title: The effects of beta-3 adrenergic innervation on bone marrow cells

first: Kaibin

last: Shi

address: 154 Anshan Rd, Heping District

department: Neurology

institute: Tianjin Medical University

summary: The activity of bone marrow hematopoeitic cells is tightly controlled by neurogenic innervations. As bone marrow cells mainly receive innervation from beta-3 adrenergic receptor, here we investigated the impact of beta3-adrenergic innervation on bone marrow cell transcriptome alterations. We sorted hematopoetic stem cells (HSCs) from wild type mice (control group) or Adrb3-/- mice (devoid of beta3-adrenergic receptor). Thereafter, Nanostring assessment was performed to compare the transcriptome alterations.

overall_design: 12 HSC samples were obtained from femur bone marrow of 6 wild type mice (C57/BL6) and 6 adregergic receptor beta 3 (Adrb3)-/- mice.

first: Samuel

first: Qiang

last: liu


title: Single-cell RNA-sequencing from mouse incisor reveals dental epithelial cell-type specific genes

status: Public on Sep 23 2020

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

type: Expression profiling by high throughput sequencing

summary: Dental epithelial stem cells give rise to all dental epithelial cell types, inner enamel epithelium, outer enamel epithelium, ameloblasts, stratum intermedium and stellate reticulum to form enamel. These all types of epithelial cells have distinct roles and are essential for enamel formation. These cell types are conventionally classified by their cell shape, however, the transcriptome and biological roles of each cell types are not fully understood. Here, we used single-cell RNA-sequencing to clarify the heterogeneity of dental epithelial cell types. Unbiased clustering of 6260 single-cells from post-natal day 7 mouse incisors are classified into 4 dental epithelial and 2 mesenchymal populations; 2 clusters of ameloblast, IEE/OEE and SI/SR clusters. Secretory-stage of ameloblasts were divided into Dspp+ or Ambn+ ameloblast. Pseudo-time analysis indicated that Dspp+ ameloblast differentiate into Ambn+ ameloblast. Further, Dspp and Ambn would be stage-specific markers of ameloblast. Gene Ontology (GO) analyses of each clusters indicate potent roles of cell types; OEE in regulation of tooth size and SR in transport of nutrition. Moreover, we identified novel dental epithelial cell marker genes, Pttg1, Atf3, Cldn10 and Krt15. These results provide a resource of transcriptome data in dental cells and contribute further molecular analyses of enamel formation.

overall_design: Examination of epithelial and mesenchymal cells in mouse incisor.

first: Kan

last: Saito

first: Daniel

last: Martin

first: Erich

middle: T

last: Boger

first: Craig

last: Rhodes

first: Keigo

last: Yoshizaki

first: Aya

last: Yamada

first: Hiroyuki

last: Inuzuka

first: Robert

middle: J

last: Morell

first: Yoshihiko

first: Satoshi

last: Fukumoto

first: Takashi

last: Nakamura


title: Metformin improves cognition of aged mice by promoting cerebral angiogenesis and neurogenesis

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model

city: Bethesda

first: Faycal

last: Guedj

state: Maryland

address: 35A Convent DR

department: NHGRI

country: USA

institute: National Institute of Health


title: Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model [Mouse]

summary:
Down syndrome (DS), a genetic condition leading to intellectual disability, is characterized by triplication of human chromosome 21. Neuropathological hallmarks of DS include abnormal central nervous system development that manifests during gestation and extends throughout life. As a result, newborns and adults with DS exhibit cognitive and motor deficits and fail to meet typical developmental and lack independent life skills. In the last two decades, a number of preclinical treatment studies showed beneficial effects in the Ts65Dn mouse model. As of summer 2020, 13 pharmacological interventions have been tested with little evidence of success in humans with DS. Potential reasons for this failure may be related to the fact that these therapeutic interventions were carried out too late, and not during the prenatal and early postnatal critical periods for brain development. To date, no prenatal treatment studies have been reported in pregnant women carrying fetuses with T21. A limited number of prenatal treatment studies using fluoxetine, maternal choline supplementation and the neuroprotective peptides NAP and SAL have been described using the Ts65Dn mouse model of DS. In our previous studies, we integrated gene expression data from nine different cellular and tissue sources in both humans with DS and mouse models to identify common dysregulated signaling pathways and cellular processes. We demonstrated that pathway abnormalities associated with DS were the result of gene-dosage specific effects and the consequence of a global stress response with activation of compensatory mechanisms. To counteract these genome-wide abnormalities, we used the Connectivity Map database (www.broadinstitute.org/CMap) to discover molecules that could be repurposed to rescue the transcriptome and promote more typical brain development in individuals with DS. One of the molecules that had the most consistent negative scores (hence, negating the dysregulated gene expression signatures in DS) across tissues and species was apigenin (4’, 5, 7-trihydroxyflavone). Here, we hypothesized that prenatal treatment with apigenin would partly rescue the global gene expression dysregulation to improve neurogenesis and postnatal cognitive outcomes in DS.
In the current study, we used a human in vitro cell model (amniocytes derived from live fetuses with Trisomy 21 and euploid fetuses) and the Ts1Cje mouse model of DS to evaluate the effects of apigenin as a potential therpay for prenatal brain defects and postnatal cognitive outcome in DS. We demonstrated that apigenin is a safe treatment that can rescue oxidative stress and total antioxidant capacity imbalance in human amniocytes from fetuses with T21. It also improved several postnatal behavioral deficits in the Ts1Cje mouse model. We also showed that apigenin achieves its therapeutic action by triggering the expression of neurogenic genes, suppressing inflammation via inhibiting NFκB and by reducing the production of pro-inflammatory cytokines, while promoting the production of anti-inflammatory cytokines, angiogenic and neurotrophic factors.

overall_design: For human studies, gene expression analysis was performed on treated and untreated amniocytes from fetuses with Trisomy 21 (T21) and age and sex matched euploid fetuses using the GeneChip® Human Transcriptome HT 2.0 array (Affymetrix, Santa Clara, CA). only one apigenin dose (2 µM) was evaluated. Twenty-eight arrays were used (seven T21 and seven euploid for both controls and treated). For mouse studies, total RNA was isolated from the developing forebrain using the RNA II kits following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA was processed and hybridized on the GeneChip® Mouse Gene ST 1.0 array. Twenty arrays were used (5 WTPow, 5 Ts1CjePow, 5 WTApig, 5 Ts1CjeApig; 3 males and 2 females/group); each array corresponded to labeled cDNA from one sample. Analyses were performed using unpaired t-tests. Data were analyzed using a repeated-measures ANOVA that included genotype, treatment, and sample pairings between T21 and control samples. Probe sets for which either genotype or treatment was significant (at p<0.001 and a Benjamini-Hochberg False Discovery Rate (BH-FDR) of 10%) were considered as differentially expressed genes (DEX). Pathway analyses were carried out using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA) on the top 1% up-/down-regulated genes (hereafter referred to as Marginally Expressed (MEX) Genes), and Gene Set Enrichment Analysis (GSEA) on the whole transcriptome.

first: Ashley

middle: E

last: Siegel

first: Jeroen

middle: L

last: Pennings

first: Fatimah

last: Alsebaa

first: Lauren

last: Massingham

first: Umadevi

last: Tantravahi

first: Diana

middle: W

last: Bianchi


title: Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model [Human]

summary:
Down syndrome (DS), a genetic condition leading to intellectual disability, is characterized by triplication of human chromosome 21. Neuropathological hallmarks of DS include abnormal central nervous system development that manifests during gestation and extends throughout life. As a result, newborns and adults with DS exhibit cognitive and motor deficits and fail to meet typical developmental and lack independent life skills. As of summer 2020, 13 pharmacological interventions have been tested with little evidence of success in improving cognition in humans with DS. Potential reasons for this failure may be related to the fact that these therapeutic interventions were carried out too late, and not during the prenatal and early postnatal critical periods for brain development. To date, no prenatal treatment studies have been reported in pregnant women carrying fetuses with T21. A limited number of prenatal treatment studies using fluoxetine, maternal choline supplementation and the neuroprotective peptides NAP and SAL have been described using the Ts65Dn mouse model of DS. In our previous studies, we integrated gene expression data from nine different cellular and tissue sources in both humans with DS and mouse models to identify common dysregulated signaling pathways and cellular processes. We demonstrated that pathway abnormalities associated with DS were the result of gene-dosage specific effects and the consequence of a global stress response with activation of compensatory mechanisms. To counteract these genome-wide abnormalities, we used the Connectivity Map database (www.broadinstitute.org/CMap) to discover molecules that could be repurposed to rescue the transcriptome and promote more typical brain development in individuals with DS. One of the molecules that had the most consistent negative scores (hence, negating the dysregulated gene expression signatures in DS) across tissues and species was apigenin (4’, 5, 7-trihydroxyflavone). Here, we hypothesized that prenatal treatment with apigenin would partly rescue the global gene expression dysregulation to improve neurogenesis and postnatal cognitive outcomes in DS.
In the current study, we used a human in vitro cell model (amniocytes derived from live fetuses with Trisomy 21 and euploid fetuses) and the Ts1Cje mouse model of DS to evaluate the effects of apigenin as a potential therpay for prenatal brain defects and postnatal cognitive outcome in DS. We demonstrated that apigenin is a safe treatment that can rescue oxidative stress and total antioxidant capacity imbalance in human amniocytes from fetuses with T21. It also improved several postnatal behavioral deficits in the Ts1Cje mouse model. We also showed that apigenin achieves its therapeutic action by triggering the expression of neurogenic genes, suppressing inflammation via inhibiting NFκB and by reducing the production of pro-inflammatory cytokines, while promoting the production of anti-inflammatory cytokines, angiogenic and neurotrophic factors.


title: RNA-Seq analysis of BEAS-2b cells stimulated with house dust mite extract with or without suppression of MD-2

city: Tokyo

last: Ishii

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

institute: The University of Tokyo

summary: We clarified MD-2 might have a protective role in house dust mite(HDM)-induced asthmatic characteristics. The purpose of RNA-Seq analysis is to identify transcriptional events regulated by MD-2 in HDM-stimulated airway epithelial cells.

overall_design: BEAS-2b cells treated with control or LY96 siRNA were stimulated with PBS or HDM extract. 24 hours after stimulation, the cells were harvested.

