title: Transcriptome-wide analyses of human neonatal articular cartilage and human mesenchymal stem cells (hMSCs)-derived cartilage provide a new molecular target for evaluating Engineered Cartilage

status: Public on Nov 23 2019

city: Cleveland

first: Rodrigo

last: Somoza

state: Ohio

address: 2080 Adelbert Rd

department: Biology

institute: Case Western Reserve University

summary:
Analysis of gene expression differences between human neonatal articular cartilage and human mesenchymal stem cells (hMSCs)-derived cartilage, to identify novel molecular signature for tissue engineered articular cartilage
Abstract: Cellular differentiation comprises a progressive, multistep program that drives cells to fabricate a tissue with specific and site distinctive structural and functional properties. Cartilage constitutes one of the potential differentiation lineages that mesenchymal stem cells (MSCs) can follow under the guidance of specific bioactive agents. Single agents such as transforming growth factor beta (TGF-b) and bone morphogenetic protein 2 in unchanging culture conditions have been historically used to induce in vitro chondrogenic differentiation of MSCs. Despite the expression of traditional chon- drogenic biomarkers such as type II collagen and aggrecan, the resulting tissue represents a transient cartilage rather than an in vivo articular cartilage (AC), differing significantly in structure, chemical composition, cellular phenotypes, and mechanical properties. Moreover, there have been no comprehensive, multicomponent parameters to define high- quality and functional engineered hyaline AC. To address these issues, we have taken an innovative approach based on the molecular interrogation of human neonatal articular cartilage (hNAC), dissected from the knees of 1-month-old cadaveric specimens. Subsequently, we compared hNAC-specific transcriptional regulatory elements and differentially expressed genes with adult human bone marrow (hBM) MSC-derived three-dimensional cartilage structures formed in vitro. Using microarray analysis, the transcriptome of hNAC was found to be globally distinct from the transient, cartilage-like tissue formed by hBM-MSCs in vitro. Specifically, over 500 genes that are highly expressed in hNAC were not expressed at any time point during in vitro human MSC chondrogenesis. The analysis also showed that the differences were less variant during the initial stages (first 7 days) of the in vitro chondrogenic differentiation program. These observations suggest that the endochondral fate of hBM-MSC-derived cartilage may be rerouted at earlier stages of the TGF-b-stimulated chondrogenic differentiation program. Based on these analyses, several key molecular dif- ferences (transcription factors and coded cartilage-related proteins) were identified in hNAC that will be useful as molecular inductors and identifiers of the in vivo AC phenotype. Our findings provide a new gold standard of a molecularly defined AC phenotype that will serve as a platform to generate novel approaches for AC tissue engineering.

overall_design: Total RNA obtained from 2 samples of knee articular cartilage derived from knees of de-identified 1-month-old cadaveric specimens and hMSC-derived cartilage at different time point during differentiation. hMSCs from the bone marrow of 2 de-identified donors

first: Diego

last: Correa

first: Ivan

last: Labat

first: Hal

last: Sternberg

first: Megan

last: Forest

first: Ahmad

last: Khalil

last: West

first: Paul

last: Tesar

first: Arnold

middle: I

last: Caplan


title: Cx3cr1-deficient microglia exhibit a premature aging transcriptome

status: Public on Nov 25 2019

city: Cambridge

first: Stefka

last: Gyoneva

state: MA

address: 225 Binney St.

country: USA

institute: Biogen, Inc

type: Expression profiling by high throughput sequencing

summary: CX3CR1, one of the highest expressed genes in microglia in mice and humans, is implicated in numerous microglial functions. However, the molecular mechanisms underlying Cx3cr1 signaling are not well understood. Here, we analyzed transcriptomes of Cx3cr1-deficient microglia under varying conditions by RNA sequencing (RNA-Seq). In 2 mos mice, Cx3cr1 deletion resulted in the downregulation of a subset of immune-related genes, without substantial epigenetic changes in markers of active chromatin. Surprisingly, Cx3cr1-deficient microglia from young mice exhibited a transcriptome consistent with that of aged Cx3cr1-sufficient animals, suggesting a premature aging transcriptomic signature.

overall_design: RNAseq analysis of sorted microglia

first: Raghavendra

last: Hosur

first: Ravi

last: Challa

first: Patrick

last: Cullen

first: Kelly

last: Miao

first: Norm

last: Allaire

first: Chris

last: Roberts


title: Food-derived Compounds Apigenin and Luteolin Modulate mRNA Splicing of Introns with Weak Splice Sites

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakawa Oiwakecho, Sakyo-ku

country: Japan

institute: Division of Integrated Life Sciences, Graduate School of Biostudies

summary: Cancer cells often exhibit extreme sensitivity to splicing inhibitors. We identified food-derived flavonoids, apigenin and luteolin, as compounds that modulate mRNA splicing at the genome-wide level, followed by proliferation inhibition. They bind to mRNA splicing-related proteins to induce a widespread change of splicing patterns in treated cells. Their inhibitory activity on splicing is relatively moderate, and introns with weak splice sites tend to be sensitive to them. Such introns remain unspliced, and the resulting intron-containing mRNAs are retained in the nucleus, resulting in the nuclear accumulation of poly(A)+ RNAs in these flavonoid-treated cells. Tumorigenic cells are more susceptible to these flavonoids than non-tumorigenic cells, both for the nuclear poly(A)+ RNA-accumulating phenotype and cell viability. This study illustrates the possible mechanism of these flavonoids to suppress tumor progression in vivo that were demonstrated by previous studies, and provides the potential of daily intake of moderate splicing inhibitors to prevent cancer development.

overall_design: U2OS cells were treated with DMSO or 75μM apigenin or 75μM luteolin for 24 h and then harvested. Total RNA was extracted from biological duplicate samples with Sepasol-RNA I super G. RNA-seq library was prepared using Truseq Stranded mRNA Library Prep Kit (Illumina, CA) and sequenced on an NextSeq Highoutput (Illumina, CA).

first: M

last: Kurata

first: S


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (BS-Seq and OxBS-Seq)

status: Public on Nov 26 2019

city: Boston

first: Lisa

middle: D.

last: Boxer

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

institute: Harvard Medical School

type: Methylation profiling by high throughput sequencing

summary: Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome, and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. Using multiple approaches, we demonstrate that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation in the brain directly, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which it binds broadly across highly methylated regions of DNA, but acts from a distance to attenuate transcriptional initiation.

overall_design: BS-seq and OxBS-seq were performed from forebrain tissue from 3 WT and 3 MeCP2 KO mice.

middle: D

first: William

last: Renthal

first: Benyam

last: Kinde

first: Michael

middle: E

last: Greenberg


title: A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation.

status: Public on Nov 21 2019

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

type: Methylation profiling by genome tiling array

summary: Maternal-effect mutations in components of the subcortical maternal complex (SCMC) of the human oocyte can cause early embryonic failure, gestational abnormalities and recurrent pregnancy loss. Enigmatically, they are also associated with DNA methylation abnormalities at imprinted genes in conceptuses, in the devastating gestational abnormality biparental complete hydatidiform mole (BiCHM) or in multi-locus imprinting disease (MLID). However, the developmental timing, genomic extent and mechanistic basis of these imprinting defects are unknown. Here, we studied methylation level of a women reported with familial recurrent hydatidiform mole and multiple pregnancy loss. Genotype analysis revealed homozygous mutation in KHDC3L. We obtained biparental mole from patient (Patient D) and compared it’s whole-genome methylation profile with respect to control placentas and sporadic mole (AnCHM) using Infinium MethylationEPIC BeadChip (WG-317-1001, Illumina). We also used endometrium samples from their respective mother for the comparison purposes. Molar conceptuses were observed with methylation defects at genome-wide level and profound loss of methylation at multiple genome-derived differentially methylated regions (gDMRs) confirming MLID.

overall_design: DNA samples from control placenta, biparental mole and sporadic mole were analysed using using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. Methylation level was assesed at genome-wide level and specific genome features (eg. gDMRs and CpG Islands).

first: Hannah

last: Demond

first: Zahra

last: Anvar

first: Bahia

middle: N

last: Jahromi

first: Angela

last: Sparago

first: Maryam

last: Davari

first: Luciano

last: Calzari

first: Silvia

last: Russo

first: Mojgan

middle: A

first: David

last: Monk

first: Simon

last: Andrews

first: Andrea

last: Riccio

first: Gavin

last: Kelsey


title: Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Progression

status: Public on Nov 27 2019

city: Philadelphia

first: Gerd

last: Blobel

state: PA

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

institute: University of Pennsylvania	Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin architecture is temporarily disrupted during mitosis. Yet, how chromatin architecture is reconfigured during M-G1 phase transition is unknown. To examine this, we performed Hi-C experiments on cell populations at defined cell cycle stages between mitosis and G1 phase.

overall_design: Uninduced G1E-ER4 (-GATA1) cells were synchronized to pro-metaphase with nocodazole treatment and was released from nocodazole for a variety of durations. Cells at different cell cycle stages were purified with FACS. Hi-C experiments were performed on purified populations to examine chromatin structure at designated cell cycle stage.

first: Haoyue

last: Zhang

first: Daniel

middle: J

last: Emerson

first: Thomas

middle: G

last: Gilgenast

first: Katelyn

middle: R

last: Titus

first: Yemin

last: Lan

first: Jennifer

last: Philips-Cremins


title: mSWI/SNF functional genomic characterization of SMARCB1 mutants in SMARCB1-null and heterozygous settings

