title: ChIP-Seq on ESR1 in human liver tissue and hepatocytes

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

summary: To improve our understanding of transcriptional regulation by ESR1 in the liver, chromatin immunoprecipitation with an antibody against ESR1 followed by high-throughput sequencing (ESR1 ChIP-Seq) was conducted in human liver samples and in hepatocytes with or without 17beta-estradiol (E2) treatment. By comparing treated and untreated hepatocytes, we identified both ligand-dependent and ligand-independent binding sites throughout the genome. Ligand-dependent binding sites include ChIP-Seq peaks that either appeared (gained peaks) or disappeared (lost peaks) upon estrogen treatment. Gained peaks occurred at the Estrogen Response Element (ERE) whereas the sites for lost peaks were instead coenriched with a variety of transcription factors. In both cases, ESR1 binding primarily occurred in enhancer regions and was associated with general liver functions, such as lipid/energy metabolism. In contrast, we also observed a subset of ESR1 sites that were maintained regardless of estrogen treatment. These ligand-independent sites mostly occurred at promoter regions and were highly enriched with several cofactor motifs.

overall_design: ESR1 chromatin binding was examined in human liver and hepatocytes with and without estradiol treatment

first: Joseph

last: Collins


title: Lamin B1 dependent transcriptional control in neural progenitor cells

status: Public on Feb 10 2021

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases

type: Expression profiling by high throughput sequencing

summary: Through knocking out Lamin B1, we found that lamin B1 regulets hundreds of genes in neural progenitor cells, which underlie differentiation of neural protenitor cells

overall_design: Knockout of floxed lamin B1 gene in neural progenitors using LV-pSox2-Cre

first: Sara

middle: B

last: Linker

first: Fred

middle: H

last: Gage


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (ChIPseq_TE_W11)

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
MYC family proteins are oncogenic transcription factors that can globally affect the function of RNA Polymerase II (RNAPII). The ability of MYC proteins to promote transcription elongation depends on their ubiquitination, but the underlying mechanism and its biological relevance are unknown. Here we show that MYC and the Polymerase II associated factor, PAF1c, interact directly and their function is mutually dependent, since the specific binding of MYC to active promoters depends on PAF1c and, conversely, PAF1c is required for MYC-dependent pause release.
Upon binding, PAF1c is rapidly transferred from MYC onto RNAPII and this transfer is driven by the HUWE1 ubiquitin ligase. Both MYC and HUWE1 globally control histone H2B ubiquitylation, which promotes transcriptional elongation and alters chromatin structure for double-strand break repair. Consistently, MYC suppresses the accumulation of double-strand breaks at promoters in response to topoisomerase II inhibition.
While depletion of PAF1c has only minor effects on MYC-dependent gene expression, MYC induces rampant transcription-dependent DNA damage in PAF1c-depleted cells. We propose that the HUWE1-dependent transfer of PAF1c from MYC onto RNAPII is critical for absorbing the topological stress accompanied with deregulated and oncogenic transcription.

overall_design: U2OS cells which stably express MYC TetOn system (Walz et al, 2014) were infected with pGIPZ shCTR9 or shCDC73 for 24 h, the infection medium was diluted 1:2 and incubated for 24 h. Cells were split In "1:3 and selectedwith puromycin (0.2 ug/ml) for 24 h. Medium was changed and cells were incubated for 24 h without MYC induction.

first: Theresa

last: Endres

first: Daniel

last: Solvie


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (ChIPseq_TE_RRL)

overall_design: U2OS cells which stably express pRRL empty (ctl) or pRRL MYC (MYC high) as well as either pInducer10 shCTR9 or pInducer10 shCDC73 were treated for 48 h either with EtOH or Dox (1ug/ml) to induce the knockdown of either CTR9 or CDC73.


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (ChIPseq_TE_MycER)

overall_design: U2OS cells which stably express a MYC-ER system. Cells were either treated with ETOH OR 4-OHT (200 nM) for 10 min.


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (BLISS)

type: Non-coding RNA profiling by high throughput sequencing

overall_design: U2OS cells expressing doxycycline-inducible MYC and shRNA targeting CTR9 or control. Treated with/without doxycycline for 24 hrs and with or without Etoposide for 3 hrs


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (ChIPseq_DS)

overall_design: U2OS cells expressing doxycycline-inducible MYC. Treated with/without doxycycline for 24 hrs and with or without BI8626 for 4 hrs


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (ChIPseq_TE_MycAID)

overall_design: K562 (2 clones: C3 and D10) which express a MYC-AID knock-in allel and a osTIR delivery vector EBFP2 (pRRL-SFFV-Tir1-3xMYC-tag-T2A-EBFP2). Where indicated, indole-3-acetic acid (IAA: 100 uM) or DMSO was added for 30 min


title: RNA-seq analysis of scat (CbyJ.Cby-Rasa3scat/Llp) and matched control mice in bone marrow and spleen

city: Bar Harbor

first: Joel

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

country: USA

institute: MDI Biological Laboratory

summary: RASA3 (RAS p21 protein activator 3), also called GAPIII or IP4BP (inositol 1,3,4,5-tetrakisphosphate, IP4, binding protein), is a member of the GAP1 family of RAS-GTPase-activating proteins (GAPs). The RAS superfamily of small GTPases includes the subfamily RAP. Small GTPases act as molecular switches, cycling between active GTP-bound and inactive GDP-bound forms. They are activated by guanine nucleotide exchange factors (GEFs), which stimulate GTP loading, and inactivated by GAPs, which accelerate GTP hydrolysis.  A major role of RASA3 in hematopoiesis was first identified upon positional cloning of the co-isogenic autosomal recessive mouse mutation, scat (severe combined anemia and thrombocytopenia. The scat phenotype, in addition to severe anemia and thrombocytopenia, includes significant leukopenia as well. The scat disease progresses episodically, with periods of severe crisis interspersed with one or two periods of remission. The RASA3 mutation (G125V) in scat causes mislocalization of RASA3 to the cytosol, abrogating RASA3 GAP activity and increasing active RAS levels in scat erythroid cells.  As part of a broader study to analyze the role of RASA3 in hematopoiesis, we performed RNAseq studies to generate hypotheses regarding the progression of the scat disease from periods of crisis to partial remission.

overall_design: We performed RNAseq using 3-5 biological replicates of whole spleen and bone marrow and flow-sorted HSPC populations from scat homozygotes mice in crisis and their WT littermates. Furthermore, as analysis of transcriptome changes occurring upon partial recovery in scat may suggest targets for disease therapy, we also compared the same tissue/cell populations from scat crisis (cr) and scat partial remission (pr) mice. Mice were classified as pr based on erythroid parameters intermediate to WT and cr with the exception of the reticulocyte percentage and spleen weight, which are expected to remain high during recovery from anemia. Flow-sorted populations obtained were megakaryocyte-erythroid progenitors (MEP) and so-called “stem and myeloid progenitors” (SMP). Because Sca1 (Ly6a) is expressed at very low levels in BALB mice, HSCs cannot be separated reliably from common myeloid progenitors. Therefore, the Lin-Sca-Kit+CD34+, CD16_32lo SMP population was used for these studies.

first: Raymond

middle: F

last: Robledo

first: Steven

middle: L

last: Ciciotte

first: Yue

last: Zhao

first: Amy

last: Lambert

first: Babette

last: Gwynn

first: Nathaniel

middle: J

last: Maki

first: Lionel

last: Blanc

first: Luanne

last: Peters


title: Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression, and drug response

city: Oxford

first: Ping

last: Zhang

address: Roosevelt Drive

department: Ludwig Institute for Cancer Research

country: United Kingdom

institute: University of Oxford

summary: Insights into oncogenesis derived from cancer susceptibility loci (single nucleotide polymorphisms, SNP) hold the potential to facilitate better cancer management and treatment through precision oncology. However, therapeutic insights have thus far been limited by our current lack of understanding regarding both interactions of these loci with somatic cancer driver mutations and their influence on tumorigenesis. For example, while both germline and somatic genetic variation to the p53 tumor suppressor pathway are known to promote tumorigenesis, little is known about the extent to which such variants cooperate to alter pathway activity. Here we hypothesize that cancer risk-associated germline variants interact with somatic TP53 mutational status to modify cancer risk, progression, and response to therapy. Focusing on a cancer risk SNP (rs78378222) with a well-documented ability to directly influence p53 activity as well as integration of germline datasets relating to cancer susceptibility with tumor data capturing somatically-acquired genetic variation provided supportive evidence for this hypothesis. Integration of germline and somatic genetic data enabled identification of a novel entry point for therapeutic manipulation of p53 activities. A cluster of cancer risk SNPs resulted in increased expression of pro-survival p53 target gene KITLG and attenuation of p53-mediated responses to genotoxic therapies, which were reversed by pharmacological inhibition of the pro-survival c-KIT signal. Together, our results offer evidence of how cancer susceptibility SNPs can interact with cancer driver genes to affect cancer progression and identify novel combinatorial therapies.

overall_design: mRNA profiles of HAP1-A-allele, HAP1-C-allele-#1 and HAP1-C-allele-#2 were generated by 3' RNA-seq, in triplicate.

first: Isaac

last: Kitchen-Smith

first: Gareth

last: Bond


title: Antibody-neutralizable major early driver of Alzheimer’s disease and vascular dementia

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Alzheimer’s disease (AD) and vascular dementia (VaD) are the two most common forms of dementia, neither of which can be effectively treated. There is growing evidence on vascular contributions to cognitive impairment and dementia such as AD, but their pathogenic molecular links are not defined yet. Notably, neurofibrillary tangles made of hyperphosphorylated tau (P-tau) are a hallmark lesion of AD, but are not found in VaD. Although brain ischemia induces some tau changes and tau knockout reduces stroke-induced acute brain damage, little is known about the role of tau in mediating progression from vascular insufficiency to later development of VaD. Cis P-tau is a pre-tangle pathology in AD and an early driver of neurodegeneration resulting from brain injury, but its role in AD treatment or in VaD is unknown. Here we identify cis P-tau as an antibody-neutralizable major common early driver of AD and VaD. We show that cis P-tau elimination using cis antibody not only prevents, but also treats AD-like neurodegeneration and memory loss in a hTau mouse model of AD. Purified cis P-tau causes and spreads neurodegeneration with behavioral changes when injected into wild-type mouse brains, but is prevented by cis antibody. Surprisingly, we also find robust cis P-tau with no evidence of tau tangles in human VaD brains and a mouse model of chronic cerebral hypoperfusion that mimics key aspects of clinical VaD. Cis mAb treatment of hypoperfusive mice for 1 or 6 months blocks VaD-like neuropathological and functional outcomes. Single-cell transcriptomic profiling reveals that cerebral hypoperfusion induces numerous global changes in diverse brain cells including those of human AD brains. Remarkably, ~90% of these global changes are fully recovered with cis antibody, correlating with tau expression in cells. Thus, cis P-tau is a major common early driver of AD and VaD, and cis antibody has a potential role in the early detection, prevention and treatment of these devastating diseases.

