic control of plant APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.

overall_design: RNA sequencing on imbibed Arabidopsis seeds

first: Tünde

last: Nyiko


title: Expression data from inducible ES stable cell line  overexpressing specifically the human gene GTF2I

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary:
In order to identify the effects of the induction of the gene of interest (GTF2I) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line
Transcriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2I

overall_design: For the analysis on the GTF2I inducible cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 24 hours; RNA extracted from un-induced clones was used as control.


title: Expression data from inducible ES stable cell line  overexpressing specifically the human gene WBSCR1

summary:
In order to identify the effects of the induction of the gene of interest (WBSCR1) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line
Transcriptome analysis of the inducible transgenic mouse ES cell line overexpressing WBSCR1

overall_design: For the analysis on the WBSCR1 inducible cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 24 hours; RNA extracted from un-induced clones was used as control.


title: Expression data from inducible ES stable cell line  overexpressing specifically the human gene GTF2IRD2

summary:
In order to identify the effects of the induction of the gene of interest (GTF2IRD2) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line
Transcriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2IRD2

overall_design: For the analysis on the GTF2IRD2 inducible cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 24 hours; RNA extracted from un-induced clones was used as control.


title: Expression data from inducible ES stable cell line  overexpressing specifically the human gene GTF2IRD1

summary:
In order to identify the effects of the induction of the gene of interest (GTF2IRD1) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line
Transcriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2IRD1.

overall_design: For the analysis on the GTF2IRD1 inducible cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 24 hours; RNA extracted from un-induced clones was used as control.


title: Gene expression profiling of iPSC-derived cardiomyocytes with BAG3 mutations

status: Public on Oct 10 2019

city: Philadelphia

first: Christopher

last: McDermott-Roe

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

summary: Gene expression profiling of wild-type, BAG3-KO and BAG3-R477H iPSC-derived cardiomyocytes

overall_design: Total RNA extracted from day 40 iPSC-derived cardiomyocytes (in triplicate) and sequenced on Illumina HiSeq2500

first: Wenjian

last: Lv

first: Chris


title: A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem


title: The in vivo endothelial cell translatome is highly heterogeneous across vascular beds

city: Ann Arbor

first: Santhi

last: Ganesh

state: Michigan

address: 1150 W Medical Center Drive

department: Department of Internal Medicine

institute: University of Michigan

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

institute: University of Zurich

summary: The RNA modification N6-methyladenosine (m6A) can modulate mRNA fate and thus affect many biological processes. We analyzed m6A modification across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, we found that viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A modification in RIOK3 and CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.

overall_design: Study of m6A changes in cellular RNA from Huh7 cells following 4 biological replicates of innate immune activation (HCV PAMP transfection, 8 hpt) or ER stress (thapsigargin (TG) treatment, 16 hpt).

first: Nandan

last: Gokhale

first: Alexa

middle: B

first: Melissa

middle: D

last: Mattocks

middle: L

last: Holley

first: Helen

last: Lazear

last: Mason

first: Stacy

last: Horner


title: The in vivo endothelial cell translatome is highly heterogeneous across vascular beds (EC-TRAP RNAseq)

summary: The interspersed anatomic distribution of endothelial cells (ECs) and their dependence on microenvironmental cues have been major challenges in studying EC function and response to (patho)physiological stimuli in vivo. Combining EC-specific translating ribosome affinity purification (EC-TRAP) with RNA sequencing provides an accurate in vivo snapshot of tissue-specific EC expression profiles, and maintains a high degree of sensitivity to detect low abundant transcripts while limiting changes in gene expression profiles due to enzymatic tissue dissociation required to generate single cell suspensions for FACS sorting or single cell analysis. In addition to demonstrating EC heterogeneity under physiologic conditions, the in vivo host response to lipopolysaccharide (LPS) revealed the induction of expression programs associated with a native defense response, with marked differences across vascular beds.

