title: Identification of conserved cis-regulatory elements impact Mecp2 level and neurological functions

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Methyl-CpG binding protein 2 (MeCP2) is a nuclear protein that binds to methylated cytosines and regulates gene expression. Normal brain function requires precise control of MeCP2 level. Loss of function mutations in the X-linked gene, MECP2 cause Rett Syndrome (RTT), a progressive neurological disorder. Increase in MeCP2 level leads to the neurological disorder MECP2 duplication syndrome (MDS). Despite the functional importance of MeCP2 in the brain, its transcriptional regulation remains poorly understood. Here, we utilized ATAC-seq in the mouse brain across development to identify five putative adult brain cis-regulatory elements (CREs) of Mecp2. We found that knocking out these CREs using CRISPR-Cas9 altered Mecp2 levels. Furthermore, two of the CREs were conserved in human, and when we delete either of these in mice, the animals show progressive neurological dysfunction. Deletion of one of the conserved CREs led to a decreased MeCP2 level and caused phenotypes similar, albeit milder, to those seen in Mecp2-null mice whereas the deletion of the second CRE led to an increased MeCP2 level and phenotypically resembled, but also milder than, MECP2 duplication mice. Deleting these two conserved CREs levels in human iPSC-derived neurons also similarly altered MECP2 levels. Taken together, our discovery of CREs that modulate Mecp2/MECP2 expression provides insight into regulation of Mecp2/MECP2 in the mouse brain and human neurons, respectively. These CREs could be candidate sites for non-coding mutations that lead to neurodevelopmental disorders characterized by partial features of RTT or MDS.

overall_design: Nuclei were isolated from adult wildtype liver and brain, P6 brain and embryonic day 12 brain for ATAC-Sequencing.

first: Yingyao

last: Shao

first: Sameer

last: Bajikar

first: Harini

last: Tirumala

first: Joshua

middle: D

last: Wythe

first: Huda

middle: Y

last: Zoghbi


title: Estrogen-driven control of diabetogenic gene networks is associated with reduced levels of miR-224/452 circulating in extracellular vesicles

status: Public on Dec 01 2020

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Exposure to Air pollution Disrupts Circadian Rhythm through Alterations in Chromatin Dynamics

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

country: USA

institute: CWRU

summary: Empirical evidence from both animals and humans suggest that PM2.5 (particulate matter < 2.5μm) exposure accelerates a variety of non-communicable diseases (NCDs) including Type 2 diabetes. We investigated whether chronic exposure to ambient air pollution (PM2.5), disrupts circadian rhythm to facilitate metabolic insulin resistance and compared the impact of inhaled ambient PM2.5 alone or in combination with continuous light exposure (LL). Exposure to PM2.5 induced peripheral IR, disrupted circadian steroid release, reduced peak oxygen consumption and altered brown adipose 18Ffluorodeoxyglucose uptake on PET imaging. These findings were identical to that seen with LL with no additive interaction between PM2.5 and LL. Transcriptome profiles in the liver revealed a number of differentially expressed circadian genes Bmal1 (Arntl/Npas2), Period (Per) and Cryptochrome (Cry) in response to PM2.5. Alteration in chromatin accessibility in circadian targets was observed with PM2.5 by Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) while chromatin immunoprecipitation (ChIP) analysis, showed a marked difference in promoter occupancy by p300.  Our data suggest a previously unrecognized role of particulate air pollution in promoting circadian disruption and metabolic dysfunction through epigenetic regulation of multiple circadian targets

overall_design: RNA Seq (transcriptomes) and ATAC Seq (open chromatin region) (to be submitted) in liver sample from mice exposed with LD-FA, LD-PM2.5, LL-FA, LL-PM2.5 (2 samples from each group) for 30 Weeks

first: Palanivel

last: Rengasamy

first: Vinesh

last: Vinayachandran

first: Bongsoo

last: Park

first: E

first: Sanjay

last: Rajagopalan


title: ATAC-seq profiling of of cell lines derived  from primary human cornea epithelial cells (hTCEpi) and human primary corneal keratocyte cells ( hTK)

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated novel genomic resources by mapping regions of open-chromatin, indicators of cis-regulatory activity, in immortalized corneal epithelial and stromal cell lines, using the assay for transposase accessible chromatin followed by sequencing (ATAC-seq).  Overlaying these data with the well-powered UK Biobank CRF-GWAS study demonstrates the keratocyte cells to be a suitable system to guide future functional characterisation of, at least some, regulatory networks modulated by CRF-associated variants.

overall_design: ATAC-seq to chart genome-wide chromatin accessibility.

first: Veronique

last: Vitart


title: A hotspot mutation p.L162R in IKZF3 drives leukemogenesis via transcriptional dysregulation

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: IKZF3 encodes an IKAROS Family transcription factor and has been recently identified as a novel mutated gene in chronic lymphocytic leukemia (CLL), with all mutations occurring at a single hotspot (L162R), located within the DNA binding domain of the protein. Here we show that B cell-restricted conditional knock-in of this mutation skews B cells development and induces CLL-like disease in elderly mice (30% penetrance), confirming its role as a CLL driver. Furthermore, this mutation alters the DNA binding specificity and target selection of IKZ3, leading to overexpression of BCR/NF-?B signaling genes and hyperactivation of these pathways. Likewise, we find an upregulated BCR signaling signature in human CLLs with IKZF3-L162R. Our studies highlight a novel mechanism by which a CLL driver activates the critical oncogenic BCR/NF-?B signaling axis in CLL

overall_design: We generated a novel conditional knock-in murine model with B-cell restricted expression of the Ikzf3-L161R mutation. RNA-seq, ChIP-seq and ATAC-seq were performed in CLL cells with Ikzf3 mutation, non-CLL cells from the same mice with the mutation, as well as WT normal B cells.

first: Shanye

last: Yin

first: Gregory

last: Lazarian

middle: J


title: Reduced Representation Bisulfite Sequencing analysis of human necrotizing enterocolitis

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

country: China

institute: 301 hospital

type: Methylation profiling by high throughput sequencing

summary: Reduced Representation Bisulfite Sequencing was used to assess that changes in intestinal DNA methylation associated with NEC outbreak.

overall_design: Preterm patients who had undergone bowel resection for stage III acute NEC constituted our positive NEC cases and preterm patients who had undergone resection for diseases other than NEC  chosen as control (CTRL) group.

first: Li

last: Lu


title: Multi-parametric profiling of a large panel of engineered nanomaterials (ENM) points to surface chemistry as a key determinant of nanomaterial effects

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Monocytic, cancer derived THP-1 cells were exposed to 31 different engineered nanomaterials (ENMs) with different core chemistries and surface modifications for 24 hours.

overall_design:
96 RNA samples treated with different ENM were analyzed against control samples. Cell culture medium without EMNs was used as negative control. Each condition was performed in triplicate.
These are dual channel microarrays processed as single-channel arrays.

first: Audrey

last: Gallud

first: Mathilde

last: Delaval

first: Pia

last: Kinaret

first: Vittorio

last: Fortino

first: Veersingh

last: Marwah

first: Jimmy

last: Ytterberg

first: Roman

last: Zubarev

first: Tiina

last: Skoog

first: Juha

last: Kere

first: Manuel

last: Correia

first: Katrin

last: Loeschner

first: Zahraa

last: Al-Ahmady

first: Jaime

last: Ruiz

first: Didier

last: Astruc

first: Marco

last: Monopoli

first: Richard

last: Handy

first: Sergio

last: Moya

first: Kai

last: Savolainen

first: Harri

last: Alenius

first: Bengt

last: Fadeel


title: Estrogen-driven control of diabetogenic gene networks is associated with reduced levels of miR-224/452 circulating in extracellular vesicles [miRNA-Seq]

first: Roel

last: Bijkerk

summary: Women with diabetes have a higher prevalence of cardiovascular complications than men, suggesting that sex-steroid hormones like estrogen may impact on female health in diabetes. Here we demonstrate that estrogen suppletion and insulin resistance in male-to-female transgenders coincides with lower plasma levels of miR-224 and miR-452 carried in extracellular vesicles. Systemic silencing of miR-224 and miR-452 in mice triggered a prediabetic phenotype with higher plasma insulin levels, increased white adipose lipogenesis and less glucose uptake and mitochondrial respiration in brown adipose tissue. Consistent with a prediabetic metabolic state, RNA sequencing demonstrated differential expression of genes involved in lipogenesis in white adipose tissue and mitochondrial respiration and glucose uptake in brown adipose tissue. In vitro studies confirmed the estrogen-dependent lowering of miR-224 (brown adipocytes) and miR-452 (white adipocytes) and their impact on adipocyte-specific metabolic processes. Collectively, we identified novel estrogen-driven, post-transcriptional networks that could drive the progression to insulin resistance in transwomen and provide potential anti-diabetic therapeutic targets in women.

overall_design: Total RNA obtained from plasma of male-to-female-transgenders

first: Barend

last: Florijn

first: Anton

last: van Zonneveld


title: Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue

city: Iowa City

first: Paul

middle: B

last: McCray

state: IA

address: 6320 PBDB

department: Pediatrics

institute: University of Iowa

summary: Cystic fibrosis (CF), caused by mutations to CFTR, leads to severe and progressive lung disease. The most common mutant, ΔF508-CFTR, undergoes proteasomal degradation, depleting its anion channel function.  “Proteostasis” pathways, i.e. those relevant to protein processing and trafficking, are altered in cells with ΔF508-CFTR and can be modulated to partially rescue protein function. However, many details regarding proteostasis modulation, and its relevance to CF and ΔF508-CFTR rescue, remain poorly understood. To shed light on this, we re-analyzed public datasets characterizing transcription in CF vs. non-CF epithelia from human and pig airways, and also profiled established temperature, genetic, and chemical interventions that rescue ΔF508-CFTR. Meta-analysis yielded a core disease signature and two core rescue signatures. To interpret these, we compiled proteostasis pathways and an original “CFTR Gene Set Library”. The disease signature revealed differential regulation of mTORC1 signaling, endocytosis, and proteasomal degradation. Overlaying functional genomics data identified candidate mediators of low-temperature rescue, while multiple rescue strategies converged on activation of unfolded protein response pathways. Remarkably, however, C18, an analog of the CFTR corrector compound Lumacaftor, induced minimal transcriptional perturbation despite its rescue activity. This work elucidates the involvement of proteostasis in both disease and rescue perturbations while highlighting that not all CFTR rescue interventions act on transcription.

overall_design: Polarized air-liquid interface cultures of CFBE cells were treated to either knockdown of SIN3A, SYVN1 or NEED8, overexpression of miR-138, treated with corrector compound 18 (C18), or cultured at temperatures associated with improving ΔF508-CFTR trafficking.