overall_design:
single cell RNA-seq from brain cortex treated with sham, BCAS + IgG or  BCAS + Cis Ptau mAb; BioProject PRJNA521781; SRP185522

BCAS: bilateral common carotid artery stenosis. This model involves the bilateral placement of permanent external microcoils (0.18 mm diameter) around the common carotid arteries to reduce parenchymal cerebral blood flow by ~50% especially in the subcortical brain region, although cerebral blood flow recovers with time notably to the cortical surficial region. This model of prolonged cerebral hypoperfusion is commonly used to mimic key aspects of clinical VaD including chronic cerebral hypoperfusion, white matter changes and working memory deficits.

first: Kun

middle: P

last: Lu


title: Expression data of the livers in mouse with iso-α-acids intake

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

summary:
Scope: Alcoholic liver disease (ALD) is a major cause of chronic liver disease and is induced by alcohol consumption. Acetaldehyde produced by alcohol metabolism enhances the fibrosis of the liver through hepatic stellate cells. Additionally, alcohol administration causes the accumulation of reactive oxygen species (ROS), which induce hepatocyte-injury-mediated lipid peroxidation. The purpose of this study was to investigate the protective effects of iso-α-acids against alcoholic liver injury in hepatocytes in mice.
Methods and results: C57BL/6N mice were fed diets containing isomerized hop extract, which mainly consists of iso-α-acids. After 7 days of feeding, acetaldehyde was administered by a single intraperitoneal injection. The acetaldehyde-induced increases in serum AST and ALT levels were suppressed by iso-α-acids intake. Hepatic gene expression analyses showed the upregulation of the glutathione-S-transferase, alcohol dehydrogenase and aldehyde dehydrogenase genes. In vitro, iso-α-acids induced the nuclear translocation of nuclear factor erythroid 2-like 2 (Nfe2l2; Nrf2), a master regulator of antioxidant and detoxifying systems, and upregulated the enzymatic activities of glutathione-S-transferase and aldehyde dehydrogenase. Conclusions: These results suggest that iso-α-acids intake prevents alcoholic liver disease injury by reducing oxidative stress via the Nrf2-mediated pathway.

overall_design: Eight-week-old male C57BL/6NCrSlc mice were purchased from Japan SLC (Shizuoka, Japan) and were housed in controlled temperature (24±1°C), humidity (50-70%), and light (12 h light-dark cycle) conditions. They were fed the AIN-93G diet (Oriental Yeast, Tokyo, Japan) for a week and then were divided into two groups based on similar average body weight. The control diet group (n = 10) was fed the AIN-93G diet, and the iso-α-acids diet group (n = 10) was fed the AIN-93G diet containing iso-α-acids (0.5%, w/w). Mice in the control group were pair-fed the control diet to the ad libitum intake of the iso-α-acid group for a week. After a week feeding period, animals were treated with an intraperitoneal (i.p.) injection of acetaldehyde (200 mg/kg). Tail vein blood samples were collected at 1, 2, and 5 h after the acetaldehyde injection. Liver samples were collected after blood sampling under deep anesthesia. The protocols for the animal experiments were approved by the Animal Use Committee of Sapporo Holdings Ltd., Research and Development Division. DNA microarray analysis was performed on liver samples from a total of ten mice (five mice each from the iso-α-acid and control diet groups) by choosing average individuals from each group on the basis of their serum enzyme values.

first: Takahito

last: Takase

first: Tsudoi

last: Toyoda

first: Naoyuki

last: Kobayashi

first: Takashi

last: Inoue

first: Tomoko

last: Ishijima

first: Youichi

last: Tsuchiya


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters

first: Martin

last: Eilers

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

overall_design: Refer to individual Series


title: Multiplex CRISPR/Cas9-Based Genome Editing of Mouse Hematopoietic Stem Cells Recapitulates Acute Erythroid Leukemia and Identifies Therapeutic Targets [RNA-Seq]

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary: Acute erythroid leukemia (AEL) is a high-risk leukemia with a distinct mutational spectrum. Here, we examined the cooperativity of loss of function alterations in leukemogenesis and tested the therapeutic tractability of each model of AEL. Using CRISPR/Cas9 genome editing, we generated six pools of lentiviral vectors with different combinations of guide RNAs and transduced Cas9-eGFP-mouse mouse hematopoietic stem and progenitor cells (HSPCs) that were used in transplant assays. Induced tumors were characterized by phenotype, genomic/epigenomic analysis and tested for sensitivity to 222 therapeutic agents. Tumor genotype determined tumor phenotype with Bcor and Tp53 driving erythroid leukemogenesis.  Tumors showed acquisition of additional somatic mutations during serial passaging and by transcriptomic analysis AEL models had overexpression of transcription factors required for differentiation of megakaryocyte-erythroid progenitors and recapitulated human AEL.  Dnmt3a-mutated models exhibited global hypomethylation, but hypermethylation when co-occurred with Tet2 mutations.   Drug response was associated with genotype. Tp53 wild-type but Dnmt3a/Tet2 double mutant cells were the most chemo-sensitive models. ViceversaTp53-mutated AEL subtypes were chemo-resistant to several conventional chemotherapeutics but highly sensitivity to PARP inhibitors, including talazoparib. Sensitivity to talazoparib was confirmed in vivo when combined with decitabine. In conclusion, combinations of recurrently mutated genes are critical determinants of leukemia phenotype, with central roles of Tp53 and Bcor mutations in driving the erythroid leukemogenesis. Using these models as preclinical tools, we have shown the potential for bromodomain and PARP inhibition as new therapeutic strategies in AEL.

overall_design: RNAseq on mouse AEL models.

first: Iacobucci

last: Ilaria

first: Qu

last: Chunxu

first: Mullighan

last: Charles


title: Quantitative Analysis of lncRNAs expression profiles between TB patients and healthy controls

city: GUANG ZHOU

first: FANG

last: YANG

state: CHINA

address: 74#，ZHONG SHAN 2nd Road

country: China

institute: SYSU

summary: To evaluate whether TB infections are associated with any lncRNA signatures in humans, we therefore used human lncRNAs microarray and hierarchical clustering analyses to compare lncRNAs expression in active TB patients and healthy controls. From 15,683 denoted lncRNAs, 5076 lncRNAs were identified to be differentially expressed (TB/HC > 2 or TB/HC< 0.5) in peripheral blood mononuclear cells (PBMCs) between TB and healthy subjects.

overall_design: Microarray were performed with RNA of PBMCs derived from six individuals with active TB disease and healthy controls, respectively

first: Gucheng

last: Zeng


title: Differential Gene Expression of Human Mural Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of BDE-153 Quantified from Follicular Fluid [BDE-153 MURAL]

city: Montreal

first: Thomas

middle: Constantine

last: Nardelli

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: This study assessed the global gene-level expression of human mural granulosa cells.

overall_design: BDE-153 MURAL

first: Nardelli

middle: C

last: Thomas

first: Lefèvre

last: Pavine

first: Monnier

last: Patricia

first: Son

last: Weon-Toung

first: Sadler

middle: R

last: Amy

first: Rawn

last: Dorothea

first: Goodyer

last: Cindy

first: Robaire

last: Bernard

first: Hales

last: Barbara


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters (RNAseq)

first: Martin

last: Eilers

overall_design: U2OS cells which stably express MYC TetOn system (Walz et al, 2014) were infected with pGIPZ shCTR9 or shCDC73 for 24 h, the infection medium was diluted 1:2 and incubated for 24 h. Cells were split 1:3 and selected with puromycin (0.2 ug/ml) for 24 h. Medium was changed and cells were either treated with doxycicline (1ug/ml) or ethanol for 24 h.

first: Theresa

last: Endres

first: Daniel

last: Solvie


title: Differential Gene Expression of Human Cumulus Granulosa and Mural Granulosa Cells in ICSI Patients


title: Differential Gene Expression of Human Cumulus Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of BDE-47 Quantified from Follicular Fluid [BDE-47 CUMULUS]

summary: This study assessed the global gene-level expression of human cumulus granulosa cells.

overall_design: BDE-47 CUMULUS


title: Differential Gene Expression of Human Mural Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of a Mixture of 10 PBDE Congeners Quantified in Follicular Fluid [10-PBDE_MURAL]


title: Differential Gene Expression of Human Cumulus Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of BDE-153 Quantified from Follicular Fluid [BDE-153 CUMULUS]

overall_design: BDE-153 CUMULUS


title: Differential Gene Expression of Human Mural Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of BDE-47 Quantified from Follicular Fluid  [BDE-47 MURAL]

overall_design: BDE-47 MURAL


title: Hoxa13 overexpression drives chromosomal instability and liver tumorigenesis in mice

status: Public on Feb 09 2021

city: Basel

first: Salvatore

last: Piscuoglio

address: Schönbeinstrasse 40

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Background and aims: Class I Homeobox (HOX) genes are fundamental components of embryonic patterning and morphogenesis, also implicated in neoplastic transformations. Among them HOXA13, in particular, has been found to be the most overexpressed in HCC and to be associated with worse prognosis. However, no previous work has shown so far a direct causal effect between HOXA13 overexpression and liver tumorigenesis. In this study we aimed to prove the direct oncogenicity of HOXA13 in the liver and to unravel the molecular mechanisms of Hoxa13-induced liver tumorigenesis.    Approach and Results:  To unravel the oncogenic mechanism of HOXA13 in vivo, a transgenic mouse model of HOXA13 overexpression in the liver was generated using hydrodynamic tail vein injection coupled with a transposase system. The mice phenotype was followed over time, from 2 weeks up to 1-year post injection. RNA-sequencing was performed to monitor the transcriptomic changes over time. HOXA13-overexpression in the liver led to highly proliferative hepatocytes and correlated with the DNA damage marker yH2AX. 1-year post-injection 50% of the injected mice developed liver tumors of various histological grades and types. RNA-sequencing analysis performed on whole liver extracts of 2 weeks-old mice and tumors showed that the main pathway deregulated by HOXA13 overexpression was cell cycle, in particular G2/M transition and mitotic spindle assembly checkpoint. Additionally, HOXA13-overexpressing livers showed a transcriptomic signature of chromosomal Instability, suggesting a possible mechanism of tumorigenesis driven by genome instability.    Conclusions: Our study highlights the role of HOXA13 as a novel oncogenic driver in hepatocarcinogenesis and strongly suggests that its oncogenic properties are least partially mediated by induction of chromosomal instability.