overall_design: Total tissue lysate and EC-TRAP RNASeq data of brain, heart, kidney, liver and lung from 10 week old Rpl22-floxed, Tek-Cre males under physiologic conditions or 4 hours after LPS treatment (n=3); total lysate and EC-TRAP RNASeq data of brain, kidney and liver after enzymatic tissue dissociation (n=3); RNASeq data from RBC-lysed whole blood before and after TRAP (n=2); RNASeq data (total lysate and EC-TRAP) from brain, heart, kidney and liver from Rpl22-floxed, Tek-Cre male after bone marrow transplantation with Cre-negative donor (n=1); RNASeq data from pooled platelets of Rpl22-floxed, Pf4-Cre before and after TRAP (n=1); total tissue lysate and TRAP data brain, heart, kidney, liver and lung from 10 week old Rpl22-floxed, EIIa-Cre males (n=3).

first: Audrey

middle: C

last: Cleuren

first: Martijn

last: van der Ent

first: Hui

last: Jiang

first: Kristina

last: Hunker

first: Andrew

last: Yee

first: David

middle: R

last: Siemieniak

first: Grietje

last: Molema

first: William

last: Aird

middle: K

last: Ginsburg


title: Evaluation of the roles of Lats1 and Lats2 in the development of the Müllerian ducts

city: St-Hyacinthe

first: Derek

last: Boerboom

state: Québec

address: 3200 rue sicotte

department: Biomédecine Vétérinaire

country: Canada

institute: Faculté de Médecine Vétérinaire (University of Montreal)

summary:
Development of the female tract results from the carefull coordination of numerous signaling pathways. Here, we evaluated the role of hippo pathway in the development of the female reproductive tract.
We used microarray to compare the gene expression changes observed in the Müllerian ducts of E17.5 mice embryos between control group and experimental (mutant) group bearing a conditional deletion of both (conjoint) Lats1 and Lats2 using the Amhr2cre strain.

overall_design: Müllerian ducts were collected from E17.5 mice (control and experimental group) for RNA extraction and hybridization on Affymetrix microarrays. Control=Lats1f/f,Lats2f/f , Mutant=Lats1f/f,Lats2f/f,Amhr2cre/+

first: Guillaume

last: St-Jean


title: Migratory DCs activate TGF-β to precondition naïve CD8+ T cells for tissue-resident memory fate

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

summary: Epithelial resident memory T (eTRM) cells serve as sentinels in barrier tissues to guard against previously encountered pathogens. How eTRM cells are generated has important implications for efforts to elicit their formation through vaccination or prevent it in autoimmune disease. Here, we show that during immune homeostasis, the cytokine transforming growth factor β (TGF-β) epigenetically conditions resting naïve CD8+ T cells and prepares them for the formation of eTRM cells in a mouse model of skin vaccination. Naïve T cell conditioning occurs in lymph nodes (LNs), but not in the spleen, through major histocompatibility complex class I–dependent interactions with peripheral tissue–derived migratory dendritic cells (DCs) and depends on DC expression of TGF-β–activating αV integrins. Thus, the preimmune T cell repertoire is actively conditioned for a specialized memory differentiation fate through signals restricted to LNs.

overall_design: Examination of chromatin accessibility in CD44low naïve CD8+ T cells isolated from lymph nodes of wild type (WT) and CD11cCre x Itgavflox/flox ("DCAV") mice, each with a biological replicate

first: Vinidhra

last: Mani

first: Äijö

last: Tarmo

first: Thorsten

last: Mempel


title: RNA-seq of human foreskin fibroblast cells lacking RB and/or p130 after doxorubicin treatment

city: Boston

first: Amy

last: Schade

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: We used human foreskin fibroblast cells with CRISPR-Cas9 mediated knockout of RB1 and p130 (RBL2) (Control, sgRB1, sgP130, sgRB1+sg130) and measured gene expression changes after doxorubicin treatmnet (24 hr, 350 nM).

overall_design: Control, sgP130, sgRB1, and sgRB1+sgP130 HFFs were contact arrested for 48 hours. Cells were released from contact inhibition by splitting into complete media containing 0 nM or 350 nM doxorubicin. Cells were collected after 24 hours and RNA was harvested for sequencing. Experiment was completed with two biological replicates for each cell line in each condition resulting in 16 samples run in a single lane for RNAseq.

first: Martin

last: Fischer

first: James

last: DeCaprio


title: RNA-seq (PolyA) of RNA from Tet-inducible SaOS2-p21 cells

city: Jena

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: RNA was extracted from SaOS2 cells harboring a tet-inducible p21 expression vector. 3 replicates from untreated and 3 replicates from 24h doxycycline-treated cells.