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

summary: Chromatin remodeling complexes regulate gene expression by shifting, evicting, and exchanging nucleosomes along the chromosomes of eukaryotic organisms.  The mammalian SWI/SNF chromatin remodeling complex (mSWI/SNF or BAF) is mutated in over 20% of human cancers and loss of the SMARCB1 gene, encoding the BAF47 protein subunit, results in one of the most aggressive and lethal pediatric cancers. An accumulation of point mutations occurs at the C-terminal end of the protein, for which the functional ramifications are unknown. We previously demonstrated that reintroduction of SMARCB1 in SMARCB1-null malignant rhabdoid tumor cells results in a genome-wide increase of mSWI/SNF complex occupancy coupled with activation of PRC2-repressed genes. Here, we study the functional consequences that these point mutations exert on mSWI/SNF complex activity in SMARCB1-deficient tumor cells and extend this investigation to a CRISPR/Cas9-mediated SMARCB1-heterozygous mutant induced pluripotent stem cell. Intriguingly, we observe that the mutant complexes bind similarly to wild-type SMARCB1 complexes at enhancers throughout the genome but often fail to transcriptionally activate nearby genes in a cis-regulatory manner.

overall_design: (1) ChIP-seq, ATAC-seq, MNase-seq and/or RNA-seq in human malignant rhaboid tumor cell lines (TTC1240 & G401) lentivirally infected with Empty vector or SMARCB1 constructs (FL, K34del, R377H, Y326*) and (2) ChIP-seq, RNA-seq, and ATAC-seq in human induced pluripotent stem cells (iPSCs) (WT control and SMARCB1 K364del heterozygous mutant)

first: Alfredo

middle: M

last: Valencia

first: Clayton

middle: K

last: Collings


title: RNA-sequencing of human peripheral blood mononuclear cells (PB MNCs) and induced neural progenitor cells derived from PB MNCs

city: Shanghai

first: Ting

address: 100 Haining Road

department: Department of Ophthalmology

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary: We have successfully generated human induced neural progenitor cells (iNPCs) from peripheral blood mononuclear cells (PB MNCs). To gain further insights into the transcriptional activation and cellular identity of human iNPCs, we compared the transcriptome of human iNPCs with PB MNCs and  published database CORTECON and BrainSpan.

overall_design: Global gene expression of PB MNCs and human iNPCs were determined by bulk RNA sequencing in two different iNPC lines at passage 15 and 25, from two individuals, respectively.

first: Ran

last: Wang

first: Guizhong

last: Cui

first: Chunmei

last: Yue

first: Naihe

last: Jing


title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (RNA-Seq I)

first: Lisa

last: Boxer

overall_design: Total RNA-seq was performed on whole-cell, nuclear, and chromatin-associated RNA from forebrain tissue from 10 MeCP2 KO and 10 WT and 10 MeCP2 R306C and 10 WT mice. Total RNA-seq was performed on visual cortex tissue from 6 Dnmt3a cKO and 6 WT mice.

first: William

last: Renthal

first: Benyam

last: Kinde

first: Michael

last: Greenberg


title: Next Generation Sequencing Facilitates Quantitative Analysis Of Wild Type And Tbk1 N129D KI Murine Embryonic Fibroblast Transcriptomes

status: Public on Nov 19 2019

first: Jea Hyun

last: Baek

address: 225 Binney Street

institute: Biogen

summary: TBK1 is a multifunctional kinase phosphorylating a variety of proteins triggering innate immune signaling and autophagy. TBK1 has recently attracted much attention of neurologists for its critical role for the pathogenesis of various neurologic diseases including ALS. Loss of function of TBK1 has been identified as a major cause of ALS and also as a sufficient cause for the disease. Existing data suggests that TBK1 or its interacting partners may be promising targets for therapeutic intervention.

overall_design: mRNA profiles of homozygous, heterozygous and wild-type  TBK1 N129D KI MEF treated with pI:pC or antimycin/oligomycin were generated by deep sequencing, in quadruplicate, on the Illumina HiSeq 2500 platform.

first: Jea-Hyun

first: Helen

last: McLaughlin


title: Helios enhances the preferential differentiation of human fetal CD4+ naïve T cells into regulatory T cells.

status: Public on Nov 22 2019

city: San Francisco

first: Melissa

last: Ng

state: California

address: 35 Medical Centre Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Impaired DNA methylation in oocytes with a mutation in KHDC3L causing recurrent hydatidiform mole

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Mutations in components of the subcortical maternal complex (SMC) of the human oocyte are enigmatically associated with DNA methylation abnormalities specifically at imprinted genes in conceptuses, but the developmental timing, genomic extent and mechanistic details of these defects are unknown.  Here, we show, by single-cell bisulphite sequencing, that mutation in human KHDC3L that causes recurrent hydatidiform mole results in a genome-wide deficit of de novo methylation in oocytes.

overall_design: BS-seq of 5 oocytes and 1 preimplantation embryo of patient D with a KHDC3L mutation and a history of 2 biparental molar pregnancies

first: H

last: Demond

first: Z

last: Anvar

first: B

last: Jahromi

first: M

last: Davari

first: S

last: Andrews

first: G

last: Kelsey


title: Transcriptomic responses in mouse blood during the first week after in vivo gamma irradiation

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

summary: Due to limitations of available human models for development of gene expression based radiation biodosimetry, many such studies have made use of mouse models.  To provide a broad view of the gene expression response to irradiation in the mouse, we have exposed male C57BL/6 mice to 0, 1.5, 3, 6 or 10 Gy of gamma rays, sacrificing groups of the mice at 1, 2, 3, 5, or 7 days after exposure.  Global gene expression was then profiled in blood from individual mice using Agilent microarrays.  In general, we found increasing numbers of genes differentially expressed with increasing dose, with more prolonged responses after the higher doses.

overall_design: Male C57BL/6 mice were either sham irradiated as controls or exposed to 1.5, 3, 6 or 10 Gy of gamma-rays.  Mice from each dose group (including controls) were sacrificed at either 1, 2, 3, 5 or 7 days after exposure, and blood collected for microarray analysis.  Ten biological replicates, representing independent mice, were done for each dose and time point, with the exception of the 10Gy dose on day 7, for which only 8 replicates were obtained.

first: Sunirmal

last: Paul


title: Single-cell characterization and metabolic profiling of in vitro cultured human skeletal progenitors with enhanced in vivo bone forming capacity

status: Public on Nov 18 2019

city: Leuven

first: Tim

last: Herpelinck

address: Herestraat 49

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Cell populations and their interplay provide the basis of a cell-based regenerative construct. Serum-free preconditioning can overcome the less predictable behaviour of serum expanded progenitor cells, but the underlying mechanism and how this is reflected in vivo remains unknown. Herein, the cellular and molecular changes associated with a cellular phenotype shift induced by serum-free preconditioning of human periosteum-derived cells was investigated. Following BMP2 stimulation, preconditioned cells displayed enhanced in vivo bone forming capacity, associated with an adapted cellular metabolism together with an elevated expression of BMPR2. Single-cell RNA sequencing confirmed the activation of pathways and transcriptional regulators involved in bone development and fracture healing, providing support for the augmentation of specified skeletal progenitor cell populations. The reported findings illustrate the importance of appropriate in vitro conditions for the in vivo outcome. In addition, BMPR2 represents a promising biomarker for the enrichment of skeletal progenitor cells for in vivo bone regeneration.

overall_design: Human periosteum-derived cells (hPDCs), pooled from 4 individuals, were cultured in growth medium (GM), i.e. DMEM-GlutaMAX supplemented with 10% foetal bovine serum and 1% antibiotic-antimycotic solution until passage 5. The hPDCs were then preconditioned in chemically-defined medium (CDM) or further cultured in GM as a control. Preconditioned and control cells were collected after 6 days and loaded onto the 10X Chromium Platform.


title: RNA-Seq of livers of male C57/BL6N and Scly KO mice on diets containing 0.08 ppm (low) and 0.25 ppm (adequate) sodium selenite

city: Honolulu

first: Lucia

last: Seale

state: Hawaii

address: 651 Ilalo st. BSB222

institute: University of Hawaii

summary: We report the application of RNA sequencing technology for transcriptomic profiling in murine livers of male wild-type (WT) and Scly knockout (KO) mouse. This study provides a framework for combined metabolomics analysis of this mouse model lacking the capacity for selenocysteine decomposition.

overall_design: 4 experimental groups: two genotypes fed two different diets containing low and medium sodium selenite concentrations

first: Vedbar

last: Khadka


title: HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge

status: Public on Nov 17 2019

city: Beijing

first: Huarong

last: Wang

address: NO. 2 Yuanmingyuan West Road

institute: China Agriculture University


title: HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge [mGC-HDACi]

summary: It is known that granulosa cells (GCs) mediate gonadotropin-induced oocyte meiosis resumption by releasing EGF-like factors in mammal, however, the detail molecular mechanisms remain unclear. Here, we demonstrate that luteinizing hormone (LH) surge induced histone deacetylase 3 (HDAC3) downregulation in GCs is essential for oocyte maturation. Before the LH surge, HDAC3 is highly expressed in GCs. Transcription factors, such as FOXO1, mediates recruitment of HDAC3 to the amphiregulin (Areg) promoter, which suppresses AREG expression. With the LH surge, decreased HDAC3 in GCs enables histone H3K14 acetylation and binding of the SP1 transcription factor to the Areg promoter to initiate AREG transcription and oocyte maturation. Conditional knockout of Hdac3 in granulosa cells in vivo or inhibition of HDAC3 activity in vitro promotes the maturation of oocytes independent of LH. Taking together, HDAC3 in GCs within ovarian follicles acts as a negative regulator of EGF-like growth factor expression before the LH surge.

overall_design: Examination of transcriptome of in vitro cultured wild type mice ovarian granulosa cells between control group and HDACi 4b-treated group for 2 repeats.