first: Shyam

last: Ramachandran


title: CRISPR repair in a preclinical model of Noonan syndrome associated cardiomyopathy II

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: We profiled RNA expression in human iPSC-derived cardiomyocytes from patients with LZTR1-associated Noonan syndrome

overall_design: 4 biological replicates of human iPSC-derived ventricular cardiomyocytes from 2 Noonan syndrome patients and 7 biological replicates of iPSC-derived ventricular cardiomyocytes from 4 CRISPR-corrected patient cell lines

first: Lukas

last: Cyganek


title: Neuro-condition media of mesenchymal stem cells (MSCs) inhibited the proliferation and pluripotency of glioma stem cells,

city: Amman

first: Deema

middle: Adnan

last: Ali

address: queen Rania street

department: cell therapy center

country: Jordan

institute: The University of Jordan

summary:
We used microarray global gene expression profiling to investigate the effect caused by neuro-condition media of MSCs on the growth and pluripotency of glioma stem cells.
The effect was specifically investigated for cell cycle arrest, cell differentiation, invasion and self renewal ability of glioma stem cells,

overall_design: Paracrine factors from six biological samples of MSCs( 3 WJ-MSCs, 3 BM-MSCs) were collected as treatment and were applied on actively growing glioma stem cells as spheroids for 7 days.

first: Nazneen

last: Aslam

first: Elham

last: abusharieh

first: Abdalla

last: Awidi

first: Abuarqoub

last: Dua'a

first: Ali

last: Dema


title: Identifying and overcoming a mechanism of resistance to Wee1 kinase inhibitor AZD1775 in high grade serous ovarian cancer cells (OVCAR8)

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: Treatment of Human high grade serous ovarian cancer cell line, OVCAR8,  with WEE1 kinase inhibitor AZD1775

overall_design: 12 samples (MKG101-112) from triplicate cultures of OVCAR8 parent treated with 100nM AZD1775 for 24 hours and three OVCAR8-derived clones resistant to 300nM AZD1775 and maintained under selection

first: David

middle: W

last: Melton

first: Miriam

middle: K

last: Gomez


title: Putative Allergens Identified in Mango (Mangifera indica Linn) leaf and fruit with transcriptome analysis

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

institute: Guizhou Normal University

summary:
Purpose: this study provided a comprehensive sequence for a systemic view of the transcriptome between mango leaf and fruit, as well as fruit allergens, which will be useful for further genomic research studies and breeding of lower allergenic mango cultivars.
Methods:Some allergens have previously been identified in mango (Mangifera indica Linn), including profilins, Bet v 1-like proteins and chitinase. In this paper, 66 potential allergen genes were identified and their relative expressions evaluated in mango fruit and leaf using Illumina RNA-Seq technology.
Results:A total of 17.63Gb Clean Data was obtained.The number of %≥Q30 was above 94.58%.RNA-Seq generated 11,751,123 contigs that were assembled into 99,328 unigenes with 16,848 unigenes of >1000 bp. A total of 230,242 unigenes were annotated using public protein databases, with a cut-off E-value above 10−5, of which 27,295, 46,030, 24,227 and 14,023 unigenes were assigned to gene ontology terms, Nr, Swiss-Prot and clusters of orthologous groups, respectively. Allergens mainly belonged to pollen allergen, pathogenesis-related protein Bet v I family and NADPH-dependent FMN reductase.

overall_design: Two tissues, including leaf and fruit from Mangifera indica, were collected and immediately stored in liquid nitrogen for RNA extraction, then sequenced via Illumina HiSeq 4000.

first: Yan

last: Huiqing

first: Huang

last: Xiaolong


title: Sphingomyelins secreted by mammosphere-derived cells present a novel mechanism for the low mammary cancer incidence observed in certain mammals

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: We describe a novel mechanism by which mammals with a low mamary cancer incidence may avert mammary cancer development.

overall_design: RNAsequencing of 2 technical replicates of 2 cell lines, each treated and untreated, for a total of 8 samples.


title: miRNA expression data from myogenic progenitor cell-derived extracellular vesicles

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

summary: In this dataset, we profiled miRNAs in extracellular vesicles derived from 24 hour cultured myoblasts (wild-type C57BL6/J)

overall_design: Myogenic progenitor cells from adult mice were isolated via fluorescence activated cell sorting, plated and allowed to proliferate until confluent on 10 cm plates, then media was conditioned by cells for 24 hours. Conditioned media was collected, extracellular vesicles were isolated, RNA was extracted, the miRNAs were profiled via microarray.

first: Murach

last: Kevin

first: Peterson

last: Charlotte


title: Identifying and overcoming a mechanism of resistance to Wee1 kinase inhibitor AZD1775 in high grade serous ovarian cancer cells (ES-2)

summary: Treatment of Human high grade serous ovarian cancer cell line, ES-2,  with WEE1 kinase inhibitor AZD1775

overall_design: The experiment comprises 16 samples (MKG1-16) from ES-2 and ES-2 derived resistant clones:  duplicate cultures of untreated ES-2 parent and ES-2 parent treated for 24 hours with 100nM AZD1775,  triplicate cultures of four resistant clones maintained in AZD1775- two clones resistant to 1000nM AZD1775 and their progenitors resistant to 250nM AZD1775


title: Mutant p53 regulates survivin to foster lung metastasis

first: Mirazul

last: Islam

address: D857A, Dana Farber Cancer Institute, 44 Binney St. Boston MA

department: Medical Oncology

institute: DFCI

summary: Esophageal cancer is one of the most common cancers where TP53 is mutated frequently. Esophageal squamous cell carcinoma (ESCC) is the major subtype of esophageal cancer, and is one of the most lethal cancers worldwide. ESCC evolves often to lung metastasis, which is associated with a dismal prognosis. P53R175H (homologous to Trp53R172H in mice) is a common hot spot mutation. How metastasis is regulated by p53R175H in ESCC, or cancers in general, remains to be elucidated. To investigate p53R175H mediated molecular mechanisms, we utilized germline Trp53R172H/- mice, and generated esophageal specific Trp53-/- mice and Trp53+/+ mice treated with the 4-NQO esophageal-specific carcinogen (a common exposure in humans) to model ESCC. In the primary Trp53R172H/- tumor cell lines established from these mouse models, we depleted Trp53R172H (shTrp53) and observed a marked reduction in cell invasion in vitro and lung metastasis burden in a tail-vein injection model in comparing isogenic cells (shCtrl). Furthermore, to understand the molecular basis for mutant p53 driven lung metastasis, we performed bulk RNA-seq to compare gene expression profiles of metastatic and primary shCtrl and shTrp53 cells. We performed Gene Set Enrichment Analysis (GSEA) and identified the YAP-BIRC5 axis as a potential mediator of Trp53R172H mediated metastasis. As a target gene of YAP, BIRC5 encodes an anti-apoptotic protein, namely survivin. We demonstrate that survivin expression increases in the presence of Trp53R172H but not wild-type Trp53.  Furthermore, depletion of survivin decreases Trp53R172H driven lung metastasis. Mechanistically, Trp53R172H but not wild-type Trp53, binds with YAP in ESCC cells, suggesting their cooperation to induce survivin expression. Furthermore, survivin high expression level is associated with increased metastasis in several GI cancer, suggesting that survivin may be a key regulator to metastasis. Taken together, this study unravels new insights into how mutant p53 mediates metastasis.

overall_design: we generated a panel of eight metastatic cell lines  from lung metastases at week 8 through YFP+ FACS sorting and confirmed that Trp53R172H depletion was maintained. To understand the molecular basis in Trp53R172H driven ESCC lung metastasis, we performed RNA-seq analysis on shCtrl-Metastatic (n=5: 376, 377, 378, 382, 383), shTrp53-Metastatic (n=3: 384, 386, 387), shCtrl-Primary (n=1: 18Ctrl) and shTrp53-Primary (n=1: 18shRNA) cell lines.

first: Qiaosi

last: Tang

first: Anil

last: Rustgi


title: Identifying cleaved and noncleaved targets of small interfering RNAs and microRNAs in mammalian cells by SpyCLIP

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

summary: we report a strategy to establish a comprehensive picture of siRNA cleaved and noncleaved off-targets by performing SpyCLIP using wild-type and catalytically inactive AGO2 mutants in parallel. Additionally, we investigated naturally occurring cleavage events mediated by endogenous miRNAs using the same strategy. Our results demonstrated that AGO2 SpyCLIP is a powerful method to identify both cleaved and noncleaved targets of siRNAs, providing valuable information for improving siRNA design rules

overall_design: Examination of AGO2 binding RNAs in conditions with SpyCLIP

first: Yao

last: Zhang

first: Yilan

last: Teng

first: Wangwen

last: Xiao

first: Beiying

last: Xu

first: Ya

last: Zhao

first: Weihua

last: Li


title: Screening of miR-379 target RNAs by comparison of WT and miR-379 KO mouse primary kidney mesangial cells by using CLASH technique [RNA-Seq]

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: We screened for miR-379 targets in primary mesangial cells from wild-type vs. miR-379KO mice using unbiased CLASH sequencing approach and identified the redox protein thioredoxin (Txn1) and mitochondrial fission-1 protein (Fis1).

overall_design: Comparison of WT and miR-379KO MMC by regular RNA-seq, Ago2IP-seq

first: Mitsuo

last: Kato

first: Zhuo

first: Xiwei

first: Jinhui

last: Wang

first: Zhen

first: Feng-Mao

last: Lin

first: Rama

last: Natarajan


title: Epigenetic gene-expression links heart failure to memory impairment [chipseq_from_saha_treatment]

first: Md Rezaul

address: von siebold str. 3a

institute: DZNE

summary: In current clinical practice care of diseased patients is often restricted to separated disciplines. However, such an organ-centered approach is not always suitable. For example, cognitive dysfunction is a severe burden in heart failure patients. Moreover, these patients have an increased risk for age-associated dementias. The underlying molecular mechanisms are presently unknown and thus corresponding therapeutic strategies to improve cognition in heart failure patients are missing. Using mice as model organisms we show that heart failure leads to specific changes in hippocampal gene-expression, a brain region intimately linked to cognition. These changes reflect increased cellular stress pathways which eventually lead to loss of neuronal euchromatin and reduced expression of a hippocampal gene cluster essential for cognition. Consequently, mice suffering from heart failure exhibit impaired memory function. These pathological changes are ameliorated via the administration of a drug that promotes neuronal euchromatin formation. Our study provides first insight to the molecular processes by which heart failure contributes to neuronal dysfunction and point to novel therapeutic avenues to treat cognitive defects in heart failure patients.

