title: H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases [Mm]

summary: Histone lysine methylations are essential components of the epigenetic regulatory mechanisms. Although major histone lysine methylations have been extensively investigated, low-abundance methylations remain largely under-studied. Among the low-abundance methylations, H3K14me3 has been identified in mammalian cells upon pathological infection by Legionella pneumophila, a gram-negative bacterium and causative agent of a severe form of pneumonia. Global host chromatin H3K14 trimethylation and transcription repression are mediated by an H3K14 methyltransferase, regulator of methylation A (RomA) encoded by the bacterial genome 1. Importantly, previous mass spectrometry studies also suggested the presence of endogenous H3K14 methylations among eukaryotes 2-7, although these findings have not been confirmed by independent means. In addition, the genomic distribution as well as the H3K14me3 regulatory enzymes have not been identified. Here, using an H3K14me3-specific antiserum we report the identification of distinct and shared H3K14me3 distribution patterns in HEK293T and human embryonic stem cells (hESCs), two cell lines with extensive epigenome profiles allowing cross comparisons with other known histone marks. H3K14me3 heavily decorates the KRAB-ZNF (Krupple-associated box containing zinc finger gene) clusters in both the HEK293T and hESC cells but is only strongly associated with active transcription in HEK293T cells, where it binds thousands of active promoters. We further profiled H3K14me3 in a mouse melanoma cell line, B16, and discovered similar distribution features as those in HEK293T cells. Importantly, we identified members of the KDM4 family of histone demethylases (KDM4A, KDM4B and KDM4C) as H3K14me3 demethylases. As the KDM4 family members have been shown to mediate H3K9me3 and H3K36me3 demethylation 8, our findings also revealed crosstalks among these modifications.

overall_design: Examination of H3K14me3 in mouse cells

first: Bin

last: Zhao


title: H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases [Hs]

status: Public on Dec 31 2018

city: Shanghai

first: Fei

last: Lan

address: 130 Dong An Road

country: China

institute: Fudan university

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of H3K14me3 in human cells


title: Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex [RNA-Seq]

city: Jerusalem

first: Avital

last: Klein Brill

address: Edmond J. Safra Campus

country: Israel

institute: The hebrew university

type: Expression profiling by high throughput sequencing

summary:
we use an induced degron system to study how rapid clearance of ATP-dependent chromatin remodelers affect nucleosome locations.
1. Screening eight remodelers
2. depletion of Sth1 leads to rapid and reversible fill-in of nucleosome-free regions at gene promoters.
3.  changes at depletion and recovery do not depend on major chromatin reassembly during DNA replication.
4. RSC is crucial in maintaining open promoters of low expressed genes.  RSC is not directly required for an acute transcriptional response.
5. Changes in nucleosome positions are tightly related to the specific TSS usage at promoters.

overall_design: We use in induced degron system in several experiments: 1. screen experiment 2. sth1 depletion experiment 3. sth1 recovery experiment 4. replication arrest experiment 5. stress response experiment. In most experiments we used both RNA seq and Mnase seq data.

last: Klein-Brill

first: Daphna

last: Joseph-Strauss

first: Nir

last: Friedman


title: Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex [MNase-Seq]


title: Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex

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

overall_design: Refer to individual Series


title: An Optofluidic Real-Time Cell Sorter for Longitudinal CTC Studies in Mouse Models of Cancer

city: Cambridge

first: Sanjay

last: Prakadan

state: MA

address: 77 Massachusetts Ave, E25-356

country: USA

institute: Massachusetts Institute of Technology

summary: Circulating tumor cells (CTCs) play a fundamental role in cancer progression. However, in mice, limited blood volume and the rarity of CTCs in the bloodstream preclude longitudinal, in-depth studies of these cells using existing liquid biopsy techniques. Here, we present an optofluidic system that continuously collects fluorescently-labeled CTCs from a genetically-engineered mouse model for several hours per day over multiple days or weeks. The system is based on a microfluidic cell-sorting chip connected serially to an un-anesthetized mouse via an implanted arteriovenous shunt. Pneumatically-controlled microfluidic valves capture CTCs as they flow through the device and CTC-depleted blood is returned back to the mouse via the shunt. To demonstrate the utility of our system, we profile CTCs isolated longitudinally from animals over a four-day treatment with the BET inhibitor JQ1 using single-cell RNA-Seq (scRNA-Seq) and show that our approach eliminates potential biases driven by inter-mouse heterogeneity that can occur when CTCs are collected across different mice. The CTC isolation and sorting technology presented here provides a research tool to help reveal details of how CTCs change over time, allowing studies to credential changes in CTCs as biomarkers of drug response and facilitating future studies to understand the role of CTCs in metastasis.