overall_design: Hoxa13 ChIP from HepG2 and huh7 cells, with IgG and input controls. HA ChIP from the same cell lines with HA tagged Hoxa13

first: Gaia

last: Bianco

first: John

last: Gallon

first: Mairene

last: Coto-Llerena

first: Venkatesh

last: Kancherla

first: Stephanie

last: Taha-Mehlitz

first: Tracy

last: O'Connor

first: Ursula

last: Ehmer

first: Rupert

last: Oellinger

first: Hesam

last: Montazeri

first: Matthias

last: Matter

first: Gerhard

last: Christofori

first: Charlotte

middle: K

last: Ng

first: Mathias

last: Heikenwälder

first: Luigi

middle: M

last: Terracciano


title: Single cell transcriptional profiling of embryonic mouse nephrogenic zone

city: Los Angeles

first: Andrew

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: A single-cell RNA-Seq data set was generated using the 10x Genomic platform from E16.5 mice kidney nephrogenic zone cells.

overall_design: We isolated and digested embryonic kidneys at E16.5 following a published protocol (Brown et al., 2015). The resultant single cell suspension was passed through 10x Genomics Chromium v1 to produce a scRNA-Seq data set.

last: Ransick

first: Qiuyu

last: Guo


title: Targeted inhibition of two specific microRNAs in the brainstem prevents the development of hypertension through the cumulative effect of gene network changes

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico


title: Targeted inhibition of two specific microRNAs in the brainstem prevents the development of hypertension through the cumulative effect of gene network changes [Fig3]

summary: We here test the concept that disease states may result not from a single cause but from small changes in a network that are collectively significant. We recently showed that development of hypertension (HTN) in the spontaneously hypertensive rat (SHR) model of human essential hypertension is accompanied by changes in microRNA expression levels in the brainstem tracking the development of HTN 1,2. This led to the hypothesis that preventing the change in microRNA levels could prevent the development of HTN. We propose that hypertension emerges from a network that has been pushed out of a normotensive equilibrium into a compensatory, pathological state. We show that small perturbations in the gene regulatory networks in the brainstem by selectively blocking two microRNAs highlighted in our previous results, miR-135a and miR-376a, is sufficient to prevent development of hypertension in the SHR model with a 38% reduction in blood pressure after one week persisting to 29% reduction after two weeks with no change in blood pressure in WKY controls at either timepoint. This effect appears driven by only modest, yet sometimes significant, changes in the expression of rate-limiting genes including IL1a, IL1b, Agtr1a, and Dbh among others. Many of these genes are direct targets of these miRNAs, suggesting that the combination of genes that are targeted in the network is responsible for the effect. The demonstration that hypertension is an emergent property of an underlying regulatory network suggests that a new treatment paradigm altogether is needed.

overall_design: Combined assay of miRNA and mRNA of single neurons in the NTS of age-matched SHR and WKY rats (4-5 animals per group).

first: Jonathan

last: Gorky

first: Danielle

last: DeCicco

first: Sirisha

last: Achanta

first: James

last: Schwaber


title: Genes regulated by both of Ten-Eleven translocation 3 and Tumor necrosis factor α in Rheumatoid arthritis fibroblast-like synoviocytes

city: Kitakyushu

first: Akio

last: Kawabe

address: 1-1, Iseigaoka Yahata-nishi

institute: University of Occupational and Environmental Health, Japan

summary:
As DNA demethylation is a dynamic epigenetic regulation in pattern formation of DNA methylation, we reasoned that DNA demethylation facilitates Rheumatoid arthritis (RA) progression. To address this point, we picked up the DNA dioxygenase family members (Ten-Eleven translocation: TET1/2/3) as these enzymes conduct the prime process of DNA demethylaion.
Tumor necrosis factor α  (TNFα) , one of the pro-inflammatory cytokines, was found effective in up-regulation in TET3 level in the cultured fibroblast-like synoviocytes (FLS), and the stimulated FLS cells exhibited high cell mobility with gene induction of cell-migration related factors in a TET3-dependent manner. From our findings, we presume that DNA demethylation mediated TET3 facilitates RA progression and chronicity as an epigenetic regulation.

overall_design: To ask whether TET3 mediates the TNFα action in the gene expression program for the transformation of FLS, we used a gene microarray analysis to profile global gene regulation in the cultured RA FLS treated by TNFα, together with TET3 knockdown by small interfering RNA (siRNA).

first: Kazuhisa

last: Nakano


title: Differential Gene Expression of Human Cumulus Granulosa Cells in ICSI Patients Exposued to Low or High Environmental Levels of a Mixture of 10 PBDE Congeners Quantified from Follicular Fluid [10-PBDE_CUMULUS]

first: Thomas

last: Nardelli

first: Nardelli

last: C Thomas

first: Lefèvre

first: Monnier

last: Patricia

first: Son

last: Weon-Toung

first: Sadler

last: RAmy

first: Rawn

last: F.K Dorothea

first: Goodyer

last: Cindy

first: Robaire

last: Bernard

first: Hales

last: FBarbara


title: Targeted inhibition of two specific microRNAs in the brainstem prevents the development of hypertension through the cumulative effect of gene network changes [Fig2]

first: Rajanikanth

overall_design: Assay of 19 mRNA of NTS of age-matched SHR and WKY rats. 4-5 rats per group.


title: Multiplex CRISPR/Cas9-Based Genome Editing of Mouse Hematopoietic Stem Cells Recapitulates Acute Erythroid Leukemia and Identifies Therapeutic Targets

first: Chunxu

last: Qu

type: Methylation profiling by high throughput sequencing


title: Expression data of mRNA and circRNA from HPV16 positive cervical cancer tissues, HSIL tissues and normal cervical epithelial tissues

city: Taiyuan

first: Haixia

last: Luo

address: 382 Wuyi Road

institute: The Second Hospital of Shanxi Medical University

summary:
CircRNAs have been found to regulate mRNA expression levels and serve an important role in cervix carcinogenesis.
To explore the circRNA expression profiles during the development and progression of cervical cancer, we performed microarray analysis with total RNA in normal cervical epithelium(n=7), HPV16 positive high-grade squamous intraepithelial lesion (HSIL)(n=6), and HPV16 positive cervical squamous cell carcinoma tissues(n=7).

overall_design: In the study presented here, we designed to analyze the mRNA and circRNA expression in  normal cervical epithelium(n=7), HPV16 positive high-grade squamous intraepithelial lesion (HSIL)(n=6), and HPV16 positive cervical squamous cell carcinoma tissues(n=7).

first: Wei

last: Wang


title: RNA Sequencing Analysis of JFK-overexpressing and ING5-depleted HepG2 cells

city: Beijing

first: Lin

last: He

address: Xueyuan Road 38

institute: Peking University

summary: To explore the functional significance of JFK-mediated ING5 degradation, we performed genome-wide analysis of the transcriptome in hepatocytes that is regulated by the JFK-ING5 axis using RNA-based deep sequencing (RNA-seq). The data obtained from RNA-seq experiments were cross-analyzed with ChIP-seq data of ING5 from HepG2 cells.

overall_design: RNA-seq from HepG2 cells transfected with vector or JFK or treated with control or ING5 siRNAs

first: Ruorong

last: Yan

first: Xinhua

last: Liu


title: Genome-wide identification of transcriptional targets for ING5

summary: In this study, we performed chromatin immunoprecipitation-coupled massive parallel DNA sequencing (ChIP-seq) to analyze the genome-wide transcriptional profile of ING5 in hepatocytes. ChIP was performed first in HepG2 cells with antibodies against ING5. Following ChIP, ING5-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with HiSeq 2500. The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked human reference genome (GRCh37, hg19) using Bowtie2, and further analyzed by MACS (Model-based Analysis for ChIP-Seq).

overall_design: Examination of transcriptional targets for ING5 in HepG2 cells.


title: Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

institute: University of Nottingham

summary: we report single cell expression and methylation profiles of embryonic cells (from day 11 to 31) of pig embryo development.

overall_design: We obtained single-cell transcriptomes of 39 male and female pig PGCs from E14 and E31 embryos as well as 89 neighbouring somatic cells from those E14 embryos with the Smart-seq2 method. DNA methylomes of male and female pig gonadal PGCs and the neighbouring somatic cells from E35 embryos were obtained using PBAT-seq.

first: Ramiro

last: Alberio


title: Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation

city: Shanghai

first: Bing

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Inadequate sleep prevails in modern society and it impairs the circadian transcriptome. However, whether acute sleep deprivation has impact on the circadian rhythms is not clear. Here, we show that in mouse lung, a 10-hour acute sleep deprivation can alter the circadian expression of approximally 3,000 genes. We found that circadian rhythm disappears in genes related to metabolism and signaling pathways regulating protein phosphorylation after acute sleep deprivation, while the core circadian regulators do not change much in rhythmicity. Importantly, the strong positive correlation between mean expression and amplitude (E-A correlation) of cycling genes has been validated in both control and sleep deprivation conditions, supporting the energetic cost optimization model of circadian gene expression. Thus, we reveal that acute sleep deprivation leads to a profound change in the circadian gene transcription that influences the biological functions in lung.