first: Han

last: Cai


title: HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge [oocyte-transcriptome]

overall_design: Examination of transcriptome of in vitro cultured oocytes in control groups and HDACi 4b-treated groups for 2 repeats


title: Genome wide maps of chromatin states of larval Drosophila neural stem cells (NSCs), their progeny and their tumorigenic counterparts

city: Vienna

first: Merve

middle: Deniz

last: Abdusselamoglu

address: Doktor. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)

summary: We develop a FACS-based method to sort different cell types of larval Drosophila brain and perform chromatin immunoprecipitation with histone modifications: H3K4me3 for active mark and H3k27me3 for repressive mark. We then sequence chromatin immunoprecipitated DNA in order to examine the chromatin state changes in neurogenesis as well as in tumorigenesis.

overall_design: examination of 2 histone modifications in four different cell types.

first: Lisa

last: Landskron

first: Elif

last: Eroglu

first: Sarah

last: Bowman

first: Thomas

last: Burkard

first: Robert

last: Kingston

first: Juergen

last: Knoblich


title: HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge [HDAC3cKO]

overall_design: Examination of transcriptome of ovarian granulosa cells of 2 mice per group


title: Detection of differences in gene expression in the noradrenergic nuclei in the brain

city: Rehovot

first: Ayelet

last: Erez

address: 234 Herzl Street

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: The goal of this study was to compare the transcriptome of neurons from the locus coeruleus (LC) from wild type and mice that are conditional KO to argininosuccinatelyase (ASL) in the LC. Using an optimized data analysis, we were able to detect difference in the transcription of key enzymes in the synthesis of catecholamine, along with changes in the catecholamine synthesis pathway. Approximately 7% of the transcripts showed differential expression between the WT and ASL-LC cKO mice. The altered expression of the releant genes was confirmed with qRT–PCR. Our study represents the detailed analysis of the LC that revealed novel metabolic regulation on this region.

overall_design: 100 cells from each mouse were collected using laser micro dissection from the LC of WT and ASL-LC cKO mice

first: Shaul

last: Lerner


title: PolII ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

status: Public on Nov 16 2019

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue D'ulm

country: France

institute: Institut Curie

summary: Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation

overall_design: This study was performed in mouse T-cells. It contains ChIP-seq data for RNA Pol II and input DNA. All sequencing were performed in paired-end sequencing runs.

first: Cyril

last: Esnault


title: Transcriptome analysis of naïve or stimulated WT and TRIM28 KO CD4 T cells (Affymetrix)

summary:
Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and effector differentiation
The study explores the role of gene silencing by TRIM28, an adaptor protein for histone binding modules , in CD4 T cell function.

overall_design: Littermate and TRIM28KO CD4 T cells, naïve or stimulated for indicated times with anti-CD3 (plate-bound) and anti-CD28 (soluble).

first: Ulf

last: Gehrmann

first: Christel

last: Goudot

first: David

last: Gentien


title: Stem and effector CD8 T-cells from human cancers

status: Public on Nov 15 2019

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

summary: Tumor infiltrating lymphocytes (TILs) are associated with a survival benefit in several tumor types and response to immunotherapy. However, the reason some tumors have high CD8 T cell infiltration while others do not remains an unanswered question. In this study, we investigated the requirements for maintaining a CD8 T cell response against human cancer. We find that CD8 T cells within tumors consist of distinct populations of terminally differentiated and stem-like cells. Upon proliferation, stem-like CD8 T cells give rise to more terminally differentiated, effector molecule expressing daughter cells. For many T-cells to infiltrate the tumor, it is critical that this effector differentiation process occur. In this study, we collected these different cell populations from human tumors and performed RNA sequencing and DNA methylation analysis.

overall_design: Cell populations were sorted from tumors and RNA and DNA extracted using qiagen all-prep kits. RNA was sequenced using the NuGen ovation protocol for prostate and bladder, and clontech smartseq2 for bladder samples. Dna methylation libraries were prepared using the Illumina DNAmethyseq protocol. Samples were sequenced on a Hiseq 3000, or Hiseq X10.


title: Transcriptome analysis of WT and TRIM28 KO CD4 T cells, naïve or stimulated with anti-CD3 (plate-bound) and anti-CD28 (soluble) in Th0, Th1, Th2, Th17 or Treg conditions

overall_design: Littermate and TRIM28KO CD4 T cells were sorted by flow cytometry, naïve or stimulated for 72h with anti-CD3 (plate-bound) and anti-CD28 (soluble) in Th0, Th1, Th2, Th17 or Treg conditions.


title: Critical role for TRIM28 and HP1beta/gamma in the epigenetic control of T cell metabolic reprograming and effector differentiation


title: Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RNA-Seq]

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

summary: Bacterial small non-coding RNAs (sRNAs) play post-transcriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV crosslinking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the P. aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5’ UTRs and sRNAs, and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that sRNAs association with Hfq is primarily a function of their expression levels, strongly supporting that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of post-transcriptional regulation in P. aeruginosa.

overall_design: To disentangle differences in gene expression from those in protein binding, we performed RNA-seq for an ad hoc normalization of CLIP-seq

first: Thorsten

last: Bischler

first: Lars

last: Barquist

first: Vivian

last: Monzon

first: Naohiro

last: Noda

first: Jörg

last: Vogel

first: Satoshi

last: Tsuneda


title: Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RIP-Seq]

overall_design: To detect the binding sites for P. aeruginosa Hfq between different conditions we collected three biological replicates of P. aeruginosa PAO1 hfq::3xFLAG strain from planktonic (OD600 = 2.0) and biofilm (48 hour-old on LB agar). Half of each replicate culture was irradiated with UV light (254 nm, 800 mJ/cm2) (+XL), while the other half was left untreated (-XL). Bacteria were lysed and the FLAG-tagged protein was immunoprecipitated using a monoclonal anti-FLAG antibody. The samples were treated with benzonase nuclease, calf intestine phosphorylase, and polynucleotide kinase in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE followed by transfer to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit. Besides, total RNA was purified from both planktonic and biofilm conditions and the high-throughput sequencing was performed at Core Unit Systems Medicine, University Hospital of Würzburg, Germany.


title: miRNA142-3p targets Tet2 and impairs Treg differentiation and stability in models of type 1 diabetes

status: Public on Nov 14 2019

city: Munich

first: Carolin

last: Daniel

address: Heidemannstrasse 1

country: Germany

institute: Helmholtz Zentrum München

type: Non-coding RNA profiling by high throughput sequencing

summary: In type 1 diabetes (T1D), the appearance of multiple islet autoantibodies indicates the onset of islet autoimmunity, often many years before clinical symptoms arise. However, the underlying molecular mechanisms in T cells that can promote aberrant activation thereby triggering autoimmune progression remain poorly understood. Here, we show that during early stages of islet autoimmunity a miRNA142-3p/Tet2 signaling axis in murine and human CD4+T cells interferes with the efficient induction of regulatory T (Treg) cells accompanied by impairments in Treg stability. Specifically, we demonstrate that miR142-3p is induced in islet autoimmunity, while its inhibition enhances Treg induction and stability accompanied by a reduction of islet autoimmunity in non-obese diabetic (NOD) mice. Mechanistically, using HITS-CLIP analyses we identify the methylcytosine dioxygenase Tet2 as a direct target of miR142-3p in CD4+T cells, thereby linking high miR142-3p levels to epigenetic remodeling and impairments in Treg induction and stability. These findings offer a new mechanistic model where during islet-autoimmunity miR142-3p/Tet2-mediated Treg instability can contribute to autoimmune activation and progression.

overall_design: We performed miRNA sequencing of four pooled samples of human naive and activate CD4+ T cell from children with and without Type 1 Diabetes islet autoimmunity

first: Martin

last: Scherm

first: Benedikt

last: Kirchner


overall_design: We performed HITS-CLIP analysis of microRNAs and mRNA fragments present in the RNA-induced silencing complex (RISC) of human CD4+ T cells.

first: Jonathan

last: Schug


title: H3K9me3 and H3K9Ac ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

first: Sebastian

last: Amigorena

overall_design: The study explores the role of gene silencing by TRIM28, an adaptor protein for histone binding modules , in CD4 T cell function.

first: Ella

last: Zueva


title: Study of sarcopenia in human muscle biopsies of elderly individuals, Jamaica Sarcopenia Study

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary:
Purpose: The main goal of this study is to compare skeletal muscle transcriptome profilings derived from muscle impaired versus healthy subjects.
Methods: We use high coverage RNA sequencing of human skeletal muscle biopsies to analyze genome-wide transcriptional changes in human sarcopenia benchmarked to healthy elderly controls.

overall_design: 14 muscle biopsies from healthy subjects, 9 muscle biopsies from sarcopenic subjects, 5 muscle biopsies from subjects with only low muscle mass, 11 muscle biopsies from subjects with only low muscle strength or low muscle function.

first: Eugenia

last: Migliavacca

first: Aline

last: Charpagne

first: Terrence

last: Forrester

first: Curtis

last: Green

first: Patrice

last: Francis

first: Gail

last: Nelson

first: Allan

last: Sheppard

first: Sherry

last: Ngo

first: Xiaoling

last: Li

first: Tony

last: Pleasants

first: Frédéric

last: Raymond

first: Descombes

last: Patrick


title: Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing

first: Kotaro

last: Chihara

overall_design: Refer to individual Series


title: Study of sarcopenia in human muscle biopsies of elderly individuals, Hertfordshire Sarcopenia Study

summary:
Purpose: The main goal of this study is to compare skeletal muscle transcriptome profilings derived from sarcopenic versus healthy subjects.
Methods: We use high coverage RNA sequencing of human skeletal muscle biopsies to analyze genome-wide transcriptional changes in human sarcopenia benchmarked to healthy elderly controls.

overall_design: 28 muscle biopsies from healthy subjects, 4 muscle biopsies from sarcopenic subjects, 5 muscle biopsies from subjects with only low muscle mass, 3 muscle biopsies from subjects with only low muscle strength or low muscle function.