overall_design: Single-cell RNA-Sequencing of CTCs and primary tumors from a murine model of non-small cell-lung cancer

middle: M

first: Alex

middle: K

last: Shalek


title: Genome-wide maps of human adenocarcinomal cell PC-9 and LINC00312 knockdown PC-9 cell

city: Changsha

first: Zhen

middle: zi

last: Peng

state: Hunan

address: Xiangya Road 87th

institute: Xiangya hospital

summary: We performed RNA-seq to analyze the transcriptional profiles of PC-9 cells with reduced expression of LINC00312 to better understand the molecular mechanisms by LINC00312

overall_design: Examination of 2 different expression in 2 cell types.

first: Zhenzi


title: Next-generation sequence analysis for transcriptome of Drosophila melanogaster whole third instar larvae of wild type (wt), hsromega66 mutant (near null allele), Hsp90GFP (over-expressing Hsp83) and hsromega66 Hsp90GFP recombinants

city: varanasi

first: subhas chandra

last: lakhotia

state: uttar pradesh

address: cytogenetics lab, department of Zoology BHU

department: Department of Zoology

country: India

institute: Brown University

summary:
Purpose: To compare transcriptomic changes in 3rd instar larvae due to near-absence of hsromega gene transcripts, or over-expression of Hsp83, or both in combination.
Method: Third instar larval total RNA profiles of WT, hsromega66, Hsp90GFP and Hsp90GFP hsromega66 were generated by sequencing, in duplicate, on Illumina Hiseq2500 platform using 50bp pair-end reads, 8 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012).
Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified 15,905 transcripts with TopHat workflow in each genotypes studied. Compared to wild type, loss of hsromega gene transcripts due to hsrɷ66 resulted in differential expression of many genes, with128 genes being down-regulated and 309 up-regulated, while that due to over expression of Hsp83 in Hsp90GFP resulted in 154 genes down regulated and 232 up-regulated. Compared to control larvae, in case of up regulation of Hsp83 and simultaneous near absence of hsrɷ transcripts, 1157 gene were up-regulated with 842 showing unique change in only this genotype but not in the former two genotypes, and 1120 were down-regulated with 1005 lowered uniquely in these individuals. Some of these (9 genes) were validated using qRT-PCR.
Conclusion: Analysis of RNA-seq data revealed that 128 and 154 genes were significantly down-regulated in hsrɷ66 and hsp90GFP larvae, respectively, when compared with similar age wild type larvae, with ~35% (45 genes) being common in hsrɷ66 and hsp90GFP larvae. Similarly, 309 and 232 genes were significantly up-regulated, compared to similar age wild type larvae, in hsrɷ66 and hsp90GFP larvae, respectively. In this case also ~37% (113) were commonly up-regulated in both these genotypes. Such common effects on a significant proportion of genes in hsrɷ66 and hsp90GFP genotypes suggest that hsrɷ transcripts and Hsp83 may be involved in several common pathways. Compared to the relatively small number of genes that were commonly affected in hsrɷ66 or hsp90GFP individuals, the proportion of genes showing unique down- or up-regulation in hsrɷ66 hsp90GFP double mutant larvae were much larger (~90% uniquely down- and ~78% uniquely up- regulated). This shows that while substantial reduction of hsrω transcripts or over-expression of Hsp83 affect several genes similarly, the effects become dramatically different and more pervasive when the hsrω transcripts are substantially reduced in a background of elevated levels of Hsp83 so that nearly 1850 genes get uniquely affected.

overall_design: Wandering third instar larval RNA profiles of wandering late third instar larvae of WT, hsromega66, Hsp90GFP and Hsp90GFP hsromega66 were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform.

first: Subhash

middle: C

last: Lakhotia

first: Mukulika

last: Ray


title: Adolescent Δ9-THC exposure and astrocyte-specific genetic vulnerability converge on NF-κB-COX-2 signaling to impair memory in adulthood

