title: GATA6 induces cell senescence to exerts lung cancer suppressive function and denotes a therapeutic opportunity for GATA6 deficient lung cancer patients

status: Public on Mar 25 2020

city: Guangzhou

first: Chen

last: Zhipeng

address: Huangpu Avenue

institute: Jinan University

summary: Lung cancer is the world-wide leading cause of cancer related deaths. Tumor suppressor genes (TSGs) play a critical role in restricting tumorigenesis and impact the therapeutic effect of various treatments. However, TSGs remain to be systemically determined in lung cancer. Here we identified GATA6 as a potent lung cancer TSG. GATA6 inhibited lung cancer cell growth in vitro and tumorigenesis in vivo. Mechanistically, GATA6 upregulated p53 expression to transcribe p21 mRNA while inhibited Akt activation to stabilize p21 protein, thus inducing lung cancer cell senescence. Furthermore, we showed that ectopic expression of GATA6 led to dramatic shrinkage of established lung tumor in vivo

overall_design: A549-TetOne-GATA6 cells were treated with(positive) or without DOX (negative)for 48 h, then total RNA was isolated from cells using Trizol reagent (TAKARA, Japan). RNA libraries and RNA sequencing were performed by The Beijing Genomics Institute (BGI)

first: Wensheng

last: Chen

first: Zhipeng


title: Insulin-Induced Serine 22 Phosphorylation of Retinoid X Receptor Alpha Is Dispensable For Adipogenesis in Brown Adipocytes

status: Public on Mar 30 2020

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

type: Expression profiling by high throughput sequencing

summary: Insulin action initiates a series of phosphorylation events regulating cellular differentiation, growth and metabolism. We have previously discovered, in a mass spectrometry-based phosphoproteomic study, that insulin/IGF-1 signaling induces phosphorylation of retinoid x receptor alpha (RXRα) at S22 in mouse brown pre-adipocytes. Here, we show that insulin induces the phosphorylation of RXRα at S22 in both brown precursor and mature adipocytes through a pathway involving ERK, downstream of IRS-1 and -2. We also found that RXRα S22 phosphorylation is promoted by insulin and upon re-feeding in brown adipose tissue in vivo, and that insulin-stimulated S22 phosphorylation of RXRα is dampened by diet-induced obesity. We used Rxra knockout cells re-expressing wild type (WT) or S22A non-phosphorylatable forms of RXRα to further characterize the role of S22 in brown adipocytes. Knockout of Rxra in brown pre-adipocytes resulted in decreased lipid accumulation and adipogenic gene expression during differentiation, and re-expression of RxraWT alleviated these effects. However, we observed no significant difference in cells re-expressing the RxraS22A mutant as compared with the cells re-expressing RxraWT. Furthermore, comparison of gene expression during adipogenesis in the WT and S22A re-expressing cells by RNA sequencing revealed similar transcriptomic profiles. Thus, our data propose a dispensable role for RXRα S22 phosphorylation in adipogenesis and transcription in differentiating brown pre-adipocytes.

overall_design: 72 samples. 2 genotypes (WT and S22A), 2 cell cultures (biological replicate). For each biological replicate 3 timepoints (D0, D2, D6), and 3 technical replicate.

first: Jacob

last: Ardenkjær-Larsen

first: Kaja

last: Rupar

first: Goda

last: Sinkevičiūtė

first: Patricia

middle: S

last: Petersen

first: Julia

last: Villarroel

first: Morthen

last: Lundh

first: Romain

last: Barrès

first: Atefeh

last: Rabiee

first: Brice

last: Emanuelli


title: Lamina Associated Domains dependent of chromatin state and A-type lamins

status: Public on Mar 27 2020

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

country: USA

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The effect of Tbx6 on the mouse heart

status: Public on Mar 20 2020

city: Tokyo

first: SHO

last: HAGINIWA

address: 5 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

summary: The Mammalian cardiomyocyte (CM) cell cycle is tightly regulated by a complex network of transcription factors; however, the gene regulatory networks depending on their developmental stages are unclear. Here, we report that Tbx6, expressed in the cardiac mesoderm, promote cell cycle re-entry in vitro and in vivo. We performed a gain of function screening for cardiac development regulator genes that promoted neonatal CM proliferation. Tbx6 activate the cell cycle and promote cultured neonatal CM proliferation. Next, we generated recombinant adeno-associated virus serotype 9 vector encoding Tbx6 (AAV9-Tbx6). Injection of AAV9-Tbx6 was shown to promote cell cycle re-entry of CMs in both postnatal and adult mice. Tbx6 overexpression activated cell cycle activators, while repressed cell cycle inhibitor gene. Thus, Tbx6 promotes neonatal CM proliferation in vitro and adult CM cell cycle re-entry in vivo.

overall_design: We analyzed gene expression levels in heart that is introduced into PBS or Tbx6 at birth and scarify after 7 days or 30 days by microarray (Clariom S Array, Mouse, Affymetrix) according to the manufacturer’s instructions. Prior to analysis, all data were normalized by using a Single Space Transformation and Robust Multichip Analysis (SST-RMA) algorithm with Affymetrix Expression Console software version1.4.

first: Sho

last: Haginiwa

first: Masaki

last: Ieda


title: Evidence of Y Chromosome LncRNAs involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells

city: Morgantown

first: Ivan

last: Martinez

state: WV

address: 1838 MBRCC PO Box 9300

department: Microbiology / Cancer Center

institute: West Virginia University

summary: Numerous studies have implicated changes in the Y chromosome in male cancers, however few have investigated the biological importance of Y chromosome non-coding RNAs. Here, we demonstrate a group of Y chromosome-expressed long non-coding RNAs (lncRNAs) involved in male non-small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. UV Cross-linking and Immunoprecipitation (CLIP) and RNA stability assays identify IGF2BP3 as a binding partner for the linc-SPRY3-2/3/4 RNAs which alters the half-life of the anti-apoptotic  HMGA2 mRNA as well as the oncogenic c-MYC mRNA. To assess the clinical relevance of these findings, we examined the presence of the Y chromosome in NSCLC tissue microarrays and the expression of linc-SPRY3-2/3/4 in NSCLC RNAseq and microarray data. We observed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiation therapy in NSCLC.

overall_design: To measure global lncRNA expression changes after 7Gy of radiation, we used the GeneChip® Human Transcriptome Array 2.0 in the NSCLC cell line H460 with 7Gy of radiation (H460_7Gy) or without radiation (H460_Control). The experiments was done in triplicates

first: Tayvia

last: Brownmiller


title: Expression data from CNE-2Z cell line transfected with TIPE1 or control vector

status: Public on Mar 21 2020

city: Zibo

first: xin

middle: xin

last: xiang

state: China

address: No. 54 Gongqingtuan West Road, Zibo, 255036, China.

country: China

institute: zibo central hospital

summary:
CNE-2Z cells transfected with an empty vector or a TIPE1 lentiviral vector were collected for gene expression detection. Some of them, for instance, the expression of the downstream mTOR signaling pathway was dramatically upregulated. We used microarrays to detail the gene expression after transfection with TIPE1 and identified distinct classes of changed genes during this process.
We used microarrays to detail the  gene expression after transfected with TIPE1 and identified distinct classes of changed genes during this process.

overall_design: CNE-2Z cells transfected with an empty vector or a TIPE1 lentiviral vector were collected for RNA extraction and hybridization on Affymetrix microarrays, and then the data were analysed.

first: Xinxin

last: Xiang

first: Yongliang

last: Liu


title: Circular RNA expression in Nasopharyngeal carcinoma

status: Public on Mar 19 2020

city: Hengyang

first: Zhifeng

state: Hunan

address: 69# Chuanshan Road, Shigu District Hengyang, Hunan

institute: The First Affiliated Hospital of University of South China

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:This study was performed to explore the circRNA profile of nasopharyngeal carcinoma (NPC).
Methods: High-throughput sequencing was performed to identify the circRNA expression profile of NPC compared with healthy controls.
Results: A total of 93 upregulated circRNAs and 77 downregulated circRNAs were identified.
Conclusion: This study provides a leading and fundamental circRNA profile of NPC.

overall_design: Examination of four matched normal tissue acquired from nasopharyngeal carcinoma and nasopharyngitis patients.

first: Jing

last: Yang

first: Yongqian

last: Gong

first: Qingshan

last: Jiang


title: Single-cell RNA sequencing of neuromesodermal progenitors of early headfold wild type embryos

status: Public on Mar 18 2020

city: Oeiras

first: Moises

last: Mallo

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary: Single-cell RNA sequencing of the caudal lateral epiblast and underlying mesoderm region of early headfold wild type embryos

overall_design: 91 single cells were isolated from the described regions

first: Andre

last: Dias


title: Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens

status: Public on Mar 14 2020

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: In order to reveal the candidate genes related to yellow plumage in Chinese chicken, a hybrid population of Huiyang Bearded chicken and White Leghorn chicken, and transcriptome data were generated from the yellow and white feather follicle of F3 population in two periods (7 and 11weeks) respectively, using RNA-seq. 127 common different expressed genes were obtained(DEGs) between two periods, these DEGs were mainly enriched in the Gene Ontology classes ‘developmental pigmentation’, ‘melanin biosynthetic process’, ‘melanosome organization’, ‘melanosome membrane’ and ‘melanosome’all related to the pigmentation process. And involved genes were considered as pigment genes that play important roles in melanogenesis. The results reveal key functional genes and possible molecular mechanisms for the elucidation of yellow plumage formation in Chinese indigenous chickens.

overall_design: RNA sequencing of 6 yellow and 6 white feather follicles in an F3 chicken population

first: Xiaotong

last: Zheng


title: Transcriptome of Pseudomonas putida KT2440 harboring plasmid RP4 during conjugative transfer

status: Public on Mar 13 2020

city: Tsukuba

first: Masatoshi

last: Miyakoshi

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

summary: We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.

overall_design: 8 samples in duplicate.