first: Naomi

last: Yamashita


title: Identification of target genes in tie1 mutant zebrafish heart by transcriptomic analysis

status: Public on Sep 22 2020

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Purpose: identifying, with RNA-seq, genes targets of Tie1 during the cardiac development in zebrafish.  Results: we identified several differential expressed genes, with an enrichment in ECM modulator genes.

overall_design: Hearts were manually extracted at 48 hpf from tie1 mutants and wild-type and heterozygote siblings.

first: Claudia

last: Carlantoni

last: Guenther


title: RNA-sequencing analysis of genetically identical female and male Daphnia magna with age

city: Birmingham

first: julia

last: constantinou

address: Edgebaston

department: Biosciences

country: United Kingdom

institute: University of Birmingham

summary: Comparison of female and male Daphnia magna gene expression with age. The sexes in Daphnia magna are genetically identical. The aim of this study was to identify possible differences in gene expression between genders with age.

overall_design: RNA was extracted from samples with approximately equivalent dry mass using RNeasy Micro Kit (Qiagen Ltd, UK). The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (2x100bp) using Illumina Hi-Seq 4000 platform at BGI, Denmark.

first: Julia

last: Constantinou

first: Jouni

last: Kvist

first: Leda

last: Mirbahai


title: Transcritomic analysis of PHF8 mediated genes in MKN28, human gastric cancer cells

city: Hsinchu

first: Lin-Lu

last: Tseng

state: Taiwan

address: 101, Section 2 Kuang Fu Road

department: Life Science

country: Taiwan

institute: National Tsing Hua University

summary: PHF8, an important epigenetic regulator of cell cycle progression, rRNA synthesis and chromatin organization, is often overexpressed in different types of cancer including gastric cancer. Notably, elevated expression of PHF8 is associated with a poor clinical outcome in patients with gastric cancer. A global transcriptomic analysis between control and PHF8-knockdown MKN28 cells reveals differentially expressed genes involved in cell mortility and cell migration, suggesting PHF8 acts as an important regulator of cell migration related genes.

overall_design: PHF8 control and knockdown cell lines were established in MKN28 cells via a lentiviral-based system: LKO (control) and shPHF8 ( PHF8 targeted shRNA )

first: Hsin-Hung

last: Cheng

first: Wen-Ching

last: Wang


title: Knockout of the Caspase 8 Associated Protein 2 (CASP8AP2) gene in HEK293 cells leads to improvement in recombinant protein expression and cell cycle arrest at the G0/G1 phase

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

summary: In this study, we focused on understanding the effect of the functional inactivation of the caspase 8 associated protein 2 (CASP8AP2) gene on gene expression in HEK293 cells, to possibly explain the improvement in recombinant protein expression engendered by its inactivation. To achieve this goal, the HEK293 cell line constitutively expressing luciferase was treated with CRISPR constructs targeting the CASP8AP2 gene, single clones isolated and a clone with a functionally compromised CASP8AP2 gene, 892-7, selected for further investigations. Recombinant luciferase expression, recombinant secreted alkaline phosphatase expression, growth and metabolic characteristics were evaluated and compared between the 892-7 clone and the parental cell line. Cells cultured to a confluence of about 80% were used for gene expression profiling.  We found that genes involved in cell cycle progression and in histone mRNA synthesis were highly differentially expressed between the two cell lines.

overall_design: mRNA profiling of HEK293 cell line expressing luciferase and HEK293 cell line expressing luciferase with a CRISPR-deleted CASP8AP2 gene

first: L

last: Abaandou

first: A

first: J

last: Shiloach


title: RNA expression of reactivated Antigen-specific memory CD4 T cells previously exposed to tolerogenic or immunogenic stimulation

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

institute: Columbia University

summary: Activated and memory CD4 T cells play important roles in many autoimmune diseases often acting as upstream co-ordinators of inflammation and tissue destruction. A major therapeutic strategy is to turn off or tolerize these CD4 T cells thereby providing a cure. While much is understood about inducing tolerance in naïve CD4 T cells, little is known about whether or how to induce tolerance in previously activated or memory CD4 T cells. Here, we use RNA-sequencing to investigate the consequences of activating mouse CD4 memory T cells with antigen delivered in the absence of adjuvant, a classic tolerance-inducing strategy for naïve T cells. To examine the long term consequences of exposing memory CD4 T cells to tolerizing signals, we first reactivated them with antigen delivered with (control) or without (experimental) adjuvant, rested the cells and then reactivated them with antigen and adjuvant 5 days prior to isolating RNA for gene expression analysis.

overall_design: We used a triple transgenic reporter mouse, TRACE, to identify antigen specific CD4 T cells. In TRACE mice, T cell activation drives expression of rtTA via the interleukin 2 promoter. Reporter mice are supplied with a diet containing doxycycline for a total of 7 days starting 2 days prior to immunisation. Binding of rtTA to doxycycline activates the tet-ON promoter that drives expression of Cre recombinase which removes a stop codon blocking EYFP expression from the Rosa locus. Thus, CD4 T cells activated in the presence of doxycycline become permanently EYFP+. TRACE mice were immunized subcutaneously in the scuff with OVA protein, conjugated to 200nm polyethylene beads delivered with anti-CD40 and polyIC. EYFP+ CD4 T cells were isolated from TRACE mice 8 days post-immunisation using a CD4 T cell enrichment kit (EasySep, StemCell Technologies) before further purification via FACS-sorting. EYFP+ CD4 T cells were transferred intravenously to sex-matched, naïve C57BL/6 recipients and administered with OVA peptide alone, or OVA peptide with LPS 14 days later. A further 30 days later, all mice were immunized with OVA protein with alum intraperitoneally. EYFP+ CD4 T cells from lymphoid organs were FACS-sorted 5 days later. Each sorted sample was then processed to extract total RNA using the RNeasy Micro kit (Qiagen).

middle: I

first: Megan

last: MacLeod

first: Thomas

last: Otto

first: Paul

last: Garside


title: CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [ATAC-seq]

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl, Memphis, TN

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We recently developed CHANGE-seq (Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing), a fast, streamlined, Tn5 tagmentation-based assay for measuring the genome-wide activity of Cas9 in vitro that is easily scalable to many targets and samples. In this study, we directly compare CIRCLE-seq to CHANGE-seq and systematically evaluate Cas9 genome-wide activity on 110 targets across 13 therapeutically-relevant loci leveraging CHANGE-seq. We validate the sensitivity of CHANGE-seq for identifying sites of bona fide cellular off-target mutations using GUIDE-seq and sensitive targeted tag sequencing. Additionally, we sought to evaluate the impact of chromatin accessibility on cellular off-target activity by comparing CHANGE-seq with matched GUIDE-seq cellular off-target, chromatin, and transcriptional profiles generated from the same human primary T-cells.

overall_design:
T-cell_ATAC_seq, Two biological replicates
Please note the processed data file was generated from both replicates and is linked to the *rep1 sample record.

first: Cicera

middle: R

last: Lazzarotto


title: CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [RNA-seq]

overall_design: T-cell_RNA_seq, two biological replicates


title: Genome-wide distribution of NSD2/WHSC1/MMSET in human fibroblast cells

city: Chuo-ku, Kumamoto

first: Mitsuyoshi

last: Nakao

state: Kumamoto

address: 2-2-1 Honjo

department: Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics

institute: Kumamoto university

summary: ChIP-seq analysis of NSD2 in IMR-90 cells. We found that NSD2 is enriched at gene bodies of actively transcribed genes and required for maintenace of H3K36me3 levels at these loci.

overall_design: Examination of NSD2/DNA interaction in IMR-90 cells in growing condition.

first: Hiroshi

last: Tanaka


title: Differences between single isolated cells and colonial cells in heteromorphic life cycle of Phaeocystis globosa：Morphology, Physiology and Transcriptome

city: Guangzhou

first: dayong

last: liang

state: Guangdong

address: 604, Huangpu Avenue West, Tianhe District

institute: Jinan University

summary:
purose:The large-scale reproduction of Phaeocystis globosa has caused serious damage to the marine ecosystem in the coastal waters of China. The outbreak of algae blooms depends on the competitive advantage of their heteromorphic life history: colonial formation is beneficial to resist zooplankton predation, and the single isolated cells can absorb nutrients rapidly. To better understand the different types of cells characteristics of P. globosa that facilitate rapid expansion, single isolated cells (GX-S) and colonial cells (GX-C) are separated by filtration.
methods:For RNA exaction, the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). mRNA profiles of 10 days GX-C  and GX-S were generated by deep sequencing, in triplicate.
results:Three biological replicates from GX-S and GX-C were ensured statistical comparability and reliability of data. Raw data ranged from 25, 608,632 to 35,516,726 reads per sample. After producing more than 24 million clean reads, removing low-quality sequences and adapter sequences. Additionally, 4386 genes were differentially expressed at statistically significant levels, which included 2268 up-regulated genes and 2118 down-regulated genes. Genes with significant differential expression were involved in several pathways, including starch and sucrose, phagosome, inositol phosphate metabolism, fatty acid degradation.
conclusions: In summary, we can find that colonial cells have stronger carbon fixation capacity. It is not used to synthesize fatty acids as reserves of energy, but to secrete EPS. The reduction of fatty acid makes P. globosa become “low-quality food” and the formation of colony from EPS reduces the chance of being ingestion by zooplankton.

overall_design: mRNA profiles of 10 days GX-C  and GX-S were generated by deep sequencing, in triplicate, using Illumina HiSeq

first: Dayong

last: Liang

first: Yan

first: Shaoshan

last: Li

first: Xiaodong

first: Yiping

last: Huo


title: RNA-seq profiling of astrocytes after microglial ablation

city: Nagoya

first: Hiroyuki

last: Konishi

state: Aichi

address: 65, Tsurumai-cho, Showa-ku

department: Department of Functional Anatomy and Neuroscience

institute: Nagoya University

summary: Astrocytes become activated in a mouse model of microglial ablation. We isolated astrocytes from hippocampus after microglial ablation, and performed RNA-seq analyses to reveal gene expression profile of activated astrocytes.