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary: Adolescent cannabis use has been associated with long-term cognitive dysfunction attributed to action of the main cannabis ingredient, delta-9-tetrahydrocannabinol (Δ9-THC), on the cannabinoid receptor 1 (CNR1). However, not all marijuana users develop cognitive impairment, suggesting a genetic vulnerability to adverse effects of cannabis. As both neurons and glial cells express CNR1, genetic vulnerability could influence Δ9-THC-induced signaling in a cell type-specific manner. Here we use an animal model of inducible expression of dominant-negative Disrupted-In-Schizophrenia-1 (DN-DISC1) selectively in astrocytes to evaluate the molecular mechanisms whereby an astrocyte genetic vulnerability could synergistically interact with adolescent Δ9-THC exposure to impair recognition memory in adulthood. We report that selective expression of DN-DISC1 in astrocytes and adolescent treatment with Δ9-THC synergistically affected recognition memory in adult mice. Similar deficits in recognition memory were observed following knockdown of endogenous Disc1 in hippocampal astrocytes in mice treated with Δ9-THC during adolescence. At the molecular level, DN-DISC1 and Δ9-THC synergistically activated the NF-kB-COX-2 (encoded by Ptgs2 gene) pathway in astrocytes and decreased immunoreactivity of parvalbumin-positive pre-synaptic inhibitory boutons around pyramidal neurons of the CA3 area of the hippocampus. The cognitive abnormalities were prevented in DN-DISC1 mice exposed to Δ9-THC by simultaneous adolescent treatment with the COX-2 inhibitor, NS389. Our data demonstrate that individual vulnerability to cannabis can be exclusively mediated by astrocytes. Results of this work suggest that genetic predisposition within astrocytes can exaggerate Δ9-THC-produced cognitive impairments via convergent inflammatory signaling, suggesting possible targets for preventing adverse effects of cannabis within susceptible individuals.

overall_design: Gene expression in  hippocampus assayed in control and aDN-DISC1 mice treated with vehicle or Δ9-THC (four groups, n=3 per group)


title: Profiling primary downstream target of LBD16 in roots of Arabidopsis thaliana

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: Rokko-dai 1-1

country: Japan

institute: Kobe University

summary: Lateral roots (LRs) are formed post-embryonically and contribute to root architecture formation in vascular plants. LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) is a key transcription factor to initiate LR formation functioning redundantly with related LBD members. To identify primary downstream targets of LBD16, we engineered a transgenic line with inducible LBD16 activity by expressing a fusion protein of LBD16 and rat glucocorticoid receptor (GR) under the regulation of its own regulatory region (gLBD16-GR) in the lbd16-1 lbd18-1 lbd33-1 mutant. Here we identified primary response genes of LBD16 from transcriptome analysis.

overall_design: LBD16-Glucocorticoid Receptor (GR) driven by its own regulatory region in lbd16-1 lbd18-1 lbd33-1 mutant was used for LBD16 induction. We collected roos from 5-day-old seedlings of gLBD16:GR lbd16 lbd18 lbd33 line 4 hours after treatment with/without dexamethazone (DEX) and cycloheximide (CHX). Two independent sets of mRNA samples for each treatment were used for this analysis

first: Tatsuaki

last: Goh


title: RNAseq to determine gene expression changes in adipose tissue macrophages (ATM1 and ATM2) and adipocyte progenitors (AP) following cold exposure or FGF21-mimetic antibody administration

city: South San Francisco

first: Junichiro

last: Sonoda

state: CA

address: 1 DNA WAY

department: Cancer Immunology

institute: Genentech

summary: Study gene expression changes in M1 and M2 macrophages and APs in visceral adipose tissue in diet-induced obese mice following cold exposure or administration of FGF21-mimetic antibody

overall_design: 3 replicates for each cell type and each condition

first: Joshua

last: Chang

first: Steffen

last: Durinck

first: Jun


title: Blood samples from COPD subjects and Healthy Volunteers taken before and after LPS challenge

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

summary: There is a need for non-invasive imaging protocols to support early phase clinical studies for drugs targeting neutrophilic inflammation. The aim of the study was to quantify whole lung neutrophil accumulation in (i) healthy volunteers (HV) following inhaled lipopolysaccharide (LPS) or saline and (ii) stable COPD patients, using radiolabelled autologous neutrophils and single-photon-emission/computed-tomography (SPECT/CT).

overall_design: Whole Blood samples for biomarker analysis were taken at baseline in  20 COPD subjects and in 18 HVs pre and post challenge with LPS


title: Genome-Wide Sequencing Reveals Small Nucleolar RNAs Downregulated in Cerebral Cavernous Malformations