first: Sheila

last: Barton

first: Cyrus

last: Cooper

first: Emma

middle: S

last: Garratt

first: Keith

last: Godfrey

first: Karen

last: Lillycrop

first: Avan

last: Sayer

first: Phil

last: Titcombe

first: Leo

last: Westbury

first: Harnish

middle: P

last: Patel

first: Holly

last: Syddall


title: SLIGRL-induced gene expression changes in NHEK cells

status: Public on Nov 13 2019

city: Berkeley

first: Diana

last: Bautista

state: CA

address: 142 Life Sciences Addition

department: Molecular and Cellular Biology

institute: UC Berkeley

summary: NHEK cells were treated with the PAR2 agonist SLIGRL to study changes in gene expression following PAR2 activation

overall_design: Comparisons were made between Vehicle and SLIGRL-treated cells

first: Rose

middle: Z

last: Hill


first: Carolin

last: Daniel


title: Monocytes and Monocyte-derived Antigen-presenting Cells have Distinct Gene Signatures in Experimental Model of Multiple Sclerosis

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Multiple sclerosis (MS) is a chronic inflammatory disease mediated by a complex interaction between the autoreactive lymphocytes and the effector myeloid cells within the central nervous system (CNS). In a murine model of MS, experimental autoimmune encephalomyelitis (EAE), Ly6Chi monocytes migrate into the CNS and further differentiate into antigen-presenting cells (APCs) during disease progression. Currently, there is no information about gene signatures that can distinguish between monocytes and the monocyte-derived APCs. We developed a surface marker-based strategy to distinguish between these two cell types during the stage of EAE when the clinical symptoms were most severe, and performed transcriptome analysis to compare their gene expression. We report here that the inflammatory CNS environment substantially alters gene expression of monocytes, compared to the monocyte differentiation process within CNS. Monocytes in the CNS express genes that encode proinflammatory cytokines and chemokines, and their expression is mostly maintained when the cells differentiate. Moreover, monocyte-derived APCs express surface markers associated with both dendritic cells and macrophages, and have a significant up-regulation of genes that are critical for antigen presentation. Furthermore, we identified Ccl17, Ccl22, and Ccr7 as signature genes for monocyte-derived APCs but not the Ly6Chi monocytes. These findings may shed light on identifying molecular signals that control monocyte differentiation and functions during EAE.

overall_design: Experimental autoimmune encephalomyelitis (EAE) was induced in mice on a C57BL/6J background by subcutaneously injection of myelin oligodendrocyte glycoprotein peptide emulsified in complete Freund’s adjuvant. Pertussis toxin (250 ng) was injected intraperitoneally at 2- and 24-hours following the injection of emulsion. At days 14-15 following EAE induction, bone marrow monocytes (CD45+ CD11b+ Ly6Chi Ly6G- CD11c-), spinal cord monocytes (CD45+ CD11b+ CD64+ Ly6Chi Ly6G-), and spinal cord monocyte-derived APCs (CD45+ CD11b+ CD64+ Ly6Clow/- Ly6G-) were isolated. RNA were purified from the cells. Gene expression was analyzed by RNA-Sequencing.

first: K

middle: L

last: Monaghan

first: W

last: Zheng

first: G

last: Wan


title: Template switching by a group II intron reverse transcriptase: biochemical analysis and implications for RNA-seq

status: Public on Nov 11 2019

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: The reverse transcriptases (RTs) encoded by mobile group II intron and other non-LTR-retro-elements differ from retroviral RTs in being able to template switch from the 5' end of one template to the 3' end of another without pre-existing complementarity between the donor and acceptor nucleic acids. Here, we used the ability of a thermostable group II intron RT (TGIRT) to template switch directly from synthetic RNA template/DNA primer duplexes having either a blunt end or a 3'-DNA overhang end to establish a complete kinetic framework for the reaction and identify conditions that more efficiently capture acceptor RNAs or DNAs. The rate and amplitude of template switching are optimal from starter duplexes with a single nucleotide 3'-DNA overhang complementary to the 3' nucleotide of the acceptor RNA, suggesting a role for non-templated nucleotide addition of a complementary nucleotide to the 3’ end of cDNAs synthesized from natural templates. Longer 3'-DNA overhangs progressively decrease the rate of template switching, even when complementary to the 3' end of the acceptor template. Although dependent upon only a single base pair between the donor and acceptor, template switching discriminates against mismatches, which coupled with the high processivity of the enzyme, enables the synthesis of full-length DNA copies of acceptor nucleic acids beginning directly at their 3' end. We discuss possible biological functions of the template-switching activity of group II intron and other non-LTR-retroelements RTs, as well as the optimization of this activity for adapter addition in RNA-and DNA-seq.

overall_design: A group II intron RT was used to template switch and reverse transcribe synthetic RNA oligonucleotides and the resulting products were sequenced by Illumina Nextseq 500, and the junctions between acceptor and donor RNA molecules were analyzed.

first: Alfred

last: Lentzsch

first: Jun

last: Yao

first: Rick

last: Russell


title: Transcriptome analysis of naïve or stimulated WT and TRIM28 KO CD4 T cells (RNA-seq)

first: Sebastian

last: Amigorena

overall_design: Littermate and TRIM28KO naïve CD4 T cells.

first: Ulf

last: Gehrmann

first: Christel

last: Goudot


title: Elimination of fukutin reveals cellular and molecular pathomechanisms in muscular dystrophy-associated heart failure

status: Public on Nov 08 2019

city: Okayama

first: Yuki

last: Katanosaka

address: Shikata-cho 2-7-1

institute: Okayama University

summary: Heart failure is the major cause of death for muscular dystrophy patients; however, the molecular pathomechanism remains unknown. Here, we show the detailed molecular pathogenesis of muscular dystrophy-associated cardiomyopathy in mice lacking the fukutin gene (Fktn), the causative gene for Fukuyama muscular dystrophy. Although cardiac Fktn elimination markedly reduced alpha-dystroglycan glycosylation and dystrophin-glycoprotein complex proteins in sarcolemma at all developmental stages, cardiac dysfunction was observed only in later adulthood, suggesting that membrane fragility is not the sole etiology of cardiac dysfunction. During young adulthood, Fktn-deficient mice were vulnerable to pathological hypertrophic stress with downregulation of Akt and the MEF2-histone deacetylase axis. Acute Fktn elimination caused severe cardiac dysfunction and accelerated mortality with myocyte contractile dysfunction and disordered Golgi-microtubule networks, which were ameliorated with colchicine treatment. These data reveal fukutin is crucial for maintaining myocyte physiology to prevent heart failure, and thus, the results may lead to strategies for therapeutic intervention.

overall_design: Microarray analysis using 10-week-old floxed and αMHC-MCM-Fktn-cKO (Fktnflox/flox;αMHC-MCM+/-) hearts treated with tamoxifen for 4 day.

first: Yoshihiro

last: Ujihara


title: Functional dissection of the regulatory mechanism of the atypical AP-1-like transcription factor, Yap1, in Cryptococcus neoformans

status: Public on Nov 07 2019

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: AP-1 like transcription factors play evolutionarily conserved roles in oxidative stress responses as redox sensors in eukaryotes. In this study, we aim to elucidate the regulatory mechanism of an atypical yeast AP-1 like protein, Yap1, in the stress response and virulence of Cryptococcus neoformans. YAP1 expression was induced not only by oxidative stresses, such as H2O2 and diamide, but also by other environmental stresses, such as osmotic and membrane destabilizing stresses. Supporting these data, Yap1 was involved in osmotic and membrane stress responses as well as oxidative stress responses. Pleiotropic roles of Yap1 in diverse biological processes were supported by transcriptome analysis data showing that more than 162 genes are differentially regulated by Yap1. This analysis also provided a clue that Yap1 is involved in carbohydrate metabolism and indeed we found that Yap1 promotes cellular resistance to toxic cellular metabolites produced during glycolysis, such as methylglyoxal. Finally, we demonstrated that Yap1 played a minor role in survival of C. neoformans within hosts.

overall_design: WT (H99) and yap1∆ mutant (YSB815) strains were incubated in liquid YPD medium overnight at 30°C. The cells were subcultured in fresh YPD medium and then further incubated at 30°C until OD600 reached 0.8 . The WT and yap1∆ mutant cells were harvested and lyophilized. Three biologically independent cultures were prepared for each strain. Total RNAs were isolated by Easy-BLUE (iNtRON) and purified with an RNeasy Mini Kit (Qiagen). cDNA libraries were constructed with the TruSeq RNA library kit v2 (Illumina) using 1 g of total RNA and sequenced by Illumina platform.

first: Yee-Seul

last: So

first: Seong-Ryong

last: Yu

first: Yong-Sun

last: Bahn


title: Effects of Spaceflight on Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Structure and Function

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: With extended stays aboard the International Space Station (ISS) becoming commonplace, there is a need to better understand the effects of microgravity on cardiac function. We utilized human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to study the effects of microgravity on cell-level cardiac function and gene expression. The hiPSC-CMs were cultured aboard the ISS for 5.5 weeks and their gene expression, structure, and functions were compared to ground control hiPSC-CMs. Exposure to microgravity on the ISS caused alterations in hiPSC-CM calcium handling. RNA-sequencing analysis demonstrated 2,635 genes were differentially expressed among flight, post-flight, and ground control samples, including genes involved in mitochondrial metabolism.  This study represents the first use of hiPSCs to model the effects of spaceflight on human cardiomyocyte structure and function.

overall_design: Examination of the effect of microgravity exposure on mRNA expression. Three cells lines examined in space-flight, post-flight, and ground control conditions.

middle: C

first: Alexa

last: Wnorowski

first: Ning-Yi

last: Shao


title: Diversity in natural transformation frequencies and regulation across Vibrio species

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street

institute: Indiana University

summary: In marine Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus.