title: MOF directs erythroid fate during hematopoiesis via RUNX1-GFI1b feedforward control (ChIP-Seq)

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The balance between self-renewal and differentiation of hematopoietic stem cells (HSCs) is orchestrated by the combinatorial function of transcription factors and epigenetic regulators. Here, we report that the H4K16 acetyl-transferase MOF regulates chromatin accessibility and hematopoietic gene expression during erythroid commitment. Mof expression is controlled via a transcriptional feedforward pathway involving Runx1 and Gfi1b, which is crucial for the erythroid lineage bias. Single-cell RNA-seq of HSCs revealed that Mof haploinsufficient mice accumulate an otherwise rare HSC subset, indicating impaired differentiation.We propose that an intricate transcription factor network ensures dynamic chromatin targeting by MOF, which defines an essential epigenetic node regulating HSC plasticity, identity and differentiation. We propose that an intricate transcription factor network ensures dynamic chromatin targeting by MOF, which defines an essential epigenetic node regulating HSC plasticity, identity and differentiation. We propose that an intricate transcription factor network ensures dynamic chromatin targeting by MOF, which defines an essential epigenetic node regulating HSC plasticity, identity and differentiation. We propose that an intricate transcription factor network ensures dynamic chromatin targeting by MOF, which defines an essential epigenetic node regulating HSC plasticity, identity and differentiation.

overall_design: Examination of MOF, H4K16ac and GATA-1 Genome-wide occupancy.

first: Cecilia

middle: P

last: Rodrigues


title: Transcriptome profiling of porcine jejunum tissue, its derived organoids over long-term culture, and transformed cell line IPECJ2 as reference model

city: Wageningen

first: Bart

last: van der Hee

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

summary:
Purpose: Organoids are gaining more traction as physiologically relevant models for host physiology, but their transcriptional stability has not been identified over long term culture. Comparing this to its host-derived tissue and a transformed cell line of this intestinal location could provide insight into the stability and maintenance of cellular programs in vitro.
Methods: Jejunum organoids were derived from 2 5-week old piglets, and grown separately in triplicate for 3 and 12 weeks. Tissue homogenate, organoids from both time points (divided in triplicate at start of experiment to monitor culture-dependent variability) and three IPEC-J2 passage rates were isolated for RNA using an RNEasy mini kit following manufacturers protocols.
Results: RNA was enriched for PolyA and sequenced on an illumina sequencer. Reads were checked for quality, trimmed, and mapped following the tuxedo suite pipeline (modified to fit our parameters) and CLC Genomics Workbench to identify unknown gene locations.
Conclusions: Organoids cultured for 12 weeks showed strong inter- and intra variability, congruence between independent cultures, and strong epithelial resemblance to host tissues. It further exemplified a more extensive transcriptome than IPEC-J2, showing more physiologically relevant genes

overall_design: Jejunum tissue, triplicate cultures of 2 biological organoid lines at 3 and 12 weeks of culture, and IPEC-J2 at three passages were subjected to RNA transcriptome profiling to check overall congruence and variation.

first: Richard

last: Crooijmans

first: Nico

last: Taverne

first: Raka

last: Choudhury

first: Linda

last: Loonen

first: Ole

last: Madsen

first: Hauke

last: Smidt

first: Jerry

last: Wells


title: A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2218 Biological Sciences III

department: Developmental and cell biology

country: Canada

institute: University of California at Irvine

summary: Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each one displayed distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than with annotated ones. These data show that TALON is a technology-agnostic long-read transcriptome discovery and quantification pipeline capable of tracking both known and novel transcript models, as well as their expression levels, across datasets for both simple studies and in larger projects. These properties will enable TALON users to move beyond the limitations of short-read data to perform isoform discovery and quantification in a uniform manner on existing and future long-read platforms.

overall_design: ONT sequencing of 2 replicates GM128278

first: Gabriela

last: Balderrama-Gutierrez


title: Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin

status: Public on Mar 17 2020

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology


title: DNA methylation analysis of blastocyst according to peripubertal age of bull (12 vs 16 months)

status: Public on Apr 02 2020

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: The DNA methylation pattern in blastocyst produced by bulls at different age was investigated. Embryos were in vitro fertilized from 4 different bulls at 12 and 16 month each with matched adult cows. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 12 and 16 months old

first: Chongyang

last: Wu

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: A deregulated HOX gene axis confers an epigenetic vulnerability in KRAS mutant lung cancers [inhibitors]

city: Boston

first: Stephanie

middle: Louise

last: Guerra

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University- Brigham Women's Hospital

summary:
MEK and BRD4 inhibitors induce cell death of subset of KRAS-mutant lung tumors in vitro and in vivo
We performed microarray analysis of MEK and BRD4 inhibition alone and in combination 24 hours after treatment, prior to the induction of cell death, to analyze transcriptional changes that might be mechanistic drivers of the therapeutic effect

overall_design: 12 samples, in triplicate, 3X vehicle, 3X PD-0325901, 3X JQ1, 3X PD-0325901 + JQ1

first: Karen

last: Cichowski


title: Genome-wide maps of chromatin state in HSC, HPC7 and lineage-committed cells

first: Asifa

last: Akhtar

summary: The correct balance between self-renewal and differentiation of hematopoietic stem cells (HSC) is orchestrated by the crosstalk between extrinsic and intrinsic factors. A combination of transcriptional regulators and chromatin-based epigenetic changes provide a fine-tuning mechanism to determine HSC fate. We report that the histone H4 lysine 16 (H4K16) specific lysine acetyl-transferase MOF (KAT8) shows dynamic chromatin occupancy during HSC differentiation. MOF regulates erythroid commitment by regulating the expression of key haematopoietic genes. Indeed, loss of just one copy of Mof perturbs HSC commitment, leading to skewed granulocytic lineage commitment and impaired erythroid maturation in mice. Wild-type MOF and strikingly, enforced expression of the transcription factor GATA-1, rescued hematopoietic skewing of this granulocytic fate bias. Furthermore, single-cell RNA-seq of Mof haploinsufficient HSCs revealed an enrichment of a novel immature heterogeneous sub-population of cells with increased proliferation potential, indicative of an enhanced pro-leukemic state. Therefore, our results demonstrate an unprecedented role of MOF in the regulation of HSC plasticity, identity and differentiation.

overall_design: We performed MOF ChIP-seq in primary HSCs and MEPs from wild type and Mof-heterozygous animals. And H4K16ac profile in the haematopoeitic progenitor cell line (HPC7). Antibodies used for ChiP anti-MOF (#A300-992A, Bethyl), GATA-1 (#181544, Abcam), H4K16ac (#07-329, Millipore)

first: C

last: Rodrigues

first: A


title: Tfam Knockdown Results in Reduction of mtDNA Copy Number, OXPHOS Deficiency and Abnormalities in Zebrafish Embryos

status: Public on Mar 10 2020

city: Maastricht

first: Rick

last: Kamps

address: P.O. Box 616

department: Genetics and Cell Biology

institute: Maastricht University

summary: High mitochondrial DNA (mtDNA) copy numbers are essential for oogenesis and embryogenesis and correlate with fertility of oocytes and viability of embryos. To understand the pathology and mechanisms associated with low mtDNA copy numbers, we knocked down mitochondrial transcription factor A (Tfam), a regulator of mtDNA replication, during early zebrafish development. Reduction of Tfam using a splice-modifying morpholino (MO) resulted in a 42%±4% decrease in mtDNA copy number in embryos at 4 days post fertilization (4 dpf). Morphant embryos displayed abnormal development of the eye, brain, heart and muscle, as well as a 50%±11% decrease in ATP production. Transcriptome analysis revealed a decrease in protein-encoding transcripts from the heavy strand of the mtDNA. In addition, various RNA translation pathways were increased, indicating an upregulation of nuclear and mitochondria-related translation. The developmental defects observed were supported by a decreased expression of pathways related to eye development and haematopoiesis. The increase in mRNA translation might serve as a compensation mechanism, but appears insufficient during prolonged periods of mtDNA depletion, highlighting the importance of high mtDNA copy numbers for early development in zebrafish.

overall_design: For gene expression studies, 12 embryos for the injected controls, 12 embryos for the injected TFAM, and 9 embryos for the non-injected control group were individually collected in sterile tubes. Dye-swap hybridizations (2+2) were performed on microarray slides (4x44K zebrafish V3, Agilent) using gasket slides and a hybridization chamber and incubated for 17 h at 65ºC and 10 rpm in the hybridization oven (Agilent Technologies). Slides were washed with Triton X-102, freshly added to the Wash Buffers. Microarray slides were scanned using a DNA Microarray scanner with SureScan High-Resolution Technology (Model 2565CA, Agilent). The arrays contained 45,220 probes. Each probe identifier was transformed to Ensembl gene IDs (ENSDARG). This resulted in 36,156 probes containing a non-empty transcript ID of which 19,459 were unique transcripts and kept for the analysis. All transcripts were analysed using a multivariate Gaussian linear regression (MVN(mu,Sigma) where mu is the mean and Sigma is the covariance matrix) including slide differences (Slide), dye swap (Dye), background level (Bg), injection (Inj) and a random effect. The inference criterion used for comparing the models is their ability to predict the observed data, i.e. models are compared directly through their minimized minus log-likelihood. When the numbers of parameters in models differ, they are penalized by adding the number of estimated parameters, a form of the Akaike information criterion (Akaike 1973). For each transcript, a model containing the relevant covariates mentioned above (E(y) =Slide+Dye+Bg+Inj) was fitted in order to obtain a reference AIC. Then a model containing the treatment group (Trt) was fitted (E(y)=Slide+Dye+Bg+Inj+Inj:Trt). The transcript under consideration was found to be differentially expressed if the AIC of this second model decreased compared to the model not containing the treatment. These statistical analysis were performed using the freely available program R (Ihaka R 1996) and the publicly available libraries 'rmutil' and ‘growth’ (Lindsey 1999).