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

type: Non-coding RNA profiling by high throughput sequencing

summary: Cerebral cavernous malformations (CCM) are vascular malformations associated with abnormally dilated blood vessels and leaky capillaries that often result in hemorrhages. Despite recent advances, precise understanding of the cellular and molecular mechanism leading to the pathogenesis of CCM remains elusive. Emerging evidence indicates that small nucleolar RNAs (snoRNAs), belonging to the class of non-coding RNAs, may play a significant role as diagnostic markers in human diseases. However, there is no report till date that studied the role of snoRNAs in CCM biology. The objective of the current study was to identify snoRNAs associated with CCM pathogenesis. Using genome-wide small RNA sequencing, we identified a total of 271 snoRNAs reliably expressed in CCM. By applying additional statistical stringency, three snoRNAs (SNORD115-32, SNORD114-22 and SNORD113-3) were found to be significantly downregulated in CCM patient tissue samples (n = 3) as compared to healthy brains (n = 3). Deregulation of the selected snoRNAs was further validated by qRT-PCR. Further, cellular localization via in situ hybridization also confirmed robust reduction in the expression of SNORD115-32 and SNORD114-22 in CCM tissues as compared to the healthy controls. By applying high throughput sequencing and cellular localization analyses, we report here for the first time the genome-wide expression profile of snoRNAs in CCM tissues and a robust downregulation of candidate snoRNAs in CCM conditions. Future studies should warrant the screening in large CCM patient cohorts and will be helpful in the development of potential biomarkers and improved clinical diagnosis.

overall_design: Differential expression of snoRNAs in CCM


title: Cytosolic copper concentration modulates spore germination and secondary metabolism in Streptomyces coelicolor

city: OVIEDO

first: Paula

last: Yagüe

state: ASTURIAS

address: JULIAN CLAVERIA SN

department: Biologia funcional

country: Spain

institute: Universidad de Oviedo

summary: We studied the influence of copper in physiological and morphological differentiation of Streptomyces coelicolor. We demonstrate differences in phenotype (germination, growth rate, antibiotic production) and genetic expression between a strain mutated at copper chaperone CopZ (SCO2730::Tn5062), the wild-type strain  and a wild-type strain sporulated in a media with 80µM CuSO4. These differences are correlated with the cytosolic copper. Our results demonstrate a pleiotropic effect of copper  modulating S. coelicolor development.

overall_design: Expression profiles from SCO2730::Tn5062 mutant, wild-type strain and a wild-type strain sporulated in a media with 80µM CuSO4 were obtained by Next Generation Sequencing from two biological replicates, in sucrose-free R5A culture media.

first: A

last: Manteca

first: N

last: González-Quiñonez

first: P


title: Hippocampal gene expression patterns linked to late-life physical activity opposes age and AD-related transcriptional decline

city: Irvine

first: Nicole

middle: Claudia

last: Berchtold

address: 1226 Gillespie Neuroscience Facility

department: Institute for Memory Impairments and Neurological Disorders

institute: UC Irvine

summary: Exercise has emerged as a powerful variable that can improve cognitive function and delay age-associated cognitive decline and Alzheimer’s disease (AD), however, the underlying mechanisms are poorly understood. To determine if protective mechanisms may occur at the transcriptional level, we used microarrays to investigate the relationship between physical activity levels and gene expression patterns in the cognitively-intact aged human hippocampus. In parallel, hippocampal gene expression patterns associated with Aging and AD were assessed using publicly available microarray data profiling hippocampus from young (20-59 yrs), cognitively-intact aging (73-95 yrs) and age-matched AD cases.  To identify “anti-Aging/AD” transcription patterns associated with physical activity, probesets significantly associated with both physical activity and Aging/AD were identified and their directions of expression change in each condition were compared.  Remarkably, of the 2138 probesets significant in both datasets, nearly 95% showed opposite transcription patterns with physical activity compared to Aging/AD.  The majority (>70%) of these anti-Aging/AD genes showed increased expression with physical activity and decreased expression in Aging/AD.  Enrichment analysis of the anti-Aging/AD genes showing increased expression in association with physical activity revealed strong overrepresentation of mitochondrial energy production and synaptic function, along with axonal function and myelin integrity. Synaptic genes were notably enriched for synaptic vesicle priming, release and recycling, glutamate and GABA signaling and synaptic spine plasticity. Anti-Aging/AD genes showing decreased expression in association with physical activity were enriched for transcription-related function.  These data suggest that physical activity preserves a more youthful profile in the hippocampus across multiple biological processes, providing a potential molecular foundation for how physical activity can delay age- and AD-related decline of hippocampal function.