overall_design: RNA-seq of cultures treated or untreated with IPTG to induce tfoX expression in Vibrio campbellii strains BB120 and DS40M4

first: Chelsea

last: Simpson

first: Ram

last: Podicheti

first: Douglas

middle: B

last: Rusch

first: Ankur

last: Dalia


title: Arabidopsis ECAP is a New Adaptor Protein that Connects JAZ Repressors with TPR2 Co-repressor to Suppress Jasmonate-Responsive Anthocyanin Accumulation

city: beijing

first: Changjiang

last: Li

address: Yuanmingyuan West Road 2,Haidian

department: College of Biological Sciences

institute: China Agricultural University

summary: Suppression mechanism employed by transcriptional repressors is commonly existed in diverse phytohormone signaling. In Arabidopsis thaliana, JASMONATE-ZIM DOMAIN (JAZ) proteins act as transcriptional repressors and involve in different aspects of the JA signaling network, through recruiting general co-repressors TOPLESS (TPL) and TPL-related proteins (TPRs). To accomplish overlapping but also finely separated functions of JAZ proteins, specificadaptor proteins are employed in JA signaling. Novel Interactor of JAZ (NINJA) is an adaptor protein mediates gene repression in JA-dependent root growth inhibition and pathogen defense. However, the adaptor protein(s) modulate other JA responsive biological processes is still a mystery. In this study, we demonstrated that a previously uncharacterized protein, ECAP(EAR-Containing Adaptor Protein) that connects JAZ6/8 and TPR to repress JA-mediated anthocyanin accumulation at low JA level. We also found ECAP-mediated transcriptional repression might play a general role in multiple aspects of plant development and responses to environments.

overall_design: 18 Samples are analyzed, wild type and mutant seedlings were treated by 50 μM JA for 0, 1 and 3 hours. Three repeats for wild type and  mutant at each time point. Wild type was set as control.

first: Lei

last: Shi

first: Yanan

last: Wang

first: Wei

first: Binqing

last: Chen

last: Zhu

first: Ming

last: Yuan

first: Ying

last: Fu


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of circular RNA derived from CUX1 gene (circ-CUX1)

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Circular RNAs (circRNAs), a subclass of noncoding RNAs characterized by covalently closed continuous loops, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating neuroblastoma progression still remain elusive. We identify one circRNA derived from CUX1 (circ-CUX1) as a novel driver of neuroblastoma progression. To investigate the mechanisms underlying the oncogenic functions of circ-CUX1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma IMR32 cells in response to stable over-expression of circ-CUX1. The results showed that stable over-expression of circ-CUX1 led to altered expression of 1215 human mRNAs, including 781 up-regulated genes and 434 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-CUX1 over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.

overall_design: Total RNA of cells stably transfected with empty vector or circ-CUX1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: The miRNAs expression in liver of Clock∆19 mutant mouse

city: Beijing

first: Yanli

state: Beijing

address: State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center

summary: Circadian clock controls the physiological functions of a lot of tissues including liver by an autoregulatory transcription-translational feedback loop, of which CLOCK is a core positive component. And, many studies have indicated that microRNAs (miRNAs) regulate liver function. However, little is known about the molecular interpretation of how CLOCK-regulated miRNAs are link to liver function. To better understand this, we performed the expression profiles of miRNAs in the liver of Clock△19 mutant mice to obtain the putative CLOCK-regulated miRNAs. A total of 61 miRNAs were differentially expressed (FCA≥2) in the liver of Clock mutant mice at zeitgeber time 2 (ZT2) and 57 miRNAs at zeitgeber time 14 (ZT14) as compared with control mice. Then, we analyzed the pathways of differentially expressed miRNAs to evaluate the roles of these miRNAs. According to the pathway analysis, the circadian rhythms and circadian entrainment pathway were found, and the target genes of differentially expressed miRNAs were mainly involved in pathways in cancer, PI3K-Akt signaling pathway and MAPK signaling pathway. The protein-protein interaction (PPI) analysis indicated that the hub genes were mostly associated with the pathway in cancer and circadian rhythms. Moreover, we verified the expression level of five miRNAs across the circadian cycle. Although the expression levels of miR-195 and miR-340 were up-regulated, the rhythms of these two miRNAs were always remained. The results identify a number of miRNAs that may be regulated by CLOCK, and these miRNAs play a role in the various physiological processes of the liver, which will provide a reference to better understanding the potential regulatory mechanisms in the liver.

overall_design: All male Clock mutant mice (Clock△19) mice at 6-8 weeks of age  were individually caged and maintained under IVC conditions with 12h light/dark cycle, lights-on at 0700hr and free access to food and water for two weeks before using. At 0900h (ZT2), 2100h (ZT14) on the first day after two weeks adaptation period, three animals of each group were sacrificed by dry ice. The liver was isolated, quickly frozen and stored in liquid nitrogen. The three RNA samples at each time point were mixed and isolated using the mirVana miRNA extraction Kit (Ambion, Austin, TX). RNA labeling, microarray hybridization and data processing were analyzed by Shanghai OE Biotech. Co., Ltd. Briefly, RNA labeled and hybridized using the Agilent mouse 4*44K microRNA microarray. Hybridization signals were detected with an Agilent DNA microarray scanner G2565BA, and scan images were analyzed using Agilent feature extraction software. Data is analyzed using Agi4x44PreProcess (Agilent Technologies).

first: Ke

last: LV

first: Mei

last: Zhao

first: Yinghui

first: Lina

last: Qu


title: Gene expression analysis in mouse brain identifies biological processes underlying stress response in Fkbp5 deficient mice

status: Public on Nov 06 2019

first: Joonhong

last: Kwon

address: 84, Heukseok-ro, Dongjak-gu

institute: Chung-Ang University

summary: Fkbp5 encodes the FK506 binding protein 5, a glucocorticoid receptor (GR) binding protein which is an important factor in stress responses that form coping behavior. However, the results of previous studies have been controversial about the relationships between variants in Fkbp5 and stress have been controversial. To clarify the effects of the loss of Fkbp5 on the stress response, we conducted behavior test with mice following chronic restraint stress with homozygous wild type (WT) and knock-out (KO) genotypes. WT mice showed anhedonia, one of depressive-like behaviors, but KO mice did not show this symptom in sucrose preference test (SPT). To examine the molecular mechanism of this stress resilience, we performed RNAseq analysis. The results of differentially expressed gene (DEG) analysis showed that diverse biological processes related with cell-cell communication are changed by chronic stress. Weighted gene co-expression network analysis detected 60 gene modules which show varied correlation patterns with stress or Fkbp5 genotype. The expression pattern of M55 module correlated with SPT results and the gene ontology (GO) enrichment analysis in this module revealed that the genes in this module are involved in nervous system development, gland morphogenesis and inflammatory response. We identify the role of Fkbp5 KO in stress response and the transcriptome study provide insight into stress-related biological processes.

overall_design: mRNA profiles of prefrontal cortex (PFC) from wild type (WT) control mice, WT stressed mice and Fkbp5-/- stressed mice were produced using Illumina HiSeq 4000. Bioinformatics analyses of the transcriptome profiles indicate that a wide variety of biological processes are affected in the PFC of WT and Fkbp5-/- stressed mice. We identified the various unique gene expression patterns altered by genotype and stress. Thus, this mouse brain transcriptome data resource provides a powerful and extensive framework to identify, prioritize and test gene targets and stress response mechanisms affected by Fkbp5-/-.

first: YeongJae

last: Kim

first: Koeul

last: Chol

first: Sihwan

last: Seol

first: Hyo

last: Kang


title: RNA-seq of tissues from MC903- and Ethanol-treated mice

first: Diana

last: Bautista

summary: We report transcript abundance in skin, spinal_cord, and trigeminal ganglia from animals treated with MC903 to induce a mouse model of atopic dermatitis across different genotypes, time points, and treatments

overall_design: Examination of gene expression in TSLPR.KO, wild-type, and neutrophil-depleted animals. For differential expression analysis, comparisons were performed between MC903 and ethanol treatments for the same condition (genotype, timepoint, etc.)

first: Rose

last: Hill


title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the consequences of oxidative stress elicited by tert-butyl-hydroperoxide in Candida albicans

status: Public on Nov 04 2019

city: Debrecen

first: Krisztina

last: Szabó

address: Egyetem tér

department: Medical Chemistry

country: Hungary

institute: University of Debrecen

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


title: single cell RNA-seq of HeLa CCL2

first: Xin

last: Zhang

address: No.5 Yiheyuan Road

department: School of Life Sciences, BIOPIC

institute: Peking University

summary: We measured 720 HeLa-CCL2 cells (288 from the 9th passage, 288 from the 14th passage and 144 from the 20th passage) in this work on an Illumina HiSeq 4000 platform (sequenced by Novogene, China) for 150 bp paired-end sequencing.  The protocol was based on Tang’s modification on SMART-Seq2.  Single cells were captured by mouth pipette under the stereomicroscope（Nikon SZM745）and followed by the protocol.  Every cell was assigned with 250 M raw data on average.

overall_design: We performed single cell RNA-seq of 720 HeLa CCL2, 288 from the 9th passage, 288 from the 14th passage and 144 from the 20th passage.

first: Wan-er

last: Hu

first: Xiao-dong

last: Su


title: Involvement of Condensin in Cellular Senescence through Gene Regulation and Compartmental Reorganization

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

summary: Cellular senescence is a state of stable cell growth arrest induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively.  Senescence is accompanied not only by global transcriptional alterations but also by 3D genome reorganization.  Here we demonstrate that the human condensin II complex participates in cellular senescence via gene regulation and reorganization of euchromatic A and heterochromatic B chromatin compartments.  OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and account for 15% of the human genome.  Mechanistically, condensin is enriched at A compartments, especially at gene promoters and typical/super enhancers, and implicated in the B-to-A transitions.  Genes present at B-to-A-switching regions tend to be up-regulated.  The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers such as the activity of senescence-associated beta-galactosidase (SA-beta-gal) and senescence-associated heterochromatic foci (SAHF).  This study describes that condensin reinforces euchromatic A compartments and is required for optimal expression of senescence genes, thereby contributing to the establishment and maintenance of the senescent state.