overall_design: Identification of p21-dependent target gene expression in SaOS2 cells


title: The in vivo endothelial cell translatome is highly heterogeneous across vascular beds (HUVEC RNAseq)

first: Santhi

last: Ganesh

summary: The interspersed anatomic distribution of endothelial cells (ECs) and their dependence on microenvironmental cues have been major challenges in studying EC function and response to (patho)physiological stimuli in vivo. Combining EC-specific translating ribosome affinity purification (EC-TRAP) with RNA sequencing provides an accurate in vivo snapshot of tissue-specific EC expression profiles, and maintains a high degree of sensitivity to detect low abundant transcripts while limiting changes in gene expression profiles due to enzymatic tissue dissociation required to generate single cell suspensions for FACS sorting or single cell analysis. In vitro HUVEC data was obtained to ensure short-term cycloheximide treatment, as used for in vivo experiments, did not alter global gene expression.

overall_design: RNASeq data from freshly isolated (passage 1) or commercially available HUVECs (passage 10), incubated with 100µg/ml cycloheximide or 2µg/ml homoharringtonine for 5 minutes (n=4 per condition per passage).

first: Audrey

last: Cleuren

last: van der Ent


title: RNA-seq of human foreskin fibroblast cells lacking RB, p130, and p107 treated with doxorubicin.

summary: We used human foreskin fibroblast cells with CRISPR-Cas9 mediated knockout of RB1 and p130 (RBL2) (sgP130, sgRB1+sg130), knocked down p107 using siRNA and measured gene expression changes after doxorubicin treatmnet (24 hr, 350 nM).

overall_design: sgP130 and sgRB1+sgP130 cells were seeded at 70% confluency and transfected with siRNA against the p107 (RBL1) transcript or a control sequence. After 48 hours, cells were split into 0 or 350 nM doxorubicin and harvested after 24 hours.


title: ATXN1-NUTM1 may define a new brain tumor entity and expand the histologic spectrum of NUTM1-rearranged neoplasia

status: Public on Oct 09 2019

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

institute: Institut Curie

type: Methylation profiling by genome tiling array

summary: An ATXN1-NUTM1 brain tumor entity

overall_design: DNA methylation profile of a single new brain tumor entity

first: Franck

last: Bourdeaut


title: FIN-Seq: Transcriptional profiling of specific cell types in frozen archived tissue from the human central nervous system

first: Ryoji

last: Amamoto

department: Genetics

institute: Harvard Medical School

summary: FIN-Seq is a method that allows transcriptional profiling of specific cell types in frozen postmortem human CNS tissues. Briefly, nuclei from frozen CNS samples are isolated, fixed, and immunolabeled with antibodies for prospective isolation. The RNA from the FACS isolated nuclei are extracted and an RNA sequencing library is generated for subsequent sequencing.

overall_design: Isolation of two cortical neuronal subtypes in mice: Corticofugal projection neurons and Callosal projection neurons using a BCL11B antibody and SATB2 antibody, respectively. Also, a comparison between cellular RNA and nuclear RNA from corticofugal neurons at P7.

first: Emanuela

last: Zuccaro

first: Paola

last: Arlotta

first: Connie

last: Cepko


title: Whole transcriptome analysis of iPSC derived hepatic organoids cultures

city: PALO ALTO

first: YUAN

last: GUAN

address: 1701 Page Mill Road

institute: Stanford University

summary: A heatmap, which focused upon 2458 genes that were involved in stem cell differentiation and liver development, was prepared to visualize the relative relationship between the transcriptomes of iPSCs, PHHs, human liver tissue and HO1. The dendrogram indicates that HO1 is more closely related to liver tissue than to PHHs; this is because cholangiocytes are present in HO1 and liver, but are absent (or rare) in PHHs. Examination of the genes within this heatmap indicated that there was a lack of expression of pluripotent genes in HO1; and that HO1 had an increased level of expression of cellular markers for liver lineages and liver development, which included mature hepatocytes, bile duct cells and NOTCH signaling components.  A cluster analysis of 1510 genes indicates that there were major changes in the transcriptome after the cells that were dissociated from an HO1 were transferred from the growth medium into the differentiation medium. As with the HO1s, the gene expression profile of HO2s resembled that of PHHs and human liver. Of importance, the level of expression of mRNAs that are of importance for various human liver functions (ADH4, CYP3A4, TTR, GSRA1, TDO2, GSTA1 and FAH) were markedly increased in HO2s.