overall_design: Analysis of H3K4me3 Chipseq data from 3 months old CamkdeltaC mice CA1 hippocampal region after 4 weeks Vorinostat/vehicle treatment

first: Islam

last: Rezaul

first: Fischer

last: Andre


title: The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [HiC]

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

summary: Recent studies suggested that crosstalk between ERα and EGFR/HER2 pathways plays a critical role in mediating endocrine therapy resistance. Several targeting EGFR/HER2 signaling inhibitors including FDA-approved lapatinib and gefitinib as well as a novel dual tyrosine kinase inhibitor (TKI) sapitnib showed greater inhibitory efficacies. However, how a 3D chromatin landscape of the response to the inhibition to EGFR/HER2 pathway remains to be elucidated. In this study, we conducted in situ Hi-C and RNA-seq in two ERα+ breast cancer cell systems, tamoxifen-sensitive MCF7 and T47D and tamoxifen-resistant MCF7TR and T47DTR before and after the treatment of sapitnib. We identified differential response of topologically associated domains (TADs), looping genes and expressed genes. Interestingly, we found that many differential TADs and looping genes are reversible, indicating that EGFR/HER2 signaling may play a role in reshaping and rewiring the high order genome organization. We further examined and recapitulated the reversible looping genes in 3D spheroids of breast cancer cells. Our data provides a rich resource for further evaluating chromatin structural response to anti-EGFR/HER2 targeted therapies in endocrine-resistant breast cancer.

overall_design: Hi-C experiment of 3 cell types, 2 biological replicates for each cell type;

first: Yini

last: Yang

first: Lavanya

last: Choppavarapu


title: The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [RNA-seq]

overall_design: RNA-seq experiment of 6 cell types with or without drugs, 3 biological replicates for each condition;


title: Differential gene expression in Hep3B and Hep3B SOX4-/- cells

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Overexpression of SOX4 in various kinds of cancers specimen was associated with poor prognosis of patients; however, the role of SOX4 in angiogenesis or tumor microenvironment modulation remains unclear. Therefore the endogenous SOX4 was knockout and the differential gene expression between Hep3B and Hep3B SOX4-/- cells were examined via genechip.
We found that the differentially expressed genes, EzH2, a SOX4-associated partner, and CXCL12, were repressed in Hep3B SOX4-/- cells compared with parental Hep3B; these results were further assessed via qRT-PCR in Hep3B SOX4-/- versus Hep3B cells.

overall_design: Endogenous SOX4 knockout in Hep3B cells via the CRISPR/cas9 system that was designed as Hep3B SOX4-/-, the transcriptome of Hep3B and Hep3B SOX4-/- cells were analyzed via an Affymetrix GeneChip™ Human Transcriptome Array 2.0.

first: Chi-Neu

last: Tsai

first: Ming-Chin

last: Yu


title: Identification of genetic susceptibility factors associated with canine gastric dilatation-volvulus

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Canine gastric dilatation-volvulus (GDV) is a common life-threatening condition occurring primarily in large and giant breeds with a 3.9% to 36.7% lifetime risk. GDV is a complex disease with risk factors including age, diet, behavior, family history, and genetics. The genetic correlates of GDV have not previously been systematically explored.
We undertook multiplatform genome-wide association analysis (GWAS) of 253 dogs including 106 healthy dogs and 147 dogs with at least one GDV episode. The study included ten dog breeds enriched for Borzoi, German Shepherd (GSD), Great Dane, and Standard Poodle. SNP array genotyping was performed on constitutional DNA from all 241 samples to identify GDV-associated SNPs and CNVs. To increase the coverage of our study we performed imputation analysis of the SNP data as well as additional whole genome sequencing (WGS) on a subset of 33 dogs (15 healthy dogs and 18 GDV patients from the three most represented breeds). Twenty-one patients were genotyped by both SNP and WGS platforms. The GWAS was conducted across breeds as well as on specific breeds using a mixed linear model adjusting for relatedness, population structure and sex.
After genome-wide Bonferroni correction, we identified a significant protective GDV-associated SNP, rs851737064, occurring in an intergenic region, across all breeds. The signal was most significant in Collies, German Shorthaired Pointers, and Great Danes. Subsequent focused analysis across these three breeds identified 12 additional independent, protective and deleterious SNPs with significant GDV association. Additional GWAS conducted on Borzoi, GSD and Great Dane yielded significant genome-wide GDV associations in 11 independent SNPs, while that in Borzoi alone identified 2 independent GDV-associated SNPs. We then used WGS data to validate the imputation analysis. Notable significant SNPs included genes involved in gastric tone and motility including VHL, NALCN, and PRKCZ. From the WGS data we also detected two independent GDV-associated SNPs in Borzoi, GSD and Great Dane breeds on an intergenic region on chromosome 7 not covered by previous analyses. These data provide important new information regarding canine GDV risk factors and facilitate generation of hypotheses regarding the genetic and molecular underpinnings this syndrome.

overall_design: We analyzed a total of 147 GDV cases and 106 healthy controls using the CanineHD Whole-Genome Genotyping BeadChip. After quality controls, the final dataset was composed by 125 GDV cases and 90 HC. Data were imputed with Beagle using a reference panel of 365 dogs from different breeds characterized with Whole Genome Sequencing (Hayward et al., 2019; Plos Genetics 15:e1008003; BioProject: PRJNA517114). GWAS was conducted on the imputed data using a mixed linear model accounting for population stratification, relatedness and sex. P-values were adjusted for multiple testing with the Bonferroni method, accounting for the number of independent SNPs with a Linkage Disequilibrium estimate.

middle: S

first: Nieves

last: Perdigones

first: Victoria

last: Zismann

first: Natalia

last: Briones

first: Salvatore

last: Facista

first: Jose

middle: L

last: Rivera

first: Elizabeth

last: Rozanski

first: Cheryl

middle: A

last: London

first: William

middle: P

last: Hendricks


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [7PMH CD302KO]

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

summary: Virus species- and tissue-tropism is governed by host dependency and restriction factors. Hepatitis C virus (HCV) exhibits a narrow species-tropism and murine hepatocytes are refractory to infection. Using murine liver cDNA library screening we identified Cd302, a lectin, and Cr1l, a complement receptor, as pan-genotypic restrictors of HCV infection. Cd302/Cr1l interact to impede virion uptake and co-operatively induce a non-canonical transcriptional program, inhibiting HCV and hepatitis B virus (HBV) infection in vitro. CAS9 disruption of murine hepatocyte Cd302 expression increased HCV permissiveness in-vivo and ex-vivo, and modulated the intrinsic hepatocyte transcriptome dysregulating metabolic process and host defense genes. In contrast, co-operative CD302/CR1L expression was absent and HCV restriction reduced in human hepatocytes. The Cd302/Cr1l axis therefore contributes to limiting hepatotropic virus cross-species transmission to mice, opening new avenues for step-wise development of mouse models for these important human pathogens, which cause substantial disease burden globally.

overall_design: Primary mouse hepatocytes from x3 entry receptor transgenic mice with conditional liver expression (human Occludin and CD81: hOChep) and x3 entry receptor transgenic mice with an additional disruption of the CD302 locus (hOChep Cd302-/-)   were isolated after liver perusion and liberase digestion. Hepatoyctes were plated onto 6-well tissue culture dishes dishes and cultured in HCM for 48 hours. RNA was then isolated for RNA-seq.

first: Richard

last: Brown

first: Thomas

last: Pietschmann


title: A Tissue-Specific Tankyrase Inhibitor Drives Key Developmental and Oncogenic Pathways

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Tissue-specific regulation of WNT and YAP/TAZ signaling is critical for optimal organismal growth, development, and maintenance. Uncontrolled activity often leads to developmental abnormalities and aggressive cancers. Tankyrase (TNKS) is a poly-ADP-ribose polymerase (PARP) that controls both WNT and YAP/TAZ signaling. However, it is unclear how TNKS activity is regulated in a tissue and cell-type specific manner. Here, we identified the previously uncharacterized prostate-associated gene 4 (PAGE4) as a tissue-specific TNKS inhibitor. Structural and biochemical studies revealed that mechanistically PAGE4 inhibits TNKS through hijacking TNKS substrate binding pockets leading to the stabilization of TNKS substrates. In vitro cell culture and in vivo zebrafish and transgenic mouse model studies showed that PAGE4 is a potent inhibitor of TNKS and WNT signaling. Interestingly, PAGE4 is physiologically restricted to expression in select tissues and cell types, including WNT producing prostatic fibroblasts where spatiotemporal regulation of WNT signaling is critical for proper organ development. Surprisingly, PAGE4 is aberrantly expressed in hepatocellular carcinomas that bypass TNKS through mutant CTNNB1 driven WNT signaling. In vitro and in vivo tumorigenic studies revealed that PAGE4 initially function as a tumor suppressor through inhibition of WNT signaling, but upon CTNNB1 mutation becomes an oncogenic driver through YAP/TAZ signaling. Thus, we establish PAGE4 as a robust tissue-specific TNKS inhibitor that physiologically coordinates developmental WNT signaling, but genetic aberration during cancer progression re-wire PAGE4 into pro-oncogenic YAP/TAZ pathway.

overall_design: Comparing WT , Mutant and RWPE samples

first: Sajjan

last: Koirala

first: Jonathon

last: Klein

first: Yumei

last: Zheng

first: Nicole

middle: O

last: Glenn

first: Travis

last: Eisemann

first: Klementina

last: Fon-Tacer

first: Ozlem

last: Kulak

first: Meifen

last: Lu

first: Geoffrey

last: Neale

first: Heather

last: Tillman

first: Peter

last: Vogel

first: Douglas

last: Strand

first: Lawrence

last: Lum

first: Chad

last: Brautigam

first: John

middle: M

last: Pascal

first: Wilson

last: Clements

first: Brenda

last: Schulman

first: Patrick

last: Potts


title: Effect of c-Myb Deficiency in Irf4/8-/- large pre-B cells

city: Charlottesville

first: Timothy

last: Bender

state: Virginia

address: 345 Crispell Dr. MR-6, RM #3707

institute: University of Virginia

summary: Differential gene expression analysis comparing c-Myb-sufficient and -deficient Irf4/8-/- large pre-B cells. The results of this study are the first to demonstrate a role for c-Myb during the large pre-B cell stage of B lymphocyte development. The results provide insight into roles for c-Myb in regulating components of glucose metabolism in large pre-B cells as well as the differentiation of large pre-B cells to the small pre-B cell compartment.