overall_design: in situ HI-C with human senescence cells. ChIP-seq and RNA-seq with human senescence cells. Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 x MEM non-essential amino acids.  Growing cells in population doublings (PD) between 26 and 32 were used for experiments.  pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging.  H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. For  CAP-H2 knockdown, pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon: CAPH2_KD1, 2, 3) and empty vector (control) were used.  Doxycycline (1ug/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression.  OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (KD1, 2, and 3) against NCAPH2 and harvested 3 days after the lentivirus infection.

first: Ken-ichi

last: Noma


title: ATAC-seq from sigmoid colon (ENCSR548QCP)

status: Public on Nov 01 2019

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ATAC-seq on human sigmoid colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: FBXW7 is a defining driver of uterine carcinosarcoma by promoting epithelial-mesenchymal transition

city: Dallas

first: Ileana

last: Cuevas

address: 5323 Harry hines Blvd. NB6.112

department: Pathology

institute: University of Texas Southwestern Medical Center

summary: Fbxw7 is a tumor supressor frequently mutated in endometrial cancer. To analyze the signaling pathways that can be altered by Fbxw7 we compared RNA expression in the presence or absence of Fbxw7 in mouse endometrial cancer cells deficient for Fbxw7 and Pten.

overall_design: Cells (UCS1 and UCS2) were isolated from mice deficient in Fbxw7 and Pten in endometrial epithelium and harboring uterine carcinosarcoma.  UCS1 and UCS2 cells were transduced with A) lentivirus expressing Fbxw7 under a Tet inducible promoter (pLVX-FBXW7) or B) lentivirus with vector only (pLVX) AND c) with lentivirus expressing TetON. Cells were selected with puromycin (pLVX) and G418 (tetON). RNA was isolated from biological replicates, RNA levels quantified and compared.

first: Diego

middle: H

last: Castrillon


title: The Msn2/4-like gene transcription factor Com2 (ORF YER130) is a key player of S. cerevisiae response and tolerance to sulphur dioxide

city: Vila Real

first: Ana

last: Mendes-Ferreira

address: Quinta de Prados

country: Portugal

institute: Universidade de Trás-os-Montes e Alto Douro

summary: Sulphur dioxide (SO2) and its derivatives are widely used as preservatives in food and beverage industries to assure the maintenance of microbiological quality of their products.  In this work it is shown, for the first time, the essential role played by the transcriptional regulator Com (ORF YER130c) in S. cerevisiae response and tolerance to SO2, this being the first biological function attributed for this regulator.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Cells of S. cerevisiae BY4741 and of the mutant BY4741_∆com2 were cultivated in MMB growth medium (at pH 3.5) either or not supplemented with 0.5mM of sulphur dioxide. For RNA extraction, cells were collected at 60 min of incubation.

first: A


title: Investigation of the host transcriptional response to intracellular bacterial infection using Dictyostelium discoideum as a host model

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary:
Background
During infection by intracellular pathogens, a highly complex interplay occurs between the infected cell trying to degrade the invader and the pathogen which actively manipulates the host cell to enable survival and proliferation. Many intracellular pathogens pose important threats to human health and major efforts have been undertaken to better understand the host-pathogen interactions that eventually determine the outcome of the infection. Over the last decades, the unicellular eukaryote Dictyostelium discoideum has become an established infection model, serving as a surrogate macrophage that can be infected with a wide range of intracellular pathogens. In this study, we use high-throughput RNA-sequencing to analyze the transcriptional response of D. discoideum when infected with Mycobacterium marinum and Legionella pneumophila. The results were compared to available data from human macrophages.
Results
The majority of the transcriptional regulation triggered by the two pathogens was found to be unique for each bacterial challenge. Hallmark transcriptional signatures were identified for each infection, e.g. induction of endosomal sorting complexes required for transport (ESCRT) and autophagy genes in response to M. marinum and inhibition of genes associated with the translation machinery and energy metabolism in response to L. pneumophila. However, a common response to the pathogenic bacteria was also identified, which was not induced by non-pathogenic food bacteria. Finally, comparison with available data sets of regulation in human monocyte derived macrophages shows that the elicited response in D. discoideum recapitulates what has been observed in human immune cells in response to Mycobacterium tuberculosis and L. pneumophila.
Conclusions
Our study presents high-throughput characterization of D. discoideum transcriptional response to intracellular pathogens using RNA-seq. We demonstrate that the transcriptional response is in essence distinct to each pathogen and to a large extent recapitulate the regulation in human macrophages after infection by mycobacteria and L. pneumophila. This indicates that host-pathogen interactions are evolutionary conserved, derived from the early interactions between free-living phagocytic cells and bacteria. Taken together, our results strengthen the use of D. discoideum as a general infection model.

sample_organism:
Dictyostelium discoideum AX4
Dictyostelium discoideum AX2

overall_design: RNA-seq of polyA enriched total RNA samples from Mycobacterium marinum infected and non-infected Dictyostelium discoideum AX2 cells. Samples were collected approximately 2.5 hours post infection (hpi). RNA-seq of polyA enriched total RNA samples from Legionella pneumophila infected D. discoideum AX4 cells at 1 and 6 hpi as well as non-infected control.

first: Jonas

last: Kjellin

first: Maria

last: Pränting

first: Frauke

last: Bach

first: Roshan

last: Vaid

first: Zhiru

last: Li

first: Marc

last: Hoeppner

first: Manfred

last: Grabherr

first: Ralph

last: Isberg

first: Monica

last: Hagedorn

first: Fredrik

last: Söderbom


title: Histone ChIP-seq from right atrium auricular region (ENCSR954TSY)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Genome-wide profiling of mTOR-dependent translation in Oikopleura dioica

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

summary: Protein synthesis is an energy-demanding process essential for cell proliferation and survival. Balancing the cost of protein synthesis with available resources has driven the evolution of its nutrient-dependent regulation. A central mechanism in this regulation is the repression of translation of the protein synthesis machinery during unfavorable growth conditions. This is mediated via mammalian target of rapamycin (mTOR), a master regulator of growth conserved from yeast to human. Despite extensive research, and the elucidation of a number of important factors, how mRNAs are translationally regulated by mTOR is still unclear. Repression depends on a 5’ Terminal Oligo Pyrimidine (TOP) motif which is conserved across vertebrates and present in Drosophila melanogaster. In Caenorhabditis elegans and the marine chordate Oikopleura dioica most TOP mRNAs are trans-spliced to a spliced leader. This results in the removal of the originally transcribed 5’ end and its replacement with a common short RNA sequence. In both species the 5’ end of the spliced leader is pyrimidine-enriched but does not meet strict requirements for a canonical TOP motif. How this affects the translational control of TOP mRNAs is unknown. Here, using transcriptome-wide ribosome profiling on whole animals treated with the mTOR inhibitor Torin 1, we show that trans-spliced TOP mRNAs in O. dioica are subject to mTOR-dependent translational control. We also show, using existing data, that trans-spliced transcripts in C. elegans are differentially translated upon recovery from starvation-induced developmental diapause. Together our results demonstrate that spliced leaders in metazoans are targets for mTOR-dependent translational control in response to nutrient availability. This indicates that trans-splicing in metazoans, the function of which has remained largely enigmatic, plays a key role in the coordinated translational regulation of growth-related genes. Moreover, our results reveal an innovative strategy for rapid evolution and developmental control of downstream targets of the ancient mTOR pathway.

overall_design: Ribosome-protected RNA fragments and total RNA extracted from animals treated with mTOR inhibitor Torin 1 and control animals (DMSO) in three biological replicates (12 samples in total) sequenced on two lanes on each of two Illumina flow cells

first: Gemma

last: Danks

first: Martina

last: Raasholm


title: Genome-wide and enzymatic analysis reveals efficient D- galacturonic acid metabolism in the basidiomycete yeast Rhodosporidium toruloides

first: Samuel

middle: Thomas

last: Coradetti

address: 1165 Glen Ave Apt B

department: Bioengineering

institute: UC Berkeley

summary: Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid and terpene derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C5/C6-sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed R. toruloides potential to assimilate Dgalacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. D-galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with D-glucose and D-xylose in R. toruloides. A genome-wide analysis by combined RNAseq/RB-TDNAseq revealed those genes with high relevance for fitness on D-galacturonic acid. While R. toruloides was found to utilize the same non-phosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. In addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for D-galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies in basidiomycetes.

overall_design: Comparitive transcriptional profiling during growth on D-galcturonic acid, D-glucose, and glycerol.

first: Ryan

last: Protzko

first: Christina

last: Hach

middle: T

first: Magdalena

last: Hackhofer

first: Sonja

last: Magosch

first: Nils

last: Thieme

first: Adam

last: Arkin

first: Jeffrey

last: Skerker

first: John

last: Dueber

first: J

last: Benz


title: Genome-wide profiling of translation in Oikopleura dioica during growth arrest and recovery

summary: Under crowded, nutrient-limiting conditions, growth in the marine chordate O. dioica arrests until favorable conditions return. We profiled translation genome-wide using ribosome profiling in O. dioica during growth arrest and growth arrest recovery. We found that initial recovery is independent of nutrient-responsive, trans-spliced genes, suggesting that animal density is the primary trigger for the resumption of development in this species.