overall_design: Whole transcriptome analysis was performed on iPSCs, primary human hepatocytes (PHH), HO1 (primary hepatic organoids) and human liver tissue. For this analysis, over 100 organoids that were generated from a single donor were analyzed. Next, whole transcriptome analysis was performed to characterize HO2s (secondary organoids) and their relationship to iPSCs, PHHs and human liver tissue. This analysis utilized 1,000 HO2s that were prepared from a single donor.

first: Yuan

last: Guan

first: Ming

last: Zheng


title: Single-cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos

city: Beijing

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: Human T lymphogenesis includes emergence, migration and thymus-seeding of T lymphoid precursor, followed by T-lymphocytes commitment in thymus, which are largely unknown. Here, we perform single-cell RNA sequencing using cells isolated from human hemogenic/hematopoietic sites such as aorto-gonad-mesonephros (AGM), liver, and thymic primordia spanning embryonic and fetal stages. The transcriptional atlas of thymic primordia illustrates the cellular trajectory of early T-lymphocyte development. Further, thymic seeding progenitors in liver and unique T lymphoid progenitors in AGM at CS14, are first unveiled. We also reveal the stepwise-specification of thymic epithelial cells，and the potential cell-cell interactions between T-lymphocyte progenitors and stromal cells during thymus organogenesis. Our data provide new insights into T lymphogenesis, which prospectively directs the efficient regeneration of T- lymphocytes from pluripotent stem cells

overall_design: Here, we performed single-cell RNA sequencing (RNA-Seq) analysis of about 26,000 individual cells from four organs and tissues of CS14 to week 10 of gestation in human embryos/fetus, including thymus, AGM region, liver and blood

first: Yang

last: Zeng

first: Chen

last: Liu

first: Yandong

last: Gong


title: Inhibition of the Dead Box RNA Helicase 3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: We have investigated the protective effect of DDX3 inhibitor RK33 on toxic damage done by combined TAT and cocaine.

overall_design: Primary neuronal cultures were treated with HIV-protein TAT and cocaine following RK33 treatment. Each treatment condition was done in biological triplicate.

first: Marina

last: Aksenova

first: Justin

last: Sybrandt

first: Biyun

last: Cui

first: Vitali

last: Sikirzhytski

first: Hao

last: Ji

first: Diana

last: Odhiambo

first: Matthew

last: Lucius

first: Jill

last: Turner

first: Eugenia

last: Broude

first: Edsel

last: Peña

first: Sofia

last: Lizarraga

first: Jun

last: Zhu

first: Ilya

last: Safro

first: Michael

last: Wyatt

last: Shtutman


title: RNA-seq analysis of A2780 and OVCAR3 human ovarian cancer cell lines after overexpression of collagen type XI alpha 1 (COL11A1)

city: Albany

first: Dong-Joo

last: Cheon

address: 47 New Scotland Ave

institute: Albany Medical COllege

summary: Collagen type XI alpha 1 (COL11A1) is identified as one of the most upregulated genes in cisplatin-resistant ovarian cancer and recurrent ovarian cancer. However, the exact functions of COL11A1 in cisplatin resistance are unknown. The goal of this study is to determine molecular mechanisms by which COL11A1 confers cisplatin resistance in ovarian cancer cells. We overexpressed COL11A1 in A2780 and OVCAR3 ovarian cancer cells, which express very low endogenous levels of COL11A1. We then compared the mRNA expression levels of various genes between COL11A1-overexpressing ovarian cancer cells and control ovarian cancer cells by RNA-Seq. Our RNA-Seq data show that COL11A1 overexpression did not consistently change the expression levels of genes involved in cisplatin efflux, glutathione metabolism, and DNA repair pathways, which are known to contribute to cisplatin resistance. This result implies that COL11A1 might confer cisplatin resistance in ovarian cancer cells through other mechanisms.