overall_design: Irf4/8-/- large pre-B cells were transduced with retroviruses that co-produce a GFP reporter and a Myb mRNA targeting shRNA (shMyb) or a a control Luciferase mRNA targeting shRNA (shLuc) in duplicate. Transduced cells were electronically sorted based on GFP expression and total cellular RNA was prepared. Next generation sequencing (RNA-seq) was performed on isolated mRNA from each sample on the Illumina NextSeq 500 for paired-end sequencing.

first: Andrea

last: Daamen


title: Expression profiling of tumor lymphatic endothelial cells upon acute Ang2 inhibition

city: Heidelberg

first: Nicolas

last: Gengenbacher

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

institute: German Cancer Research Center

summary: Lymphatic endothelial cells (LEC) were isolated from MT-ret tumor tissue 12h after treatment with an Ang2-blocking antibody or control-IgG

overall_design: Total RNA-sequencing of FACS-sorted LEC. Five independent biological replicates for each treatment

first: Hellmut

middle: G

last: Augustin


title: Screening of miR-379 target RNAs by comparison of WT and miR-379 KO mouse primary kidney mesangial cells by using CLASH technique [CLASH-Seq]

first: Nancy

last: Chen

overall_design: Comparison of WT and miR-379KO MMC by Ago2IP-ligation-seq (CLASH)

first: Mitsuo

last: Kato

first: Zhuo

first: Xiwei

last: Wu

first: Jinhui

last: Wang

first: Zhen

first: Feng-Mao

last: Lin

first: Rama

last: Natarajan


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice

first: Birthe

last: Tegtmeyer

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

overall_design: Refer to individual Series


title: Screening of miR-379 target RNAs by comparison of WT and miR-379 KO mouse primary kidney mesangial cells by using CLASH technique


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [5PHH]

overall_design: Primary human hepatocytes were isolated from livers of three different donors undergoing partial hepatectomy. Hepatoyctes were plated onto 6-well tissue culture dishes dishes and cultured in HCM, followed by RNA extraction.

first: Richard

last: Brown

first: Thomas

last: Pietschmann


title: Identifying and overcoming a mechanism of resistance to Wee1 kinase inhibitor AZD1775 in high grade serous ovarian cancer cells

city: Edinburgh

first: Graeme

last: Grimes


title: Expression data from MT-ret tumor tissue

summary: Expression analysis of total MT-ret tumor RNA upon neo-adjuvant Ang2 targeting

overall_design: MT-ret tumor bearing mice were treated with an Ang2-blocking antibody or a corresponding isotype control during primary tumor growth. Total tumor RNA was analyzed.

first: G

middle: H


title: The postprandial transcriptomic response of adipose tissue to high fat meals in middle-aged men with metabolic syndrome

city: Notting Hill

first: Aimee

last: Dordevic

state: VIC

address: Level 1, 264 Ferntree Gully Rd

department: Nutrition, Dietetics & Food

country: Australia

institute: Monash University

summary: This study aimed to examine the postprandial transcriptome of adipose tissue middle-aged men selectively recruited on the basis of MetS (defined by the International Diabetes Federation (IDF) criteria) and healthy control participants. Two breakfast meals that provided different macronutrient composition, and were indicative of major patterns of dietary habits (animal-based versus plant-based) were given, postprandial adipose gene expression was measured by microarray at fasting (0 h) and 4 hours post-meal.

overall_design: Total RNA obtained from adipose tissue biopsies at fasting (0 h) and 4 h postprandial.

first: Susan

last: Coort

first: Chiara

last: Murgia

first: Chirs

last: Evelo

first: Amy

last: Larsen

first: Petra

last: Gran

first: Andrew

last: Sinclair

first: Maxine

last: Bonham

first: David

last: Cameron-Smith


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [6PMH siRNA]

overall_design: Primary mouse hepatocytes from x3 entry receptor transgenic mice with conditional liver expression (human Occludin and CD81: hOChep) and one wildtype control mouse were isolated after liver perfusion and liberase digestion. Hepatoyctes were plated onto 6-well tissue culture dishes dishes and cultured in HCM. 24 hours after plating hepatocytes were transfected with siRNAs targeting the genes of interest or a control siRNA. 24 hours after siRNA transfection hepatocytes were infected with HCV (strain Jc1, MOI 1) or left uninfected. 24 hours post infection RNA was isolated for RNA-seq.


title: Identification of ERα AF-1 or AF-2 mediated genes in mouse uterus

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Estrogen receptor alpha (ERα) is a ligand dependent transcription regulator, which contains two transactivation functional domains, AF-1 and AF-2. These activities are regulated differently by the ligands. Specifically, the selective estrogen receptor modulators (SERMs) regulate AF-1 rather than AF-2. It is important to know whether AF-1/AF-2 predominantly regulated genes exist in the tissues for a better understanding of the SERMs functionality. We sought out AF-1 dependent estrogenic genes by using the AF-2 mutated knock-in (KI) mouse model, AF2ERKI. AF2ER is an estrogen-insensitive AF-2 disrupted ERα mutant mouse but unique to this model, AF-1 can be activated by the estrogen-antagonist, fulvestrant (ICI), in vitro and in vivo. The information of ICI-mediated gene expression profile of AF2ERKI could define whether AF-1/AF-2 predominantly regulated genes exist in the tissues.

overall_design: Ovariectomized (OVX) mice were treated with vehicle or chemicals for 6h. Uterus was collected from the 3 mice in each treatment for microarray samples (three biological replicas).

first: Yukitomo

last: Arao

first: Katherine

last: Hamilton

first: Kenneth

last: Korach


title: LSH facilitates DNA methylation primarily by promoting UHRF1 DNA accessibility and DNA methylation by DNMT1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Accumulative studies indicate that DNA maintenance methylation by DNMT1 is initiated by binding of UHRF1 to replication fork. However, how UHRF1 gains access to chromatin in S phase is poorly understood. Here we report that LSH, a SNF2 family chromatin remodeler, facilitates DNA methylation in somatic cells primarily by promoting DNA methylation by DNMT1. We show that knockout of LSH in various somatic cells resulted in substantial reduction of DNA methylation, whereas knockout of DNMT3A and DNMT3B only moderately reduced the level of DNA methylation. Consistent with a role in maintenance methylation, genome-wide analysis of DNA methylation revealed a widespread reduction of DNA methylation in all genomic elements in LSH null cells. Mechanistically, we demonstrate that LSH interacts with UHRF1 but not DNMT1 and facilitates UHRF1 chromatin association, UHRF1-catalyzed H3 ubiquitination, and subsequent DNMT1 recruitment to replication fork. Notably, UHRF1 also enhances LSH association with replication fork. Thus, our study identifies LSH as an essential factor for maintenance methylation and provides novel insight into how LSH facilitates maintenance methylation.

overall_design: Reduced representation bisulfite sequencing (RRBS) were first carried out for LSH KO/WT cells of HCT116 and HeLa. RNA-seq was carried out for LSH KO/WT cells of HeLa.

first: Mengmeng

last: Han

first: Jiemin

last: Wong


title: Genome-wide chromatin interactions identify characteristic promoter-distal loops

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: We developed a novel computational model, HiSIF (Hi-C Significant Interacting Fragments), which uses a Poisson Mixture Model (PMM) with a power-law decay background. We compared its performance to some existing programs with publicly available Hi-C data, and then applied it to in situ Hi-C data in breast cancer sensitive and resistant cells.

overall_design: In this study, we tested the model in our newly generated Hi-C data in three ERα positive breast cancer cell lines, MCF7, tamoxifen-resistant MCF7 (MCF7-TamR) (MCF7 and MCF7-TamR data have been deposited in GEO under accession number GSE108787), T47D and tamoxifen-resistant T47D (T47D-TamR), ZR75-1 and tamoxifen-resistant ZR75-1 (ZR75-1-TamR).

first: Victor

last: Jin


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [4Total liver]

first: Birthe

last: Tegtmeyer

overall_design: After perfusion to remove blood cell contaminants, total livers of x3 inbred mouse strains were removed and flash-frozen in liquid nitrogen. Flash-frozen liver sections were homogenised in RA1 buffer prior to total RNA extraction and RNA-seq.

first: Richard

last: Brown

first: Thomas

last: Pietschmann


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [2Ectopic expression]

overall_design: Huh-7.5 cell-lines stably overexpressing the indicated murine gene(s) were used for infection experiments. To determine whether the over expression of murine genes modulated the intrinsic transcriptome of these x4 over-expressing cell-lines, 3 different passages of each cell-line were taken. RNA was extracted and used for RNA-seq.


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [3PMH]

overall_design: Primary mouse hepatocytes from x3 inbred mouse strains were isolated after liver perusion and liberase digestion. Hepatoyctes were plated onto tissue culture dishes dishes and cultured in HCM, followed by RNA extraction.


title: ABA-responsive gene expression under shade

city: Albany

first: ByungHoon

middle: Brian

last: Kim

state: GA

address: 504 College Dr.

institute: Albany State University

summary: Microarray analysis to investigate the global gene expression patterns in response to ABA under different light quality backgrounds

overall_design: Samples treated with four different conditions were used to monitor the effect of one factor in the background context of another factor.


title: Analysis of Escherichia coli adaptation to a sublethal concentration of sodium bisulfite

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

country: Spain

institute: University of the Basque Country

summary:
Little is known about cell responses and survival in the presence if reducing agents that could change the redox state of living organisms potentially conferring a negative effect on major metabolic pathways and respiration. As many reducing reagents, in particular sulfur-containing compounds, are widely used as food preservatives, we decided to study effects of sublethal concentrations of reducing reagents on bacterial adaptation.
The aim of this study was to analyse and compare the transcriptome profils of untreated and sulfite-treated Escherichia coli cells obtained by employing microarray analysis.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA was isolated from Echerichia coli MG1655 cultures grown in M9 supplemented with 0.4% glucose prior and after sulfite treatment and submited for microarray analysis

first: Vladimir

middle: R

last: Kaberdin

first: Itxaso

last: Montánchez

first: Ion

last: Recio


title: Regulatory network of SlDof1 in fruit ripening

city: Beijing

first: Yuying

last: Wang

address: No.20 Nanxincun, Xiangshan

institute: Institute of botany, the chinese academy of sciences


title: Expression profiling of tumor endothelial cells [single cells]

first: Nicolas

last: Gengenbacher

summary: Blood (BEC) and lymphatic (LEC) endothelial cells were isolated from MT-ret tumors and 10x Genomics-based single-cell RNA-seq analysis was performed.

overall_design: 10000 FACS-sorted BEC and 10000 FACS-sorted LEC were used for the library preparation. For each sample four libraries were generated. Multiplexed samples were sequenced with a HiSeq 4000 machine.