last: Lindsey


title: Haematopoetic RNA-seq from ultra low input

overall_design: 15 cells from 6 different progenitor cells: HSCs (LSK+CD34-Flt3-CD48-CD150+), MPP2 (LSK+CD34+Flt3-CD48+CD150+), MPP3 (LSK+CD34+Flt3-CD48+CD150-), MPP4 LSK+CD34+Flt3+CD48+CD150-), CMP Lin-Sca-1-cKit+CD34+IL7r-CD16/32low) and MEP (Linegae-Sca-1-cKit+CD34-IL7r-CD16/32-) were sorted by Aria FACS Fusion II (BD)

last: Rodrigures

first: J

last: Herman

first: D

last: Grun


title: Single-cell RNA from Haematopoetic progenitor cells

overall_design: 768 single-cell RNA: HSCs (LSK+CD34-Flt3-CD48-CD150+), Pre-MeP (Lin-cKit High Sca1-CD41-CD16/32-CD150+CD105-),MEP (Lin-cKithighSca1-CD34-CD127-CD16/32-), Pre-CFU-E (Lin-cKit High Sca1-CD41-CD16/32-CD150+CD105+), Pro-E (CD44-CD71-Ter119+), Pre-GMP (Lin-cKit High Sca1-CD41-CD16/32-CD150-CD105-), GMP (Lin-cKit High Sca1-CD41-CD16/32+CD150-CD105-) and Megakaryocte progenitor (Lin-cKit High Sca1-CD41+CD16/32-CD150-CD105-) from wild type and Mof heterozygous mice


title: Identifying candidate genes whose expression is regulated by the HutC transcriptional repressor in Pseudomonas fluorescens SBW25

status: Public on Mar 06 2020

city: Auckland

first: Xue-Xian

last: Zhang

address: 14.02 The Station Cre., Albany

department: School of Natural and Computational Sciences

country: New Zealand

institute: Massey University

summary: HutC in Pseudomonas is a representative member of the HutC/GntR family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate binding domain. HutC is generally known to represses expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here we first describe the detailed molecular interactions between HutC and its PhutU target site in a plant growth promoting bacterium P. fluorescens SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization in planta.

overall_design: Gene expression was compared between wild-type P. fluorescens SBW25 and its derived hutC deletion mutant.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, arr1, and AOE Transcriptomes

city: Qingdao

first: Zhenhua

last: Liu

address: Binhai Road 72

institute: Shandong University

summary:
Purpose: The goals of this study are to identify the downstream regulated genes of ARR1.
Methods: RNA was extracted from wild-type, arr1 single mutant, and AOE root explants at the nascent SAM formation stage. Library construction and RNA-Seq were performed by Biomarker Co. (www.biomarker.com.cn, Beijing, China). DESeq and the Q value were used to identify differentially transcribed genes (DTGs). Differential transcription was inferred by applying a false discovery rate threshold of 0.001 and the |log2 Ratio| ≥ 1. Functional categorization was inferred from a BLAST search of the non-redundant GenBank (http://www.ncbi.nlm.nih.gov/genbank/), KEGG Pathway (http://www.genome.jp/kegg/pathway.html), and UniProt protein databases (http://www.uniprot.org/), and was further analyzed by the Gene Ontology (http://geneontology.org/) method.
Results: In the transcriptomes of arr1 vs. wild-type explants, we detected 177 up- and 260 downregulated DTGs, and in the AOE vs. wild-type transcriptomes, we detected 129 and 6 DTGs, respectively. The pathways involved in hormone signal transduction and indole alkaloid synthesis were well represented among the DTGs in arr1 vs. wild type. These DTGs also included genes involved in auxin transport and signaling, as well as IAA17, an Aux/IAA repressor gene, which was downregulated in arr1 root explants.
Conclusions: Our study showed that IAA17 was downstream gene of ARR1 in root explants.

overall_design: RNA  profiles of wild-type, arr1 single mutant, and AOE root explants at the nascent SAM formation stage were generated by deep sequencing, in duplicate, using Illumina system.

first: Fengning

last: Xiang


title: MOF directs erythroid fate during hematopoiesis via RUNX1-GFI1b feedforward control (scRNA-Seq)

overall_design: Single-cell RNA-seq from hematopoietic stem cells

first: Cecilia


title: Decoding the regulatory circuit by epigenetic regulator MOF in haematopoiesis

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

overall_design: Refer to individual Series


title: Microarray result of human skin derived from normal, atopic dermatitis and atopic march patients

status: Public on Mar 05 2020

city: Seoul

first: Bomi

last: Kim

address: 50-1, Yonsei-Ro

country: South Korea

institute: Yonsei University college of medicine

summary: The patho-mechanism of atopic dermatitis showing systemic involvement may be explained by Th17-related cytokines induced by FABP5 through systemic sensitization to a major allergen of a house dust mite.

overall_design: To find a possible mechanism of atopic march(AM), we designed a study in search of immune signatures and specific biomarker for AM by RNA microarray. Informed consent was obtained from all subjects, and the protocols were approved by the Institutional Review Board (no. 4-2013-0624).

first: Chang

middle: O

last: Park

first: Kwang

middle: H

last: Lee


first: Michael

last: Borg

summary: Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In most animal species, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamine. Precisely how the paternal epigenome is reprogrammed in flowering plants remains unclear since sperm chromatin is not demethylated and histones are retained. Here, we show that the sperm-specific histone, H3.10, is immune to lysine 27 methylation and that its deposition in sperm contributes to the global and specific resetting of the epigenetic mark H3K27me3 by uncoupling its inheritance during DNA replication. The loss of H3K27me3 facilitates transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation, revealing a global wave of epigenetic resetting that coordinates with early plant life. Thus, in contrast to the indiscriminate removal of epigenetic marks in animal sperm, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.

overall_design:
Smart-Seq2 library from mature pollen and sperm cells

Publicly-available RNA-seq datasets were processed in the same pipeline and are included for reference.
Type SRA_ID Tissue
RNA-seq SRR800753 Floral bud
RNA-seq SRR800754 Floral bud
RNA-seq SRR1207194 Carpel
RNA-seq SRR1207195 Carpel
RNA-seq SRR401413 Receptacle
RNA-seq SRR401414 Receptacle
RNA-seq SRR401415 Receptacle
RNA-seq SRR401416 Receptacle
RNA-seq SRR401417 Receptacle
RNA-seq SRR401418 Receptacle
RNA-seq SRR401419 Receptacle
RNA-seq SRR401420 Receptacle
RNA-seq SRR401421 Receptacle
RNA-seq SRR1260032 Root apical meristem
RNA-seq SRR1260033 Root apical meristem
RNA-seq SRR949956 Shoot apical meristen
RNA-seq SRR949965 Shoot apical meristen
RNA-seq SRR949988 Shoot apical meristen
RNA-seq SRR949989 Shoot apical meristen
RNA-seq SRR515073 Seedling
RNA-seq SRR515074 Seedling
RNA-seq SRR527164 Seedling
RNA-seq SRR527165 Seedling
RNA-seq SRR493097 Leaf
RNA-seq SRR493098 Leaf
RNA-seq SRR493101 Leaf
RNA-seq SRR1046909 Roots
RNA-seq SRR1046910 Roots
RNA-seq SRR5227391 Dry seeds
RNA-seq SRR5227392 Dry seeds
RNA-seq SRR5227393 Dry seeds
RNA-seq SRR364465 1-cell/2-cell embryos
RNA-seq SRR364466 1-cell/2-cell embryos
RNA-seq SRR364467 8-cell embryos
RNA-seq SRR364468 8-cell embryos
RNA-seq SRR364469 ~32-cell embryos
RNA-seq SRR364470 ~32-cell embryos


title: Pancreatic Circulating Tumour Cell Profiling Identifies LIN28B as a Metastasis Driver and Drug Target

status: Public on Mar 01 2020

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Gene expression profiling of circulating tumor cells purified from human patients with pancreatic cancer led to identification of LIN28B as possible metastasis driver. Functional studies in model systems confirmed the importance of this pathway.

overall_design: RNA-seq of primary purified circulating tumor cells from pancreatic cancer patients and healthy donors.

first: Joseph

last: Franses


title: Microarray result of human T cells. T cells were harvested from atopic march patients' peripheral blood mononuclear cells (PBMCs)


title: RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

summary: Arabis alpina, similar to woody perennials, has a complex architecture with a zone of axillary vegetative branches and a zone of dormant buds that serve as perennating organs. We show that floral development during vernalization is the key for shaping the dormant bud zone by facilitating a synchronized and rapid growth after vernalization and thereby causing an increase in auxin transport, response and endogenous indole-3-acetic acid (IAA) levels in the stem. Floral development during vernalization is associated with the development of axillary buds in subapical nodes. Our transcriptome analysis indicated that these buds are not dormant during vernalization but only reach sustained growth after the return to warm temperatures. Floral and subapical vegetative branches grow after vernalization and inhibit the development of the buds below. Dormancy in these buds is regulated across the A. alpina life cycle by low temperatures and by apical dominance in a BRANCHED 1 dependent mechanism.

overall_design: 12 samples, 3 biological replicates per condition

first: Alice

last: Vayssieres

first: Priyanka

last: Mishra

middle: C


title: Genome-wide maps of chromatin state in mouse B16 melanoma cancer cells in response to interfacial geometry

city: Kensington

first: Kristopher

middle: A

last: Kilian

state: UNSW

address: Hilmer Building 740

country: Australia

institute: University of New South Wales

summary: Chromatin immunoprecipitation and sequencing (ChIP-Seq) analysis specific for the identified histones (H3K4me2/H3K9ac)

overall_design: Examination of murine B16 melanoma cancer cells cultured on patterned or non-patterned substrates

first: Junmin

first: Thomas

middle: G

last: Molley

first: Christopher

last: Seward

first: Amr

last: Abdeen

first: Huimin

first: Xiaochun

last: Wang

first: Hetvi

last: Gandhi

first: Jia-Lin

last: Yang

first: Katharina

last: Gaus


title: BRN2 expression increases anoikis resistance in melanoma.