overall_design: We overexpressed COL11A1 in A2780 and OVCAR3 ovarian cancer cell lines (A2780-COL11A1, OVCAR3-COL11A1) and performed RNA-Seq. We also performed RNA-Seq in A2780CIS ovarian cancer cell line expressing high endogenous levels of COL11A1 and A2780-shCOL11A1 cell line where COL11A1 is knocked down with short hairpin RNA. We then compared the differential expression of mRNAs in ovarian cancer cell lines overexpressing COL11A1 (A2780-COL11A1, OVCAR3-COL11A1, and A2780CIS, ) to control cells which express no or very low COL11A1 (A2780, A2780shCOL11A1, and OVCAR3).

first: Sandra

last: Orsulic

first: Vincent

last: Funari


title: Reconstruction of the global neural crest gene regulatory network in vivo [RNA-seq]

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits t hat define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.

overall_design: Genome-wide transcriptome profiling avian neural crest (NC) at 2 different stages of the NC ontogeny isolted from their in vivo context.

first: Ruth

middle: M

last: Williams

first: Ivan

last: Candido-Ferreira

first: Emmanouela

last: Repapi

first: Daria

last: Gavriouchkina

first: Upeka

last: Senanayake

first: Jelena

last: Telenius

first: Irving

last: Ling

first: Stephen

last: Taylor

first: Jim

last: Hughes


title: Reconstruction of the global neural crest gene regulatory network in vivo [ChIP-seq]

overall_design: ChiP-seq was performed against BRD4 and H3K27Ac to determine "super-enhancer"-like cluster of cis-regulatory elements in neural crest cells dissected from the developing chick embryo.


title: ChIP-seq with Mucor circinelloides Mis12- and Dsn1-mCherry proteins

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

institute: Universidad de Murcia

summary: ChIP-seq experiment with two outer kinetochore proteins to identify the centromeric sequences of Mucor circinelloides

overall_design: Chromatin Immunoprecipitation and sequencing assay with two different proteins, Mis12 and Dsn1 tagged with mCherry, using a-mCherry antibodies, including an input control for each sample and a mock control without antibody

first: María Isabel

last: Navarro-Mendoza


title: Reconstruction of the global neural crest gene regulatory network in vivo [CRISPR_RNA-seq]

overall_design: Bulk RNA-seq was performed on neural crest cells dissected from the developing chick embryo to determine the effect of CRISPR/Cas9 knock down and its downstream effects on a set of putative core transcription factors.


title: Reconstruction of the global neural crest gene regulatory network in vivo [Capture-C]

overall_design: Capture-C was performed in key neural crest regulators to determine their topologically associated domains and promoter-enhancer communications in vivo.


title: Reconstruction of the global neural crest gene regulatory network in vivo [ATAC-seq]

overall_design: High-resolution, genome-wide chromatin accessibility maps were determined by ATAC-seq at several stages of pure avian neural crest populations and non-neural crest cells isolated from developing chick embryos.


title: Reconstruction of the global neural crest gene regulatory network in vivo [bulk RNA-seq]

overall_design: Transcriptional profilling of avian neural crest populations and non-neural crest cells isolated from developing chick embryos.


title: eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5’UTR

city: Glasgow

first: Ania

last: Wilczynska

address: Switchback Road

institute: Beatson Insistute for Cancer Research

summary:
Background: Regulation of the mRNA life cycle is central to gene expression control and determination of cell fate. miRNAs represent a critical mRNA regulatory mechanism, but despite decades of research, their mode of action is still not fully understood.
Results: Here, we show that eIF4A2 is a major effector of the repressive miRNA pathway functioning via the Ccr4-Not complex. We demonstrate that while DDX6 interacts with Ccr4-Not, its effects in the mechanism are not as pronounced. Through its interaction with the Ccr4- Not complex, eIF4A2 represses mRNAs at translation initiation. We show evidence that native eIF4A2 has similar RNA-selectivity to chemically inhibited eIF4A1. eIF4A2 exerts its repressive effect by binding purine-rich motifs which are enriched in the 5’UTR of target mRNAs directly upstream of the AUG start codon.
Conclusions: Our data support a model whereby purine motifs towards the 3’ end of the 5’UTR are associated with increased ribosome occupancy and possible uORF activation upon eIF4A2 binding.