overall_design: Hippocampus was dissected from two Siglechdtr/dtr mice 2 days after PBS or DT injection, and astrocytes were isolated using magnetic-activated cell sorting system with anti-astrocyte cell surface antigen-2 MicroBeads (Miltenyi Biotec). Three pools of RNA were obtained from three independent experiments. Libraries were prepared using the SMARTer Stranded RNA-seq Kit (Clontech Laboratories) followed by sequencing with NovaSeq6000 (Illumina).

first: Yuichiro

last: Hara

first: Okiru

last: Komine

first: Koji

last: Yamanaka

first: Tomoo

last: Ogi

last: Kiyama


title: Re-localization of CENP-A at centromeres upon depletion and re-expression

city: Paris

first: Riccardo

last: Gamba

address: 12 rue Lhomond

country: France

institute: Insitut Curie

summary: In a human cell line centromeric protein CENP-A was removed and then re-expressed. Possible subsequent changes in CENP-A localization were investigated with CUT&RUN-seq.

overall_design: One cell line with induced CENP-A depletion followed by CENP-A re-expression.

first: Sebastian

last: Hoffmann

first: Helena

middle: M

last: Izquierdo

first: Florian

last: Chardon

first: Marie

last: Dumont

first: Veer

last: Keizer

first: Solène

last: Hervé

first: Shannon

last: McNulty

first: Beth

last: Sullivan

first: Nicolas

last: Manel

first: Daniele

last: Fachinetti


title: Novel mirnas participate in Atherosclerosis through inflammation and apoptosis pathways (HAEC mRNA)

first: Zhen

last: Sheng

address: F13, Building 2, 4560 Jinke Road

institute: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd

summary: Atherosclerosis (AS), which is a chronic inflammatory disease, is the leading cause of death worldwide. Although several miRNAs have been reported to participate in regulating the progression of AS, there is a lack of systematic study of miRNA profile in AS. We combined miRNA and mRNA array analysis to study the global miRNAs in two AS models-oxidative LDL treated human aortic endothelial cells (HAEC) and high fat diet fed ldlr W483Stop knockin mouse. Novel miRNAs were identified to function in AS through inflammation and apoptosis pathways.

overall_design: Totally, there were six mRNA samples divided into two equal-sized groups, AS group and nornal control group.

first: Jia-Yan

last: Guo

first: Han-Bing

last: Mei

first: Qing-Yuan

last: Meng

first: Murielle

last: Véniant

first: Hong

last: Yin


title: High-throughput microRNA profile in adult and pediatric primary glioblastomas: the role of miR-10b-5p and miR-630 in the tumor aggressiveness

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Glioblastoma (GBM) is the most common primary malignant neoplasm of the central nervous system and, despite the standard therapy; the patients’ prognoses remain dismal. The miRNA expression profiles have been associated with patient prognosis, suggesting that they may be helpful for tumor diagnosis and classification as well as predictive of tumor response to treatment. We described the microRNA expression profile of 29 primary GBM samples (9 pediatric GBMs) and 11 non-neoplastic white matter samples as controls (WM) by microarray analysis and we performed functional in vitro assays on these 2 most differentially expressed miRNAs. Hierarchical clustering analysis showed 3 distinct miRNA profiles, two of them in the GBM samples and a group consisting only of cerebral white matter. When adult and pediatric GBMs were compared to WM, 37 human miRNAs were found to be differentially expressed, with miR-10b-5p being the most overexpressed and miR-630 the most underexpressed. The overexpression of miR-630 was associated with reduced cell proliferation and invasion in the U87 GBM cell line, whereas the inhibition of miR-10b-5p reduced cell proliferation and colony formation in the U251 GBM cell line, suggesting that these miRNAs may act as tumor-suppressive and oncogenic miRNAs, respectively. The present study highlights the distinct epigenetic profiling of adult and pediatric GBMs and underscores the biological importance of mir-10b-5p and miR-630 for the pathobiology of these lethal tumors.

first: Luiz

middle: G

last: Júnior

first: Mirella

last: Baroni

first: Régia

middle: C

last: Lira

first: Silvia

last: Teixeira

first: Paola

middle: F

last: Fedatto

first: Vanessa

middle: S

last: Silveira

first: Veridiana

last: Suazo

first: Luciana

last: Veronez

first: Rodrigo

middle: A

last: Panepucci

first: David

last: Antonio

first: José

last: Yunes

last: Brandalise

first: Simone

last: Aguiar

first: Luciano

last: Neder

first: Ricardo

last: Oliveira

first: Hélio

last: Machado

last: Carlotti Jr

last: Tone

first: Elvis

last: Valera


title: Prenatal and ancestral exposure to di(2-ethylhexyl) phthalate alters gene expression and DNA methylation in mouse ovaries.

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

summary: Di(2-ethylhexyl) phthalate (DEHP) is a commonly used plasticizer and known endocrine disrupting chemical, which causes transgenerational reproductive toxicity in female rodents. However, the mechanisms of action underlying the transgenerational toxicity of DEHP are not understood. Therefore, this study determined the effects of prenatal and ancestral DEHP exposure on various ovarian pathways in the F1, F2, and F3 generations of mice. Pregnant CD-1 dams were orally exposed to corn oil (vehicle control) or DEHP (20 μg/kg/day-750 mg/kg/day) from gestation day 10.5 until birth. At postnatal day 21 for all generations, ovaries were removed for gene expression analysis of various ovarian pathways and for 5-methyl cytosine (5-mC) quantification. In the F1 generation, prenatal DEHP exposure disrupted the expression of cell cycle regulators, the expression of peroxisome-proliferator activating receptors, and the percentage of 5-mC compared to control. In the F2 generation, exposure to DEHP decreased the expression of steroidogenic enzymes, apoptosis factors, and ten-eleven translocation compared to controls. It also dysregulated the expression of phosphoinositide 3-kinase (PI3K) factors. In the F3 generation, ancestral DEHP exposure decreased the expression of steroidogenic enzymes, PI3K factors, cell cycle regulators, apoptosis factors, Esr2, DNA methylation mediators, and the percentage of 5-mC compared to controls. Overall, the data show that prenatal and ancestral DEHP exposure greatly suppress gene expression of pathways required for folliculogenesis and steroidogenesis in the ovary in a transgenerational manner and that gene expression may be influenced by DNA methylation. These results provide insight into some of the mechanisms of DEHP-mediated toxicity in the ovary across generations.

overall_design:
Murine ovarian mRNA profile of post natal day (PND) 21 mice from the F3 generaion of F0 generation dams treated with 20ug/kg/day DEHP or tocopherol-stripped corn oil control. Three ovaries of each treatment group are analyzed individually for three replicates in each treatment group.

GRANT: EPA RD83 543401 Project 2: Endocrine Disrupting Chemicals, Diet and Gonadal Toxicity (Flaws) UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN Jodi A Flaws

first: Saniya

last: Rattan

first: Hannah

last: Beers

first: Athilakshmi

last: Kannan

first: Anujaianthi

last: Ramakrishnan

first: Emily

last: Brehm

first: Indrani

last: Bagchi

first: Joseph

last: Irudayaraj

first: Jodi

last: Flaws


title: Differential expression analysis of HaCaT and HaSKpw keratinocytes

city: Darmstadt

first: Alexander

last: Rapp

address: Schnittspahnstr. 10

department: Biology

institute: Technische Universität Darmstadt

summary:
Basal expression levels in untreated human keratinocytes were determined to compare the HaSKpw cell line with the HaCat cell line. Cells were grown without synchronisation until confluency was reached and three biological replciates per cell line were analysed.
Expression profiles were generated using Illumina HumanHT-12 V4.0 expression beadchip and the HiScan system (Illumina)

overall_design: Total RNA was extracted from independent cell cultures, reverse transcribed into cDNA

first: Elisabeth

last: Pavez Lorie

first: Nicola

last: Stricker

first: Beata

last: Plitta-Michalak

first: I-Peng

last: Chen

first: Beate

last: Volkmer

first: Rüdiger

last: Greinert

first: Anna

last: Jauch

first: Petra

last: Boukamp


title: The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage [scRNA-Seq]

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

institute: Henry Ford Health System

summary: Tissue-resident macrophages (TRMs) play central roles in local tissue development and immunity. However, how to control TRM ontogeny and maintenance remains unclear. We performed transcriptional and histone modification analyses of alveolar macrophages in mice with myeloid-specific (Csf1rCre) deletion of HDAC3 using bulk RNA-seq, single-cell RNA-seq and ChIP-seq. We report that HDAC3 deficiency results in metabolic disorders and increased cell death of the fetal lung TRMs, which is partially regulated through directly targeting PPAR-γ. Although the loss of AMs in the absence of HDAC3 is not AM subset specific, the transcriptome changes in HDAC3 deficient AM subsets are different. We propose that HDAC3 serves a key epigenetic regulator that controls embryonic TRM ontogeny and maintenance.

overall_design: scRNA-sequencing of Csf1rCre+HDAC3fl/fl and Csf1rCre-HDAC3fl/fl adult lung alveolar macrophage

first: Yi

last: Yao

first: Queping

last: Liu

first: Indra

last: Adrianto

first: James

last: Glassbrook

first: Xiaojun

last: Wu

first: Congcong

last: Yin

first: Yu

last: Wang

first: Jun

last: Zhang

first: Hongmei

last: Peng

last: Yang

first: Zheng

last: Dong

first: Frederic

last: Geissmann

first: Li

last: Zhou


title: Reciprocal regulation of EGR1 and EZH2 in breast cancer cells

city: Macau

first: Gang

last: Li

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: We found that EGR1 stimulates the expression of EZH2, which in turn inhibited the expression of EGR1 through a silencer region and deletion of the silencer resulted in upregulation of EGR1, which reduced the malignancy of breast cancer cells.

overall_design: RNA sequencing of MDA-MB-231 and MCF-7 with wildtype and silencer knockout. Two clones of silencer knockout were included.

first: Xiaowen

last: Guan

first: Un

last: Choi


title: Transcriptomic and epigenomic profiling of H3K27me3 demethylases inhibitor GSK-J4 induced changes in colon cancer cells (RNA-Seq)

status: Public on Sep 21 2020

city: Shenzhen

first: Xing-sheng

last: Shu

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

summary: H3K27me3 demethylases UTX and JMJD3 play vital roles in development and disease, including cancer. Therefore, we systematically investigated the impact of inhibition of these two demethylases using a small molecule inhibitor in colon cancer cells.