status: Public on Feb 25 2020

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: Melanoma tumors are highly heterogeneous, comprising of many cell populations that vary in their potential for growth and invasion.  Differential transcription factor expression contributes to these phenotypic traits.  BRN2, a member of the POU domain family of transcription factors is thought to play important roles in melanoma invasion and metastasis.  However, how BRN2 functions during the metastatic process of melanoma remains largely unknown.  We therefore investigated the effects of BRN2 expression in melanoma cells with no or low constitutive expression using a doxycycline-inducible system.  Induction of BRN2 expression led to reduced proliferation and partial resistance to an inhibitor of mutated BRAF.  Whole genome profiling analysis revealed novel targets and signaling pathway changes related to prevention of cell death induced by detachment from the extracellular matrix, known as anoikis resistance.  Further investigation confirmed increased survival of BRN2 expressing cell lines in non-adherent conditions.  Functionally, expression of BRN2 promoted induction of c-MET levels as well as increased phosphorylation of STAT3.  Treatment with crizotinib, a c-MET inhibitor, decreased cellular viability of BRN2 expressing cells under non-adherent conditions to death by anoikis.  These results highlight the importance of a largely overlooked transcription factor in the progression and metastasis of melanoma, and may suggest a strategy to target BRN2 expressing cells resistant to therapy and cell death by anoikis.

overall_design: melanoma cells, expressing BRN2 or vector, were treated with 50 ng/ml doxycycline for either 24 or 48 hours; Single colour, Illumina Human HT12v4 Beadarrays.

first: Carly

middle: J

last: Pierce

first: Jacinta

middle: L

last: Simmons

first: Natasa

last: Broit

first: Deshapriya

last: Karunarathne

first: MeiFong

last: Ng


title: Whole transcriptome analysis of mouse aortas and kidneys with or without deletion of the EGFR in vascular smooth muscle cells after 18 weeks of high fat diet

city: Halle (Saale)

first: Barbara

last: Schreier

address: Magdeburgerstr. 6

institute: Martin Luther University Halle-Wittenberg

summary: Obesity causes diabetes type 2 (DMT2) leading to vascular dysfunction and finally renal end-organ damage. Vascular smooth muscle (VSM) EGF receptor (EGFR) modulates vascular wall homeostasis in part via serum response factor (SRF), a major regulator of VSM differentiation and a sensor for glucose. We investigated the role of VSM-EGFR during obesity-induced renovascular dysfunction and the EGFR-hyperglycemia crosstalk.

overall_design:
RNASequencing of aortas and kidneys from mice with or without deletion of the EGFR in VSMC after 18 weeks of high fat or standard fat diet
Raw RNASequencing data were treated successively with Cutadapt (adaptor removal), Tophat (mapping) and featureCounts (counting).

first: Alexander

last: Nolze

first: Michael

last: Gekle

first: Christian

last: Stern

first: Sindy

last: Rabe

first: Sigrid

last: Mildenberger


title: RNA-Seq Analysis of Wild Type and pSTK::amiRNACWIN24 (4-3) Transcriptomes

status: Public on Feb 29 2020

city: Callaghan

first: Shengjin

last: Liao

state: NSW

address: University Drive

institute: The University of Newcastle, Australia

summary: Ovule formation is essential for realizing crop yield as it determines seed number. The underlying molecular mechanism, however, remains elusive. Here, we show that cell wall invertase (CWIN) functions as a positive regulator of ovule initiation in Arabidopsis. In situ hybridization revealed that CWIN2 and CWIN4 were expressed at the placenta region where ovule primordia initiated. Specific silencing of CWIN2 and 4 by using targeted artificial microRNA driven by an ovule-specific SEEDSTICK promoter (pSTK) resulted in a significant reduction of CWIN transcript and activity, which blocked ovule initiation and aggravated ovule abortion. Surprisingly, there was no induction of carbon starvation genes in the transgenic lines and supplement of extra carbon to newly forming floral buds failed to recover the ovule phenotype. The findings indicate that suppression of CWIN did not lead to carbon starvation. Interestingly, a group of hexose transporters was downregulated in the transgenic plants and two representative transporter genes, STP9 and SWEET8 were spatially co-expressed with CWIN2 and CWIN4, suggesting a coupling between CWIN and hexose transporters for ovule initiation. RNA-Seq analysis identified differentially expressed genes encoding putative extracellular receptor-like-kinases (RLKs), MADS-box transcription factors including STK and early auxin response genes, SAURs, in response to CWIN-silencing. Collectively, our data demonstrate the essential role that CWIN plays in ovule initiation likely through sugar signalling instead of carbon nutrient contribution. We propose that CWIN-mediated sugar signalling may be perceived by, and transmitted through, hexose transporters or RLKs to regulate ovule formation by modulating downstream auxin signalling and MADS-box transcription factors.

overall_design: To explore the underlying basis of CWIN-mediated ovule initiation, RNA-seq was conducted to compare the transcript profiles of flower buds pooled from stage 8 to 10 in a representative transgenic line, 4-3 and WT. Four biological replicates were used for each genotype in this RNA-Seq analysis


title: Peptidylarginine deiminase 4 promotes the renal infiltration of neutrophils and exacerbates the TLR7 agonist-induced lupus mice

status: Public on Feb 19 2020

city: Tokyo

first: Hiroaki

last: Hatano

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Allergy and Rheumatology

institute: The University of Tokyo

summary: Peptidylarginine deiminase 4 (PAD4), encoded by PADI4, plays critical roles in the immune system. The pathological roles of PAD4 were investigated in lupus model mice. PAD4-regulated pathways were identified by RNA-sequencing of WT and Padi4 KO neutrophils.

overall_design: Neutrophil mRNA profiles of 8 week-old wild type and Padi4-/-, in response to TLR7 agonost (R848), were generated.

first: Norio

last: Hanata

first: Hirofumi

last: Shoda

first: Yasuo

last: Nagafuchi

first: Toshihiko

last: Komai

first: Tomohisa

last: Okamura

first: Akari

last: Suzuki

first: I

middle: K

last: Gunarta

first: Katsuji

last: Yoshioka

first: Kazuhiko

last: Yamamoto

first: Keishi

last: Fujio


title: Gene expression profiling reveals that ERα controls the mitochondrial biogenesis in LysM-Cre targeted cells

status: Public on Feb 14 2020

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Estrogens decrease osteoclast numbers via direct and indirect effects. In trabecular bone, the anti-osteoporotic efficacy of estrogens is mediated via the estrogen receptor α (ERα) present in myeloid lineage cells, but the molecular mechanism mediating these effects remain controversial. In contrast to published findings by others, FasLgld/gld mice which lack functional FasL lost cortical and cancellous bone following OVX indistinguishably from FasL-intact controls. Microarray analysis of osteoclast progenitors isolated from the bone marrow of ERαf/f;LysM-Cre mice and ERαf/f controls indicated that ERα deleted macrophages exhibited significant enrichment for the term “oxidative phosphorylation”, suggesting that estrogen signaling via ERα inhibits this process

overall_design: Erα knock out is compare with control in osteoclast progenitors, pre-osteoclasts and mature osteoclasts

first: Ha-Neui

last: Kim

first: Serra

last: Ucer

first: Srividhya

last: Iyer

first: Nukhet

last: Aykin-Burns

first: Kim

last: Krager

first: Li

last: Han

first: Rafael

last: de Cabo

first: Haibo

last: Zhao

first: Stavros

last: Manolagas

first: Maria

last: Almeida


title: Differential impacts on host transcription by ROP and GRA effectors from the intracellular parasite Toxoplasma gondii

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: The intracellular parasite Toxoplasma gondii employs a vast array of effector proteins from the rhoptry and dense granule organelles to modulate host cell biology; these effectors are known as ROPs and GRAs, respectively. To examine the individual impacts of ROPs and GRAs on host gene expression, we developed a robust, novel protocol to enrich for ultra-pure populations of a naturally occurring and reproducible population of host cells called uninfected-injected (U-I) cells, which Toxoplasma injects with ROPs but subsequently fails to invade. We then performed single cell transcriptomic analysis at 1-3 hours post-infection on U-I cells (as well as on uninfected and infected controls) arising from infection with either wild type parasites or parasites lacking the MYR1 protein, which is required for soluble GRAs to  cross the parasitophorous vacuole membrane (PVM) and reach the host cell cytosol. Based on comparisons of infected and U-I cells, the hostâ€™s earliest response to infection appears to be driven primarily by the injected ROPs, which appear to induce immune and cellular stress pathways. These ROP-dependent pro-inflammatory signatures appear to be counteracted by at least some of the MYR1-dependent GRAs and may be enhanced by the MYR-independent GRAs, (which are found embedded within the PVM). Finally, signatures detected in uninfected bystander cells from the infected monolayers suggests that MYR1-dependent paracrine effects also counteract inflammatory ROP-dependent processes.

overall_design: A total of 8395 cells were sequenced and a total of 5354 cells passed quality control and were sequenced. Samples were treated for three timepoints. For each treatment, we have measured a negative control sample treated with mock infection.