first: Hellmut

last: Augustin


title: RNA sequencing Reveals the Differentially Expressed Genes between Wild-type and SlDof1-RNAi Fruits

summary:
Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage.
Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays.
Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.

overall_design: Expression profiles of wt and SlDof1-RNAi fruits at 38 dpa were generated by RNA deep sequencing, with three replicates, using Illumina HiSeqTM 2000

first: Guozheng

last: Qin


title: The impact of defective cholesterol metabolism on sex-specific hepatocarcinogenesis in hepatocyte specific deletion of Cyp51 in mice

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
The potential role of defective cholesterol metabolism in HCC development and exposition the Cyp51 gene as a promising marker with tumor suppressor potential in sex-dimorphic chronic liver pathogenesis in mice.
Hepatocyte-specific Cyp51 knock-out (KO) and wild type (WT) mice on a mixed background (129/Pas (10%) × C57BL/6J (90%)) of both sexes (F and M) were investigated at the age of 24 months. From each of KO mice, two samples (a tumor and a surrounding tissue) were considered.

overall_design: Microarrays were hybridized with individual samples from livers of 14 mice (6 male, 8 female) at 24 months of age. 8 samples were hybridized from WT mice, i.e. 4 from male and 4 from female mice. 6 KO mice were investigated, i.e. 2 male and 4 female. From each of KO mice, two samples (a tumor and a surrounding tissue) were taken; altogether, 6 tumor and 6 corresponding surrounding-tissue samples were hybridized from KO mice.

first: Kaja

last: Blagotinsek Cokan

first: Damjana

last: Rozman


title: Genome-wide profiling reveals the distribution pattern of abasic sites in mammalian genomes

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary:
The AP-seq provides a genome-wide method for detecting abasic sites among the human and mouse genomes
Purpose: Abasic sites are one of the most frequent DNA damage among the genome , which often carries harmful consequences for the genome stability and the normal cell functions. So it is necessary to develop a whole genome abasic sites (AP sites) profiling method to detect all the AP sites among the genome, which we called the AP-seq.
Methods: The human and mouse genome are processed with enzymatic fragmentation, damage repair, biotin-dU labeling, and pull-down steps. After the sequencing library preparation, the  FASTQ files are produced by the Illumina HiSeq XTen platform. To guarantee the reproducibility, each case of the experiment is present with two biological replicates.
Results:   The reproducibility of our two biological replicates shows a high correlation which larger than 0.95. And the overlap AP site peaks between the HEK293T and MCF-7 cell line are over 50%, which show a great similarity between the different cell lines. Totally, we identified more than 2000 and 1000 abasic site peaks in human, and mouse cell lines separately. Moreover, the distribution of these AP sites prefer to locate in the intergenic regions and introns.

overall_design: We explored a genome-wide efficient method to map the abasic sites in human and mouse genome called AP-seq. And perform the AP-seq with human HEK293T, MCF-7, and mouse embryo stem cells (mESC).

first: Liu

last: Menghao

first: Meng

last: Haowei

first: Lv

last: Zhicong

first: Yi

last: Chengqi


title: Genome-wide binding analysis of SlDof1 in tomato fruit

summary: We used the mode-based analysis of ChIP-seq (MACS) to identify a total of 18375, 14938, and 13680 peaks from the three biological replicates, respectively. SlDof1 target genes are involved in a variety of metabolic pathways and further analysis verified that SlDof1 direct regulates some well-known ripening-related genes.Our data suggest that SlDof1 acts as both activator and repressor, and these findings contribute to understanding the transcriptional regulatory networks underlying fruit ripening.

overall_design: Examination of SlDof1-binding sites in wild-type fruits at 38 days after polination (dap)


title: ChIP of SMC2 at defined cell cycle stages

first: Lora

last: Boteva

state: City of Edinburgh, Midlothian

address: Crewe Road

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary: Investigating binding of the SMC2 protein genome-wide in synchronised HCT116 cells at early S, late S and G2/M

overall_design: HCT116 cells were synchronised at the G1/S boundary and released either in normal media or in media supplemented with 0.4microM aphidicolin to induce replication stress. Cells were harvested at 4, 8 and 10h post release, corresponding to early S, late S and G2/M. Cells were fixed and ChIP for SMC2 was performed

first: Ryu-suke

last: Nozawa

first: Nick

last: Gilbert


title: Deregulation of the Hippo pathway promotestumor cell proliferation through YAP activity in human sporadic vestibular schwannoma

city: beijing

first: zhao

last: fu

address: No. 6 Tiantan Xili Dongcheng District

institute: Beijing Neurosurgical Institute

summary:
Object: The main limitation of treatment strategies for vestibular schwannomas (VSs) is loss of function of vestibulocochlear and facial nerves, which has driven investigations into new pharmaceutical therapies. The most common genetic alteration in human VSs is loss ofthe NF2 gene which encodes the protein merlin. It is well established that merlin achieves tumor suppressive functions through regulation of the Hippo pathway. The aim of this study was to analyze dysregulation of the Hippo pathway in sporadic VSs and to identify whether Hippo signaling could be potential targetable pathway for treatment of VS.
Methods: In this study, we performed gene expression profiling of ten human sporadic VSs and four normal control vestibular nerves to identify aberrant expression of the Hippo pathway in VSs. Molecular subtypes in VSs was evaluated using unsupervised hierarchical clustering analysis. Western blot analysis and immunohistochemical staining were used to examine the expression of Hippo pathway core components in twenty human sporadic VSs. NF2 gene sequencing and mutation analysis were performed in all VS samples. Ki67 marker was used to investigate proliferation of tumor cells. Verteporfin was used to determine whether the inhibitor of YAP-TEAD reduced proliferation of human primary VS cells with NF2 mutations and RT4-D6P2T cell line. Results: We found fifty-one differentially expressed genes between VSs and controls. Unsupervised analysis of transcriptional profiles identified the two distinct molecular variants, which was significantly associated with NF2 mutation status. The protein level of MST2, LAST2,phospho-LAST1, and phospho-YAP were significantly decreased in VSs compared with normal tissues. Nuclear YAP staining was positively correlated with Ki-67 indexin VS samples. Finally, verteporfin reduced viability of human primary VS cells and in a dose-dependent manner by decreasing YAP expression. Conclusions: Our findings implicate that deregulation of the Hippo pathway as a molecular mechanism of pathogenesis in human sporadic VSs, and suggest inhibition of this pathway as a potential treatment strategy.

overall_design: Affymetrix GeneChip Human Genome HTA_2_0 Array was used to test global gene expression in  ten human sporadic VSs and four normal control vestibular nerves to identify aberrant expression of the Hippo pathway in VSs. Molecular subtypes in VSs was evaluated using unsupervised hierarchical clustering analysis.

first: Fu

last: Zhao

first: Zhijun

last: Yang

first: Yang

last: Chen

first: Qiangyi

last: Zhou

first: Jing

last: Zhang

first: Jiang

last: Liu

first: Bo

first: Qiyang

last: He

first: Li

first: Yanbin

last: Yu

first: Pinan


title: Klf4 has an unexpected protective role in perivascular cells within the microvasculature

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

summary: Recent smooth muscle cell (SMC) lineage tracing studies have demonstrated that SMCs undergo remarkable changes in phenotype during development of atherosclerosis, including loss of typical SMC markers such as ACTA2 and Klf4 dependent activation of multiple markers of macrophages and mesenchymal stem cells. Of major interest, we showed Klf4 in SMC is critical for overall lesion pathogenesis as SMC-specific conditional knockout (KO) of Klf4 resulted in smaller, more stable lesions that exhibited marked reductions in the numbers of SMC-derived macrophage-like and mesenchymal stem cell like cells. Herein we tested the hypothesis that Klf4 dependent SMC transitions are beneficial following myocardial infarction (MI). Utilizing SMC-specific lineage tracing mice +/- simultaneous SMC-specific conditional KO of Klf4, we demonstrate that SMCs express Klf4 and transition to a Klf4 dependent macrophage-like state as well as a Klf4 independent myofibroblast-like state. SMC specific, conditional KO of Klf4  resulted in marked exacerbation of heart failure following MI. Surprisingly, significant cardiac dilation was seen in SMC-Klf4 KO mice prior to MI. This cardiac dilation was accompanied by a reduction in peripheral resistance, as evidenced by a reduction in blood pressure, an increase in blood flow, and a larger passive diameter of mesenteric resistance arteries as measured by pressure myography. Klf4 ChIP-Seq analysis on the mesenteric resistance arteries identified potential Klf4 target genes in SMC at baseline in pathways including PDGF and FGF signaling previously shown to be important for perivascular cell investment. Interestingly, examination of microvascular tissue beds revealed gaps in lineage traced SMC coverage along the resistance arteries. Taken together, these results provide novel evidence that Klf4 has a critical maintenance role within microvascular SMCs, including being required for normal SMC coverage of resistance arteries as well as their function.

overall_design: Examination of Klf4 transcription factor at base line in micro-vessels

first: Ryan

last: Haskins

first: Anh

middle: T

last: Nguyen

first: Gabriel

middle: F

last: Alencar

first: Marie

last: Billaud

first: Miranda

middle: E

last: Good

first: Katharina

last: Bottermann

first: Alexander

last: Klibanov

first: Brent

last: French

first: Thurl

last: Harris

first: Brant

last: Isakson


title: RRBS (reduced representation bisulfite sequencing) analysis of hepatocyte-specific  STAT5a/STAT5b Knockout (STAT5ab-KO) mouse liver to identify differentially methylated regions (DMRs)

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: The impact of STAT5 on liver DNA methylation was assessed by performing RRBS analysis on male and female mouse liver with a hepatocyte-specific loss of STAT5a and STAT5b. Extensive changes in CpG-methylation were seen in STAT5-deficient liver, where sex differences were abolished at 88% of ~1,500 sex-differentially methylated regions, largely due to increased DNA methylation upon STAT5 loss. STAT5-dependent CpG-hypomethylation was rarely found at proximal promoters of STAT5-dependent genes. Rather, STAT5 primarily regulated the methylation of distal enhancers, where STAT5 deficiency induced widespread hypermethylation at genomic regions enriched for accessible chromatin, enhancer histone marks (H3K4me1, H3K27ac), STAT5 binding, and DNA motifs for STAT5 and other transcription factors implicated in liver sex differences. Thus, the sex-dependent binding of STAT5 to liver chromatin is closely linked to the sex-dependent demethylation of distal regulatory elements linked to STAT5-dependent genes important for liver sex bias.