overall_design: HCT116 colon cancer cells were treated with 15 μm GSK-J4 or veichle for 48 hours and the cells were harvested for analysis as described below.

first: Xingsheng


title: Transcriptomic and epigenomic profiling of H3K27me3 demethylases inhibitor GSK-J4 induced changes in colon cancer cells

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

overall_design: Refer to individual Series


title: miR-199 Family Regulates Sonic Hedgehog Expression During Craniofacial Development

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Through microarray analyses of three SHH conditions, we were able to identify the miR-199 family as a family of miRNAs that is regulated by SHH signaling from the brain.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: To identify miRNAs that are regulated by SHH signaling within the brain and are active during the development of the upper jaw, we performed miRNA microarray analysis on the chick frontonasal ectodermal zone in normal embryos before (HH18) and after (HH22) the onset of SHH expression, after activating SHH (SHH-N or PBS control) or blocking SHH (5E1 or 40-1A control) signaling in the neural tube at HH10 and examined gene expression at HH22.

first: Diane

last: Hu

first: Ralph

last: Marcucio


title: Transcriptomic and epigenomic profiling of H3K27me3 demethylases inhibitor GSK-J4 induced changes in colon cancer cells (ChIP-Seq)


title: miR-199 Family Regulates Sonic Hedgehog Expression During Craniofacial Development.

type: Non-coding RNA profiling by high throughput sequencing

summary: miR-199 is a family of SHH-regulated microRNAs that participates in morphogenesis of the upper jaw.

overall_design: To identify miRNAs that are regulated by SHH signaling within the brain and are active during the development of the upper jaw, we performed RNA-sequencing analysis on the chick frontonasal ectodermal zone in normal embryos before (HH18) and after (HH22) the onset of SHH expression.


title: Mir-483 regulates the senescence of human adipose-derived mesenchymal stem cells through IGF1

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We performed small-RNA sequencing using adipogenic differentiation samples from day 0 (undifferentiated) and day 14.

overall_design: To identify putative miRNAs that may simultaneously affect adipogenic differentiation and replicative senescence in hADSCs, we performed small-RNA sequencing using adipogenic differentiation samples from day 0 (undifferentiated) and day 14.


title: Epigenome analysis of statin-treated SGBS pre-adipocytes during differentiation

city: Lille

first: Mickaël

last: Canouil

address: 1, Place de Verdun

institute: CNRS UMR1283/8199 - EGID

type: Methylation profiling by genome tiling array

summary: We investigated the role of statin treatment in adipocyte differentiation by using the in vitro pre-adipocyte SGBS cell line. We found that statins induced a reduction in adipogenesis by decreasing the mRNA expression of key transcriptional regulators, such as ADIPOQ and GLUT4. Therefore, we analysed the whole methylome of statin-treated cells, compared to DMSO-vehicle controls, using the 850K methylation arrays (Illumina) to identify putative effective genes.

overall_design: Human pre-adipocyte SGBS cell line was differentiatied using standard protocol. The cells were treated with either 10 µM mevastatin, 10 µM atorvastatin or DMSO-vehicle control at day 6 of differentiation and continued until adipocyte maturation (day 12). This experiment was performed in 4 biological replicates. At day 12, DNA was isolated from the cells and methylation arrays were performed.

first: Amna

last: KHAMIS

last: CANOUIL

first: Stephane

last: LOBBENS

first: Philippe

last: FROGUEL


title: Restoring chromatin accessibility for MLL reactivates latent tumor suppression-mediated vulnerability to proteasome inhibitors.

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

summary: MLL undergoes multiple distinct chromosomal translocations to yield aggressive leukemia with dismal outcomes. Besides their well-established role in leukemogenesis, MLL fusions also possess latent tumor suppressive activity which can be exploited as effective cancer treatment strategies using pharmacological means such as proteasome inhibitors (PIs). Here, we show that wild-type MLL is indispensable for the latent tumor suppressive activity of MLL fusions. MLL dysfunction, shown as loss of the chromatin accessibility and subsequent degradation of MLL, compromises the latent tumor suppressive activity of MLL fusions and is instrumental for the acquired PI resistance. Mechanistically, MLL dysfunction is caused by chronic PI treatment-induced epigenetic reprogramming and can be specifically restored by histone deacetylase (HDAC) inhibitors.

overall_design: Examination of differential expressive genes in parental and resistant MLL leukemia cell lines SEM and RS4;11, and drug-resistant cells treated with DMSO or HDAC inhibitors (LBH589 and SAHA).

first: Han


title: β-Globin Lentiviral Vectors Have Reduced Titers Due to Incomplete Vector RNA Genomes and Lowered Virion Production

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Lentiviral vectors (LV) commonly used for the treatment of hemoglobinopathies often have low titers and sub-optimal gene transfer efficiency for human hematopoietic stem and progenitor cells (HSPC), hindering clinical translation and commercialization for ex vivo gene therapy. We observed that a high percentage of β-globin LV viral genomic RNAs were incomplete towards the 3’ end in packaging cells and in released vector particles.  The incomplete vector genomes impeded reverse transcription in target cells, limiting stable gene transfer to HSPC. By combining three modifications to vector design and production (shortening the vector length to 5.3-kb; expressing TAT protein during packaging; and packaging in PKR-/- cells) there was a 30-fold increase in vector titer and a 3-fold increase in vector infectivity in HSPC. These approaches may improve the manufacturing of β-globin and other complex LVs for enhanced gene delivery and may facilitate clinical applications.

overall_design: Examination of viral RNA truncation in 3 lentiviral vectors of different lengths

first: Jiaying

last: Han

first: Matteo

last: Pellegrini

first: Donald

middle: B

last: Kohn


title: Differentially-expressed-transcriptome study of Non-Small Cell Lung Carcinoma

city: Lucknow

first: Neetu

last: Singh

address: Chowk

department: Center for Advance Research

country: India

institute: King George's Medical University

summary:
We systematically profiled the genome-wide alternative splicing events in Lung Adenocarcinoma (LUAD) and Lung Squomous Cell Carcinoma (LUSC) against Lung Control through Human Transcriptome Array2.0.
Non-invasive Stage IIIA non-small cell lung cancer (NSCLC) is heterogeneous in nature which makes it difficult to predict, diagnose and prognose owing to lower 5-year survival rate and 75-85% brain or bone metastasis. Hence, we hypothesized to develop transcript-based signature to categorize Stage IIIA-NSCLC-LUAD and LUSC, as well as identify markers which could indicate towards prognosis of disease. We were able to molecularly-categorize LUAD- and LUSC-tissue more precisely through HTA array2.0.

overall_design: The Non-Small Cell Lung Cancer Stage IIIA patients were clustered into LUAD, LUSC and control based-on transcriptional-profile through Human-Transcriptome-array2.0 (HTA2.0).

first: Archana

last: Mishra

first: Dinesh

last: Sahu

first: Mayank

last: Jain

first: Hari

last: Shyam

first: Ratnesh

last: Tripathi

first: Pratap

last: Shankar

first: Anil

last: Kumar

first: Nawazish

last: Alam


first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo

institute: Kumamoto university

summary: Transcriptome analysis of NSD2/WHSC1/MMSET-depleted human fibroblast cells revealed that loss of NSD2 downregulates the expression of cell cycle-related genes.

overall_design: We depleted NSD2 in IMR-90 human fibroblast cells using three different siRNAs, and then carried out an mRNA-seq analysis.

first: Hiroshi

last: Tanaka


title: Genome-wide distribution of NSD2 and transcriptome analysis of NSD2-depleted human fibroblast cells


title: Aldosterone induces trained immunity: the role of fatty acid synthesis.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Supranormal levels of aldosterone are associated with increased cardiovascular risk in humans, and with accelerated atherosclerosis in animal models. Atherosclerosis is a low-grade inflammatory disorder, with monocyte-derived macrophages as major drivers of plaque formation. Monocytes can adopt a long-term pro-inflammatory phenotype after brief stimulation with microbial pathogens or endogenous atherogenic lipoproteins via a process termed trained immunity. Using a primary human in vitro model, we demonstrate that aldosterone induces trained immunity via the mineralocorticoid receptor. We identify fatty acid synthesis as a crucial pathway necessary for the induction of trained immunity in monocyte-derived macrophages and demonstrate that pharmacological inhibition of this pathway blunts aldosterone-induced trained immunity. At the level of gene regulation, aldosterone promotes enrichment of the transcriptionally-permissive H3K4me3 modification at promoters of genes central to the fatty acid synthesis pathway. These data provide mechanistic insight into the contribution of aldosterone to inflammation, atherosclerosis and cardiovascular disease.

overall_design: After isolation, human monocyte-derived macrophages were stimulated (trained) with aldosterone (10nM) or vehicle (ethanol) for 24h, which was followed by a resting period of 5 days in medium. On day 6, before or after 4h of restimulation with Pam3Cys, RNA was isolated and subjected to gene expression profiling.

first: Charlotte

last: van der Heijden

first: Samuel

middle: T

last: Keating

first: Laszlo

last: Groh

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Niels

middle: P

last: Riksen


title: mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana [smallRNAs]

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: In order to assess the possible effects of m6A on miRNA biogenesis we performed small RNA (sRNA) sequencing to compare their levels in WT Col-0 plants to those in mutant lines with severely reduced m6A levels. The reduced mta line contains MTA cDNA under the ABI3 promoter in MTA null mutant background (ABI3:MTA) and ABI3 being an embryo specific promoter rescues the embryo lethal phenotype of MTA knockout while keeping the levels of MTA in mature plants severely low34. sRNAs isolated from 4 week old WT and mta plants were used to make libraries that were sequenced using HiSeq® (Illumina) and the results were analyzed using NOISeq package in R-Studio.