overall_design: Ribosome-protected RNA fragments and total RNA extracted from animals during growth arrest and half an hour after release from arrest in two biological replicates sequenced on two Illumina flow cells

first: Heloisa

last: Galbiati


title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the consequences of oxidative stress elicited by tert-butyl-hydroperoxide in Candida albicans (RNAseq data set)

first: Krisztina

last: Szabó

summary: Candida albicans is an opportunistic pathogen which is responsible for widespread nosocomial infections. It encompasses a fungus specific serine/threonine protein phosphatase gene CaPPZ1 that is involved in cation transport, cell wall integrity, oxidative stress response, morphological alterations, and virulence. We demonstrated that tert-butyl-hydoperoxide induced oxidative stress suppressed the growth rate and blocked the proliferation of the fungal cells without effecting their viability, both in the cappz1 KO mutant and in the genetically matching QMY23 control strains. To reveal the gene expression changes behind the above observation we carried out a global transcriptome analysis by DNA microarray hybridization as well as RNA sequencing, and confirmed our results by quantitative RT-PCR. The numbers of genes affected and the amplitudes of the transcript-level changes revealed that the deletion of CaPPZ1 enhances the effects of oxidative stress. Thus the roles of this fungus specific protein phosphatase in important physiological processes like membrane transport, cell surface interactions, oxidoreductase activity, cell signaling, translation, and RNA processing becomes more pronounced under oxidative conditions.  We conclude that in the wild type C. albicans CaPPZ1 has a protective role against oxidative damage, and suggest that the specific inhibition of this phosphatase combined with mild oxidative treatment could be a feasible approach of topical antifungal therapy.

overall_design: Examination of untreated and 0.4 mM tBOOH-treated control and cappz1 mutant Candida albicans cultures in three- three replicates.

first: Viktor

last: Dombrádi


title: ATAC-seq from breast epithelium (ENCSR846ZBX)

first: ENCODE

last: DCC

summary:
ATAC-seq on human breast epithelium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from esophagus muscularis mucosa (ENCSR944JCE)


title: Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization

city: University of Helsinki

first: Nicolas

last: Di-Poi

address: Viikinkaari 1

department: Institute of Biotechnology, Helsinki Institute of Life Sciences

country: Finland

institute: University of Helsinki

summary: We exploited the extraordinary  ecomorphological diversity of squamates to assess  brain phenotypic diversification with respect to locomotor specialization, by integrating transcriptomic data along with other methods. We reveal significant changes in cerebellar morphology as well as dynamic gene expression that all correlate with locomotor behaviours.

sample_organism:
Python regius
Eryx colubrinus
Pantherophis guttatus
Pogona vitticeps
Trioceros jacksonii
Basiliscus vittatus
Pseudopus apodus
Dasypeltis gansi
Chrysopelea ornata
Mochlus fernandi

overall_design:
RNA sequencing of adult cerebellum tissues from ten different squamate species, using NextSeq 500 platform (Illumina, U.S.A.).
Conclusions is only based on the 630 orthologous genes (present in the current table) identified among all ten species analyzed. We have not used all genes in our work, but only orthologous genes.

first: Simone

last: Macrì

first: Yoland

last: Savriama

first: Imran

last: Khan

last: Di-Poï


title: Gene expression changes caused by KRAS in MCF-10A

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

summary: Tumor formation hinges on the acquisition of  two or more driver genes that cause normal cells  to progress from proliferation to abnormal  expansion and malignancy. In order to understand  the minimum genetic alterations involved in this  process, we compared the transcriptomes of an  isogenic set of breast epithelial cell lines that are  non-transformed, or contain a single or double  knock-in (DKI) of mutant PIK3CA (H1047R) or  KRAS (G12V). Gene set enrichment analysis  revealed that DKI cells were enriched over single  mutant cells for genes that characterize a MYC-  target gene signature. This gene signature was  mediated in part by the bromodomain-containing  protein, 9 (BRD9) that was found in the SWI-SNF  chromatin-remodeling complex, bound to the MYC  super-enhancer locus. Small molecule inhibition of  BRD9 reduced the MYC transcript and increased  the MYC-negatively regulated target, NDRG1.  Critically, only DKI cells had the capacity for  anchorage-independent growth in semi-solid  medium, and CRISPR/Cas9 manipulations showed  that PIK3CA and BRD9 expression were essential  for this phenotype. In contrast, KRAS was  necessary for DKI cell migration, and  overexpression of BRD9 partially rescued the  growth of KRAS single mutant cells in semi-solid  medium. These results provide new insight into  the earliest transforming events driven by  oncogene cooperation, and suggest BRD9 is an  important mediator of mutant PIK3CA/KRAS-  driven transformation.

overall_design: MCF-10A cells were modified by knock-in of KRAS-G12V mutation in a single endogenous locus or by the combination of PIK3CA-H1047R and KRAS-G12V.  Total RNA was extracted from these cell lines and compared with existing RNAseq data of MCF-10A and MCF-10A PIK3CA-H1047R.

first: Peter

last: Vogt


title: DNase-seq from esophagus squamous epithelium (ENCSR783OCW)


title: DNase-seq from tibial artery (ENCSR332MRT)


title: Formula Feeding and Immature Gut Microcirculation Promote Intestinal Hypoxia leading to Necrotizing Enterocolitis

status: Public on Nov 05 2019

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Major risk factors for necrotizing enterocolitis (NEC) are formula feeding and prematurity, however, their pathogenic mechanisms are unknown. We found that insufficient arginine/nitric oxide synthesis limits blood flow in the intestinal microvasculature, leading to hypoxia, mucosa damage and NEC in the premature intestine after formula feeding. Formula feeding led to increased intestinal hypoxia in pups at postnatal day 1(P1) and P5, but not in more mature pups at P9. Accordingly, blood flow in the intestinal microvasculature increased after formula feeding only in P9 pups. mRNA profiling revealed that regulators of arginine/nitric oxide synthesis are at higher levels in endothelial cells of the intestine of P9 than P1 pups. Importantly, arginine supplementation increased intestinal microvasculature blood flow, and prevented NEC, whereas an arginine antagonist exacerbated NEC. Our results suggest that balancing intestinal oxygen demand and supply in the premature intestine by modulating arginine/nitric oxide could be used to prevent NEC.

overall_design: Examination of  gene expression profile in intetsinal endothelial cells of early (Postnatal day 1,P1) and late (P9) postnatal mice

first: Yong

last: Chen

first: Abdalla

last: Ahmed

first: Agostino

last: Pierro


title: Whole transcriptome analysis of obese adipose tissue suggests u001kfc.1 as a potential regulator to glucose metabolism

city: Shijiazhuang

first: Linlin

last: Yang

state: Hebei

address: 348, Heping west road

institute: Hebei General Hospital

summary:
LncRNAs are newly proposed key factors controlling brown adipogenesis and development, but their regulatory effect to white adipocyte is still merely understood. Deciphering the underlying mechanism could be a novel way to discovering potential targets of obesity.
In the present study, the whole transcriptome of adipose tissues collected from obese individuals and control subjects were analyzed by HTA2.0. A stepwise network reconstruction strategy was proposed to explore lncRNA-related functional modules altered in obesity. A lncRNA named uc001kfc.1, which was recognized from the core network, was suggested to be down regulated in obesity group and might regulate glucose metabolism of adipocytes through PI3K/PTEN pathway. Our study highlighted the potential of lncRNA regulating glucose homeostasis in human adipose tissue from a global perspective, which would facilitate deeply understanding pathology of obesity as well as developing novel therapeutic targets.

overall_design: Our study was approved by the IRB of Hebei General Hospital and conducted according to the principles expressed in the Declaration of Helsinki. The use of these subjects was approved by the hospital’s Ethics Committee and all participants provided their written informed consents. All participants were recruited when they were hospitalized due to cholecystolithiasis. 11 obese patients and 22 controls were enrolled in this study. Separately, 6 and 5 subjects were randomly selected from the obesity and control group for microarray assay.

first: Xing

last: Wang

first: Huaibin

last: Guo

first: Wanxing

last: Zhang

first: Wei

first: huijuan

last: Ma


title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the consequences of oxidative stress elicited by tert-butyl-hydroperoxide in Candida albicans (Microarray expression)

first: Krisztina

last: Szabó

overall_design: Examination of untreated and 0.4 mM tert-butyl-hydroperoxide (tBOOH) treated cultures of control (QMY23) and cappz1 mutant Candida albicans strains in single pilot experiment.

first: Viktor

last: Dombrádi


title: DNase-seq from upper lobe of left lung (ENCSR164WOF)

first: ENCODE

last: DCC


title: DNase-seq from breast epithelium (ENCSR600KUR)


title: Mitochondrial Arginase-2 deletion enhances the function of in vivo activated murine CD8+ T cells

status: Public on Nov 02 2019

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: As sufficient extracellular arginine is crucial for T cell function, depletion of extracellular arginine by elevated Arginase 1 (Arg1) activity has emerged as a hallmark immunosuppressive mechanism. However, the potential cell-autonomous roles of arginases in T cells have remained unexplored. Here we show that the arginase isoform expressed by T cells, the mitochondrial Arginase 2 (Arg2), is a cell-intrinsic regulator of CD8+ T cell activity. Both germ-line Arg2 deletion and adoptive transfer of Arg2-/- CD8+ T cells significantly reduced tumor growth in preclinical cancer models by enhancing CD8+ T cell activation, effector function and persistence. Transcriptomic, proteomic and high-dimensional flow cytometry characterization revealed a CD8+ T cell-intrinsic role of Arg2 in modulating T cell activation, anti-tumor cytoxicity and memory formation, independently of extracellular arginine availability. Furthermore, specific deletion of Arg2 in CD8+ T cells strongly synergized with PD-1 blockade for the control of tumor growth and animal survival. These observations coupled with the finding that pharmacologic arginase inhibition accelerates activation of ex vivo human T cells unveil Arg2 as a new therapeutic target for T cell-based cancer therapies.