overall_design: Liver genomic DNA was isolated from livers of individual male and female control and hepatocyte-specific STAT5ab-KO mice and subjected to RRBS analysis

first: Pengying

last: Hao

middle: J


title: RNA-seq in livers of wild-type (WT) controls, PiZ and PIZ mice deleted for Chop (PiZ/Chop-/-)

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: Transgenic PiZ mice have been genetically engineered to express ATZ and have been a valuable experimental model for liver disease due to AAT polymerization. ATZ accumulates in these mice within the endoplamic reticulum (ER) of hepatocytes in a nearly identical manner to livers of affected patients. To investigate the role of the transcription factor CHOP in the pathogenesis of liver damage induced by ATZ, we performed RNA-seq in livers of 6-week-old wild type, PiZ and PiZ mice deleted for Chop. All groups were matched for the strain, age, and the gender.

overall_design: RNA sequencing in 6 week-old wild-type (WT), PiZ and PIZ deleted for Chop (PiZ/Chop-/-) mouse livers mice using QuantSeq 3'mRNA-Seq

first: Sergio

last: Attanasio

first: Nicola

last: Brunetti-Pierri


title: Cd302 and Cr1l restrict human hepatotropic virus cross-species transmission to mice [1Library screen]

first: Birthe

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

summary: Virus species- and tissue-tropism is governed by host dependency and restriction factors. Hepatitis C virus (HCV) exhibits a narrow species-tropism and murine hepatocytes are refractory to infection. Using murine liver cDNA library screening we identified Cd302, a lectin, and Cr1l, a complement receptor, as pan-genotypic restrictors of HCV infection. Cd302/Cr1l interact to impede virion uptake and co-operatively induce a non-canonical transcriptional program, inhibiting HCV and hepatitis B virus (HBV) infection in vitro. CAS9 disruption of murine hepatocyte Cd302 expression increased HCV permissiveness in-vivo and ex-vivo, and modulated the intrinsic hepatocyte transcriptome dysregulating metabolic process and host defense genes. In contrast, co-operative CD302/CR1L expression was absent and HCV restriction reduced in human hepatocytes. The Cd302/Cr1l axis therefore contributes to limiting hepatotropic virus cross-species transmission to mice, opening new avenues for step-wise development of mouse models for these important human pathogens, which cause substantial disease burden globally.

overall_design: We performed a murine hepatic restriction factor screening using a cDNA library generated from the liver of an IFN-treated mouse. The library was packaged in chimeric lentiviral/VSV pseudoparticles and transduced into HCV-permissive n4mBid cells which are highly permissive for HCV but undergo apoptosis upon HCV replication due to HCV NS3 protease-mediated cleavage of the modified BH3 interacting domain death agonist (mBID) protein. Two rounds of selection with HCV were then performed, with surviving cells expanded after each round of selection. Total RNA-Seq of cell population S0, the initial n4mBid cell population after delivery of the cDNA library, and cell population S2, the population of cells after two consecutive challenges with HCV, were performed. Two technical replicates were performed for each sample. Transcriptomes were mapped against the human hg19 reference to ascertain the host cell background, and the mm9 mouse reference to quantify the integrated murine library. S0 and S2 mouse integrations were then compared to identify restriction factors.

first: Richard

last: Brown

first: Thomas

last: Pietschmann


title: An alternative sensing strategy of microglia for pathogen infection: Odorant receptor-pathogen-derived metabolite axis

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: The goals of this study are to identify ectopic expression of microglial odorant receptors and to demonstrate that microglial odorant receptor have a role in sensing pathogen-derived metabolite for global neuroinflammation. We compared the genetic and functional similarity between S.pneumoniae supernatant-treated and S.pneumoniae-derived metabolite, 2-pentylfuran- treated microglia by analyzing the relationship between DEGs. A significant (p < 0.01) portion of these DEGs, 213 were shared between the DEGs by the supernatant and 2-pentylfuran, including 135 up-regulated and 78 down-regulated genes. To examine cellular processes associated with these shared genes, we performed the enrichment analysis of gene ontology biological processes (GOBPs). These shared up-regulated genes were found mainly associated with the processes related to microglia-mediated neuroinflammation with downstream signaling. Taken together, our study represents the first analysis of primary microglia for identifying ectopic odorant receptors. Our result suggest an alternative sensing strategy of microglia for pathogen infection via odorant receptor-pathogen derived metabolites axis with functional similarity by trascriptome profiling (RNA-seq).

overall_design: Examination of relationship between DEGs in the two comparisons of Sup-treated (n=3) versus control (n=3) microglia (Sup/Ctrl) and 2-PF-treated (n=2) versus control (n=3) microglia (2-PF/Ctrl)

first: JaeHyung

last: Koo

first: Deahee

last: Hwang

first: NaHye

last: Lee


title: Analysis of SIN3A/B functions within HEK293T cells.

city: Kansas City

first: Gaye

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

summary: Transcription products influenced by decreased SIN3A or SIN3B are analyzed and compared.

overall_design: HEK293T cells were transfected with control siRNA, siRNA targeting SIN3A, or siRNA targeting SIN3B. Total RNA was isolated from cells for RNA-seq analysis.

first: Mark

last: Adams

first: Mike

last: Washburn


title: Gene expression profiling of mouse liver with hepatocyte-specific knockout of STAT5a/STAT5b genes (STAT5ab-KO)

summary: rRNA-depleted RNA isolated from livers of control male and female mice and from male mice with hepatocyte-specific STAT5ab-KO was analyzed by RNA-seq. This study revealed a substantial, albeit incomplete loss of liver sex bias in hepatocyte-specific STAT5a/STAT5b (collectively, STAT5)-deficient mouse liver. Notably, in male liver, many male-biased genes were down regulated in direct association with the loss of STAT5 binding; many female-biased genes, which show low STAT5 binding, were de-repressed, indicating an indirect mechanism for repression by STAT5.

overall_design: Liver RNA was isolated from male and female mice with hepatocyte-specific STAT5a and STAT5b gene inactivation (STAT5ab-KO), and corresponding (floxed) control mice and subjected to RNA-seq analysis.


title: Examination of Glis3 binding and affects on gene expression in mouse pancreas

city: Research Triangle Park

first: Anton

last: Jetten

address: 111 TW Alexander Drive

institute: NIEHS, NIH

summary: RNA sequencing of mouse islets from mice containing a pancreas-specific deletion of Glis3, and control littermates. Also, ChIP-seq analysis of Glis3 binding using a Glis3-eGFP mouse (endogenous Glis3 fused to enhanced GFP) and GFP antibody.

overall_design: Isolated Islets from 4 WT and 3 KO mice for RNAseq. Isolated islets from Glis3-eGFP mice, ChIP-seq using commercial GFP antibody

middle: W

last: Scoville

last: Jetton

first: Sara

last: Grimm


title: Genome-wide maps of DPF2 and H3K14 modifications in K562 cells

first: fan

last: feng

address: Tsinghua West Road

institute: Tsinghua University

summary: we report DPF2 and H3K14 modifications in K562 cells

overall_design: Examination of DPF2 and  H3K14 modifications in K562 cells

first: Fan

last: Feng

first: Wenhao

last: Zhang

first: Jiaxin

last: Huang


title: Inhaled multi-walled carbon nanotubes-induced gene expression profile in rat lung

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

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

overall_design: Refer to individual Series


title: RalA and RalB are potential therapeutic targets in multiple myeloma which mediate cell survival independently of oncogenic RAS

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary: NRAS and KRAS are frequently mutated  oncogenic drivers in multiple myeloma, however, their use as drug targets has not been successful. Hence, we reached out to characterize the role of the RAS-like (RAL) oncogenic signaling cascade and compare transcriptomic changes after knockdown af KRAS and RALA.

overall_design: Differential expression experiment after KRAS and RALA knockdown in multiple myeloma cell line.

first: Marcel

last: Seibold

first: Thorsten

last: Stühmer

first: Nadine

last: Schmiedl

first: Anja

last: Mottok

first: Ellen

last: Leich

first: Andreas

last: Rosenwald

first: Manik

last: Chatterjee

first: Hermann

last: Einsele

first: Ralf

middle: C

last: Bargou

first: Torsten

last: Steinbrunn


title: Establishing a foothold in the desert: a transcriptomic view of survival from the extremophyte, Haloxylon ammodendron

city: Lanzhou

first: Quan-Sheng

last: Qiu

state: Gansu

address: 222 South Tianshui Road

department: MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences

institute: Lanzhou University

summary: Drought is an inevitable stress almost all terrestrial plants face in their life cycles. Desert dwelling plants show extreme adaptations to drought but their genomes are largely unexplored compared to drought sensitive model plants generally studied to understand plant drought tolerance. Haloxylon ammodendron is a pioneer species extremely tolerant to drought and capable of colonizing desert sand dunes. Seedling establishment is the most critical development stage in the survival of H. ammodendron. H. ammodendron seedlings are able to withstand high light, and low temperature stresses characteristic of temperate desert environments in addition to drought. We have investigated the genome-wide transcript responses under induced drought stress during early seedling establishment to identify prevailing basal and induced gene clusters that likely contribute to survival and stress adapted growth in H. ammodendron. We find staggering support for drought response transcript accumulation together with other transcripts that may transform the cellular expression space into a preadapted state for salt, light, osmotic, and temperature stress tolerance. While transcript accumulation is excessive for genes associated with abiotic stress tolerance under an induced drought treatment, H. ammodendron seems to enhance biotic stress tolerance simultaneously by down-regulation of several genes that would be found at an up-regulated state during pathogen entry in susceptible plants. We detected enriched basal level transcript allocation that suggests preadaptation to abiotic stresses as well as pathogen defense in H. ammodendron when compared to other Amaranthaceae family transcriptomes under stress neutral conditions. Amaranthaceae is one of the most enriched plant families for extremophytes. We found transcripts that are generally maintained at low levels and some induced only under abiotic stress in Arabidopsis thaliana to be highly expressed under basal conditions in the Amaranthaceae transcriptomes including H. ammodendron. These could be novel candidates to expand or initiate discovery of new stress adaptive gene networks and mechanisms naturally selected in extremophytes that allow survival under environmental stresses.

overall_design: RNA from Haloxylon ammodendron whole seedlings grown for seven days under control and 5% PEG treatments for Illumina paired-end sequencing.

first: Ligang

last: Fan

first: Guannan

last: Wang

first: Wei

last: Hu

first: Pramod

last: Pantha

first: Kieu-Nga

last: Tran

first: Lizhe

last: An

first: Maheshi

last: Dassanayake


title: PHF6 keeps hematopoietic lineage development in check [OP9-DLL1]