overall_design: We used hippocampus from clinically well-defined cases where late-life physical activity levels (exercise and non-exercise) had been objectively measured on an annual basis. In parallel, hippocampal gene expression patterns associated with Aging and AD were assessed in young (20-59 yrs), cognitively-intact aging (73-95 yrs) and age-matched AD cases.  To identify “anti-Aging/AD” transcription patterns associated with physical activity, probesets significantly associated with both physical activity and Aging/AD were identified and their directions of expression change in each condition were compared. Multiple linear regression was used to assess the strength of the relationship between physical activity and gene expression across all samples after adjusting for technical variables (batch, post-mortem interval, RNA integrity)

first: G

middle: A

last: Prieto

first: M

last: Phelan

first: D

middle: L

last: Gillen

last: Baldi

last: Bennett

middle: S

last: Buchman

first: C

middle: W

last: Cotman


title: Expression data from 17 patients with colorectal cancer

city: Athens

first: Aristotelis

last: Chatziioannou

state: Not in US

address: 48 Vassileos Constantinou Avenue

department: Institute of Biology, Medicinal Chemistry and Biotechnology

country: Greece

institute: National Hellenic Research Foundation

summary:
Colorectal cancer is a highly heterogeneous disease, with variable molecular pathogenesis, involving multiple genomic and epigenetic alterations. Despite the significant advances in the diagnosis and treatment of colorectal cancer, it remains a major cause of morbidity and mortality, especially for countries in Northern America and Europe, as also in New Zealand & Australia. In this direction, the introduction of gene expression signatures derived from multiple layers of molecular & clinical dissection, may resolve the problems of heterogeneity and improve robust disease stratification
We used microarrays to monitor the global gene expression alterations of primary adenocarcinomas and matched normal samples from each patient, to unravel the critical biological processes that are involved in CRC progression

overall_design:
A total of 17 patients with histologically confirmed colorectal adenocarcinomas were studied. The tissue specimens of the tumor and normal colon were removed during surgery and immediately frozen in liquid nitrogen. Total RNA was extracted for further processing with the affymetrix microarray platform HG-U133A.

The patients assayed in this study are independent from those assayed in GSE110223.

first: Efstathios

last: Vlachavas

first: Olga

last: Papadodima

first: Eleftherios

last: Pilalis

first: Dirk

last: Koczan

first: Stefan

last: Willis

first: Sven

last: Klippel

first: Antonia

last: Dimitrakopoulou-Strauss

first: Caixia

last: Cheng

first: Leyun

last: Pan

first: Christos

last: Sachpekidis


title: Expression data from 30 patients with colorectal cancer


title: Expression data from 13 patients with colorectal cancer

summary:
Colorectal cancer is a highly heterogeneous disease, with variable molecular pathogenesis, involving multiple genomic and epigenetic alterations. Despite the significant advances in the diagnosis and treatment of colorectal cancer, it remains a major cause of morbidity and mortality, especially for countries in Northern America and Europe, as also in New Zealand & Australia. In this direction, the introduction of gene expression signatures derived from multiple layers of molecular & clinical dissection, may resolve the problems of heterogeneity and improve robust disease stratification.
We used microarrays to monitor the global gene expression alterations of primary adenocarcinomas and matched normal samples from each patient, to unravel the critical biological processes that are involved in CRC progression.

overall_design:
A total of 13 patients with histologically confirmed colorectal adenocarcinomas were studied. The tissue specimens of the tumor and normal colon were removed during surgery and immediately frozen in liquid nitrogen. Total RNA was extracted for further processing with the affymetrix microarray platform HG-U133A.

The patients assayed in this study are independent from those assayed in GSE110224.


title: RNA-seq of cultured human kidney peritubular microvascular endothelial cells following exposure to cyclosporine A

city: Seattle

first: Ying

last: Zheng

state: WA

address: 850 Republican

department: Bioengineering

institute: University of Washington

summary: This study represents the first time human kidney endothelial cells were exposed to cyclosporine A (CsA), a calcineurin inhibitor known to contribute to nephrotoxicity with symptoms including microvascular injury. This toxicity has been found to be unique to human trials and human kidneys are particularly susceptible to injury. We found that human kidney peritubular microvascular endothelilal cells (HKMECs) that were exposed to CsA exhibited transcriptomic changes around genes important to VEGF signaling and endothelial inflammation.

overall_design: HKMECs from three donors were cultured then exposed to CsA or control for 1 hour and lysed for RNA collection after 18 hours, these were performed in duplicate

first: Jonathan

last: Himmelfarb


title: Transcriptome comparisons of TRIM45 overexpressing and vector control U251 cells

city: Guangzhou

first: Jindong

last: Zhang

address: Zhongshan road 74#

institute: Sun Yat-sen University

summary: We used microarrays to detail the global gene expression in TRIM45-overexpressing and control U251 cells.