overall_design: Splenic CD8+ T cells were isolated from naive WT or Arg2-/- mice and activated in vitro for 0, 2, 6, 12 and 24 hours. For each genotype, five independent biological replicates were analysed at all time points.

first: Adrià-Arnau

last: Martí i Líndez

first: Isabelle

last: Dunand-Sauthier

first: Walter

last: Reith

first: Mark

last: Conti

first: Emmanuèlle

last: Barras


title: DNase-seq from prostate gland (ENCSR958QXU)


title: ATAC-seq from right atrium auricular region (ENCSR062SVK)

summary:
ATAC-seq on human right atrium auricular region

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from right atrium auricular region (ENCSR668EVA)


title: The gene expression profiles of gallbladder cancer

city: Shanghai

first: Sunwang

last: Xu

address: 160 Pujian Road, Shanghai, China

institute: Renji Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Gallbladder cancer is a rare but highly malignant cancer. We performed the transcriptional profile sequencing to figure out the potential mechanisms, which might significantly affect gallbladder cancer progression.

overall_design: 10 cases of  gallbladder cancer tumorous tissue samples with matched normal tissue were obtained from surgery and perform next-generation sequencing.

first: Jian


title: Multi-Parameter Analysis of Biobanked Human Bone Marrow Stromal Cells Shows Little Influence for Donor Age and Mild Comorbidities on Phenotypic and Functional Properties

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary: Heterogeneous populations of human bone marrow-derived stromal cells (BMSC) are among the most frequently tested cellular therapeutics for treating degenerative and immune disorders, which occur predominantly in the aging population. Currently, it is unclear whether advanced donor age and commonly associated comorbidities affect the properties of ex vivo-expanded BMSCs. Thus, we stratified cells from adult and elderly donors from our biobank (n = 10 and n = 13, mean age 38 and 72 years, respectively) and compared their phenotypic and functional performance, using multiple assays typically employed as minimal criteria for defining multipotent mesenchymal stromal cells (MSCs).We found that BMSCs from both cohorts meet the standard criteria for MSC, exhibiting similar morphology, growth kinetics, gene expression profiles, and pro-angiogenic and immunosuppressive potential and the capacity to differentiate toward adipogenic, chondrogenic, and osteogenic lineages.We found no substantial differences between cells from the adult and elderly cohorts. As positive controls, we studied the impact of in vitro aging and inflammatory cytokine stimulation. Both conditions clearly affected the cellular properties, independent of donor age. We conclude that in vitro aging rather than in vivo donor aging influences BMSC characteristics.

overall_design: RNA-Seq transcriptome analysis of human bone marrow stromal cells at different passages from healthy and diabetic donors, with and without stimulation

first: Guido

last: Moll

first: Sven

last: Geissler


title: Nanog regulates Pou3f1 expression at the exit from pluripotency during gastrulation

status: Public on Oct 31 2019

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Pluripotency is regulated by a network of transcription factors that maintains early embryonic cells in an undifferentiated state while allowing them to proliferate. NANOG is a critical factor for maintaining pluripotency and its role in primordial germ cell differentiation has been well described. However, Nanog is expressed during gastrulation across all the posterior epiblast, and only later in development its expression is restricted to primordial germ cells. In this work, we unveiled a previously unknown mechanism by which Nanog specifically represses genes involved in anterior epiblast lineage. Analysis of transcriptional data from both embryonic stem cells and gastrulating mouse embryos revealed Pou3f1 expression to be negatively correlated with that of Nanog during the early stages of differentiation. We have functionally demonstrated Pou3f1 to be a direct target of NANOG by using a dual transgene system for the controlled expression of Nanog. Use of Nanog null ES cells further demonstrated a role for Nanog in repressing a subset of anterior neural genes. Deletion of a NANOG binding site (BS) located nine kilobases downstream of the transcription start site of Pou3f1 revealed this BS to have a specific role in the regionalization of the expression of this gene in the embryo. Our results indicate an active role of Nanog inhibiting neural regulatory networks by repressing Pou3f1 at the onset of gastrulation.

overall_design: Mouse embryonic stem cells were maintained in 2i+Lif conditions and at time 0h serum was add to the medium and 2i and Lif were removed, allowing the cells to differentiate. Three timepoints were obtain by triplicate: 0h, 12h and 24 starting at the adding of serum. RNA from NanogKO ES cells and their parental line was extracted using the RNeasy Mini Kit (Qiagen). Library preparation (New England Biolabs Nest Ultra RNA library prep Kit) and single read Next generation sequencing (Illumina HiSeq 2500) were performed at the Genomics Unit at Centro Nacional de Investigaciones Cardiovasculares (CNIC).

first: Julio

last: Sainz de Aja

first: Miguel

last: Manzanares


title: RNA-seq in NT, CAP-D3, and CAP-H2 expressing cells treated with DMSO or menadione

status: Public on Oct 30 2019

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

state: OH

address: 9500 Euclid Ave NE20

institute: Cleveland Clinic Foundation

summary: The goal of this experiment was to identify transcripts that are differentially expressed in CAP-D3 and CAP-H2 depleted cells with and without exposure to menadione

overall_design: RNA was isoalted from HT cells expressing Non-Target, CAP-D3, and CAP-H2 shRNA, post DMSO or menadione treatment. cDNA libraries (50 bp, paired end) were made at the University of Chicago Genomics Core and sequenced on an Illumina HiSeq2500, according to standard protocols.


title: DNase-seq from Peyer's patch (ENCSR954AJK)

city: Stanford


title: DNase-seq from right atrium auricular region (ENCSR278SKG)


title: RNA-seq of Wild type Arabidopisis and two Nup96 mutants

city: Beijing

first: Xu

last: Wang

address: No. 12 Zhongguancun south road

country: China

institute: Institute of crop sciences, CAAS

summary: Lines of evidence indicate that nuclear pore complex profoundly affects the timing of plant flowering, but the underlying mechanisms remain poorly elucidated. Here, we report that Nucleoporin 96 (Nup96) acts as a negative regulator of long-day photoperiodic flowering in Arabidopsis. Through multiple approaches, we identified and verified an E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) interacting in vivo with Nup96. Nup96 and HOS1 proteins mainly localize and interact on nuclear membrane. Loss-of-function of Nup96 leads to destruction of HOS1 proteins without changing its mRNA abundance, which results in over-accumulation of the key activator of long-dayphotoperiodic flowering, CONSTANS (CO) proteins, as that in hos1 mutants. Unexpectedly, we observed that mutation of HOS1 gene strikingly diminishes Nup96 protein level, suggesting that Nup96 and HOS1 are mutually stabilized and thus they form a novel repressive module to regulate CO protein turnover.  Therefore, the nup96 and hos1 single mutants and nup96 hos1 double mutant have very much similar early-flowering phenotypes and overlapping transcriptome changes. Together, this study reveals a new repression mechanism, where the Nup96-HOS1 repressive module gates the level of CO proteins, to prevent precocious flowering of Arabidopsis under long day conditions.

overall_design: RNA-seq of Wild type and two mutation.


title: Global gene expression profile of CD4+ T cells activated and infected with Tox2- or GFP-only virus under different conditions (RNA-Seq)

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: T Follicular helper (Tfh) cell is an effector CD4+ T cell subset specialized in helping B cells in germinal centers (GC) reactions. Although Bcl6 was identified as a Tfh-specific transcription factor essential for their development, the molecular mechanisms underlying Bcl6 regulation and Tfh cell commitment remain unclear. Here, we report that Tox2 transcription factor is highly expressed in Tfh cells, regulated by Bcl6 and STAT3. Forced expression of Tox2 drives Bcl6 expression and Tfh development. Mechanistically, Tox2 directly binds to Tfh-associated genes, including Bcl6, and functions to promote their chromatin accessibility and modulate the activities of other Tfh-regulating factors. Conversely, genetic deletion of Tox2 results in defective Tfh differentiation, and inhibiting both Tox and Tox2 in T cells abolishes Tfh differentiation and GC response. Thus, our results demonstrate that Tox2 is a key transcription factor that regulates Bcl6 expression and Tfh development and suggest a Tox2-Bcl6 axis in feed-forward regulation of Tfh program.

overall_design: To gain insights into the mechanism whereby Tox2 regulates Tfh differentiation, we performed RNA-seq analysis on Tox2-overexpressing (Tox2-RV-GFP+) and control (Empty-RV-GFP+) CD4+ T cells cultured in both Th0 (αIFNγ+αIL-4+αIL-2) and Tfh-like (αIFNγ+αIL-4+αIL-2+IL-6) conditions.

first: Wei

first: Xiaohong

last: Zhao


title: Transcription factor Tox2 functions to promote chromatin remodeling during T follicular helper (Tfh) cell development (ATAC-seq)

overall_design: The in vivo-generated CD4+CD44hiCXCR5hiBcl6-RFPhiFoxp3-GFP- Tfh cells sorted from Bcl6-RFPFoxp3-GFP mice immunized with KLH/CFA and the T cells activated in vitro under indicated conditions were harvest for ATAC-seq analysis.


title: Genome-wide maping of chromatin state and gene exoression in hematopoietic stem and progenitor cells.

status: Public on Oct 29 2019

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

summary: We report the application of H3K27me3 ChI-seq assays in hematopoietic stem and progenitors cells (HSPCs) from p53+/+ and p53R248W/+ mutant mice. We also performed RNA-seq assays to examine the impact of p53 on gene expression in hematopoietic stem and progenitor cells.

overall_design: Examination of histone modification H3K27me3 in p53+/+ and p53R248W/+ HSPCs (Lin-Kit+). Examine gene expression in p53+/+, p53R248W/+, and p53-/- HSPCs (LSKs)

first: Sisi

last: Chen

first: Qiang

first: Zhonghua

last: Gao