overall_design: The animals in the control group were housed under 12 h: 12h light/dark cycle, while the animals in the acute sleep deprivation group (SD) were kept awake for 10 hours from 6 a.m. to 4 p.m. according to a sleep deprivation paradigm. After 10-hour sleep deprivation, we harvested the lung tissue at 6 time points with 4-hour intervals during the following 24 hours. Transcriptome analyses were performed by total RNA-sequencing (whole-transcriptome sequencing).

first: Yuntao

last: Lu

first: Ju

last: Huang


title: Multiple bleomycin exposed mouse lung epithelial type 2 cells

first: xiaoxi

last: lv

address: No Jia2, Nanwei road, Xi Cheng district

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: We analyze the mRNA level in multiple PBS or bleomycin exposed mouse lung alveolar epithelial type 2 cells

overall_design: Examination of mRNA level in multiple PBS exposed mouse lung alveolar epithelial type 2 cells from 3 mice and mRNA level in multiple bleomycin exposed mouse lung alveolar epithelial type 2 cells  from 3 mice

first: Xiao-xi

last: Lv

first: Shan-shan

first: Zhuo-wei

last: Hu


title: Histone lysine methyltransferase Pr-set7/SETD8 promotes neural stem cell reactivation

city: Singapore

first: Hongyan

state: Singapore

address: 8 College Rd

country: Singapore

institute: Duke-NUS

summary: The ability of neural stem cells (NSCs) to switch between quiescence and proliferation is crucial for brain development and homeostasis. Increasing evidence suggest that variants of histone lysine methyltransferases including KMT5A are associated with neurodevelopmental disorders. However, the function of KMT5A/Pr-set7/SETD8 in the central nervous system is not well established. Here, we show that Drosophila Pr-Set7 is a novel regulator of NSC reactivation. Loss-of-function of pr-set7 causes a delay in NSC reactivation and loss of H4K20 monomethylation in the brain. Through NSC-specific in vivo profiling, we demonstrate that Pr-set7 binds to the promoter region of cyclin dependent kinase 1 (cdk1) and Wnt pathway transcriptional co-activator earthbound1/jerky (ebd1). Further validation indicates that Pr-set7 is required for the expression of cdk1 and ebd1 in the brain. Similar to Pr-set7, Cdk1 and Ebd1 promote NSC reactivation. Moreover, Cdk1 upregulates the Ebd1 levels in NSCs, while Ebd1 appears to downregulate Cdk1 expression, suggesting a negative feedback regulation. Finally, overexpression of Cdk1 and Ebd1 significantly suppressed NSC reactivation defects observed in pr-set7-depleted brains. Therefore, Pr-set7, the sole H4K20 methyltransferase, promotes NSC reactivation through regulating Wnt signaling and cell-cycle progression. Given the conservation of Pr-set7, our findings may contribute to the understanding of mammalian KMT5A/PR-SET7/SETD8 in NSC proliferation and associated neurodevelopmental disorders.

overall_design: Examination of gene regions targeted by Pr-set7 in NSCs. Two batches of experiments were conducted. In each batch, one control (UAS-Dam) and one gene-of-interest (UAS-Dam-Pr-set7) were included. UAS contructs were induced under NSC-specific driver, grh-Gal4. Dam-Pr-set7 then bound to DNA and methylated adenines (m6A) at the nearby GATC motifs. By examining the DNA methlyation status through next generation sequencing, Pr-set7 target regions could be identified.

first: Jiawen

first: Wing-Kin

last: Sung

first: Mahekta

last: Gujar

first: Qiannan

last: Deng

first: Sook-Yoong

last: Chia

first: Patrick

last: Tan


title: Analyzing the Effect of the K27M Mutation in Histone H3.3 on Gene Expression in Pluripotent Stem Cells and Neural Stem Cells.

city: Heidelberg

first: Daniel

last: Haag

state: Baden-Wuerttemberg

address: INF 580

department: Pediatric Neurooncology

institute: German Cancer Research Cernter (DKFZ)

summary: Diffuse intrinsic pontine glioma (DIPG) is an aggressive childhood tumor of the brainstem with currently no curative treatment available. The vast majority of DIPGs carry a mutation in histone H3 leading to a lysine 27-to-methionine exchange (H3K27M). The H3K27M mutation has been shown to inhibit EZH2, the catalytic subunit of the polycomb repressive complex 2, which presumably leads to global reduction of H3K27 trimethylation and upregulation of tumor-driving genes. However, the exact pathomechanism and cellular context remain elusive. Recent single cell transcriptome data suggested the DIPG cell of origin to be of oligodendroglial lineage, whereas in vivo studies demonstrated neural stem or progenitor cells (NPCs, NSCs) to be susceptible for malignant transformation upon H3K27M expression. Here, we used targeted human induced pluripotent stem cells (iPSCs) carrying an inducible H3.3-K27M allele in the endogenous H3F3A locus together with specific differentiation methods to study the effects of the mutation in disease-relevant cell identities of the neural lineage. Phenotypic, transcriptomic, and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed a distinct role of H3.3-K27M for deregulating bivalent promoter-associated developmental genes producing diverse outcomes in different cell types. While being fatal for iPSCs, H3.3-K27M increased proliferation in NSCs and to a lesser extent in oligodendroglial progenitor cells (OPCs) but not in astroglial-restricted precursors. Importantly, we demonstrated that only NSCs but not OPCs gave rise to tumors upon induction of the H3.3-K27M and TP53 inactivation in an orthotopic xenograft model faithfully recapitulating human DIPGs. Thus, we provide evidence that indeed only NSCs can develop H3.3-K27M-driven DIPG-like tumors but that the mutation actively drives acquisition of oligodendroglial characteristics, thus explaining the different observations of cell identity. Identification of the originating cell type may help to determine specific vulnerabilities of this tumor for developing targeted therapies.

overall_design: We sought to investigate the gene expression changes in induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) upon endogenous expression of the H3.3-K27M mutation. Further, we wanted to perform transcriptome profiling of iPSC-NSC-derived xenograft tumors. For this purpose, we generated human iPSCs carrying a Cre-inducible H3.3-K27M reading frame in one copy of the H3F3A locus. Lentiviral infection delivering Flp enzyme expression loops out the selection marker from the initial targeting cassette and preserves the wildtype H3.3 variant (control). Lentiviral delivery of Cre enzyme loops out the wildtype H3.3 reading frame and activates expression of the H3.3-K27M variant (mutation). Lentiviral infection of Cre and Flp was conducted at the iPSC stage for two engineered lines from two individuals as well as after NSC differentiation of one engineered iPSC line. For xenograft experiments, iPSC-derived NSCs were infected with lentivirus expressing Cre-GFP and retrovirus expressing shRNA against TP53 before orthotopic injection into immunodeficient mice.  Total RNA from control and mutant iPSCs was extracted between 5-6 days after lentiviral infection encompassing two biological replicates per cell line. Total RNA from control and mutant iPSC-derived NSCs was extracted around day 10, 18, 26, and 30 after lentiviral infection encompassing one biological replicate per time point. Total RNA from iPSC-NSC-derived tumors was extracted from lesion areas after sacrificing sick animals according to defined endpoints of tumor burden. Two tumors were harvested for molecular analysis. Transcriptome analysis were performed on Affymetrix HG-U133_Plus 2 arrays.

first: Stefan

last: Pfister


title: Expression data from HepG2 and LX2 cells treated with a dual epigenetic inhibitor of G9A and DNMT1.

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary:
Hepatocarcinogenesis involves epigenetic abnormalities of great relevance. Both the histone methyltransferase G9A and the DNA methyltransferase DNMT1 are overexpressed in fibrosis and liver tumor development.
We used microarrays to evaluate the global programme of gene expression in the human HCC cell line HepG2 and in the human Hepatic Stellate Cell LX2, trated with CM272. This molecule is an epigenetic inhibitor that simultaneously targets the methyltransferase activities of G9a and DNMT1.

overall_design: HepG2 (HCC cell line) and LX2 (HSC cell line) were treated with CM272 at 400nM during 48 hours. RNA extraction and hybridization on Affymetrix microarrays were performed in order to obtain a transcriptomic profile after the simultaneous inhibition of G9a and DNMT1 in these two cell types.

first: Matias

last: Avila


title: Restoration of type I interferon signaling in intrahepatically primed CD8+ T cells promotes functional differentiation

city: Nagoya

first: masaya

last: onishi

address: Kawasumi, Mizuho

department: Virology & Liver unit

institute: Nagoya City University Graduate School of Medical Sciences

summary: Hepatitis B virus-specific (HBV-specific) CD8+ T cells fail to acquire effector functions after priming in the liver, but the molecular basis for the dysfunction is poorly understood. By comparing the gene expression profile of intrahepatically primed, dysfunctional HBV-specific CD8+ T cells with that of systemically primed, functional effector counterparts, we found that the expression of interferon-stimulated genes (ISGs) is selectively suppressed in the dysfunctional CD8+ T cells. The ISG suppression was associated with impaired phosphorylation of STAT1 in response to IFN-α treatment. Importantly, a strong induction of type I interferons (IFN-Is) in the liver facilitated the functional differentiation of intrahepatically primed HBV-specific CD8+ T cells in association with the restoration of ISGs' expression in the T cells. These results suggest that intrahepatic priming suppresses IFN-I signaling in CD8+ T cells, which may contribute to the dysfunction. The data also suggest a therapeutic value of the robust induction of intrahepatic IFN-Is for the treatment of chronic HBV infection.

overall_design: We compared the gene expression profile between naïve, dysfunctional and effector HBV-specific CD8+ T cells by using microarray .Specifically, HBcAg derived peptide (COR93)-specific CD8+ T cells were adoptively transferred into HBV-Tg mice (lineage 1.3.32, inbred B6, H-2b) to obtain tolerant COR93-specific T cells. To obtain effector COR93-specific T cells, we adoptively transferred the same T cells into B6 mice treated with an agonistic anti-CD40 antibody and COR93 peptide . Seven days later, adoptively transferred COR93-specific CD8+ T cells were purified from Intrahepatic lymphocytes of HBV-Tg mice.  Donor naïve COR93-specific CD8 T cells were also purified for comparison.

first: Keigo

last: Kawashima

first: Masanori

last: Isogawa

first: Masaya

last: Onishi


title: PRC2-mediated epigenetic signatures associate with pathogn-induced programmed cell death in Arabidopsis

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated H3K27me3 histone modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.

overall_design:
With modification of two-component vector system (Brand et al., 2006) we designed system for inducible expression of two different constructs mimicking the pathogen infection. The activator vector (pMDC150::XVE) contains chimeric transcription factor XVE under control of minimal 35S promoter. Both respondant vectors (pMDC160::NPP1 and pMDC160::RPT2) contain XVE-responsive promoter OlexA TATA. Constructs were introduced to Arabidopsis thaliana Columbia ecotype containing activator vector pMDC150::XVE by Agrobacterium-mediated transformation (Clough and Bent, 1998).