overall_design: The TRIM45-overexpressing and control U251 cells were for RNA extraction and hybridization on Affymetrix microarrays.


title: Microfluidic MeDIP-seq for low-input methylomic analysis of mammary tumorigenesis in mice

status: Public on Dec 30 2018

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

type: Methylation profiling by high throughput sequencing

summary: Studies of dynamic epigenomic changes during tumorigenesis using mice often require profiling epigenomes using a tiny quantity of tissue samples. Conventional epigenomic tests do not support such analysis due to the large amount of materials required by these assays. In this study, we developed an ultrasensitive microfluidics-based methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) technology for profiling methylomes using as little as 0.5 ng DNA (or ~100 cells) with 1.5 h on-chip process for immunoprecipitation. This technology enabled us to examine genome-wide DNA methylation in a C3(1)/SV40 T-antigen transgenic mouse model during different stages of mammary cancer development. Using our data, we identified differentially methylated regions and their associated genes in different periods of cancer development. Our results showed that unique methylomic features were presented in various tumor developmental stages.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We examined genome-wide DNA methylation profiles for GM12878 cell line (with starting DNA sample amounts in the range of 0.5-100 ng), and mammary tissue/tumor harvested from C3(1)/SV40 T-antigen transgenic mouse model during mammary cancer development (6, 16, 23 weeks, with starting DNA sample amount of 10ng).

first: Yan

last: Zhu


title: Affymetrix microarray analysis of the effects of nicotinamide on HEK293 cells

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

summary:
Sirtuin deacetylases and forkhead box class O (FOXO) transcription factors are central regulators of cell survival, cell cycle and cellular resistance to stress in response to signals from hormones, growth factors and oxidative stress. FOXO activity is modulated by the sirtuins, which function in a NAD+-dependent manner. Sirtuin activity, on the other hand is subject to inhibition by a natural compound nicotinamide (NAM). This study aims to investigate the effects of NAM on the
sirtuin pathway and cellular homeostasis. It was hypothesized that NAM inhibits the sirtuin deacetylase activity, which then shifts FOXO-dependent responses away from stress resistance and towards apoptosis. Expression analysis using Affymetrix microarray was employed to determine differential gene expression in HEK293 cells in response to NAM treatment. Data analyses were performed using multiple algorithms, computational methods and interaction analyses. Significant changes in gene expression were detected with the generation of an expansive list of genes and interaction amongst gene groups were identified from the NAM treatment at different concentration. Substantial changes in expression profiles were detected for genes involved in a number of unique cellular pathways and functions, including cell cycle arrest, cellular proliferation and differentiation, metabolism, apoptotic signaling, inflammatory regulation and various disease conditions such as
cancer. In addition, this study observed that sirtuin activities exhibit complex cell- and contextdependent behavior in modulating FOXO signaling. Contrasting roles of FOXOs and sirtuins appear to have opposite effects on cellular homeostasis. In addition, the coexistence of reciprocal regulations in this cell system suggested several levels of feedback control and illustrated the complexity of an existing fine-tuned regulatory network system between these two proteins. Future
work aims to characterize putative regulators and effectors of sirtuin- and FOXO-related pathways using molecular approaches such and RNA interference knockdown of individual FOXO-isoforms.
Inter-connectivity of the pathways will provide invaluable insight into current understanding of cell degeneration diseases such as diabetes, cancers and neurological disorders.
Keywords: Serial concentration experiment

overall_design: Expression variation at the transcriptional level was studied with RNA samples(Batch 1) obtained from cells treated with nicotinamide (NAM) at five different concentrations i.e., 0, 5, 10, 15 and 20 mM. The cytotoxicity of these concentrations was previously determined by Mark Pinese (Honours thesis 2005). This first experiment was to determine which concentration caused the most gene expression changes. Once this was determined, 2 replicate RNA samples (Batch 2 and 3) were subsequently assayed. In this case, 3 replicates of HEK293 cells treated at 0 and 5 mM NAM were used.

first: JackieKY

last: Lau

first: RubyCY

first: Ian

last: Dawes

first: Brian

middle: J

last: Morris


title: Genome-wide chromatin profiling usign ATAC-seq of diabetic or non-diabetic murine bone marrow derived macrophages (BMDM)

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

summary: Previous ATAC-seq analysis revealed changes in bone marrow HSC chromatin structure and transcription factor binding site accessibility. Here, we use ATAC-seq analyses on bone marrow derived macrophages to characterise whether HSC chromatin changes are long-lasting, and differences persist in diabetic macrophages, after glucose normalisation, and helps to drive pro-inflammatory gene expression and function.