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: Analysis of the mutational landscape of various hematological malignancies has shown that key regulators implicated in lineage commitment and differentiation are frequently implicated in leukemic transformation. In T-cell acute lymphoblastic leukemia, the role of various oncogenic and tumor suppressing transcription factors has been investigated. More recently, an exceptional high prevalence of mutations affecting epigenetic modifiers in T-ALL has also been noted. In order to understand the exact contribution of such lesions to normal differentiation and oncogenic transformation, further functional characterization of this subclass of proteins is warranted. PHF6 is one of these key epigenetic players, which was described as a frequently mutated and deleted novel tumor suppressor in T-ALL. In a first step towards unraveling the role of PHF6 in normal and malignant hematopoiesis, we characterized the function of PHF6 in both normal T-cell differentiation and other hematopoietic lineages as a prelude to understand its contribution to leukemogenesis. Here, we show for the first time that PHF6 controlled epigenetic regulation positively controls a NOTCH1 gene signature and the effects observed on T-lineage differentiation seem to be additive with Notch1. In this study, we show for the first time that PHF6 is a master regulator of early hematopoietic differentiation along the T-cell, B-cell, myeloid and NK-cell lineages.

overall_design: Gene expression was measured in cord blood (CB) CD34+ progenitors upon lentiviral infetion with scrambled or a PHF6 targeting shRNA. Cells were collected after 72h of co-culture (96h post-transduction) on an OP9-DLL1 stromal feeder layer. This was performed for 3 independent donors.

first: Siebe

last: Loontiens

first: Inge

last: Van de Walle

first: Pieter

last: Van Vlierberghe

first: Frank

last: Speleman

first: Tom

last: Taghon


title: PHF6 keeps hematopoietic lineage development in check [OP9-GFP]

overall_design: Gene expression was measured in cord blood (CB) CD34+ progenitors upon lentiviral infetion with control or a PHF6 targeting shRNA. Cells were collected after 72h of co-culture (96h post-transduction) on an OP9-GFP stromal feeder layer. This was performed for 3 independent donors.


title: SMARCB1 knockdown in liver cancer cells

city: seoul

first: Seong Hwi

last: Hong

address: 120 Neungdong-ro

department: School of Medicine

country: South Korea

institute: Konkuk University

summary: Transcriptome analysis after loss of SMARCB1 in two liver cancer cell lines

overall_design: generating stable SMARCB1 knockdown cells using shRNA in SK-Hep1, Huh7 liver cancer cell line.

first: Jueng

last: You

first: Seong


title: PHF6 keeps hematopoietic lineage development in check [ALLSIL]

overall_design: Gene expression was measured in ALL-SIL T-ALL lymphoblasts upon electroporation with a control or PHF6 targeting siRNA. Cells were collected after 96h post-electroporation. This was performed for 3 independent biological replicates.


title: Gene expression for treatment of bioceramic water

first: Minhyung

last: Kim

state: CA

summary: Increased oxidative stress induces impairment of the antioxidant defense systems and defects in regeneration of injured tissues. We aim to evaluate the effects of antioxidant bioactive ceramic water (JJ101) on tissue repairing and anti-aging. In vitro, myogenic and antioxidant factors were determined in satellite cells cultured in JJ101 media. Satellite cells grown in JJ101 medium displayed increased expression of Notch1, Pax7, AMP-activating protein kinase-alpha (AMPK-alpha) and anti-oxidant enzymes and significant protection against hydrogen peroxide-induced cell death. In vivo, JJ101 enhanced muscle regeneration via increased number of regenerating muscle fibers and reduced muscle fibrosis. The lifespan in SMP30 KO mice fed with a VC-deficient diet was extended by drinking JJ101. Moreover, the hepatic expression of AMPK-α in JJ101-fed SMP30 KO mice was comparable to that of VC-fed SMP30 KO mice, whereas it was suppressed in tap water-fed SMP30 KO mice. These results suggest that bioactive ceramic water improves antioxidant status through up-regulating antioxidant enzymes and AMPK and thereby provides a favorable niche for satellite cells, leading to an increase in muscle regeneration and compensates oxidative stress.

overall_design: Gene expression in muscle of bioceramic water treatment was analyzed. B10 and MDX mice fed tap water were used as control. Each group has two samples.

first: Kyu-Shik

last: Jeong

first: Eun-Joo

last: Lee

first: Daehee

last: Hwang


title: Expression data from murine TLR5 overexpressing HEK293 cells treated with flagellins of E. coli Nissle (EcN) and Salmonella Typhimurium SL1344 (ST)

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary:
The healthy gut microbiota is composed of three different functional subgroups, symbionts, commensals and pathobionts. Additionally, infection with pathogenic bacteria can occur. Microbe Associated Molecular Patterns (MAMPs) are expressed by most members of both, microbiota and pathogens and interact with Pattern Recognition Receptors (PRRs), resulting in activation of the innate immune system. It is still unclear whether the interaction of PRRs with MAMPs of different origin, leads to a differential activation of innate immunity and whether thereby, distinction can be made between symbionts, commensals, pathobionts and pathogens. Here we addressed the question whether the interaction of flagellin with Toll-like receptor 5 (TLR5) might be a possible mechanism of the innate immune system to distinguish between the different microbial subgroups and initiate the respective immune response. To characterize distinct cellular immune responses to symbiont or pathogen derived flagellin we run transcriptomics, phosphoproteomics and proteomics of TLR5 overexpressing cells. Responses to different flagellins were characterized by differential kinetics and regulation of protein phosphorylation as well as variant protein expression patterns. In vivo experiments revealed that commensal derived flagellin mediated an inert TLR5 signal, thus not affecting Dextran-Sodium-Sulfate (DSS) induced intestinal inflammation. In vitro pathogenic derived flagellin induced a strong pro-inflammatory TLR5 response and did not ameliorate intestinal inflammation. In contrast, symbiont derived flagellin revealed an intermediate TLR5 activation and clearly ameliorated DSS induced intestinal inflammation thus shifting the host immune response in favor of mucosal immune balance. Bone marrow chimeric mice proofed that CD11c+TLR5+ intestinal lamina propria cells mediate the anti-inflammatory symbiotic effect of flagellin.   We suggest that the quality of flagellin-induced TL signal might determine the balance between homeostasis and intestinal inflammation and may help the innate immune system to distinguish between symbionts, commensals, pathobionts and pathogenic microbes.
We used microarrays to analyze differential expression of genes between treatments with flagellins of E. coli Nissle (EcN) and Salmonella Typhimurium SL1344 (ST).

overall_design: TLR5 overexpressing human embryonic kidney cells (HEK293) were treated with flagellins of E. coli Nissle (EcN) and Salmonella Typhimurium SL1344 (ST) and a mock control for a period of 120min taking samples at 60min (timepoint t1) and 120min (timepoint t2). To analyze gene expression changes related to either EcN or ST treatment total RNA was extracted for subsequent array hybridization and microarray analysis using the Affymetrix Human Gene 2.1 ST Array chip.

first: Julia-Stefanie

last: Frick

first: Sarah

last: Menz

first: Marius

last: Codrea


title: Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

summary: In mammalian embryos, the stepwise generation of hematopoietic stem cells (HSCs) from endothelial precursors and pre-hematopoietic stem cells (pre-HSCs) is stringently modulated by signaling pathways and transcription factors. Nevertheless, the understanding of regulatory strength and mechanism by non-coding RNA (ncRNA) remains entirely lacking. Taking advantage of our capacity to capture rare single pre-HSCs and HSCs in vivo and accordingly generate the single-cell transcriptome datasets, here we presented the first long non-coding RNA (lncRNA) landscape of HSC development at single-cell resolution. Combining bioinformatics analysis and functional screening, we identified 6 lncRNAs showing influence on hematopoietic progenitor generation in vitro. Moreover, endothelial disruption of H19 in vivo resulted in defective emergence of functional pre-HSCs and HSCs in aorta-gonad-mesonephros region, albeit with unperturbed development of erythro-myeloid progenitors in yolk sac. Single-cell RNA sequencing revealed that H19 deficient pre-HSCs (The DMR region of H19 was knocked out in the "KO" samples) possessed similar molecular pattern with endothelial cells, suggesting their severe blockade during hematopoietic transition. Methylation sequencing of pre-HSCs further demonstrated hyper methylation on promoter region of several master hematopoietic transcription factors, including Runx1 and Spi1, by H19 deficiency. Taken together, our study identified H19 as the first non-coding gene indispensable for endothelial-to-HSC transition, and the single-cell lncRNAomics map should be valuable for exploring epigenetic control of HSC generation and regeneration.

overall_design: Build the single-cell lncRNAomics map during HSC generation and regeneration

first: Jie

last: Zhou

first: Jiayue

last: Xu

first: Linlin

last: Zhang

first: Siqi

last: Liu

first: Yanni

last: Ma

first: Fuchou

last: Tang

first: Bing

first: Jia

last: Yu

first: Yu

last: Lan


title: Expression data of human bone marrow mesenchymal cells (BM-MSC) from follicular patients (FL) or normal healthy donors (N)

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on in vitro expanded bone marrow mesenchymal stroma cells

overall_design: GEP was performed on 8 BM-MSC from FL patients and 8 from healthy donors.

first: Patricia

last: Amé-Thomas

first: Karin

last: Tarte

first: Thierry

last: Fest


title: Selective lymphoma cell killing by a PRC2 small molecule inhibitor (ChIP-Seq set 1)

city: Cambridge

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Genomewide H3K27me3 and H3K4me3 patterns and EZH2 binding profiles in HT and SUDHL6 cell lines by chromatin immunoprecipitation and deep sequencing (ChIP-seq).

overall_design: Histone marks (H3K27me3, H3K4me3) and EZH2 binding by ChIP-seq in SUDHL6 and HT DLBCL cell lines.

first: Patrick

last: Trojer

first: Shivani

last: Garapaty

first: Fei

first: Charlie

last: Hatton


title: PHF6 keeps hematopoietic lineage development in check [Jurkat]

first: Kaat

last: Durinck

overall_design: Gene expression was measured in Jurkat T-ALL lymphoblasts upon lentiviral infetion with scrambled or a PHF6 targeting shRNA. Cells were collected after 96h post-transduction. This was performed for 3 independent biological replicates.

first: Siebe

last: Loontiens

first: Inge

last: Van de Walle

first: Pieter

last: Van Vlierberghe

first: Frank

last: Speleman

first: Tom

last: Taghon


title: Swr1 mediated H2A.ZPht1 incorporation designates centromere DNA for de novo CENP-ACnp1 assembly