Each ChIP-seq *.bed file was generated from all replicates together and is linked to the corresponding rep1 sample records.
The RNA-seq DESeq*.txt files (linked as Series supplementary files) are comparison between different sample groups as indicated in the corresponding sample description field.

first: Eva

middle: D

last: Tomastíková

first: Anders

last: Hafrén

middle: S

last: Trejo-Arellano

first: Sheena

last: Rasmussen

first: Juan

last: Santos-González

first: Lars

last: Hennig

first: Claudia

last: Köhler

last: Hofius


title: DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

overall_design: Two MCF-7 cell samples, including Mock and Rnase H treated samples

first: Benjamin

last: Delatte

first: Anjana

last: Rao


title: Analyzing the Effect of the K27M Mutation in Histone H3.3 on Chromatin Regulation in Pluripotent Stem Cells, Neural Stem Cells, and Oligodendroglial Progenitor Cells

first: Daniel

last: Haag

overall_design: To investigate the genomic distribution of the histone variant H3.3 in human pluripotent stem cells and during glioma-relevant stages of neural lineage commitment we performed chromatin immunoprecipitation sequencing (ChIP-seq) against an HA tag fused to a wildtype H3.3 reading frame inserted into the endogenous H3F3A locus. ChIP-seq against the HA-tag (H3.3) was performed in H3.3-wildtype iPSC, iPSC-derived neural stem cells (NSCs), and iPSC-derived oligodendroglial progenitor cells (OPCs). To further investigate the effect of the H3.3-K27M mutation on chromatin regulation, we performed ChIP-seq with spike-in normalization against the repressive histone modification H3K27me3 as well as the activating histone modification H3K4me3.

first: Stefan

last: Pfister


title: Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

city: Tokyo

first: Kohei

last: Kashima

address: 7-3-1 Hongo Bunkyo-ku

department: Pediatrics

institute: The University of Tokyo Hospital

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Slug-Ad infected mouse lung alveolar type 2 cells

first: xiaoxi

last: lv

summary: We analyze the mRNA level in Slug-Ad or Con-Ad infected mouse lung alveolar epithelial type 2 cells

overall_design: Examination of mRNA level in Slug-Ad infected AEC2s from 3 mice and Con-Ad infected AEC2s from 3 mice

first: Xiao-xi

last: Lv

first: Shan-shan

last: Liu

first: Zhuo-wei

last: Hu


title: Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

summary:
Preterm or small for gestational age (SGA) infants are to be at high risk of noncommunicable diseases in adolescence, because they are exposed to hypoxia and malnutrition in and ex utero during perinatal period. Epigenetics could be one of the most important mechanisms of DOHaD.In the field of premature babies, previous studies investigated the methylation alterations related to gestational age and birthweight by using cord blood samples.
In the field of preterm or SGA babies, there were few EWAS studies that examine whether methylation changes relate to RNA expression using cord blood samples, and the interpretation of postnatal blood methylation were different by studies.The objective is to investigate the epigenetic alterations associated with preterm birth and SGA by using methylation and expression microarray, and to explore the epigenetic changes which may persist after birth.

overall_design: Cross-sectional study using 110 cord blood samples and 47 postnatal peripheral blood samples.

first: Naoto

last: Takahashi

first: Takeshi

last: Nagamatsu

first: Tomoyuki

last: Fujii

first: Isaku

last: Omori

first: Mitsumasa

last: Shimizu

first: Hironobu

last: Hyodo

first: Hiromi

last: Kamura

first: Tomoko

last: Kawai

first: Kazuhiko

last: Nakabayashi

first: Kenichiro

last: Hata

first: Koji

last: Kugu


title: Gut microbiota derived metabolites 3-idoleacetic acid promotes IL-35+B cell production

status: Public on Feb 08 2021

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: Disruptions of microbiota composition by factors such as genetics have been suggested to be critical contributing factors to the growth of the worldwide epidemics of chronic illness such as metabolic diseases. IL-35-producing regulatory B and T regulatory cells are critical regulators to these illnesses. Whether microbiota-derived metabolites can regulate these IL-35+ cells maintain elusive. Here, we found gut genetic factor Reg4 associated lactobacillus could promote the generation of IL-35+ B cells through producing 3-idoleacetic acid (IAA). HuREG4IEC tg mice had markedly accumulation of IL-35+ not only in adipose tissues but also in colon tissues; whereas significantly decreased IL-35+ cells in adipose tissues and colon tissues could be detected in Reg4 KO mice. On the mechanism, IAA-mediated IL35+ B cells was through PXR), RXR and CAR in the presence of LPS. PXR KO, CAR KO and NF-B KO mice impaired the generation of IAA- IL-35+B cells. Interestingly, lower levels of IAA and IL-35 were also detected in the peripheral blood of individuals with obesity. Thus, IAA is a factor to promote the generation of IL-35+B cells to impede the development of obesity.

overall_design: Examination  of the enrichment of PXR in the promoter region of P35 gene in WEHI231 cells.

first: Xiaomin

last: Su

first: Houbao

last: Qi


title: Oil Palm Fruit Abscission Zone Transcriptome

city: Montpellier

first: Timothy

middle: John

last: TRANBARGER

address: 911 avenue agropolis BP 64501

department: Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)

country: France

institute: Institut de Recherche pour le Développement

summary: To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.

overall_design: As a first step to screen for genes involved in oil palm ripe fruit abscission, we examined the short-term gene expression response in the fruit abscission zone (AZ) at 150 Days after pollination (DAP) to an exogenous ethylene treatment. Transcriptome analysis was assessed every 3h over a period of 12h, while cell separation was already observed after 9h of treatment. We identified 1957 differentially expressed genes (DEGs) during at least one time point of the ethylene treatment in the 150 DAP sample (AZ150) compared to the control (time 0h AZ150). As a second step to screen the 1957 DEGs for AZ specific expression, we compared the short-term response of AZ150 to exogenous ethylene with those from the AZ from immature fruit at 30 DAP (AZ30) and the pedicel from ripe fruit (P150) samples (also treated with ethylene at same time intervals) at each ethylene treatment time point. From this analysis, a total of 502 DEG candidates were retained based on their higher or lower expression level in AZ150 compared to that observed in both AZ30 and P150. As a third step to screen for AZ genes involved in abscission, we analysed gene expression in the AZ of ripe fruit undergoing natural abscission in the field and aimed at finding genes with similar expression profiles between ethylene induced and natural abscission in the field. The natural abscission study (RNA-Seq) was conducted with AZ samples collected in the field at 30 DAP, 120 DAP, during which time no abscission was observed, and 160 DAP collected from a fruit bunch where abscission was observed.

last: Tranbarger

first: Fabienne

last: Morcillo

first: Sithichoke

last: Tangphatsornruang


title: Next Generation Sequencing Facilitates Quantitative Analysis of CTU treated Human breast MDA-MB-231 cells Transcriptomes

city: Camperdown

first: Michael

middle: Khalilur

last: Murray

state: NSW

address: 92 Parramatta Road

department: Pharmacology

country: Australia

institute: The University of Sydney

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived CTU-treated MDA-MB-231 cell's transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Purified RNA of CTU-treated MDA-MB-231 cells (10 μM, 6 h) were sent to the Australian Genome Research Facility for RNA-Seq analysis. Differential expression analysis was performed by edgeR and pathway enrichment was performed using the Reactome database as a reference.qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results:  RNA-Seq profiling identified a total of 14,951 genes in MDA-MB-231 cells, and detected 382 differentially expressed genes greater than or equal to (≥) 2-fold after 10 μM CTU treatment at 6 h. Genes whose expression was changed significantly were identified using the false discovery rate (FDR), an adjusted P-value for multiple testing. The expression of 250 and 132 genes was significantly up-regulated and down-regulated, respectively, to ≥2-fold of control in CTU-treated cells (FDR<0.05). Secondary pathway analysis was performed using the Reactome database to identify the principal biological pathways that were altered in CTU-treated MDA-MB-231 cells. This analysis implicated several mechanisms, including disruption of the tumour microenvironment, activation of cellular stress signalling and activation of cell cycle arrest. ER stress via the UPR survival mechanism was a major dysregulated pathway in MDA-MB-231 cells that had been treated with CTU (10 μM, 6 h) compared with control (FDR= 0.0001).
Conclusions: Our study represents the first detailed analysis of CTU-treated MDA-MB-231 cells (10 μM, 6 h) l 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 NGS 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: mRNA profiles of CTU-treated MDA-MB-231 cells (10 μM, 6 h)

first: Hassan

last: Choucair

first: Md

last: Rahman


title: Bulk RNA sequencing of WT and Pim1 -/- bone-marrow-derived myeloid-derived suppressor cells

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: There is a strong correlation between myeloid derived suppressor cells (MDSCs) and resistance to immune checkpoint blockade (ICB), but the detailed  underlying this correlation are largely unknown. Using single-cell RNA-seq analysis in a bilateral tumor model, we found that immunosuppressive myeloid cells with characteristics of fatty acid oxidative metabolism dominate the immune-cell landscape in ICB-resistant subjects. In addition, we uncovered a previously underappreciated role of a serine/threonine kinase, PIM1, in regulating lipid oxidative metabolism via PPARγ-mediated activities. Enforced PPARγ expression sufficiently rescued metabolic and functional defects of Pim1-/- MDSCs. Consistent with this, pharmacological inhibition of PIM kinase by AZD1208 treatment significantly disrupted myeloid cell–mediated immunosuppression microenvironment and unleashed CD8+ T cell–mediated antitumor immunity, which enhanced PD-L1 blockade in preclinical cancer models. PIM kinase inhibition also sensitized non-responders to PD-L1 blockade by selectively targeting suppressive myeloid cells. Overall, we have identified PIM1 as a metabolic modulator in MDSCs that is associated with ICB resistance and can be therapeutically targeted to overcome ICB resistance.