first: Suchita

last: Rastogi

first: Stephen

middle: R

last: Quake

first: John

last: Boothroyd


title: Differential gene expression and pathway analysis by RNA sequencing in human OPTN(E50K) retinal ganglion cells

status: Public on Feb 11 2020

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Retinal ganglion cells (RGCs) serve as the essential connection between the eye and the brain, with this connection disrupted in blinding disorders such as glaucoma. Numerous cellular mechanisms have been associated with glaucomatous neurodegeneration, and useful models for the study of glaucoma allow for the precise analysis of these degenerative phenotypes. Human pluripotent stem cells (hPSCs) serve as powerful tools for the in vitro analysis of human neurodegenerative diseases, particularly those cellular mechanisms underlying degeneration. Thus, efforts of the current study were initially focused upon the use of hPSCs with an E50K mutation in the Optineurin (OPTN) gene underlying glaucomatous neurodegeneration. CRISPR/Cas9 gene editing approaches were used to introduce the OPTN(E50K) mutation into existing lines of hPSCs, as well as the generation of isogenic control lines from existing OPTN(E50K) patient-derived hPSC lines. When grown from glaucomatous sources, hPSC-derived RGCs developed similarly to isogenic controls. Conversely, at later stages of maturation, OPTN(E50K) RGCs exhibited numerous deficits associated with a neurodegenerative phenotype, including neurite retraction, autophagy pathway disruption, apoptosis, and increased excitability. The results of this study provide an extensive analysis of the OPTN(E50K) mutation in hPSC-derived RGCs, with a number of biochemical and molecular alterations associated with functional changes to these RGCs. The opportunity now exists to further explore the precise cellular pathways leading to RGC death in glaucoma, as well as develop novel translational approaches for glaucoma including pharmacological screening and cell replacement therapies.

overall_design: Examination the differential gene expression from mRNA in human pluripotent stem cell-derived retinal ganglion cells underlying OPTN E50K mutation in comparison with wild-type OPTN

first: Kang-Chieh

last: Huang

first: Kirstin

last: VanderWall

first: Jason

last: Meyer


title: Transcriptome analysis of CHI3L1 silencing in thyroid cancer cells

status: Public on Feb 12 2020

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: CHI3L1 (Chitinase-3-like protein 1), also known as YKL-40, has been associated with inflammation and cancer. Transcription profiling analysis was performed in FTC-133 thyroid cancer cells transfected with control siRNA or siRNAs against CHI3L1.

overall_design: CHI3L1 expression was knocked-down in FTC-133 cells. RNA was extracted from cells transfected with control siRNA or siRNAs against CHI3L1 and submitted to RNA sequencing.


title: HIF-1 directly induces TET3 expression to redistribute 5-hydroxymethylcytosine and induce erythroid gene expression in hypoxia [5-hmC]

status: Public on Feb 01 2020

city: Chicago

first: Lucy

last: Godley

state: IL

address: 5841 S. Maryland Ave. MC 2115

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: We characterized genome-wide 5-hydroxymerhylcytosine (5-hmC) distribution  of CD34+ cells undergoing erythroid differentiation in normoxia vs. hypoxia by chemically labeling 5-hmC followed by pull-down and sequencing (hMe-SEAL). We found that hypoxia increases both the number and the prominance of 5-hmC peaks at each time point, especially at day 7 and 10.

overall_design: DNA was extracted from erythropoietic cells cultured in normoxia or hypoxia at various stages of differentiation (days 0, 3, 7, and 10). 5-hmC containing DNA was pulled-down and submitted for deep sequencing

middle: Z

last: Cao

first: Hui

last: Liu

first: Amittha

last: Wickrema


title: HIF-1 directly induces TET3 expression to redistribute 5-hydroxymethylcytosine and induce erythroid gene expression in hypoxia


title: Serine racemase is required for colorectal tumor growth and a potential therapeutic target.

status: Public on Jan 29 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Serine racemase (SRR) is an enzyme that catalyzes two reactions, the racemization and the dehydration of L-Ser and D-Ser and has been studied mainly in the fields of central nervous system. The function of SRR in cancer metabolism has not been elucidated. Here we show that SRR expression is upregulated in colorectal adenoma and adenocarcinoma lesions compared to non-neoplastic mucosa in human colorectal cancer specimens. Further analysis by using CRISPR/CRISPR-associated protein 9 system reveals that SRR enhances colorectal cancer cell proliferation via maintaining intracellular pyruvate and mitochondrial mass resulting in higher basal reactive oxygen species level, and has anti-apoptotic function.

overall_design: To investigate the effects of SRR on gene expression, we performed RNA-seq analysis and found 1,571 genes downregulated in SRR-KO DLD-1 cells and 977 genes in SRR-KO HCT116 cells.

first: Kenji

last: Ohshima

first: Eiichi

last: Morii


title: Highly multiplexed proteomic assessment of the human bone marrow microenvironment reveals elevated levels of CCL23 in acute myeloid leukemia

status: Public on Feb 03 2020

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

summary: Acute myeloid leukemia (AML) is a genetically heterogeneous disease that is characterized by abnormal clonal proliferation of myeloid progenitor cells found predominately within the bone marrow (BM) and blood. Recent studies suggest that genetic and phenotypic alterations in the BM microenvironment support leukemogenesis and allow leukemic cells to survive and evade chemotherapy-induced death. However, despite substantial evidence indicating the role of tumor-host interactions in AML pathogenesis, little is known about the complex microenvironment of the BM. To address this, we performed novel proteomic profiling of the non-cellular compartment of the BM microenvironment in AML patients (n=10) and age- and sex-matched healthy controls (n=10) using an aptamer-based, highly multiplexed, affinity proteomics platform (SOMAscan). We demonstrate that proteomic assessment of blood or RNA-sequencing of BM are suboptimal alternate screening strategies to determine the true proteomic composition of the extracellular compartment of the AML marrow microenvironment. Proteomic analysis showed 168 proteins significantly differed in abundance, with 91 proteins up-regulated and 77 proteins down-regulated in leukemic BM. A highly connected signaling network of cytokines and chemokines, including IL-8, was found to be the most prominent proteomic signature associated with AML in the BM microenvironment. We report the first description of significantly elevated levels of the myelosuppressive chemokine CCL23 (MPIF–1) in both AML and MDS patients and perform functional experiments supportive of a role in the suppression of normal hematopoiesis. This unique paired RNA-sequencing and proteomics dataset provides innovative mechanistic insights into AML and healthy aging and should serve as a useful public resource.

overall_design: Total RNA sequencing of rRNA-depleted RNA was performed using the Illumina TruSeq Stranded Total RNA kit.  Sequencing was performed on RNA isolated from bone marrow PAXgene tubes of 10 acute myeloid leukemia patients and 10 age- and sex-matched healthy donor controls.

first: Gege

last: Gui

first: Christopher

last: Hourigan


title: Next generation sequencing comparing effects of FFSS, FAK inhibitor and FAK gene deletion. [FFSS]

status: Public on Jan 28 2020

city: Boston

first: Marc

last: Wein

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

summary: Purpose: The goals of this study are to compare the effect of FFSS, HDAC4 and HDAC5 gene deletion on gene expression of NGS-derived RNA-sequencing.

overall_design: Methods: Ocy454 cells were grown at 37c for 14 days. Cells were then treated with FFSS (3h). Total RNA was isolated using PureLink RNA mini columns, and submitted for NGS library generation and sequenccing. All experiments performed in triplicate.

first: Tadatoshi

last: Sato

first: Murat

last: Cetinbas


title: RNA-seq on DMSO and EPZ6438 treated CD34+ HSPCs

status: Public on Jan 24 2020

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

summary: The overall goal is to understand how does the DNA methylation Canyon interactions in CD34+ HSPCs can be impacted by the inhibition of EZH2

overall_design: We has thus treat the CD34+ HSPCs in the ex vivo culture condition with DMSO and EZH2 inhibitor, we then utilzed the in situ HiC to detect the interactions of chromosomal loops, DNA methylation Canyons.We also use H3K27me3 ChIP-seq to detect the H3K27me3 in the EZH2 inhibitor treatment setting and use RNA-seq to test if the DNA methylation Canyon associated genes will be altered in the gene expresion

first: Haley

last: Gore


title: In Situ on DMSO and EPZ6438 treated CD34+ HSPCs


title: HIF-1 directly induces TET3 expression to redistribute 5-hydroxymethylcytosine and induce erythroid gene expression in hypoxia [ChIP-seq]

summary: We performed HIF-1alpha ChIP-seq in K562 cells cultured in normoxia vs. hypoxia for 3 days. We identified two new HIF binding sites in TET3 intron 2 that control TET3 expression in hypoxia

overall_design: K562 cells were cultured in normoxia or hypoxia for 72 hours. HIF-1alpha ChIP were performed on fixed chromatin

first: John


title: H3K27me3 and H3K4me3 ChIP-seq on DMSO and EPZ6438 treated CD34+ HSPCs


title: Transcriptional Programming of Human Mechanosensory Neuron Subtypes from Pluripotent Stem Cells

status: Public on Jan 21 2020

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: In vitro generation of human peripheral sensory neurons may provide a framework for novel drug screening platforms and disease models of touch and pain. However, derivation of a functionally pure sensory neuron population remains a major unmet challenge. We discovered that, by expressing the transcription factors NGN2 and BRN3A, human pluripotent stem cells can be induced to differentiate into a surprisingly homogenous culture of cold- and mechano-sensing neurons. Although such a neuronal subtype has not been reported in mice, we found molecular evidence of its existence in adult human sensory ganglia. Combining NGN2 and BRN3A programming with neural crest patterning, we produced two additional populations of sensory neurons, including a more specialized mechanosensory neuron subtype. Finally, we applied this system to model a rare inherited sensory disorder, characterized by profound impairment of touch sensation and proprioception, caused by inactivating mutations in PIEZO2. Together these findings establish an approach to specify distinct sensory neuron subtypes in vitro, underscoring the utility of stem cell technology to capture human-specific features of physiology and disease.

overall_design: RNA sequencing was performed on a total of 13 human samples. Of these samples, one represented a pool of human Dorsal Root Ganglia (hDRG), three represented human undifferentiated induced pluripotent stem cells (iPSC), three represented sensory neurons induced by NGN2-BRN3A expression in iPSCs (iSN), three represented sensory neurons induced by long term NGN2-BRN3A expression in iPSC-derived neural crest (NC_iSN1), and three represented sensory neurons induced by short term NGN2-BRN3A expression in iPSC-derived neural crest (NC_iSN2).