overall_design: wt and mta mutant small RNA sequencing

first: Dawid

last: Bielewicz

first: Artur

last: Jarmolowski


title: mTOR Inhibition Enables Long-Term Expansion of Human Neonatal Tracheal Aspirate-Derived Airway Basal Stem Cells

city: Cambridge

first: Todd

last: Gierahn

state: MA

address: 500 Main St

institute: MIT

summary: Bronchopulmonary dysplasia remains one of the most common complication of prematurity, despite significant improvements in perinatal care.  Functional modeling of human lung development and disease, like BPD, is limited by our ability to access the lung and to maintain relevant stem cell populations in culture. Single cell RNA-sequencing confirmed the presence of epithelial cells in tracheal aspirates obtained from intubated neonates.  Using combined SMAD signaling inhibition and mTOR inhibition neonatal tracheal-aspirate derived (nTAD) basal stem cells can be expanded long-term and retain the ability to differentiate into pseudo-stratified airway epithelium.  Conclusions: Our data demonstrate that neonatal tracheal aspirate-derived epithelial cells can provide a novel ex vivo human cellular model to study neonatal lung development and disease.

overall_design: Fresh aspirates collected from preterm infants intubated with endotracheal tubes were subjected to Seq-Well single cell RNA sequencing to identify cellular composition.

first: Junjie

last: Lu


title: Novel mirnas participate in Atherosclerosis through inflammation and apoptosis pathways (Mouse miRNA)

first: Zhen

last: Sheng

address: F13, Building 2, 4560 Jinke Road

institute: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd

summary: Atherosclerosis (AS), which is a chronic inflammatory disease, is the leading cause of death worldwide. Although several miRNAs have been reported to participate in regulating the progression of AS, there is a lack of systematic study of miRNA profile in AS. We combined miRNA and mRNA array analysis to study the global miRNAs in two AS models-oxidative LDL treated human aortic endothelial cells (HAEC) and high fat diet fed ldlr W483Stop knockin mouse. Novel miRNAs were identified to function in AS through inflammation and apoptosis pathways.

overall_design: Totally, there were six miRNA samples divided into two equal-sized groups, AS group and normal control group.

first: Jia-Yan

last: Guo

first: Han-Bing

last: Mei

first: Qing-Yuan

last: Meng

first: Murielle

last: Véniant

first: Hong

last: Yin


title: Effects of chronic intermittent ethanol exposure and withdrawal on neuroblastoma cell transcriptome

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary: Cycles of heavy drinking and abstinence can lead to ethanol abuse disorder. We studied the effects of chronic intermittent ethanol exposure (CIE) over three weeks on neuroblastoma cells, using an ethanol concentration frequently attained in binge drinking (40 mM, 184 mg/dl). There were many changes in gene expression but most were small. CIE affected pathways instrumental in the development or plasticity of neurons, including axonal guidance, reelin signaling and synaptogenesis. Genes involved in dopamine and serotonin signaling were also affected. Changes in transporters and receptors could dampen both NMDA and norepinephrine transmissions. Decreased expression of the GABA transporter SLC6A11 could increase GABA transmission and has been associated with a switch from sweet drinking to ethanol consumption in rats. Ethanol increased stress responses such as unfolded protein response. TGF-β and NFκB signaling were increased. Most of the genes involved in cholesterol biosynthesis were decreased in expression. Withdrawal for 24 h after CIE caused most of the CIE-induced expression changes to move back toward unexposed levels.

overall_design: comparison of cell-lines treated intermittenly with 40mM ethanol to control cells and those allowed to withdraw for 24h post-treatment

middle: N

first: Howard

middle: J

last: Edenberg


title: Novel mirnas participate in Atherosclerosis through inflammation and apoptosis pathways (Mouse mRNA)

overall_design: Totally, there were six mRNA samples divided into two equal-sized groups, AS group and normal control group.


title: Holistic characterization of single hepatocyte transcriptome responses to high fat diet

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary:
Purpose: The goals of this study are to investigate the effects of the long-term high-fat diet to transcriptome of mouse hepatocytes utilizing single cell RNA-seq (scRNA-seq) technology.
Methods: Hepatocytes were obtained from three mice that had been fed with the high-fat diet (HFD) and two mice that had been treated with the regular diet (LFD). After isolation and enrichment, hepatocytes were subjected to Drop-seq.

overall_design: A total of 5 Drop-seq experiments (2 LFD and 3 HFD mice) were run.  Sequencing was performed through Illumina HiSeq-4000 High-Output system.

first: Sung

last: Park

first: Hyun

last: Kang

first: Jun

middle: H


title: HRI depletion cooperates with pharmacologic inducers to elevate fetal hemoglobin and reduce sickle cell formation

city: Philadelphia

first: Gerd

last: Blobel

state: Pennsylvania

address: 3615 Civic Center Blvd., Abramson Research Center 316H

department: Hematology

institute: Children's Hospital of Philadelphia

summary: Increasing fetal hemoglobin (HbF) provides clinical benefit in patients with sickle cell disease (SCD). We recently identified heme-regulated inhibitor (HRI, EIF2AK1) as a novel HbF regulator. Since HRI is an erythroid-specific protein kinase it presents a potential target for pharmacologic intervention. We find that maximal HbF induction requires >80-85% HRI depletion. As it remains unclear whether this degree of HRI inhibition can be achieved pharmacologically, we explored whether HRI knockdown can be combined with pharmacologic HbF inducers to achieve greater HbF production and minimize potential adverse effects associated with treatments. Strongly cooperative HbF induction was observed when HRI depletion was combined with exposure to pomalidomide or the EHMT1/2 inhibitor UNC0638, but not hydroxyurea. Mechanistically, reduction in the levels of the HbF repressor BCL11A reflected the cooperativity of HRI loss and pomalidomide treatment, whereas UNC0638 did not modulate BCL11A levels. In conjunction with HRI loss, pomalidomide maintained its HbF inducing activity at 10-fold lower concentrations, at which condition there were minimal observed detrimental effects on erythroid cell maturation and viability as well as fewer alterations in the erythroid transcriptome. In sum, this study provides a foundation for the exploration of combining future small molecule HRI inhibitors with additional pharmacologic HbF inducers to maximize HbF production and preserve erythroid cell functionality for the treatment of SCD and other hemoglobinopathies.

overall_design: RNA-seq analysis of HRI-depleted primary CD34-derived erythroid cultures treated with the fetal hemoglobin pharmacologic inducers pomalidomide and UNC0638

first: Scott

last: Peslak


title: mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana

first: Zofia

last: Szweykowska-Kulinska

overall_design: Refer to individual Series


title: mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana [m6A_IP]

summary: We performed m6A-RNA immunoprecipitation followed by sequencing (m6A-IP Seq) using libraries produced with unfragmented ployA+ RNA from 4 week old WT Col-0 and mta plants.

overall_design: wt and mta mutant m6A-IP followed by RNA sequencing

first: Dawid

last: Bielewicz

first: Artur

last: Jarmolowski


title: C. elegans cnd-1/NeuroD1 functions with the Hox gene ceh-13/labial to control multiple genes required for nervous system development and function

city: Kennesaw

first: Martin

middle: Lyn

last: Hudson

state: GA

address: 370 Paulding Avenue, Suite SC507, MD1201

department: Molecular and Cellular Biology

institute: Kennesaw State University

summary: Identifying the mechanisms behind neuronal fate specification are key to understanding neurodevelopmental disorders such as autism and schizophrenia. In vivo nervous system fate specification is difficult to study in vertebrates. However, the nematode Caenorhabditis elegans, with its invariant cell lineage and simple nervous system of 302 neurons, is an ideal organism to explore the earliest stages of neural development. We took a comparative transcriptome approach to understanding the role of cnd-1/NeuroD1 in C. elegans nervous system development and function. This basic helix-loop-helix transcription factor is deeply conserved across phyla, and plays a crucial role in cell fate specification in both the vertebrate nervous system and pancreas. We find that cnd-1 partially represses its own expression during C. elegans embryogenesis. In addition, we show that cnd-1 controls the expression of ceh-5, a Vax2-like homeobox class transcription factor expressed in the nervous system and in head muscles. We also demonstrate a role for the Hox gene ceh-13/labial in defining the fate of cnd-1-expressing motorneurons. Finally, we show that cnd-1 also controls the expression levels of genes required for post-mitotic function, including the RING-finger ubiquitin ligase rpm-1. These data highlight the utility of comparative transcriptomes for understanding the nuances of transcription factor control, and establish a paradigm for future transcriptome-based studies.

overall_design: RNAseq analysis of Caenorhabditis elegans embryogenesis in N2 wild type (n = 3) and cnd-1(ju29) mutants (n = 3)

middle: L

first: Wendy

last: Aquino-Nunez

first: Zachery

middle: E

last: Mielko


title: Assaying 6xIAPP toxicity

first: Can

last: Kayatekin

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Measuring the change in gene expression profiles in yeast in response to 6xIAPP expression in high toxicity conditions

overall_design: Cells were grown in 5 mL total volume in log phase and induced for 6 hours. Expression profiles were compared in two biological replicates, both with and without IAPP expression.

first: M

middle: I

last: Barrasa


title: Novel mirnas participate in Atherosclerosis through inflammation and apoptosis pathways (HAEC miRNA)

first: Zhen

last: Sheng

overall_design: Totally, there were six miRNA samples divided into two equal-sized groups, AS group and nornal control group.

first: Jia-Yan

last: Guo

first: Han-Bing

last: Mei

first: Qing-Yuan

last: Meng

first: Murielle

middle: M

last: Véniant

first: Hong


first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

summary: 16 rats were mated and the dams continued pregnancy (controls) or were subsequently caloric restricted (CR) for 20% during days 1-12. Control female/male offspring continued normal lactation, while offspring of CR-treated dams received either normal lactation (CR group) or received during lactation until PN21 leptin supplementation. Leptin treatment of offspring during lactation after caloric restriction of dams during pregnancy reverts CR-induced dysfunction.

overall_design: 16 rats were mated and the dams continued pregnancy (controls) or were subsequently caloric restricted (CR) for 20% during days 1-12. Control female/male offspring continued normal lactation, while offspring of CR-treated dams received either normal lactation (CR group) or received during lactation until PN21 leptin supplementation (physiological doses given on subsequent days: 1.0; 2.0; 3.0; 4.0; 5.0; 6.3; 7.5; 8.8; 10.0; 11.3; 15.6; 17.2; 18.8; 20.3; 21.9; 23.5; 25.0; 26.6; 39.4; 43.8 ng of leptin; CR-L group. These doses represent five times the average amount of daily leptin intake from the mother's milk). After four months ad libitum feeding with chow, a blood sample was drawn and PBMC were isolated.  Snap frozen in liquid nitrogen and used for RNA isolation and whole genome gene expression microarray hybridisation using Agilent arrays.