overall_design: 6 diabetic mice samples and 6 non-diabetic control mice samples were used. Each sample was split in half, one half submitted as a baseline, unstimulated control and the other was stimulated with LPS + IFNy.

first: Thomas

last: Krausgruber

first: Madeleine

middle: E

last: Lemieux

first: Robin

middle: P

last: Choudhury


title: Maternal siRNAs mediate spatial and temporal regulation of gene expression and seed development in Arabidopsis

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: In Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1 pathway. To investigate their biological functions we characterized siRNAs in the endosperm and seed coat that were separated by laser capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatio-temporal activity of the NRPD1 pathway on seed development using AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches we identified four distinct groups of siRNA loci that were dependent on or independent of the maternal NRPD1 allele in the endosperm or seed coat. A group of maternally expressed NRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using the sensor AGL40:GUS and AGL91:GUS constructs we demonstrate that spatial and temporal expression patterns of these genes in the endosperm were regulated by the NRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Modified expression of these siRNA-targeted genes affects seed size and we propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

overall_design: 1. Examination of small RNAs in embryo, endosperm and seed coat of Arabidopsis seeds. 2. Examiniation of small RNAs in reciprocal crosses between wild type and nrpd1a mutant as well as rdr2 mutant. 7 crosses were made including 3 self pollination of parent strains.

first: Ryan

last: Kirkbride

first: Jie

first: Changqing

first: Rebecca

last: Mosher

first: David

last: Baulcombe

first: Z


title: Affymetrix microarray analysis of the effects of isonicotinamide on HEK293 cells

overall_design: Expression variation at the transcriptional level was studied with RNA samples(Batch 1) obtained from cells treated with isonicotinamide (INAM) at five different concentrations i.e., 0, 5, and 10 mM. The cytotoxicity of these concentrations was previously determined by Mark Pinese (Honours thesis 2005). This first experiment was to determine which concentration caused the most gene expression changes. Once this was determined, 2 replicate RNA samples (Batch 2 and 3) were subsequently assayed. In this case, 3 replicates of HEK293 cells treated at 0, 5 and 10 mM NAM were used.

first: Zi-Hui

last: Lo

first: Helen

last: Speirs


title: An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages

status: Public on Dec 29 2018

city: Urbana

first: Soumya

last: Negi

state: Illinois

address: Institute of Genomic Biology, 1206 W Gregory Dr

department: Cell and Developmental Biology

institute: University of Illinois

summary: The evolutionarily conserved transcription factor, Tbx18, is expressed in a dynamic pattern throughout embryonic and early postnatal life and plays crucial roles in the development of multiple organ systems. Previous studies have indicated that this dynamic function is controlled by an expansive regulatory architecture, extending far upstream and downstream of the gene. With the goal of identifying elements that interact with the Tbx18 promoter in developing prostate, we coupled chromatin conformation capture (4C) and ATAC-seq from embryonic day 18.5 (E18.5) mouse urogenital sinus (UGS), where Tbx18 is highly expressed. The data revealed dozens of active chromatin elements distributed throughout a 1.5 million base pair topologically associating domain (TAD). To identify cell types contributing to this chromatin signal, we used lineage tracing methods with a Tbx18 Cre “knock-in” allele; these data show clearly that Tbx18-expressing precursors differentiate into wide array of cell types in multiple tissue compartments, most of which have not been previously reported. We also used a 209 kb Cre-expressing Tbx18 transgene, to partition enhancers for specific precursor types into two rough spatial domains. Within this central 209 kb compartment, we identified ECR1, previously described to regulate Tbx18 expression in ureter, as an active regulator of UGS expression. Together these data define the diverse fates of Tbx18+ precursors in prostate-associated tissues for the first time, and identify a highly active TAD controlling the gene’s essential function in this tissue.

overall_design: 2 replicates of 4C-seq performed in male mouse UGS at E18.5 using Tbx18 promoter as view-point. 1 replicate of ATAC-seq of male UGS at E18.5

first: Christopher

last: Bolt

first: Lisa

last: Stubbs


title: Mitochondrial Proteostatic Stress Induces Aggrephagy to Triage Unimported Proteins