first: Alec

last: Nickolls

first: Michelle

last: Lee

first: David

middle: F

last: Espinoza

first: Marcin

last: Szczot

first: Ruby

last: Lam

first: Qi

last: Wang

first: Jeanette

last: Beers

first: Jizhong

last: Zou

first: Minh

middle: Q

last: Nguyen

first: Hans

last: Solinski

first: Aisha

last: AlJanahi

first: Michael

middle: E

last: Ward

first: Alexander

last: Chesler

first: Carsten

last: Bönnemann


title: Single-Cell Transcriptomics of Genome-Edited Kidney Organoids

city: Evanston

first: Behram

middle: Sarosh

last: Radmanesh

address: 633 Clark St

institute: Northwestern University

summary: We report the first use of genome-edited human kidney organoids, combined with single-cell transcriptomics, to study APOL1 risk variants at the native genomic locus in different nephron cell types. This approach captures interferon-mediated induction of APOL1 gene expression and cellular dedifferentiation with a secondary insult“second hit” of endoplasmic reticulum stress.

overall_design: Examination of interferon gamma +/- tunicamycin in G0 and G1 APOL1 kidney organoids. A, B, C, etc refer to independent experimental replicates.

first: Jennie

last: Lin


title: Influence of the putative transcription factor ClbR and the thioesterase ClbQ on colibactin synthesis regulation and characterization of critical transcription start sites in Escherichia coli

status: Public on Jan 17 2020

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

summary: By comparing the transcriptome profile upon deletion or overexpression of ClbR or ClbQ, we addressed the role of these proteins in regulation of colibactin expression. Our global screen indicates that ClbR is the key transcriptional activator of colibactin expression. In addition, we further investigated potential transcription start sites of the colibactin determinant.

overall_design: Bacterial cultures with an OD600nm of 0.4 (three biological triplicates with eight technical replicates, 140µl each), were pooled. The pools of five different samples (wildtype reference strain, and four different mutants) were included into RNA-seq analysis. In addition, a sample of the reference strain was TEX-treated for transcription start mapping by differential RNA-seq.

last: Wallenstein


title: HIF-1 directly induces TET3 expression to redistribute 5-hydroxymethylcytosine and induce erythroid gene expression in hypoxia [RNA-seq]

first: Lucy

last: Godley

summary: We performed RNA-sequencing on erythropoietic cells cultured in normoxia or hypoxia at days 3,7, and 10. We found numerous expression changes induced by hypoxia, including the canonical hypoxia targets as well as a number of genes encoding genes involved in epigenetic processes.

overall_design: RNA was extracted from erythropoietic cells cultured in normoxia or hypoxia at various stages of differentiation (days 0, 3, 7, and 10) and submitted for deep sequencing

first: John

last: Cao

first: Hui

last: Liu

first: Amittha

last: Wickrema


title: RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia.

status: Public on Jan 14 2020

city: Richland

first: Daniel

middle: Torres

last: Naylor

state: WA

address: 3300 Stevens Drive, MSIN. J4-18

department: Biological Systems Division

institute: Pacific Northwest National Laboratory

summary:
Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia.
Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases.
Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test.
Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.

overall_design: mRNA profiles of enriched functional consortia were sequenced using an Illumina HiSeq platform.

first: Dan

first: Ryan

last: McClue


title: Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

status: Public on Jan 13 2020

city: Bloomington

first: Gabriel

last: Zentner

address: 915 E 3rd St

department: Biology

institute: Indiana University

summary: Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: STRIPE-seq and RNA-seq in two organisms.

first: Robert

last: Policastro


title: Fallopian tube vs Fimbria

status: Public on Apr 04 2020

city: Miami

first: Sophia

middle: HL

last: George

state: FL

address: 1550 NW 10th Ave

department: Obstetrics and Gynecology

institute: University of Miami

summary:
Compare luteal and follicular phases of fimbria and ampulla tissue
Fallopian tube epithelial cells for gene expression analysis of fimbria and ampulla  specimens were obtained using LCM

overall_design: Expression arrays were preprocessed using the frma package (McCall et al., 2010) from  Bioconductor for hgu133plus2 arrays, and the oligo Bioconductor package (Carvalho and  Irizarry, 2010) for human genome HTA-2.0 arrays, to generate gene level summary  expression levels. Ovarian cycle at the time of surgery (6 luteal phase and 7 follicular phase)  was determined by histological review of the endometrium.

first: Patricia

last: Shaw


title: Genome-wide CRISPR/Cas9 library screening identifies genes regulating the IFN signalling pathways.

status: Public on Jan 11 2020

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Innate immunity is a non-specific host immune response against pathogen invasion. It exists widely in most of cells and is considered as the first line of defense against pathogen infection. Upon virus infection, the natural immune system is activated to generate immune response, thereby exerting the antiviral effect and effectively inhibiting the spread of virus in the body. With recent decades of research, people have found and identified the key regulatory factors of the natural immune response and the signal transduction. However the regulatory mechanisms of the factors are still unclear and need to be further explored. Our work used the CRISPR/Cas9 library to perform large-scale genome-wide, unbiased screening in immune cells, and discovered some novel genes involved in the regulation of type I IFN responses.

overall_design: First, we constructed a lentiviral vector encoding a fluorescence reporter (EGFP, enhanced green fluorescent protein) driven by the IFN-β promoter. Then, the reporter system was stably integrated into A549 cells. The stable clones were selected with puromycin and the capacity of EGFP-induction of the clones were examined by the infection of SeV. The clone with high homogeneity was chosen as the IFN-β-EGFP reporter cell line. The GeCKO library (#1000000048, Addgene) was amplified in Stbl3 bacteria and packaged into lentivirus in HEK293T cells. The reporter cells were transduced with lentivirus carrying the GeCKO library for 4 h, and the medium was replaced with fresh medium. Forty-eight hours post transduction, the cells were selected for 7 days with the treatment of puromycin. The GeCKO library-containing reporter cells were infected with SeV for 10 h and then subjected to flow cytometry sorting. Cells with drastically either enhanced or decreased fluorescence intensities of EGFP were collected for genomic DNA extraction. CRISPR library guides were amplified by PCR and then deep sequenced. After alignment, the differentially expressed sgRNAs were calculated and the corresponding genes are ranked.

first: Guo

last: Deyin

first: Hou

last: Panpan


title: Transcriptomic responses of human monocyte-derived dendritic cells to HIV and other innate stimuli

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: Transcriptional programming of the innate immune response is pivotal for host protection. The transcriptional mechanisms that link pathogen sensing with innate activation remain poorly understood. During infection with HIV-1, human dendritic cells (DCs) can detect the virus through an innate sensing pathway leading to antiviral type I interferon and DC maturation. Here, we have developed an iterative experimental and computational approach to map the innate response circuitry during HIV-1 infection. By integrating genome-wide chromatin accessibility with expression kinetics, we have inferred a gene regulatory network that links 542 transcription factors (TFs) with 21,862 target genes. Through genetic perturbation and drug treatments we identify PRDM1 and RARA as essential regulators of the interferon response and DC maturation, respectively. This work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting the complexity and cooperativity in the regulatory circuit controlling the DC response to HIV-1 infection.

overall_design: DCs were derived from the peripheral blood from seven deidentified human donors and infected with HIV or stimulated with innate immune agonists.  Conditions include infection with HIV-1-GFP in the presence or absence of Vpx, infection with wild type HIV-1, HIV-2, mutated HIV-2 capsid, or stimulation with LPS ( 100ng/ml), polyIC (10ug/ml) , cGAMP, recombinant IFN, R848, and polydCdG. Bulk RNA-Seq was performed on cells at 0, 2, 6, 24, and 48 hours after infection or stimulation as indicated.  For some samples, cells were sorted by flow cytometry prior to sequencing based on GFP or CD86 expression as indicated.

first: Jarrod

middle: S

last: Johnson

first: Nicholas

last: De Veaux

first: Alexander

middle: W

last: Rives

first: Lynn

last: Amon

first: Nicolas

last: Manel

first: Alan

last: Aderem

last: Littman

first: Richard

last: Bonneau


title: Regulation of nitrous oxide production in low oxygen waters off the coast of Peru [BC016]

status: Public on Jan 07 2020

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

summary:
Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 Â± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 Â± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 Âµmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 Âµmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation.
[SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287

sample_organism:
synthetic construct
seawater metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (labeled with Cy3) within 15% identithy of the 70-mer conjugated to a 20-mer oligo (labeled with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: Claudia

last: Frey

first: Eric

last: Achterberg

first: Amal

last: Jayakumar

first: Carolin

last: Löscher

first: Damian

last: Arévalo-Martínez

first: Elizabeth

last: León-Palmero

first: Mingshuang

last: Sun

first: Hermann

last: Bange

first: Ruifang

middle: C

last: Xie

first: Sun

last: Xin

first: Sergey

last: Oleynik


title: Neocartilage gene expression in microtia and normal auricular chondrocytes with and without BMP7

status: Public on Jan 03 2020

city: Akron

first: Robin

last: DiFeo Childs

state: Ohio

address: 215 W. Bowery St., Suite3300

department: Plastic & Reconstructive Surgery

institute: Childrens Hospital Medical Center of Akron

summary:
To gain understanding in the tissue engineering of a human auricle, neocartilages generated from microtia and normal surgical remnants were compared by microarray anlaysis.  Comparison of these two groups after 10 weeks development in vivo (nude mouse) revealed no statistically significant differences
Comparison of normal and microtia cells, each seeded on nanoPGA and supplemented with BMP7 in a slow-release hydrogel, showed statistically significant differences in certain genes identified by microarray analysis.  Such differences were also noted in several analyses comparing counterpart seeded cells without BMP7. Normal cells with and without growth factor showed several transcription and proliferative genes upregulated with addition of BMP7. Microtia with added BMP7 compared to normal neocartilage with added BMP7 was statistically significantly increased in gene levels of homeobox A10, DEAD box polypeptide 17, and arginine vasopressin.