first: Nara

last: Szostaczuk

first: Melissa

last: Bekkenkamp

first: Cati

last: Pico

first: Andreu

last: Palou

first: Jaap

last: Keijer


title: Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease

status: Public on Sep 20 2020

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

summary: Vogt-Koyanagi-Harada (VKH) disease is a systemic autoimmune disorder affecting multiple organs, including eyes, skin, and central nervous system. It is known that monocytes significantly contribute to the development of autoimmune disease. However, the subset heterogeneity with unique functions and signatures in human circulating monocytes and the identity of disease-specific monocytic populations remain largely unknown. Here, we employed an advanced single-cell RNA sequencing technology to systematically analyze 11259 human circulating monocytes and genetically defined their subpopulations. We constructed a precise atlas of human blood monocytes，identified 6 subpopulations: including S100A12-; HLA-; CD16-; proinflammatory-; megakaryocyte-like-; and NK-like-monocytes subsets, and uncovered 2 previously unidentified subsets: HLA- and megakaryocyte-like monocyte subsets. Relative to healthy individuals, cellular composition, gene expression signatures, and activation states were markedly alternated in VKH patients utilizing cell type-specific programs, especially the CD16- and proinflammatory monocyte subpopulation. Notably, we discovered a disease-relevant subgroup, proinflammatory monocytes, which showed a discriminative gene expression signature indicative of inflammation, antiviral activity, and pathologic activation, and converted into pathologic activation state implicating the active inflammation during VKH disease. Additionally, we found the cell type-specific transcriptional signature of proinflammatory monocytes, ISG15, which could act as a disease biomarker to more accurately reflect disease activity and treatment response than symptom evaluation. Taken together, in this landmark study we present novel discoveries on accurate classification, molecular markers, and signaling pathways for VKH disease-associated monocytes and therapeutically targeting this proinflammatory monocyte subpopulation would provide an attractive approach for treating VKH as well as other autoimmune diseases.

overall_design: 10X single cell RNA-seq from 3 normal people and 3 VHK patient

first: Yixin

last: Hu

first: Yuhua

last: Xiao


title: Expression data from NRK-52E cells treated with chlorothalonil for 6h, 24h and 72h.

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

summary:
Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile) is a widely used broad spectrum fungicide. Despite its common use, chlorothalonil is classified by IARC as Group 2B, a possible human carcinogen, with formation of renal tubular adenomas and carcinomas in rats of both sexes and in male mice. In this study we have examined the effect of sub-cytotoxic exposure to chlorothalonil at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E).
We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity.

overall_design: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to chlorothalonil dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 μM CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

first: Katarzyna

first: Edward

last: Lock


title: miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line.

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery.
Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using miRNA microarray expressions.

overall_design: miRNA expression profiles of MCF-7 enriched CSCs spheroids and monolayer cultures were generated in triplicates by Affymetrix GeneChip miRNA_4.0 array.

first: Lily

last: Boo

first: Wan

middle: Y

last: Ho

first: Norlaily

last: Ali

first: Swee

middle: K

last: Yeap

first: Huynh

last: Ky

first: Kok

middle: G

last: Chan

first: Wai

last: Yin

first: Dilan

last: Satharasinghe

first: Woan

middle: C

last: Liew

first: Sheau

middle: W

last: Tan

first: Han

last: Ong

first: Soon

last: Cheong


title: RNA sequencing of the stomachs of H. pylori-infected WT and Mincle–/– mice after 8 weeks

status: Public on Sep 19 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Helicobacter pylori (H. pylori) causes assorted gastrointestinal disorders. H. pylori-specific T cells develop during infection, which is a prerequisite for the induction of gastritis and malignancy. How the innate immune system senses H. pylori to prime T cells remains unclear. We report that cholesteryl glucosides in H. pylori activate innate immunity through C-type lectin receptors (CLRs). Cholesteryl acyl α-glucoside (αCAG) was identified as a ligand for Mincle (Clec4e). Upon H. pylori infection, T cell responses and gastritis were ameliorated in Mincle-deficient mice, although bacterial numbers were comparable.Thus the cholesteryl lipid–CLR axis exacerbates H. pylori-induced gastric inflammation with limited contribution to protective immunity.

overall_design: RNAseq analysis was performed by using RNA extracted from the stomachs of H. pylori-infected WT and Mincle–/– mice after 8 weeks in triplicates.

first: Masahiro

last: Nagata

first: Sho

last: Yamasaki


title: RNA-seq and ChIP-seq for human-specific regulation of neural maturation identified by cross-primate transcriptomics

city: La Jolla

first: Fred

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary:
Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding often termed neoteny. Signatures of neoteny, including a protracted proliferation of apical and basal progenitors as well as a delay in physiological activity of mature neurons, have been revealed in part through the use of induced pluripotent stem cell (iPSC) modeling of primate neurogenesis. IPSC modeling is particularly useful when examining the molecular drivers of a cellular phenotype such as gene transcription. It has long been proposed that phenotypic differences between closely related species may be driven, in part, by divergent transcriptional regulation rather than novel protein-coding sequence, however, how these regulatory mechanisms play a role in the protracted maturation process in human neurons remains largely unknown.
Here we show that the transcription factor GATA3 directly regulates the rate of physiological maturity in human neurons.  We modeled neurogenesis across 5 primate species consisting of 4 genera and 2 families and assessed the differences in transcriptional dynamics. We discovered that GATA3, a pioneer transcription factor, exhibited a unique up-regulation during human neurogenesis and was highly correlated with species-specific transcription. Strikingly, we also found that down-regulating GATA3 generated a gain-of-function, speeding up the rate of physiological maturity in human neurons. These findings indicate that the rate of physiological maturity in human neurons can be directly controlled by modulating a single, conserved transcription factor, providing evidence for the divergence of gene regulation as a major contributor to human neoteny.

sample_organism:
Macaca mulatta
Gorilla
Pan paniscus
Pan troglodytes
Homo sapiens

overall_design: RNA- and ChIP-sequencing from human, chimpanzee, bonobo, gorilla, and rhesus macaque neurons throughout pan-neuronal differentiation, sampled at 2 week intervals over an 8 week period.

first: Sara

middle: B

last: Linker


title: Plasma Cell Fate is Orchestrated by Large-Scale Changes in Compartmentalization

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

institute: UCSD

summary: Plasma cell differentiation is characterized by differentiation of progenitor cells into short-lived and long-lived compartments. Here we examine how gene expression and nuclear architecture are linked to instruct short-lived and long-lived plasma cell fate. We find that plasma cell commitment is concurrent with the nuclear repositioning of transcription start sites associated with activation or repression of genes including the Irf4 and Bcl6 loci, respectively. Intergenic regions associated with the Ebf1 and Prdm1 loci also reposition concomitant with altered patterns of gene expression. Plasma cell differentiation is also enriched for inter-chromosomal associations concurrent at a global scale with alterations in gene expression. Finally, we find that the onset of plasma cell development is associated with a gain in euchromatic strength for genes encoding for cell cycle regulation and DNA repair that characterize in part the long-lived plasma cell fate. We conclude that at the onset of plasma cell development different strategies are applied to modulate genes that dictate short-lived and long-lived plasma cell gene programs.

overall_design: 6 samples

first: Alexandra

last: Bortnick

first: Zhaoren

last: He

first: Cornelis


title: Oncogenic KRAS recruits an  expansive transcriptional network through mutant p53

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: We utilized genetically engineered mouse models that do and do not express mutant p53 to identify gain of function mechanisms in pancreatic cancer. Human pancreatic cancer (PDAC) patient derived xenografts with high and low p53 levels underwent transcriptional profiling

overall_design: Bulk RNA-sequencing was performed on 4 KPC tumors that express mutant p53 and 4 KPC tumors that are p53 null. DE analysis was performed. 19 PDAC PDX tumors were identified that express high levels of mutant p53 and 11 PDAC PDX tumors were identified that do not express any p53. Differential gene expression analysis was performed.

first: Michael

last: Kim

first: Gigi

last: Lozano


title: A study to investigate the effects of long-term organic and integrated fertilization on soil microbial community

city: Beijing

first: Long-Jun

last: Ding

address: 18 Shuangqing Road, Haidian District

department: Research Center for Eco-Environmental Sciences

institute: Chinese Academy of Sciences

summary:
Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear.
Here we used  microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. fertilization at various regimes.

overall_design: Soil samples from upper layer (0–15 cm) were taken from six fertilization treatments as follows: Control (no fertilizer), rice straw (R), rice straw plus chemical fertilizers nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Each treatment has three replications. A total of eighteen samples were analyzed by Geochip.

first: Longjun

first: Jianqiang

last: Su

first: Guoxin

last: Sun

first: Jinshui

last: Wu

first: Wenxue

last: Wei


title: RNA-Seq analysis of HCT-116 colon cancer cells upon lysophosphatidic acid treatment

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: We report the differential gene expression upon the LPA treatment depicting the invasion/metastasisphenomenon and the lipogenesis effect on the colorectal cancer cells HCT-116

overall_design: Cellular RNA profile of the HCT-116 cells, one with LPA treatment and one without treatment

first: Sib

middle: S

last: Roy


title: Investigsting the role of NF-ĸB p50 S80 phosphorylation in regulating LPS-induced transcription in THP-1 cells

city: Glasgow

first: Emma

last: Smith

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary: Phosphorylation of the NF-ĸB p50 subunit is known to regulate target gene expression. The role of p50 S80 phosphorylation in regulating LPS-induced transcription by utilising wild type (WT) and NFKB1S80A THP-1 cells is investigated.