overall_design: Bulk RNA sequencing, 2 samples (WT and Pim1-/- MDSC), 3 biological replicates per sample, from bone-marrow-derived myeloid-derived suppressor cells

first: Gang

last: Xin

first: Yao

last: Chen


title: Whole genome expression analysis of primary head and neck squamous cell carcinoma (HNSCC) cell lines and their isogenic gefitinib resistant cell lines

first: Joo-Leng

last: Low

address: 60 Biopolis Street, #02-01 Genome

institute: Genome Institute of Singapore

summary: Gene expression analysis of primary HNSCC cell lines and their corresponding gefitinib resistant cell lines

overall_design: RNA from three primary HNSCC cell lines and their corresponding gefitinib resistant cell lines were isolated and sequenced. The gefitinib resistant cell lines were cultured in 6.4 uM gefitinib before RNA isolation.

first: Ramanuj

last: DasGupta

first: N

last: Iyer


title: Surprising Phenotypic Diversity of Cancer-associated mutations at Gly 34 in the Histone H3 tail

city: Memphis

first: Patrick

middle: Allen

last: Schreiner

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

summary: Deep sequencing of cancer genomes has identified frequent mutation of core histones, termed oncohistones, but the role of some mutants is poorly understood. Here, using fission yeast as a model, we determine the consequences of mutation of histone H3.3 at Gly 34, a site frequently mutated in pediatric cortical high-grade glioma (G34R/V), and in virtually all giant cell tumors of bone (G34W). H3-G34 mutations cause a surprising diversity of outcomes, differentially affecting modification of the nearby H3K36 residue, subtelomeric silencing, genomic stability, sensitivity to irradiation, alkylating agents, hydroxyurea and influencing DNA repair. Since fifteen genes encode H3 isoforms, and only one allele is targeted in cancer, G34R/V/W H3 likely represents a small portion of total cellular H3. Whilst the presence of wild type H3 rescues most G34 mutant phenotypes, hydroxyurea sensitivity, subtelomeric silencing and homologous recombination defects dominate in cells expressing G34R and wild type H3. Together, these studies demonstrate the complexity associated with different substitutions at even a single residue in histone H3 and highlight the utility of genetically tractable systems for their analysis.

overall_design: Examination of total RNA in S.pombe with single copy H3 and H4 histone genes (hht2 and hhf2) bearing H3 WT, H3 G34R, H3 G34V, H3 G34K mutations or deleted for set2. Also examination of H3 G34R and H3 G34K mutants compared to WT H3 in strains retaining 2 wild type copies of H3 and H4.

first: Brandon

last: Lowe

first: Rajesh

last: Yadav

first: Ryan

middle: A

last: Henry

first: Atsushi

last: Matsuda

first: Alfonso

last: Fernandez

first: David

last: Finkelstein

first: Margaret

last: Campbell

first: Satish

last: Kallappagoudar

first: Carolyn

last: Jablonowski

first: Andrew

last: Andrews

first: Yasushi

last: Hiraoka

first: Janet

last: Partridge


title: RNA-seq analysis of Scx-lineage cell depletion to investigate tendon cell functions during flexor tendon healing

city: Rochester

first: Alayna

middle: E

last: Loiselle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: Little is understood about the roles of tendon cells during flexor tendon healing. To better understand tendon cell functions, the Scx-Cre mouse was crossed to the DTR mouse model to facilitate scleraxis lineage cell depletion prior to acute flexor tendon injury and repair. WT (cre-) and experimental (cre+) mice underwent complete transection and repair of the flexor digitorum longus tendon. Repaired tendons were harvested at 14 and 28 days post-repair for bulk RNA-Seq analysis to examine possible mechanisms driving differential healing due to Scx lineage cell depletion.

overall_design: Transcriptomes of D14 and D28 repaired tendons with or without scleraxis lineage depletion driven by the DTR mouse model were generated in triplicate.

first: Katherine

middle: T

last: Best


title: Thymoproteasome-expressing mesenchymal stromal cells confer protective anti-tumor immunity via cross-priming of endogenous dendritic cells

city: Montréal

first: Moutih

last: Rafei

state: Québec

address: 2900 Boul. Édouard-Montpetit

institute: Université de Montréal

summary: Raw RNA-seq counts from reads aligned to the mouse genome (mm10 assembly) were generated with Htseq-count (PMID: 25260700). Differentially expressed genes between TPr and Ctl MSCs were calculated by DESeq2 (PMID: 25516281). Pre-ranked gene set enrichment was performed as recommended for RNA-seq data (PMID: 16199517). Custom R scripts were used to filter highly redundant biological processes. A false discovery rate of 0.05 was considered as an acceptable threshold for further investigation. All analyses were conducted in R (v3.6) or Python (v3.7) programming language. The ggplot2, ClusterProfiler and dplyr packages were used for data visualization. Student’s t-test was performed for normally distributed data to compute the p-value and the Benjamini-Hochberg procedure was used for adjusting the statistical inference of multiple comparisons.

overall_design: We report in this study the effect of TPr subunit expression on the antigen cross-presenting abilities of MSCs.

first: Nehme

last: El-Hachem


title: RNAseq of nasal cells from volunteers experimentally infected with RSV

city: London

first: Christopher

last: Chiu

address: Hammersmith Campus, Du Cane Road

department: Infectious Disease

institute: Imperial College London

overall_design: We report the analysis of nasal curettage cells by RNAseq collected at multiple timepoints in healthy adults experimentally challenged with respiratory syncytial virus (RSV). Following inoculation, 57% of participants developed PCR-confirmed infection. Prior to viral challenge, 80 differentially expressed genes were identified that associated with susceptibility to symptomatic infection. At day 3, 87 differentially expressed genes were associated with protection. Thus, we showed that the nasal mucosa at the time of virus exposure and during the incubation phase correlate with susceptibiltiy and protection from respiratory viral infection.


title: Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

first: Kohei

last: Kashima

overall_design: Cross-sectional study using 55 cord blood samples which had valid methylation data.

first: Naoto

last: Takahashi

first: Takeshi

last: Nagamatsu

first: Tomoyuki

last: Fujii

first: Isaku

last: Omori

first: Mitsumasa

last: Shimizu

first: Hironobu

last: Hyodo

first: Koji

last: Kugu

first: Kazue

last: Takeda

first: Kenji

last: Matsumoto

first: Tomoko

last: Kawai

first: Kazuhiko

last: Nakabayashi

first: Kenichiro

last: Hata


title: Transcriptomic profiling of cerebrum, liver, and muscle tissues of 50 days fetuses in response to early maternal nutrient restriction

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

summary:
We addressed the molecular mechanisms and biological processes underlying the differences in cerebrum, liver, and muscle gene expression of 50 days fetuses in response to early maternal nutrient restriction. To this end, we employed tissue-to-tissue and tissue-specific network approaches using the genome-wide expression profile of 14 samples for two experimental conditions [Control – CON (n = 7) and 40% nutrient restriction – RES (n = 7)]. After RNA quality control, read mapping was performed with STAR aligner to the bovine ARS-UCD1.2 reference genome. Count normalization was performed by using the VST function from DESEq2. Gene networks were constructed using the PCIT algorithm, whereas differentially co-expressed genes were identified based on the R-package DGCA. Significant gene-gene co-expression was taken based on r > | 0.9| and then filtered by differentially expressed genes and transcription factors. Networks were visualized in Cytoscape, and functional analyses were carried out on Cluego and ShinyGo tools. We found that the cerebrum, liver, and muscle tissues were affected by nutrient restriction leading to differences in transcriptional regulation between CON and RES groups. Furthermore, we shed light on the nutrient-sensing pathways across tissues such as mTOR, PI3K/Akt, and insulin.
This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2016-67016-24946 from the USDA National Institute of Food and Agriculture as well as the USDA-NIFA-AFRI (2018-67011-31708).

overall_design: Angus-cross heifers (n = 14) with average initial body weight = 313 ± 24.9 kg were randomly assigned at breeding to receive dietary intake of either 100% of NRC energy requirements for 0.45 kg/day of body weight gain (control; CON, n = 7) or were fed a diet to delivery 60% of CON intake (restricted; RES, n = 7). On day 50 of gestation, cerebrum (n = 14), liver (n = 14), and muscle (n = 14) were collected from fetuses following ovariohysterectomy.

middle: J

first: Matthew

last: Crouse

first: Robert

last: Cushman

first: Kyle

last: McLean

first: Joel

last: Caton

first: Carl

last: Dahlen

first: Lawrence

last: Reynolds

first: Alison

last: Ward


title: Next Generation Sequencing Facilitates Quantitative Analysis of Osteoarthritis related long non-coding RNAs (LcnRNAs)

city: Shanghai

first: liying

last: Jiang

address: Pudong

institute: collaboration research centre

summary:
Purpose: LncRNAs are important moleculars in immune responses. The goals of this study are to identify osteoarthritis related lncRNAs.
Methods: PBMCs from healthy control and osteoarthritis patients were collected. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed lncRNAs were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed lncRNAs was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories.
Results: 18 lncRNAs decreased significantly in osteoarthritis patients.

overall_design: LncRNA profiles of PBMC from healthy controls and osteoarthritis patients were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system


title: Transcriptome in WT Col-0 and mik2-1 mutant upon SCOOP12 treatment.

city: Jinan

first: Shuguo

last: Hou

state: Shandong

address: Fengming Road 1000, Shandong Jianzhu University

department: School of Municipal & Environmental Engineering

institute: Shandong Jianzhu University

summary: We tested SCOOP12-regulated gene transcription in Arabidopsis Wt (Col-0) and mik2-1.

overall_design: Ten-day old seedlings grown on 1/2MS medium were treated with or without 1 uM SCOOP12 for 1 or 6 hours. RNA was isolated for RNA sequencing analysis.Three biologic replicates were used for each treatment. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform with 150-nucleotide pair-end reads.