overall_design: RIP-Seq of endogenous IPs of eIF4A1, eIF4A2 ad DDX6 with total RNA; RNA-Seq of subpolysomal and polysomal fractions from sucrose density gradients from HEK293 cells treated with control siRNA or CNOT1 siRNA with total RNA; RNA-Seq of total RNA of HEK293 cells transfected with either a control siRNA or siRNA against TNRC6A and TNRC6B

first: Sarah

last: Gillen

first: Hedda

last: Meijer

first: Claudia

last: Langlais

first: Rebekah

last: Jukes-Jones

first: Wei-Ting

last: Lu

first: Jack

last: Godfrey

first: Benjamin

last: Hawley

first: Kelvin

last: Cain

first: John

last: Le Quesne

first: Martin

last: Bushell

first: Tobias

last: Schmidt


title: Interdependent photo- and chemosensory systems regulate larval settlement in a marine sponge

city: Brisbane

first: Tahsha

last: Say

state: QLD

address: The University of Queensland

department: School of Biological Sciences

institute: The University of Queensland

summary: Marine pelagic larvae from throughout the animal kingdom use a hierarchy of environmental cues to identify a suitable benthic habitat on which to settle and metamorphose into the reproductive phase of the life cycle. The majority of larvae are induced to settle by biochemical cues and many species have long been known to preferentially settle in the dark. Combined, these data suggest that larval responses to light and biochemical cues may be linked, but this is yet to be explored at the molecular level. Here, we track vertical position of larvae of the sponge Amphimedon queenslandica to show that they descend to the benthos at twilight, by which time they are competent to respond to biochemical cues, consistent with them naturally settling in the dark. We then conduct larval settlement assays under three different light regimes (natural day-night, constant dark or constant light), and use transcriptomics on individual larvae to identify candidate molecular pathways underlying the different settlement responses that we observe. We find that constant light prevents larval settlement in response to biochemical cues, likely via actively repressing chemostransduction; this is consistent with the sustained upregulation of a photosensory cryptochrome and two putative inactivators of G-protein signalling in the constant light only. We hypothesise that photo- and chemosensory systems may be hierarchically integrated into ontogeny to regulate larval settlement via nitric oxide (NO) and cyclic guanosine monophosphate (cGMP) signalling in this sponge that belongs to one of the earliest branching of the extant animal lineages.

overall_design: Transcriptomic data for 43 individual larvae of the sponge Amphimedon queenslandica aged 1 and 9 hours post emergence (hpe) that were exposed to one of three experimental light regimes. Larvae were collected within a 30-minute window beginning at 11 am and were distributed into 0.22 μm filtered sea water, under one of three experimental light regimes, by 0.5 hours post emergence (hpe). The light regimes were (1) natural day-night, (2) constant dark (using LEE filter model 299, 1.2 neutral density, allowing 6.6% transmission of ambient daylight), and (3) constant light (full spectrum Lumilux T5 HE tube). For RNA-sequencing, two timepoints (1 and 9 hpe) were chosen to represent precompetent and competent larvae, respectively.