overall_design: 12 samples in total (3 replicates of 4 conditions)

first: Domenico

last: Somma

first: David

last: Kerrigan

first: Ruaidhrí

last: Carmody


title: scRNAseq of DIO-NASH mouse livers

city: Hørsholm

first: Kristoffer

last: Rigbolt

address: Hørsholm Kongevej 11B

country: Denmark

institute: Gubra

summary: To improve the understanding of the complex biological processes underlying the development of non-alcoholic steatohepatitis (NASH), a multi-omics approach combining bulk RNA-sequencing based transcriptomics, quantitative proteomics and single-cell RNA-sequencing was used to characterize tissue biopsies from histologically validated diet-induced obese (DIO) NASH mice compared to chow-fed controls. Bulk RNA-sequencing and proteomics showed a clear distinction between phenotypes and a good correspondence between mRNA and protein level regulations, apart from specific regulatory events discovered by each technology. Transcriptomics-based gene set enrichment analysis revealed changes associated with key clinical manifestations of NASH, including impaired lipid metabolism, increased extracellular matrix formation/remodeling and pro-inflammatory responses, whereas proteomics-based gene set enrichment analysis pinpointed metabolic pathway perturbations. Integration with single-cell RNA-sequencing data identified key regulated cell types involved in development of NASH demonstrating the cellular heterogeneity and complexity of NASH pathogenesis.

overall_design: Examination of liver biopsies from 4 healthy and 2 DIO-NASH mice.

first: Helene

last: Ægidius


title: Effects of mechanical stress and deficiency of dihydrotestosterone or 17β-estradiol on temporomandibular joint osteoarthritis in mice

status: Public on Sep 18 2020

city: Chiyoda-ku

first: Tomohisa

last: Ootake

state: Tokyo

address: 2-9-18 Kanda-Misakicho

institute: Tokyo Dental College

summary:
Temporomandibular joint osteoarthritis (TMJ-OA), a subtype of temporomandibular joint dysfunction (TMD), is characterized by progressive cartilage degradation, subchondral bone erosion, and chronic pain. Although there has been extensive research on TMJ-OA, its etiology remains unknown. Age, hormonal factors, and excessive mechanical stress on the TMJ are proposed risk factors for TMJ-OA.
Using microarrays, we discovered two disease susceptibility genes that have been suggested to be involved in the pathogenic mechanism of TMJ-OA.

overall_design: For experimental groups, orchiectomy (ORX) or ovariectomy (OVX) was performed on sexually mature 8-week old mice. To apply excessive mechanical stress (MS) on mandibular condyles, a metal plate was attached to the posterior surface of the maxillary incisors. Male mice were divided into control, ORX, MS, and ORX+MS group, while female mice were divided into control, OVX, MS, and OVX+MS groups. Microarray analysis was conducted using a Clariom S Assay (Mouse, Thermo Fisher Scientific) for comprehensive analysis of related genes.

first: Takenobu

last: Ishii

first: Kenji

last: Sueishi

first: Akira

last: Watanabe

first: Yoichi

last: Ishizuka

first: Katsuhiko

last: Amano

first: Masashi

last: Nagao

first: Kazuaki

last: Nishimura

first: Yasushi

last: Nishii


title: Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [ChIP-Seq]

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

summary: Currently, the epigenetic mechanisms governing the osteoclast differentiation process remains poorly understood. To investigate the combinatorial activity of TFs, cis-regulatory elements, and the enhancer landscape that establish and maintain osteoclast transcriptional identity, we profiled histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and PU.1 and IRF8 binding by ChIP-seq. RNA-seq data from sorted Ly6Chi, Ly6Cint, and Ly6C– cells were overlaid with ChIP-seq data to identify epigenetic changes specific to each subset and genotype. Our data suggest that the Ly6Chi inflammatory monocytes and Ly6Cint cells are transcriptionally and epigenetically programmed to differentiate in mature osteoclasts when compared to Ly6C– anti-inflammatory monocytes. A combinatorial activity of TFs and cis-regulatory elements in the vicinity of several osteoclast-specific genes are responsible for establishing and maintaining osteoclast identity in these subsets. In Irf8 cKO mice, several promoters and enhancers established during the progenitor stage may be critical for initiating early lineage commitment and priming monocyte subsets to differentiate into robust osteoclasts.

overall_design: ChIP-seq analysis of epigenetic changes in BMMs stimulated with MCSF (day 0) and OCs stimulated with MCSF plus RANKL (day 4). We performed ChIP-seq for H3K4me1, H3K4me3, H3K27ac, H3K27me3, and PU.1 in BMMs and OCs. Both male and female mice and cells obtained from both genders were analyzed in this study.

first: Thumbigere-Math

last: Vivek

first: Shetty

last: Amol

first: Das

last: Amitabh

first: Brooks

last: Stephen

first: Dell'Orso

last: Stefania


title: Human G-MDSCs are Neutrophils at Distinct Maturation Stages that Promote Tumor Growth and Immune Cell Exclusion in Breast Cancer

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

summary: Myeloid-derived suppressor cells (MDSC) are known to contribute to immune evasion in cancer. However, the function of the human granulocytic (G)-MDSC subset during tumor progression is largely unknown, and there are no established markers for their identification in human tumor specimens. Using gene expression profiling, mass cytometry and tumor microarrays, we here demonstrate that human G-MDSCs occur as neutrophils at distinct maturation stages, with a disease-specific profile. G-MDSCs derived from patients with metastatic breast cancer (MBC) and malignant melanoma display a unique immature neutrophil profile, that is more similar to healthy donor neutrophils than to G-MDSCs from sepsis patients. Finally, we show that primary G-MDSCs from MBC patients co-transplanted with breast cancer cells, promote tumor growth and affect vessel formation, leading to myeloid immune cell exclusion. Our findings reveal a role for human G-MDSC in tumor progression and have clinical implications also for targeted immunotherapy.

overall_design: Triplicate blood sample cells, per condition, were FACS sorted, RNA was extracted and hybridized to Affymetrix 1.0 ST arrays.

first: Karin

last: Leandersson

first: Meliha

last: Mehmeti-Ajradini


title: Transcriptome of thyroid cancer (TC) cells after coculture with TC-induced macrophages

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: RNA sequencing data of TPC-1  cells (TC cell line) after co-culture with TC-induced macrophages. We used an in vitro co-culture model of a human TC cell line, TPC1 (RET/PTC rearrangement), and human primary monocytes.

overall_design: Co-incubation in trans-well system between TPC1 cell lines and human primary macrophages, which were stimulated with medium (control, "none") or a TLR-4 ligand ("LPS").

first: Yvette

last: Sloot

first: Katrin

last: Rabold

first: Bas

last: Heinhuis

first: Thomas

last: Ulas

first: Kristian

last: Händler

first: Dennis

last: de Graaf

first: Mihai

last: Netea

first: Johannes

last: Smit

first: Leo

middle: A

last: Joosten

first: Romana

middle: T

last: Netea-Maier


title: Maternal high-fat-diet alters lactation-specific miRNA expression and programs the DNA methylome in female offspring

city: Toronto

first: Patrick

middle: O

last: McGowan

state: ON

address: 1265, Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto

type: Methylation profiling by high throughput sequencing

summary: Reduced representation bisulfite sequencing was used to explore differentially methylated regions and sites within the amygdala of female rat offspring during earlylife and adulthood, in response to maternal high fat diet exposure. DMRs shared across early life and adulthood included pathways involved in neurodevelopment and genes regulating the DNMT machinery and protein function. To our knowledge, this is the first study to identify persistent genome-wide DNA methylation modifications associated with mHFD exposure in offspring from early life to adulthood.

overall_design: We measured differences in 5mC levels across aintergenic, promoter, and genebody at postnatal day 7 and postnatal day 90 in the amygdala of female offspring. N=4 per treatment per age

first: Sameera

last: Abuaish

first: Sanoji

last: Wijenayake

first: Wilfred

last: de Vega


title: DNMT3.1 controls life span and trade-off between growth and fecundity under the starved condition in the cladoceran crustacean Daphnia magna

first: Hajime

last: Watanabe

address: Yamadaoka 2-1

institute: Osaka University

summary:
Purpose: We aim to clarify the physiological function of DNMT3.1 in extending longevity and energy allocation to reproduction under starved condition. In this study, we introduced a mutation into DNMT3.1 and analyzed the transcriptional changes, corresponded to phenotypic changes, of the mutant compared to wild type under starved condition.
Methods: Whole body mRNA profiles of 12 days old daphnids from wild type (WT) and mutant (MT) cultured in nutrient rich (HF) and starved (LF) conditions were proceeded by using Illumina sequencing (provided by Novogene). Data analysis was performed by using CLC Genomics Workbench 12 (Qiagen) software.
Results: In nutrient rich and starved conditions, numbers of differentially expressed genes were 220 and 2770 respectively, between wild type and mutant.
Conclusions: Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to larger difference of transcriptome between the mutant and wild type. This findind reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog.

overall_design: mRNA profile of 3 groups: starved wild type (WTLF),  nutrient rich mutant (MTHF) and starved mutant (MTLF) were screened from 12 days old Daphnia magna in triplicates (total 9 samples). For comparision in nutrient rich and starved condition, 9 libraries of the above samples combined with 3 libraries of the triplicates from wild type in nutrient rich condition deposited in NCBI’s Gene Expression Omnibus (GEO) through the accession number: GSE150821.

first: Nhan

middle: D

last: Nguyen

first: Tomoaki

last: Matsuura

first: Yasuhiko

last: Kato


title: Repolarization of HSC attenuates HSCs failure in Shwachman-Diamond syndrome

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: Shwachman-Diamond syndrome (SDS) is a bone marrow failure (BMF) syndrome associated with an increased risk of myelodysplasia and leukemia. The molecular mechanisms of SDS are not fully understood. We report that primitive hematopoietic cells from SDS patients present with a reduced activity of the small Rho GTPase Cdc42 and concomitantly a reduced frequency of HSCs polar for polarity proteins. The level of apolarity of SDS HSCs correlated with the magnitude of HSC depletion in SDS patients. Importantly, exogenously provided Wnt5a or GDF11 that elevates the activity of Cdc42 restored polarity in SDS HSCs and increased the number of HSCs in SDS patient samples in surrogate ex vivo assays. Single cell level RNA-Seq analyses of SDS HSCs and daughter cells demonstrated that SDS-HSC treated with GDF11 are transcriptionally more similar to control than to SDS-HSCs. Treatment with GDF11 reverted pathways in SDS HSCs associated with rRNA processing and ribosome function, but also viral infection and immune function, p53-dependent DNA damage, spindle checkpoints, and metabolism, further implying a role of these pathways in HSC failure in SDS. Our data suggest that HSC failure in SDS is driven at least in part by low Cdc42 activity in SDS HSCs. Our data thus identify novel rationale approaches to attenuate HSCs failure in SDS.