title: Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth


title: Cell-penetrant SELENOT mimetic protects dopaminergic neurons and ameliorates motor function

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Parkinson’s disease (PD) is a neurodegenerative disorder characterized by motor dysfunction for which there is an unmet need for better treatment options. Although oxidative stress is a common feature of neurodegenerative diseases, notably PD, there is currently no efficient therapeutic strategy able to tackle this system-wide pathophysiological process. Based on our previous observations of the potent antioxidant and neuroprotective activity of SELENOT, a vital thioredoxin-like selenoprotein, we designed the small peptide PSELT from its redox active site in order to determine its potential polyfunctional activity in PD models. PSELT proved to site in order to be protective for neurotoxin-treated dopaminergic neurons and fibers against oxidative stress determine its potential polyfunctional activity in PD models. PSELT proved to be protective for neurotoxin-treated dopaminergic neurons and fibers against oxidative stress and cell death. We demonstrate that PSELT is cell-permeable and acts in different subcellular compartments of dopaminergic neurons where oxidative stress exerts its deleterious effects. This protective activity prevented neurodegeneration and restored phosphorylated tyrosine hydroxylase levels, leading to improved motor skills in rodent models of PD

overall_design: The human SH-SY5Y neuroblastoma cell line treated or not with 500 μM or 1 mM MPP+ for 36 h in the presence or absence of PSELT (10 μM).

first: Abdel

first: Lee

last: Eiden

first: Youssef

last: Anouar


title: Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis [RNA-Seq]

summary: Astrocytes are the predominant component of the scar and play crucial roles in spinal cord injury (SCI) at acute injury stage. Understanding the complex reactive astroglial contributions to SCI pathophysiologies is important for developing therapeutic strategies. To understand the mechanisms of astrogliosis in SCI, and to identify novel molecular targets to improve the injury environment and axonal regeneration, we have studied gene expression changes in SCI epicenter tissue using RNA-Seq at chronic stages (1 month and 3 months) in mouse moderate contusive injury models. Importantly, we have also FACS purified cells successfully from adult spinal cord using transgenic mice and generated RNA-Seq results for both acute (7 days) and chronic (1 month and 3 months) injury stages. The SCI RNA-Seq analysis provided valuable information on the gene expression in injury environment and astrocytes after SCI. In addition to protein coding genes, we were the first to systematically analyze the expression profiles of Long Noncoding RNAs (lncRNAs) in SCI and purified astrocytes. We have tested a number of candidates and found gene of interest Zeb2os which is a highly conserved lncRNA in human. Zeb2os expression has high correlation with an essential transcription factor (TF) in astrogliosis, Stat3, and its antisense protein coding gene Zeb2.  Furthermore, our ChIP-seq experiment showed STAT3 bound to Zeb2 promoter region, thus Zeb2os may regulate Zeb2 and Stat3 directly or indirectly and STAT3 may regulate Zeb2 expression. Moreover, we have demonstrated for the first time by shRNA gene knockdown (KD) and functional assays that Zeb2os plays an important functional role in astrogliosis. We found Zeb2os KD in primary astrocytes affected a number of downstream genes by RNA-Seq, for example, Gfap, Zeb2, and Stat3 level decreased and reduced astrocyte proliferation.

overall_design: We analyzed total 25 RNA-Seq libraries, including 6 tissue samples (3 replicates at each time points, each replicates contained 3 mice), 11 purified astrocyte samples (3 replicates in sham, 7D, 1M and 2 replicated in 3M, each replicates contained 3 mice), 4 Zeb2os KD primary astrocyte samples (2 replicates for control and Zeb2os KD, respectively), and 4 Zeb2 KD primary astrocyte samples (2 replicates for control and Zeb2 KD, respectively).

first: Jia

middle: Q

last: Wu

first: Yanan

last: You

first: Raquel

last: Cuevas-Diaz Duran

first: Xizi

first: Bo

last: Hai


title: Characterisation of Multipotent Stem Cells Generated by Direct Conversion of Human Adipoctyes using PDGF-AB and 5-Azacytidine

city: Sydney

first: Dominik

last: Beck

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

summary: This submission represents the RNAseq component of the study.

overall_design: Bulk RNA sequencing of full-length transcripts (RNA-seq) was used to identify differences and similarities between the tested populations of primary adipocytes, Adipose derived MSCs (AdMSCs) and reprogrammed induced multipotent stem (iMS) cells.

first: Avani

last: Yeola

first: Vashe

last: Chandrakanthan

first: John

last: Pimanda

first: Diego

last: Chacon


title: Induction of Muscle Regenerative Multipotent Stem Cells from Human Adipocytes by PDGF-AB and 5-Azacytidine [RRBS]

city: Kensington

address: Cnr High and Botany St

institute: UNSW

summary: Terminally differentiated murine osteocytes and adipocytes can be reprogrammed using platelet-derived growth factor–AB and 5-Azacytidine into multipotent stem cells with stromal cell characteristics. To generate a product that is amenable for therapeutic application, we have modified and optimised culture conditions to reprogram human adipocytes into induced multipotent stem cells (iMS) and expand them in vitro. The basal transcriptomes of adipocyte-derived iMS cells and matched adipose-tissue-derived mesenchymal stem cells were remarkably similar. However, there were distinct changes in histone modifications and CpG methylation at cis-regulatory regions consistent with an epigenetic landscape that was primed for tissue development and differentiation. In a non-specific tissue injury xenograft model, iMS cells contributed directly to new muscle, bone, cartilage and blood vessels with no evidence of teratogenic potential. In a cardiotoxin muscle injury model, iMS cells contributed specifically to satellite cells and myofibres without ectopic tissue formation. Taken together, human adipocyte derived iMS cells regenerate tissues in a context dependent manner without ectopic or neoplastic growth.

overall_design:
Distribution of regions with CpG methylation in AdMSCs and iMS cells.
This submission represents the Reduced Representation Bisulphite Sequencing (RRBS) component of the study.

first: Shruthi

last: Subramanian

first: Jason

last: Wong

first: Feng

last: Yan


title: Induction of Muscle Regenerative Multipotent Stem Cells from Human Adipocytes by PDGF-AB and 5-Azacytidine

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

overall_design: Refer to individual Series


title: Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis [ChIP-Seq]

first: Haichao

summary: Astrocytes are the predominant component of the scar and play crucial roles in spinal cord injury (SCI) at acute injury stage. Understanding the complex reactive astroglial contributions to SCI pathophysiologies is important for developing therapeutic strategies. To understand the mechanisms of astrogliosis in SCI, and to identify novel molecular targets to improve the injury environment and axonal regeneration, we have studied gene expression changes in SCI epicenter tissue using RNA-Seq at chronic stages (1 month and 3 months) in mouse moderate contusive injury models. Importantly, we have also FACS purified cells successfully from adult spinal cord using transgenic mice and generated RNA-Seq results for both acute (7 days) and chronic (1 month and 3 months) injury stages. The SCI RNA-Seq analysis provided valuable information on the gene expression in injury environment and astrocytes after SCI. In addition to protein coding genes, we were the first to systematically analyze the expression profiles of Long Noncoding RNAs (lncRNAs) in SCI and purified astrocytes. We have tested a number of candidates and found gene of interest Zeb2os which is a highly conserved lncRNA in human. Zeb2os expression has high correlation with an essential transcription factor (TF) in astrogliosis, Stat3, and its antisense protein coding gene Zeb2.  Furthermore, our ChIP-seq experiment showed STAT3 bound to Zeb2 promoter region, thus Zeb2os may regulate Zeb2 and Stat3 directly or indirectly and STAT3 may regulate zeb2 expression. Moreover, we have demonstrated for the first time by shRNA gene knockdown (KD) and functional assays that Zeb2os plays an important functional role in astrogliosis. We found Zeb2os KD in primary astrocytes affected a number of downstream genes by RNA-Seq, for example, Gfap, Zeb2, and Stat3 level decreased and reduced astrocyte proliferation.

overall_design: We analyzed total 4 STAT3 Chip-Seq samples, including 1 input sample and 1 STAT3 binding sample for sham, 1 input sample and 1 STAT3 binding sample for SCI. Each sample contained  pooled epicenter spinal cord tissue from 3 mice.


title: Induction of Muscle Regenerative Multipotent Stem Cells from Human Adipocytes by PDGF-AB and 5-Azacytidine [ChIP-seq]

overall_design:
Distribution of regions with differential histone marks in AdMSCs and iMS cells.
This submission represents the ChIP-seq component of the study.


title: miRNA sequencing of RJ423EV and RJ423c141 cells

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

summary: miRNA sequencing of RJ423 cells expressing an empty vector (RJ423EV) or a vector containing the miR-200c/141 cluster (RJ423c141)

overall_design: two cell lines, RJ423EV and RJ423c141 with 3 replicates for each cell line


title: miRNA sequencing of RJ423EV and RJ423ba429 cells

summary: miRNA sequencing of RJ423 cells expressing an empty vector (RJ423EV) or a vector containing the miR-200b/200a/429 cluster (RJ423ba429)

overall_design: two cell lines, RJ423EV and RJ423ba429 with 3 replicates for each cell line


title: miRNA sequencing of MDA-231EV, MDA-231c141 and MDA-231ba429 cells

type: Non-coding RNA profiling by genome tiling array

summary: miRNA sequencing of MDA-M-231 cells expressing an empty vector (MDA231EV), a vector containing the miR-200c/141 cluster (MDA-231c141) or a vector containing the miR-200b/200a/429 cluster (MDA-231ba429)

overall_design: three cell lines, MDA-231EV, MDA231ba429 and MDA-231ba429 with 4 replicates for each cell line


title: Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity [ChIPmentation]

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer associated and preferentially downregulated by pharmacologic transcriptional CDK inhibition, leading to cell death. To understand the underlying basis of this sensitivity, we dissect the brachyury transcription regulatory network and compare the consequences of brachyury degradation with transcriptional CDK inhibition. Brachyury defines the chordoma super-enhancer landscape and autoregulates through binding its super-enhancer, and its locus forms a transcriptional condensate. Transcriptional CDK inhibition and brachyury degradation disrupt brachyury autoregulation, leading to loss of its transcriptional condensate and transcriptional program. Compared with transcriptional CDK inhibition, which globally downregulates transcription, leading to cell death, brachyury degradation is much more selective, inducing senescence and sensitizing cells to anti-apoptotic inhibition. These data suggest that brachyury downregulation is a core tenet of transcriptional CDK inhibition and motivates developing strategies to target brachyury and its autoregulatory feedback loop.