overall_design:
Chondrocytes were isolated from two types of human auricular surgical remnants, microtia and conchal.  Isolated chondrocytes were expanded in culture for 2 weeks and subsequently counted and seeded onto nanopolyglycolic fiber mats with and without the growth factor BMP7.  After 10 weeks of implantation in a nude mouse model, total RNA from harvested samples were compared.
contributor: NCH Biomedical Genomics Core, Nationwide Hospital, Columbus, OH

middle: D

last: Childs


title: Next generation sequencing facilitates quantitative analysis of maize 35 mitochondrial genes in dek53-ref and wild-type (WT) kernels

status: Public on Jan 01 2020

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

summary: Analysis of 35 mitochondrial genes expression level in dek53-ref and WT kernels at 15 days after pollination (DAP)

overall_design:
mRNA profiles of 35 mitochondrial genes in dek53-ref and WT kernels at 15 DAP were generated by deep sequencing, using Illumina Hiseq 4000 (2 × 150bp read length)

Public accession IDs for dek53:
GRMZM2G480380: MaizeGDB (https://www.maizegdb.org/)
ONM32820.1: Genbank (https://www.ncbi.nlm.nih.gov/genbank/)


title: Regulation of nitrous oxide production in low oxygen waters off the coast of Peru

summary:
This SuperSeries is composed of the SubSeries listed below.
[SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287

overall_design: Refer to individual Series


title: Dissecting the early steps of MLL induced leukaemogenic transformation using a new mouse model of AML [ATAC-seq]

status: Public on Feb 07 2020

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Leukaemogenic mutations commonly disrupt cellular differentiation and/or enhance proliferation, thus perturbing the intricate regulatory programs that control multi-lineage differentiation and self-renewal in haematopoietic stem and progenitor cells. Translocations involving the Mll1 gene generate particularly powerful oncogenic fusion proteins, predominantly affecting infant and paediatric AML and ALL patients. The early stages of leukaemogenic transformation are typically inaccessible from human patient samples, and are not captured by conventional mouse models. Here, we took advantage of conditionally immortalised multipotent haematopoietic progenitor cells to develop a new MLL-r model capturing the early cellular and molecular consequences of MLL-ENL expression based on a clear clonal relationship between the parental and MLL-leukaemic cells. Through a combination of scRNA-seq, ATAC-seq and genome-scale CRISPR-Cas9 screening, we identified pathways and genes likely to be important during the early phases of leukaemogenesis. Finally, we demonstrate the broad utility of using matched parental and transformed cells for small molecule inhibitor studies by validating both known and new potential therapeutic targets.

overall_design: ATAC-Seq of parental and MLLENL transformed Hoxb8 cells

first: Silvia

last: Basilico

first: Alison

last: Kennedy

first: Konstantinos

last: Tzelepis

first: George

last: Giotopoulos

first: Sarah

middle: J

last: Kinston

first: Pedro

middle: M

last: Quiros

first: Kim

last: Wong

first: David

last: Adams

first: Larissa

last: Carnevalli

first: Brian

last: Huntly

last: Vassiliou

first: Fernando

last: Calero-Nieto

first: Berthold

last: Gottgens


title: Distinct SOX signature determines neuroblastoma origin and predicts clinical outcome

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: Multimodality treatment of high-risk neuroblastoma can be effective, but up to 50%  of children experience recurrent disease with fatal outcome. Extensive genetic intratumoral heterogeneity and diverse clinical outcomes pose therapeutic challenges in treating children affected by this aggressive disease. Several hypotheses have been proposed to explain the heterogeneity of neuroblastoma, including a possible origin from multipotent neural crest stem cells (NCSCs). Utilizing an in vivo mouse genetics approach, we demonstrate that lineage-restricted sympathoadrenal (SA) progenitors and not NCSCs are the cellular origin of neuroblastoma. Human neuroblastoma tissue is composed of two spatially juxtaposed cell types, neuroblasts and Schwann cells, both cell types derive from neural crest (NC) lineage. This composition mimics the architecture of sympathetic ganglions (SG) as well as of adrenal medulla at the late stage of neural crest (NC)  development. Similarly to SG, SOX10 is restricted to Schwannian cells and is not present in tumorigenic neuroblasts. Transcriptional landscape of Sox genes can serve as paradigmatic model for stage identification along NC lineage development. While early multipotent NCSCs are characterized by the expression of Sox9/Sox10 transcription factors (TF), committed SA progenitor identity is defined by the presence of Sox4/Sox11 TFs. Molecularly, we show that the core transcriptional network that orchestrate neuroblastoma maintenance is highly reminiscent of the SA progenitors. Taken together, the data presented here show that neuroblastoma cells functionally resemble the committed SA progenitors, while lacking specific stem cell program.

overall_design: RNA-seq of human neuroblastoma cell lines overexpress or knockdown SOX9

first: Chia-Lung

last: Yang

first: André

last: Serra-Roma

first: Olga

last: Shakhova


title: Regulation of nitrous oxide production in low oxygen waters off the coast of Peru [BC015]

first: Bess

last: Ward

first: Claudia

last: Frey

first: Eric

last: Achterberg

first: Amal

last: Jayakumar

first: Carolin

last: Löscher

first: Damian

middle: L

last: Arévalo-Martínez

first: Elizabeth

last: León-Palmero

first: Mingshuang

last: Sun

first: Hermann

last: Bange

first: Ruifang

last: Xie

first: Sun

last: Xin

first: Sergey

last: Oleynik


title: MNase sensitivity of promoter chromatin in GM12878 cells during stimulation with heat-killed Salmonella typhimurium

city: TALLAHASSEE

first: LAUREN

middle: A

last: COLE

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

summary: We employed an MNase-Transcription Start Site Sequence Capture method to map and determine the accessibility of all nucleosomes during immune stimulus, at high coverage for all human Pol II promoters. We uncovered features of nucleosomal organization and sensitivity to MNase digestion in B-lymphoblastoid cells. We also find that transcription factor binding is associated with sensitive nucleosomes.

overall_design: Nucleosome mapping via MNase-seq during heat-killed Salmonella typhimurium (HKST) stimulation in GM12878 cells.

first: Lauren

last: Cole

first: Jonathan

last: Dennis


title: Epithelial Vegfa specifies a distinct endothelial population in the mouse lung

city: Chicago

first: Lisandra

last: Vila Ellis

address: 303 E Superior

department: Cell and Developmental Biology

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


title: A genome-wide CRISPR screen identifies mediators of ferroptosis sensitivity in polyunsaturated fatty acid-treated cells

city: La Jolla

first: Haoxin

last: Li

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: Polyunsaturated fatty acids (PUFA) sensitize cells to ferroptotic cell death. In the study associated with this dataset, we used UACC257 as a model cell line (intrinsically resistant to ferroptosis) induced to be sensitive to ferroptosis with different PUFAs. We performed genome-wide CRISPR knockout screen to identify genes that mediate the sensitivity to ML210, a selective inhibitor of glutathione peroxidase 4 (GPX4) and a potent inducer of ferroptotic cell death. We identified cytochrome P450 oxidoreductase (POR, CYPOR) as a key player required for ferroptotic cell death among other genes.

overall_design: UACC257 cells with Cas9 expression were infected with a genome-wide lentiviral sgRNA library, selected with puromycin, expanded for incubation with different PUFAs before DMSO or ML210 treatment respectively. sgRNA-barcodes that were enriched in ML210-treated conditions were identified by high-throughput sequencing.

first: Mudra

last: Hegde

first: John

last: Doench

first: Stuart

last: Schreiber


title: RNA-seq analysis of scramble microPEP(Scr) or microPEP155(P155) treated THP1-derived dendritic cells

status: Public on Dec 31 2019

city: shanghai

first: Niu

last: liman

address: Building No.5(West Area),No.280 South Chongqing Road

department: Shanghai Institute of Immunology,Department of Immunology and Microbiology

summary:
The goals of this study are to compare the clusters and pathways of differential genes in scramble microPEP(Scr) and microPEP155(P155) treated THP1-derived dendritic cells.
Methods: THP1-derived DCs were treated with P155 or Scr for 2 h and then treated with R848 (1 µg/ml) for another 2 h. All samples were washed twice with PBS, and total RNA was extracted with RNAiso Plus (Takara Bio) and purified with magnetic oligo (dT) beads after denaturation. Purified mRNA samples were reverse transcribed into fragmented DNA samples and adenylated at the 3’ ends. Adaptors were ligated to construct a library. DNA was quantified by Qubit (Invitrogen). After cBot cluster generation, DNA samples were then sequenced by an Illumina HiSeq X Ten SBS instrument from Genergy Bio (Shanghai). Raw data were converted into Fastq format and transcript per million fragments mapped (FPKM) was calculated and log2 transformed with Cuffnorm. Differential gene transcripts were analyzed with DESeq and enriched for the GO/Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.
Results:RNA-seq data of THP1-derived DCs treated with P155 or Scr revealed that Gene Ontology (GO) pathways mainly involving vesicle-mediated transport and T cell receptor signaling pathway.

overall_design: Examination of mRNA profiles in Scramble microPEP(Scr) and microPEP155(P155) treated THP1-derived dendritic cells,totally 4 samples (2/group) were analyzed by deep sequencing.

first: N

middle: I

last: Liman


title: RNA-seq analysis of the spinal cord cells in scramble microPEP(Scr) or microPEP155(P155) treated EAE mouse model

summary:
The goals of this study are to analyze the DEGs of the spinal cord cells in scramble microPEP(Scr) or microPEP155(P155) treated EAE mouse model.
Methods: mononuclear cells of the spinal cord were isolated using Percol™ gradient centrifugation, washed twice with PBS, and total RNA was extracted with RNAiso Plus (Takara Bio) and purified with magnetic oligo (dT) beads after denaturation. Purified mRNA samples were reverse transcribed into fragmented DNA samples and adenylated at the 3’ ends. Adaptors were ligated to construct a library. DNA was quantified by Qubit (Invitrogen). After cBot cluster generation, DNA samples were then sequenced by an Illumina HiSeq X Ten SBS instrument from Genergy Bio (Shanghai). Raw data were converted into Fastq format and transcript per million fragments mapped (FPKM) was calculated and log2 transformed with Cuffnorm. Differential gene transcripts were analyzed with DESeq and enriched for the GO/Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.
Results:Gene Ontology (GO) pathways analysis of RNA-seq data revealed that genes downregulated by P155 treatment were mainly involved in the immune respones signaling pathway.