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

summary: The centromere is the location on each chromosome that directs the assembly of the kinetochore. The underlying hallmark of centromeres in most eukaryotes is the presence of specialised nucleosomes in which canonical histone H3 is replaced by the histone H3 variant CENP-A. The molecular events that mediate a programme to install CENP-A in place of histone H3, at centromeres and how the centromeric chromatin is reorganised for CENP-A assembly during cell cycle remain poorly characterised. Histone H2A variant, H2A.Z is linked to transcriptional competence, in maintaining heterochromatin silencing and enriched in CENP-A chromatin. Our analyses demonstrate that H2A.ZPht1 and the Swr1 complex are associated with CENP-ACnp1 chromatin in fission yeast. Swr1 and Msc1 regulate H2A.ZPht1 deposition at centromeres and along with H2A.ZPht1 maintain CENP-ACnp1 chromatin integrity. Additionally, they coordinate the deposition of CENP-ACnp1 through the cell cycle, coupled with eviction of histone H3 from centromeres. Based on our results, we propose that the centromere is programmed to the widespread incorporation of H2A.ZPht1 via Swr1, and that H2A.ZPht1 dynamics likely play a role in regulating centromeric chromatin by influencing CENP-A incorporation.

overall_design: ChIP-seq for CENP-A, H2A.Z and SWR1 chromatin remodeling complex

first: Raghavendran

last: Kulasegaran-Shylini

first: Robin

last: Allshire


title: Expression profiling of immature ovule and pistil samples of sexual and apomictic Boechera (Brassicaceae)

status: Public on Nov 30 2020

city: Logan

first: John

middle: G.

last: Carman

state: UT

address: 4820 Old Main Hill

department: Plants, Soils and Climate Department

institute: Utah State University

summary:
Sexual reproduction (meiosis and syngamy) is the major form of reproduction in diploid Boechera species, but most species hybrids reproduce by apomixis (unreduced gametophyte formation followed by parthenogenesis of the unreduced egg).
In this study, we used Arabidopsis microarrays to detail global programs of gene expression underlying sexual and apomictic modes of reproduction.

sample_organism:
Boechera stricta
Boechera lignifera
Boechera microphylla
Boechera formosa x Boechera sp. JC-2020

overall_design: For apomictic B. x formosa, B. lignifera and B. microphylla, ovules were microexcised from ovaries at the megaspore mother cell, meiosis, early gametophyte and late gametophyte stages. For sexual B. stricta, pistils were excised at the meiosis and early gametophyte stages. RNA was extracted, amplified and hybridized to Affymetrix ATH1 microarrays.


title: Selective lymphoma cell killing by a PRC2 small molecule inhibitor

middle: M


title: Selective lymphoma cell killing by a PRC2 small molecule inhibitor (Exon array)

summary: Microarray-based expression analysis in HT and SUDHL6 cell lines.

overall_design: Expression profiling by Affymetrix exon array of HT and SUDHL6 cell lines.

last: Lan


title: PHF6 is a key regulator of normal human hematopoiesis by modulating NOTCH1 signaling activity


title: Selective lymphoma cell killing by a PRC2 small molecule inhibitor (RNA-Seq)

summary: Genome-wide gene expression changes in response to iEZH treatment in HT and SUDHL6 cells using RNA sequencing (RNA-seq).

overall_design: Expression profiling by RNA-seq of HT and SUDHL6 cell lines after 96 hours of treatment with iEZH.


title: Selective lymphoma cell killing by a PRC2 small molecule inhibitor (ChIP-Seq set 2)

summary: Genome-wide distribution of EZH2, H3K27me3 and H3K36me1 determined by ChIP-seq in SUDHL6 cells in the absence or presence of iEZH

overall_design: Histone marks (H3K27me3, H3K36me1) and EZH2 binding by ChIP-seq in SUDHL6 DLBCL cell line after 96 hours of treatment with iEZH (1.5 uM).


title: Expression data from E17.5 mouse brain regions

city: Suita

first: Tokuichi

last: Iguchi

state: Osaka

address: 2-2 Yamada-oka

country: Japan

institute: Osaka University

summary:
During brain development, layer 5 neurons distributed across most areas of the neocortex innervate the pontine nuclei (basilar pons) by the initiation and extension of collateral branches interstitially along their corticospinally extending axons.
We used microarrays to compare gene expression profiles of brain areas that were projected (pontine nucleus, superior colliculus) and were not projected (cerebellum, olfactory bulb) by axon collaterals from the corticospinal tract in order to understand genetic programs that regulate axon collaterals formation.

overall_design: Each brain region was dissected out and subjected to total RNA preparation and hybridization on Affymetrix microarrays.

first: Makoto

last: Sato


title: Influence of  hsd17b4 knockout in gene expression of RAW 264.7 cells

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: Hsd17b4 is a very important for beta oxidation. However, influence of hsd17b4 on gene expression in RAW 264.7 cells is unknown yet. In this study, the influence of hsd17b4 knockout on gene expression in RAW 264.7 cells was investigated.

overall_design: Differential gene expression between wild type  and hsd17b4 knockouted RAW 264.7 cultured cells was measured, and  infuence of treatment of LPS on these cells was investigated.

first: Naoya

last: Matsunaga

first: Akito

last: Tsuruta

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: Mesenchymal transition and acquired therapy resistance of glioblastoma cells is connected to astrocyte reactivity (DNA methylation data set)

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

type: Methylation profiling by genome tiling array

summary: We show that Glioma initiating cells (GICs) can, through MES transition, enter a reactive-astrocyte-like cell state which is connected to increased therapy resistance

overall_design: Illumina Infinium Methylation EPIC array analyses were performed according to the manufacturer's directions on genomic DNA extracted from clonal malignant glioma cells in time series of IL1 stimulation (1-42 days) and corresponding control cells.

first: Anna


title: Microarray data of human moDC treated with IFNβ and TNFα

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L Levy Pl

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Human moDC were treated with IFNβ and TNFα or the combination of both for either 1 h or 2.5 h in triplicate and profiled by gene expression microarray

overall_design: DC were treated with 4500 pg/mL TNFα, 3000 pg/mL IFNβ, or the combination of both for either 1 h or 2.5 h. Untreated DC served as a negative control. Three samples were taken per treatment and time point. RNA was extracted with the RNeasy plus kit (Qiagen) following the manufacturer’s instructions. Gene expression was assayed using broad human genome specific HG-U133_Plus_2 GeneChip expression probe arrays (Affymetrix).

first: Boris

last: Hartmann


title: An Investigation into the Biological Effects of Indirect Potable Reuse Water Using Zebrafish Embryos

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

institute: University of Liverpool

summary: In the search for sustainable drinking water, many countries are weighing up the benefits of advanced treatment technologies as a proactive measure to assist with the transformation of treated wastewater into a source of water used for the production of potable water. We investigated the biological effects along a pilot plant with an advanced water treatment process, using zebrafish embryos at different stages of development. The study took an innovative approach, comparing phenotypic observations with whole genome responses. This enabled us to keep an open mind about which chemicals might be influencing the biological activity. There was no evidence of acute toxicity at any stage of treatment, but distinctive abnormalities – skeletal, cardiovascular and pigmentation – occurred in a small proportion of embryos along the treatment process, and in a tap water, that were not detected in the aquarium water control. Reverse osmosis (RO) reduced the concentration of measured chemical contaminants in the water the most, whilst eliminating the occurrence of abnormalities detected in the fish. In contrast, advanced oxidation appeared to reverse the benefits of RO treatment by increasing the frequency of teratogenic and sub-lethal abnormalities seen in embryos.  Genomic analysis found alterations to the retinoid system, which was consistent with the teratogenic abnormalities observed.  In addition, we found evidence of changes to metabolic pathways, including tryptophan metabolism associated with the production of melatonin required for the control of normal circadian rhythms.  Although we cannot extrapolate these preliminary findings in zebrafish embryos to human or environmental health, we show that underexplored forms of biological activity (that existing Test Guidelines are not designed to capture) occur in treated wastewater effluent, and/or may be created depending on the type of advanced treatment process used.  Although the identity of the culprit chemicals are unknown at this time, our innovative approach highlights the need for more research into the effects of chemicals on the retinoid system (and metabolism).

overall_design: Analysis of water from a indirect potable reuse water plant. Stages of the water purification were tested on effects on Zebrafish embryos. These stages included AOP-1, AOP-2, MF, RAW, RO, Tap, a separate water control and the Final effluent. Exposures were performed over time (8,12,16,24,36, and 48h). In total 132 samples were generated.

first: Elizabeth

last: Lawton

first: Sopie

last: Walker

first: Eve

last: Germain-Cripps

first: Francesco

last: Falciani

first: Edwin

last: Routledge


title: Mesenchymal transition and acquired therapy resistance of glioblastoma cells is connected to astrocyte reactivity

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

overall_design: Refer to individual Series


title: AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (ChIP-seq)

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

summary: Photomorphogenesis is a critical developmental process bridging light-regulated transcriptional reprogramming with morphological changes in organisms. Strikingly, the chromatin-based transcriptional control of photomorphogenesis remains poorly understood. Here, we show that both light-induced genes and dark-induced genes were affected in the atino80 mutant. Genome-wide occupancy of the H2A.Z histone variant and levels of histone H3 were reduced in atino80.

overall_design: examination of 2 different histone modifications in 2 samples with 2 replicates. Samples without antibody were used as input control.

first: Aiwu

last: Dong

first: Lin

last: Li


title: AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (RNA-seq)


overall_design: RNAseq for atino80 mutant at dark condition, 2 genotypes with 3 replicates

first: Chuanwi

last: Yang


title: Analysis of somatic copy number alterations in ApcΔ716 mouse intestinal tumors [aCGH]

city: Kobe

first: Yuko

last: Kiyosue

address: 2-2-3 Minatojima-Minamimachi, Chuo-ku

institute: RIKEN Center for Biosystems Dynamics Research

summary: To detect somatic copy number alterations in APC mutant tumors, we analyzed intestinal tumors from heterozygous ApcΔ716 mice, in which polyposis initiates upon loss of heterozygosity without losing the mutant allele (Proc Natl Acad Sci U S A. 1995 May 9;92(10):4482-6).

overall_design: The genomic DNAs from ApcΔ716 mouse normal small intestines (control) and polyps were fragmented, amplified, and then labelled with Cy3 or Cy5 dyes. Dye-swap replication experiments were performed for each polyp sample vs. control DNA. The hybridized DNAs were applied to the microarray and scanned on an Agilent SureScan Microarray Scanner.

first: Yoshihiro

last: Kawasaki

first: Hiroko

last: Oshima

first: Masanobu

first: M.

last: Taketo

last: Mimori-Kiyosue