overall_design: Genome binding/occupancy profiling (ChIPmentation) by high throughput sequencing

first: Hadley

last: Sheppard


title: RNA sequencing of RJ423EV and RJ423c141 cells

summary: RNA sequencing of RJ423 cells expressing an empty vector (RJ423EV) or a vector containing the miR-200c/141 cluster (RJ423c141)


title: Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity


title: RNA sequencing of MDA-231EV, MDA-231c141 and MDA-231ba429 cells

summary: RNA sequencing of MDA-MB-231 cells expressing an empty vector (MDA-231EV), a vector containing the miR-200c/141 cluster (MDA-231c141) or a vector containing the miR-200b/200a/429 cluster

overall_design: three cell lines, MDA-231EV, MDA-231c141 and MDA-231ba429 with 4 replicates for each cell line


title: DNA methylation of leukocytes from sporadic breast cancer patients and healthy controls in Latin American population

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: The study aimed to compare the DNA methylation differences between blood samples from sporadic breast cancer patients and healthy controls from a well-defined cohort in Uruguayan population. Infinium methylation arrays (450K Illumina) are used to identify genome-wide methylation differences between groups. The identified differently methylated CpG were further analyzed in an independent cohort of 80 breast cancer patients and 80 healthy controls.

first: Monica

last: Cappetta

first: Maria

last: Berdasco


title: Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle

city: Bunkyo

first: Ryuichi

last: Yamada

state: Tokyo

address: Yayoi 1-1-1

department: Veterinary Anatomy

institute: The Univerisity of Tokyo

summary: The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRNA-seq) using 7,989 cells from the presumptive eye area in mouse embryos at the 12–26-somite stages at five developmental time points. We demonstrated the presence of seven optic vesicle populations, including three unique cell types located in the ventricular surface or dorsoventral areas of the optic vesicle structure. Moreover, the remaining four populations of retinal progenitor cells could be classified according to their stage-dependent time point, and these cells exhibited altered expression of several structural and metabolic key genes, such as Col9a1 and Ckb, just before regionalization of the optic cup. From these data, we provide the first report on stage-dependent transcriptional profiles during initial retinal specification at single-cell resolution and highlight the unexpected developmental heterogeneity of the murine optic vesicle structure.

overall_design: Ocular area scRNA-seq profiles of 12-26 somite stages wild type (WT) mice were generated using a 10X Chromium system.

first: Katsunori

last: Fujiki

first: Hirotaka

last: Takezoe


title: microRNA expression profile in colorectal cancer

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

summary:
Background: circRNAs, a recently identified new member of non-coding RNAs, have been proved to play an essential role in the development and progression of various cancers. However, the functions and mechanisms of circRNAs in colorectal liver metastasis have not been fully elucidated.
Methods: We performed circRNA microarray to screen differentially expressed novel circRNAs in the pathology of colorectal liver metastasis. Quantitative real-time PCR was used to detect the circ102049 expression in colorectal cancer (CRC) samples. Then CRC cells were transfected with a circ102049 over-expression vector or siRNAs, and the effects of circ102049 on biological functions in CRC cells were accessed in vitro. Mechanistically, the bioinformatics analysis, fluorescence in situ hybridization, RIP assay, RNA pull down assay and luciferase reporter assay were conducted to confirm the relationships among circ102049, miR-761, miR-192-3p and FRAS1. Moreover, the mechanism of circ102049 how to recruit and distribute DGCR8 protein in cytoplasm was elucidated.
Results: The results showed that circ102049 was highly expressed in primary CRC tumors with liver metastasis and closely correlated with the CRC patients' prognosis. Circ102049 might act as a novel metastasis-related non-coding RNA, and significantly promote the adhesion, migration and invasion abilities of CRC cells. Mechanistically, we verified that circ102049 promoted the CRC development and progression via a miR-761/miR-192-3p-FRAS1-dependent mechanism. Notably, due to the distribution of DGCR8 protein, circ102049 might also reduce the mature products of miR-761 and miR-192-3p in cytoplasm indirectly. In addition, the role of circ102049 in promoting colorectal liver metastasis was also confirmed in vivo.
Conclusions: Our findings provided new clues that circ102049 might be a potential prognostic factor in CRC, and the circ102049-miR-761/miR-192-3p-FRAS1 axis could be further explored as a therapeutic target for anti-metastatic therapy in CRC patients with liver metastases.
Keywords: Hsa_circ_102049, miR-761, miR-192-3p, FRAS1, Colorectal liver metastasis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: To detect the miRNAs expression profiles in 10 colorectal cancer (CRC) tissues from patients with liver metatasis and 10 CRC tissues from patients without liver metatasis by human miRNAs expression profile chips and to identify the differentially expressed miRNAs between two groups based on the chip data. In this way, this study provided the basis for identifying novel CRC biomarkers and further studying the roles and functions of differentially expressed miRNAs in different stage and metastaic potential of CRC. The function of the differentially expressed miRNAs were analyzed by bioinformatic methods.

first: Daiwei

last: Wan

first: Ye

last: Han

first: Zhihua

last: Xu

first: Rui

last: Ren

first: Zhenlong

last: Chen

first: Dai


title: Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity [Total RNA-seq, SLAM-seq]

overall_design: Gene expression profiling (RNA-seq and SLAM-seq) by high throughput sequencing


title: Circular RNAs expression profiling in  human colorectal cancer

overall_design: To detect the circRNAs expression profiles in 20 colorectal cancer tissues from patients with liver metastasis and without liver metastasis.


title: Hsa_circ_102049 promotes liver metastasis of colorectal cancer by up-regulating Fraser extracellular matrix complex subunit 1

type:
Non-coding RNA profiling by array
Expression profiling by array


title: Long Noncoding RNA and mRNA Expression Profile in colorectal cancer

overall_design: To detect the lncRNA/mRNAs expression profiles in 10 colorectal cancer (CRC) tissues from patients with liver metatasis and 10 CRC tissues from patients without liver metatasis by human lncRNA/mRNAs expression profile chips and to identify the differentially expressed lncRNA/mRNAs between two groups based on the chip data. In this way, this study provided the basis for identifying novel CRC biomarkers and further studying the roles and functions of differentially expressed lncRNA/mRNAs in different stage and metastaic potential of CRC. The function of the differentially expressed lncRNA/mRNAs were analyzed by bioinformatic methods.


title: Transcriptome of plants cells in the G2/M phase of the cell cycle

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary: Gene expression must be reconfigured rapidly during the subsequent phases of the cell cycle to execute the cellular functions specific of each phase. Post-transcriptional regulation has a predominant role in modulating gene expression during the mitotic cell cycle, including among other mechanisms, protein phosphorylation and ubiquitination, differential protein stability and mRNA localization and translatability. Regulation at the transcriptional level is also important, as studies conducted in synchronized plant cell suspension cultures have identified hundreds of genes with periodic patterns of genes expression across the phases of the cell cycle.  We describe here an alternative strategy to cell suspension cultures to profile the transcriptome of Arabidopsis root cells in the G2/M phase of the cell cycle.  Through fluorescence activated cell sorting we first isolated cells in G2/M using CYCB1;1-GFP, a reporter of a mitotic cyclin. The analysis of the transcriptome of these cells allowed us to identify hundreds of genes whose expression is depleted or enriched in G2/M cells.

overall_design: We analyzed the transcriptome of 3 biological replicates of complete root meristems and G2/M cells obtained by FACS from roots expressing CYCB1;1-GFP.

first: R


title: S1PR3–G12-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation [HeLa RNA-seq]

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary: Cancer tissues possess less glucose than surrounding normal tissue, because cancer cells predominantly produce energy by glycolysis than oxidative phosphorylation even in the presence of an adequate oxygen supply (Warburg effect). We found a novel compound ALESIA which causes apoptosis of malignant cells at a low glucose condition from an original phenotypic screening. Identified target molecule of ALESIA was Sphingosine-1-phosphate receptor 3 (S1PR3). Being different from the natural ligand, ALESIA selectively stimulated S1PR3-G12 coupling to S1PR3 without suppression by β-arrestin recruitment and continuously promoted NO synthesis. To reduce the enhanced oxidative stress, NAPDH production through pentose-phosphate pathway and resulting consumption of glucose were promoted in ALESIA-treated cells. ALESIA therefore accelerated glucose starvation of cancer cells and preferentially killed them both in vitro and in vivo.

overall_design: We analyzed polyA-tailed RNA profiles including transcribing RNAs in HeLa cells of ALESIA racemate treatment (n=3) and control (n=3) under normal culture condition using NovaSeq 6000

first: Masayasu

last: Toyomoto

last: Iida

first: Masatoshi

last: Hagiwara


title: S1PR3–G12-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation


title: TBC1D3 suppression of the Histone Lysine N-methyltransferase G9a promotes the generation of neural progenitors and cortical expansion

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

institute: shanghaitech university


title: TBC1D3 suppression of the Histone Lysine N-methyltransferase G9a promotes the generation of neural progenitors and cortical expansion [RNA-seq]

summary: we conducted RNA sequencing using human cerebral organoids treated with TAT peptides. Each group with one replicates.

overall_design: Human cerebral organoids were treated with TAT peptides for two groups, that is, TAT-Scrambled (Short for TAT-Scr) with the sequence of YGRKKRRQRRR-FRVRYWFQGCHSEDPWR and TAT-465-481, a special peoptide designed for inhibition of TBC1D3, with the sequence of YGRKKRRQRRR-EGPWFRHYDFRQSCWVR. After 4 days incubation, human cerebral organoid tissues were extracted at cultured day 16 and bulk RNA from TAT-Scr group or TAT-465-481 group was extracted to be sequenced. TAT-Scr group has two replicates as TAT-S1 and TAT-S2. TAT-465-481 group has two replicates as TAT-E1 and TAT-E2.

first: Qiongqiong

last: Hou

first: Zhen-Ge

last: Luo