first: Sandie

last: Degnan


title: Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells

status: Public on Oct 08 2019

city: New Haven

first: Rolando

last: Garcia-Milian

address: 333 Cedar St

department: CWML

institute: Yale University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. An integrated systems approach was used with bioinformatics tools to understand the the role of aldehyde dehydrogenase 1A1 (ALDH1A1) in human colon cancer cells. We combined transcriptomics, proteomics and untargeted metabolomics to gain insight into the mechanisms affected by the suppression of the ALDH1A1 gene in COLO320 cells
Methods: COLO 320 cells. Cellular ALDH1A1 expression was suppressed using MISSION shRNA lentiviral transduction particles containing validated ALDH1A1 shRNA in a pLKO plasmid vector. Scramble control shRNA in pLKO plasmid vector was used to generate control cells. Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Primary analysis sample de-multiplexing and alignment to the human genome was performed using Illumina's CASAVA 1.8.2 software suite. The reads were trimmed for quality and aligned with the hg19 reference genome using TopHat2. The transcripts were assembled using Cufflinks. The assembled transcripts were used to estimate transcript abundance and differential gene expression using Cuffdiff. The results were visualized using R (CRAN) and CummeRbund
Results: We combined transcriptomics, proteomics and untargeted metabolomics to gain insight into the mechanisms affected by the suppression of the ALDH1A1 gene in COLO320 cells. RNA-seq and proteomics analyses revealed 1747 transcripts and 336 proteins that were differentially expressed in cells in which the ALDH1A1 had been suppressed by shRNA transfection. Transcriptomics pathway analysis showed significant signaling pathways, such as Wnt/β-catenin (p=3.47E-6), molecular mechanisms of cancer (7.41E-5) and others relevant to lipid metabolism, such as cholesterol biosynthesis I, II and III (p=1.82E-4). Proteomics pathway analysis identified oxidative phosphorylation to be the most highly significant pathway (p=5.01E-31). Pathway  analysis of the genes common to the transcriptomics and proteomics analyses revealed the asparagine biosynthesis (p=3.16E-3) and cholesterol biosynthesis the most statistically significant (p=3.36E-3). Univariate analysis of the  untargeted metabolomics dataset revealed 859 ions statistically significant. Network analysis showed alterations in pathways linked to energy and lipid metabolism, such carnitine shuttle (p=5.3E-4) and fatty acid oxidation (p=2.9E-2). A systems biology approach was used to integrate all three datasets and a total of 61 pathways were generated. A direct association between the suppression of ALDH1A1 and the Vitamin A (retinol) metabolism pathway and downregulation of retinol and the UGT2B17, UGT2A3 and PRDX6 genes was shown
Conclusions: the present results confirm the role of ALDH1A1 in retinol metabolism and shows for the first time the influence of this gene on lipid metabolism pathways that may be crucial for cholesterol synthesis in human colon cancer cells. In addition, they demonstrate how an integrated systems approach using unbiased bioinformatics tools can be used to understand the interplay of cellular pathways.

first: Vasiliou

last: Vasilis

first: Garcia-Milian

last: Rolando


title: RNA Sequencing analysis of xenografts for mouse gene expression changes

city: Dallas

first: Yuqing

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UTSouthwestern Medical Center

summary: Control and 2G8-treated MiaPaca-2 and Colo375 xenografts were subjected to RNA-seq analysis for mouse gene expression changes

overall_design: Tumor tissues were harvested in RLT lysis buffer and purified according to instructions of the RNeasy Plus Kit (QIAGEN). RNA concentration was determined by a Qubit fluorometer  (Thermo Fisher Scientific) and then prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina). Samples were quantified, normalized, and sequenced on the Illumina HiSeq 2500 with at least 25 million reads per sample. FASTQ files were aligned to mouse mm10 reference transcriptome.

first: Huocong

last: Huang


title: Gene expression profiles in HMC3 cells after exposure to ketamine or its active metabolites: 2R6R-HNK and 2S6S-HNK

status: Public on Oct 07 2019

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: This study was designed to clarify mechanisms of action for ketamine and its active metabolites, (2R,6R;2S,6S)-hydroxynorketamine (HNK), which also appear to play a major role in ketamine’s rapid antidepressant effects. An HMC3 human microglial cell line was used as a model system to test a possible role for ketamine in immune response regulation that might contribute to its antidepressant effects. Our results highlight the fact that ketamine and its two active metabolites can regulate the type I interferon pathway mediated, at least partially, through STAT3 which plays a major role in the immune response. Specifically, STAT3 downstream genes that were modulated by either ketamine or its active metabolites were enriched in the “response to type I interferon” pathway. Our data also suggest that STAT3 might play a role in ketamine’s antidepressant effects, mediated, at least in part, through EEF2, resulting in the augmentation of BDNF expression and promoting the synthesis of synaptic proteins PSD95 and SYN1.

overall_design: To determine gene expression profiles in HMC3 cells after exposure to vehicle, Estradiol (E2), ketamine, (2R,6R)-HNK, (2S,6S)-HNK, E2+ketamine, E2+(2R,6R)-HNK, and E2+(2S,6S)-HNK.

first: Richard

last: Weinshilboum


title: Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation

city: Houston

first: Min

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series