overall_design: Single-cell RNA-seq of mother and daughter human HSCs (Control, SDS, and SDS-HSC treated with GDF11)

first: Hartmut

last: Geiger


title: Synergistic action of the Arabidopsis spliceosome components PRP39 and SmD1 in promoting post-transcriptional transgene silencing

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

institute: CNRS

summary:
The goals of this study is understand the role of spliceosome component PRP39 and SmD1 in post transcriptional transgene silencing
Conclusions: MiEFF18 overexpression modifies the expression of genes important for the ontogenesis of giant cells, notably those involved in microtubule cytoskeleton reorganization and cell cycle regulation, strongly suggesting that MiEFF18-mediated SmD1 inactivation in plants leads to a loss of susceptibility to root-knot nematodes.

overall_design: mRNA profiles of PolyA RNA from  whole 14-day-old Col-0, prp39a-3 (SAIL_1249A03), smd1b-3 (Elvirat-Matelot et al., 2016) and Col-0 plants grown on 1/2MS medium. Three independent biological replicates were produced per genotype. For each biological repetition and each point.

first: Hervé

last: Vaucheret


title: RNA sequencing analysis of gene expression profiles of OLFM4-RET fusion in HEK293 cells

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The purpose of this assay is to determine the gene expression profiles induced by OLFM4-RET fusion, therefore further understanding the molecular mechanim of oncognesis by OLFM4-RET

overall_design: HEK293 cells were transfected with empty vector, RET or OLFM4-RET expression plasmid. After 48h, the total RNA were extracted for RNA sequencing analysis

first: Wenli

last: Liu


title: Reduced Representational Bisulfite Sequencing of R1 and Dnmt1 Tet/Tet mouse embryonic stem cell lines

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Telangana

address: shameerpet, Jawaharnagar

institute: Birla Institute of Technology, Pilan- Hyderabad Campus

summary: We generated RRBS data to enable a comparative DNA methylation analysis of Dnmt1 Tet/Tet, a mouse embyonic stem cell line (ESC) that overexpresses DNMT1 and the WT R1 ESCs and their neuronal derivatives. The optimized data analysis workflows provides a framework for comparative investigations of methylation profiles. This platform offers a comprehensive and more accurate quantitative and qualitative evaluation of methylated cytosines in ESCs and neurons. We expect that RRBS-based methylome analysis permits to understand the epigenetic basis of abnormal neurogenesis.

overall_design: Study of the methylation profiles of R1 and Dnmt1 Tet/Tet ESCs and their neuronal derivatives.

middle: N

first: Sonal

last: Saxena

first: Sumana

last: Choudhury


title: Next generation sequencing facilitates quantitative analysis of wild type and overexpression of LbDREB6 transgenic line transcriptomes

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary:
Purpose:  we performed comparative RNA-seq analyses to identify differentially expressed genes between overexpression of LbDREB6 transgenic lines and Wild Type expose to pathogen stress

Methods:After 2 days of inoculation with the pathogen, leaves of WT, OE14 and OE18 plants were harvested and frozen in liquid nitrogen immediately for RNA extraction. For each sample, ~20 μg total RNA of stem tip with 2 pieces of leaves was sent to Annoroad Gene Technology Co., Ltd, Beijing, China for high throughout Illumina HiSeq 4000 sequencing (Illumina, San Diego, CA, USA).

Results: To determine the possible pathways of LbDREB6 in pathogen defense, we conduct the transcriptomotic sequencing. After sequence, we achieved 53.20 Gb clean reads (18.2–24.7 million per library, Q30 ≥95.02%). About 68.3%-70.42% clean reads per library could be mapped to the Populus trichocarpa genome (see Table S2). The quality of the assembled transcriptome is good enough for functional annotation and further analysis compared with WT.

Conclusions: Our study represents the detailed analysis of pathogen response transcriptomes , with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that next generation sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: With pathogen stress, stem tip mRNA profiles of wild type (WT) and  transgenic Populus ussuriensis  were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jingli

last: Yang

first: Haizhen

last: Zhang


title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding transcripts in adult mouse somatic (non-reproductive) cells (Lexogen)

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

institute: Université de Montréal

summary: In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class (RNA-Seq)   of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes,   which include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes.  However, the impact   of targeted mutations of these genes on the functions of adult non-reproductive somatic cells   is still unknown due to lack of experimental evidence.  We thus compared adult male mice   carrying a gene trap within their Uty gene (UtyGT) to wild-type (WT) isogenic controls, and   performed deep sequencing of RNA and genome-wide profiling of chromatin in extracts   from either cardiac tissue, cardiomyocyte-specific nuclei and purified cardiomyocytes.    The impact of UtyGT on gene transcription was mostly limited to its effects on genes   surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs)   contained within their introns, Eif2s3y, as well as on the autosomal Malat1 lncRNA.    Notwithstanding, UtyGT also caused coordinate changes in the abundance of   hundreds of mRNA transcripts related to particular cell functions, including   RNA processing and translation.  The results altogether indicated that tightly   co-regulated chrY genes had nonetheless more widespread effects on the   autosomal transcriptome in adult somatic cells, most likely due to mechanisms   other than just transcriptional regulation of protein-coding genes.

overall_design: Frozen left ventricles were obtained from either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th   intron of the Uty gene) or their wild-type counterparts from the isogenic strain C57BL/6.Y<129P2> adult mice.  For each group, samples were obtained from 7 different mice.


title: The ubiquitin ligase TRIM37 controls cancer-specific vulnerability to PLK4 inhibition

city: San Diego

first: Karen

last: Oegema

state: California

address: 9500 Gilman Drive, CMM East

institute: UCSD

summary: We show synthetic lethality between PLK4 inhibition-mediated centrosome loss and the overexpression of the ubiquitin ligase TRIM37 in cancer cells with amplification of Chr17q

overall_design: Compare the effect of differential TRIM37 expression on global gene expression in untransformed hTERT RPE1 and neuroblastoma CHP-134 cells.

first: Franz

last: Meitinger

first: Arshad

last: Desai


title: ScRNA-Seq of Fresh Mouse Glioblastoma Cells and Mouse Glioblastoma Cell line

city: Zhejiang

first: Chong

address: NO.866 of Yuhang Tong Road

institute: Medical College of Zhejiang University

summary:
Methods: In our study, we added tdTomato gene inherent in our mouse model gene list to obtain the final matrics by modifying the reference genome. Finally, we separated the matrix by the cell type judgment result obtained by the cellranger. Cells with high quality were selected with the following criteria: (1) Genes detected in < 3 cells were removed; (2) Cells with unique molecular identified (UMI) ≤ 150 or ≥ 4500 were removed. (3) Cells with ≥ 20% mitochondrial counts were removed.
Results:  scRNA-seq for the cells dissociated from a CKO_NG2-CreER tumor (Figure 1B) identified 12 distinct clusters, visualized using t-distributed stochastic neighbor embedding (t-SNE). Referring to known cellular markers in the brain 24, we could identify the cell identities/states of 10 clusters, including two for OPCs (C5 and C7), two for microglia (C1 and C4), one each for astrocytes (C2), endothelial cells (C3), oligodendrocytes (C6), pericytes (C9), neurons (C11) and T/dendritic cells (C12). Projection of lineage marker tdTomato onto the t-SNE map further revealed that 4 clusters (C2, C6, C7 and C9) were likely derived from NG2-CreER labeled cells and/or their progeny
Conclusions: scRNA-seq suggests that tumor OPCs in adult OPC-originated gliomas may function as TICs given their strong stemness feature.

overall_design: Glioma cells from genetic mouse model were generated by ScRNA sequencing,single cells were processed through the 10X Chromium 5’ (for the primary tumor sample) or 3’ (for all cell lines) Single Cell Platform using the Chromium™ Single Cell 5’ or 3’ Reagent Kits v3 , Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol (Illumina).


title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding transcripts in adult mouse somatic (non-reproductive) cells

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

overall_design: Refer to individual Series


title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding transcripts in adult mouse somatic (non-reproductive) cells (RNA-Seq)

summary: In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class   of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes,   which include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes.  However, the impact   of targeted mutations of these genes on the functions of adult non-reproductive somatic cells   is still unknown due to lack of experimental evidence.  We thus compared adult male mice   carrying a gene trap within their Uty gene (UtyGT) to wild-type (WT) isogenic controls, and   performed deep sequencing of RNA and genome-wide profiling of chromatin in extracts   from either cardiac tissue, cardiomyocyte-specific nuclei and purified cardiomyocytes.    The impact of UtyGT on gene transcription was mostly limited to its effects on genes   surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs)   contained within their introns, Eif2s3y, as well as on the autosomal Malat1 lncRNA.    Notwithstanding, UtyGT also caused coordinate changes in the abundance of   hundreds of mRNA transcripts related to particular cell functions, including   RNA processing and translation.  The results altogether indicated that tightly   co-regulated chrY genes had nonetheless more widespread effects on the   autosomal transcriptome in adult somatic cells, most likely due to mechanisms   other than just transcriptional regulation of protein-coding genes.

overall_design: Adult cardiomyocytes were obtained from ventricles from either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th intron of the Uty gene) or their wild-type counterparts from the isogenic strain C57BL/6.Y<129P2> adult mice.  The hearts were digested by retrograde perfusion of a solution of collagenase type 2 (Worthington, Lakewood, NJ) in calcium-free solutions, followed by gravity sedimentation within 5% bovine serum albumin (BSA) solutions supplemented in a step-wise fashion with increasing CaCl2 concentrations.  After isolation, the cells were plated on laminin-coated dishes, and used 4 hours after plating for RNA isolation.  For each strain, the procedure was repeated three times to obtain triplicate samples for the RNA-Seq analysis.


title: Impact of a Uty gene trap on the regulation of genes and the abundance of corresponding   transcripts in adult mouse somatic (non-reproductive) cells (ATAC-Seq)

overall_design: Frozen left ventricles were obtained from either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th intron of the Uty gene) or their wild-type counterparts from the isogenic strain C57BL/6.Y<129P2> adult mice.  For each strain, the procedure was repeated on three different days in order to obtain triplicate samples for the ATAC-Seq analysis.