overall_design: Examination of mRNA profiles in Scramble microPEP(Scr) and microPEP155(P155) treated EAE mouse model,totally 4 samples (2/group) were analyzed by deep sequencing.


title: Essential functions of the Glucocorticoid Receptor require direct DNA binding [ChIP-seq]

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: We performed ChIP-Sequencing for GR in GR wild-type, GR Zn mutant and GR Knock-Out Mouse Embryonic Fibroblasts (MEFs). We show that GR Zn mutant chromatin binding is mostly lost except for some tethered binding sites. Together with the corresponding RNA-Seq data, our results illustrate how GR requires direct DNA binding for activation and repression of target genes.

overall_design: ChIP-Sequencing of GR in GR wild-type, GR Zn mutant and GR Knock-Out MEFs with 3, 4 and 2 biological replicates each.

first: Laura

last: Escoter-Torres

first: Nina

middle: H

last: Uhlenhaut


title: Muscle specific MyD88-/- confers a sexual dimorphism protecting female mice from inactivity-induced fat accumulation

status: Public on Dec 30 2019

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: We demonstrate whole body inflammation (miR146a-/-) exacerbated inactivity-induced fat gain and glucose dysregulation, while muscle specific MyD88 KO mitigated these outcomes in female mice.  Higher gene expression of Igf1 and decreased expression of Ip6k3 in muscle of MyD88 KO female mice may explain enhancement of glucose uptake in the soleus. Whereas protection from fat accumulation may be related to visceral fat gene changes in adipose tissue expansion (Prc1↓, Gulp1↑, Anxa2↓, Cav2↓, EHD1↓), adipose beiging (Fgf10↑), metainflammation (Hmox1↓), and genes involved in perfusion.  Of noteworthy to mention, two genes decreased in common between muscle and fat with the ablation of muscle MyD88. These were expression of the negative regulator for GLUT4 translocation, Ralgapa2, and uncharacterized 993011J21Rik2, a potential interferon interacting gene. We conclude that future therapeutic strategies for prevention or treatment of obesity and metabolic disturbances in populations unable to be physically active should focus on further understanding how skeletal muscle inflammation communicates with fat storage depots, and how this cross-talk is influenced by sex hormones.

overall_design: Total RNA was isolated from visceral fat and the red portion of the gastrocnemius muscle as described previously (25).  Briefly, tissue was homogenized in Tri Reagent LS (Molecular Research Center, Cincinnati, OH, USA) and disrupted via hand-held homogenizer (Bio-Gen PRO200; Pro Scientific, Oxford, CT, USA).  Chloroform separation was used and RNA was precipitated using isopropanol.  RNA was purified using TURBO DNase (AM2238) with Zymo RNA Clean and Concentrator-5 clean up.  RNA sequencing and library construction was performed by the University of Utah High Throughput Genomics Core.  Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583), and average RIN was 8.3.  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.  Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).  Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 51 cycle paired end sequence run was performed (NovaSeq 2 x 50 bp Sequencing_100 M Read-Pairs) using a NovaSeq S1 reagent Kit (20027465).

first: Ziad

last: Mahmassani

first: Paul

middle: T

last: Reidy

first: Alec

last: McKenzie

last: Petrocelli

first: O'Connor

last: Matthews

first: Naomi

last: de Hart

first: Patrick

last: Ferrara

first: Ryan

last: O'Connell

first: Katsuhiko

last: Funai


title: Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: Breast cancer is a heterogeneous collection of disease arising from the breast with distinct molecular and phenotypic features. Certain subsets of patients have tumors that are particularly difficult-to-treat, which include triple-negative breast cancer (TNBC), metastatic/recurrent disease and rare histological variants. To delineate the underlying biology and identify therapeutic candidates for these patients, a series of 37 breast cancer patient-derived xenografts (PDX) from both chemo-naïve and pre-treated specimens was generated from 81 transplant attempts. Whole-genome and transcriptome sequencing revealed marked fidelity of the molecular landscape for the majority of PDXs in comparison to parental tumors. Reverse-phase protein array analysis of PDXs further identified potential therapeutic targets. Metastatic potential varied between PDXs, where low-penetrance lung micrometastases was the most common pattern of dissemination and observed in 34.5% of models. Three PDXs recapitulated the metastatic localization seen in the corresponding patients, including two lines with high-frequency metastases to multiple vital organ systems, while another PDX displayed tropism to the skull-base. Chemosensitivity profiling was performed in vivo with standard-of-care agents (doxorubicin, cisplatin, gemcitabine or paclitaxel), where multi-drug chemoresistance was found in 60.0% of PDXs and 64.7% of responses were concordant with pre-engraftment responses observed in the patient. Consolidating chemogenomic data identified potentially actionable features in 97.2% of PDXs, and marked regressions were seen in vivo when a subset of these underwent proof-of-concept functional studies. This included FGFR inhibitor sensitivity in a FGFR1-amplified lobular carcinoma, mTOR inhibitor sensitivity in a recurrent neuroendocrine breast cancer with proteomic evidence of mTOR/PI3K activation, and platinum sensitivity in a TNBC with BRCA1 germline mutation predicted as benign. Together, this clinically-annotated PDX library with comprehensive molecular and phenotypic profiling serves as a resource for both discovery and validation preclinical studies on difficult-to-treat breast tumors.

overall_design: RNA sequencing data from breast cancer pairs of primary tumors and PDXs.

last: Savage

first: Hellen

last: Kuasne

first: Leah

last: Liu

first: Daniel

last: Lai

first: Adrian

last: Wan

first: Valentina

last: Muñoz-Ramos

first: Virginie

last: Pilon

first: Anie

last: Monast

first: Hong

last: Zhao

first: Margarita

last: Souleimanova

first: Matthew

middle: G

last: Dankner

last: Annis

first: Adriana

last: Aguilar-Mahecha

first: Nicholas

middle: R

last: Bertos

first: Jamil

last: Asselah

first: Nathaniel

last: Bouganim

first: Kevin

last: Petrecca

first: Peter

last: Siegel

first: Atilla

last: Omeroglu

first: Sohrab

middle: P

last: Shah

first: Samuel

last: Aparicio

first: Mark

last: Basik

first: Sarkis

last: Meterissian

first: Morag

last: Park


title: Epithelial Vegfa specifies a distinct endothelial population in the mouse lung [scRNA-seq]

first: Lisandra

last: Vila Ellis

institute: Northwestern University

summary: The lung microvasculature is essential for gas exchange and commonly considered homogeneous.  We show that Vascular endothelial growth factor A (Vegfa) from the epithelium specifies a distinct endothelial cell (EC) population in the postnatal mouse lung.  Vegfa is predominantly expressed by alveolar type 1 (AT1) cells and locally required to specify a subset of ECs.  Single cell RNA-seq identified 15~20% lung ECs as transcriptionally distinct and marked by Carbonic anhydrase 4 (Car4), which are specifically lost upon epithelial Vegfa deletion.  Car4 ECs, unlike bulk ECs, have extensive cellular projections and are separated from AT1 cells by a limited basement membrane without any intervening pericytes.  Without Car4 ECs, the alveolar space is aberrantly enlarged despite the normal appearance of myofibroblasts.  Lung Car4 ECs and retina tip ECs have common and distinct transcriptional profiles.  These findings support a signaling role of AT1 cells and shed light on alveologenesis.

overall_design: FACS-purified lung endothelial cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics)

first: Jichao

last: Chen


title: The Adipocyte acquires a Fibroblast-like Transcriptional Signature in response to a High Fat Diet.

status: Public on Dec 18 2019

city: Cambrdge

first: Ramya

last: Gamini

state: MA

address: 1 Portland st

institute: Pfizer Inc.,

summary:
RNA-seq analysis of isolated adipocytes after 8, 20 and 34 weeks high fat diet. Our data demonstrate that the adipocyte responds to the HFD by adopting a fibroblast-like phenotype, characterized by enhanced expression of ECM, focal adhesion and cytoskeletal genes and suppression of many adipocyte programs most notably those associated with mitochondria.
Purpose: Visceral white adipose tissue (vWAT) expands and undergoes extensive remodeling during diet-induced obesity. Much is known about the contribution of various stromal vascular cells to the remodeling process, but less is known of the changes that occur within the adipocyte as it becomes progressively dysfunctional. Here, we performed a transcriptome analysis of isolated vWAT adipocytes to assess global pathway changes occurring in response to a chronic high fat diet (HFD).
Methods: C57BL/6J mice were fed a high fat diet (HFD) or chow for 8, 20 and 34 weeks. At each time, metabolic parameters were measured and RNAseq performed on RNA isolated from adipocyte and stromal vascular cell fractions of the corresponding perigonadal white adipose tissue (eWAT).
Results: Our data demonstrate that the adipocyte responds to the HFD by adopting a fibroblast-like phenotype, characterized by enhanced expression of ECM, focal adhesion and cytoskeletal genes and suppression of many adipocyte programs most notably those associated with mitochondria.
Conclusions: This study reveals that during obesity the adipocyte progressively becomes metabolically dysfunctional due to its acquisition of fibrogenic functions. We propose that mechano-responsive transcription factors such as MRTFA and SRF contribute to both upregulation of morphological genes as well as suppression of mitochondrial programs.

overall_design: C57BL/6J mice were fed a high fat diet (HFD) or chow for 8, 20 and 34 weeks. At each time, RNAseq was performed on RNA isolated from the adipocyte fraction of the perigonadal white adipose tissue (eWAT).

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