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We report the results of overexpression of the wildtype and mutant ANT1 (SLC25A4) gene in human embryonic kidney 293T (HEK293T) cells from the cytomegalovirus (CMV) promoter. Libraries were prepared from three independent replicates per condition using stranded RNA sequencing and run at 2 x 75 read length at a targeted output of 60 million paired-end reads per sample. We found only a limited number of nuclear genes whose expression is altered by wildtype ANT1-overexpression. Among the most upregulated genes is the zinc-finger proteins Egr1, a transcriptional factor with diverse cellular functions, including the repression of genes encoding mitochondrial inner membrane protein. The upregulation of EGR1 likely serves as a retrograde mechanism to reduce protein loading on the IMM and to alleviate mPOS.  Overexpression of the triple and quadruple mutant alleles altered the expression of 206 and 560 genes, respectively, with 32 commonly up-regulated in both. These include EGR1, ZCCHC12 and SFPQ, which were also upregulated in cells overexpressing the wild-type ANT1. The 32 up-regulated genes are involved in functions including RNA-processing, autophagy/intracellular structure/trafficking, transcriptional control, ribosomal biogenesis/translational control, chaperones/proteasomal function and mitochondrial biogenesis. Upstream regulator analysis subsequently revealed 42 pathways predicted to be either activated or inhibited by these genes, including PPARGC1A, ATF4, Heat Shock Factor 1 (HSF1), mechanistic Target of Rapamycin (mTOR), Myc, EGFR and HMGA1.

overall_design: Examination of effects of overexpression of wildtype and mutant ANT1 alleles in HEK293T cells

first: Xin


title: A Foxp3 mutation drives Th2 effector function in regulatory T cells

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

summary: Regulatory T (Treg) cells maintain immune tolerance through the action of the master  regulator FOXP3, a transcription factor crucial for Treg cells function and homeostasis.  We identified an IPEX patient with a FOXP3 mutation in the domain swap interface of  the protein (mutant M370I). Recapitulation of this Foxp3 variant in mice led to an autoimmune syndrome  similar to the patient and consistent with an unrestrained Th2 immune response.  Genomic analysis of Treg cells by RNA-seq, Foxp3 ChIP-seq and H3K27ac-HiChIP  revealed a specific de-repression of the T helper type 2 (Th2) transcriptional program  leading to the generation of Th2-like Treg cells that are unable to suppress extrinsic Th2  cells. Th2-like Treg cells are characterized by increased intra-chromosomal interactions  in the Th2 locus leading to type-2 cytokines production. Our research provides cellular  and molecular characterizations of mechanisms used by Foxp3 to restrain Th2 transdifferentiation  and promote optimal Treg suppressive function and stability.

overall_design: Wild-type (WT) and mutant M370I (MT) mouse Treg cells were analysed for: gene expression by RNA-seq, Foxp3 binding profile by Foxp3 ChIP-seq and for 3-dimensional genome structure by H3K27ac HiChIP

first: Frederic

middle: V

last: Gool

first: Michelle

last: Nguyen

first: Ansuman

middle: T

last: Satpathy

first: Maxwell

middle: R

last: Mumbach

first: Alexander

last: Marson

first: Howard

middle: Y

last: Chang

first: Jeffrey

last: Bluestone


title: Single-cell RNA-seq of Mesp1+ mesoderm from ES cells

city: Minneapolis

first: Sunny

last: Chan

state: MN

address: 2231 6th St SE

department: Pediatrics

institute: University of Minnesota

summary: We have developed a protocol to generate hematopoietic and cardiac derivatives in vitro by Mesp1 induction in ES cells.  The goal of this study is to analyze the heterogeneity of Mesp1+ mesoderm by single-cell RNA-seq

overall_design: 48 Mesp1-induced single cells were captured using the Fluidigm C1 microfluidic system.  RNA extraction, RT and cDNA amplication were then performed according to the manufacturer's manual.

first: Michael

last: Kyba


title: RNA m6A-Ythdf1 in dendritic cells triggers anti-tumor immunity (ribo-seq and m6a-seq in GMDCs)

city: Bethesda

first: Chuanyuan

last: Chen

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

summary: Emerging evidence emphasizes the important role of tumor neoantigen in generating the spontaneous antitumor immune response and predicting the clinical response to immunotherapies. Despite the presence of numerous neoantigens, complete tumor elimination rarely occurs in majority of patients due to failures in mounting a sufficient and lasting antitumor immunity. Here we show that the durable neoanitgen-specific immunity is regulated by a m6A-binding protein, Ythdf1. In contrast to wild-type mice, Ythdf1-deficient (Ythdf1-/-) mice generate more antigen-specific CD8+ T cell response for persistent tumor control. Loss of Ythdf1 in dendritic cell (DC) results in an enhanced cross-presentation of tumor antigen and cross-priming of CD8+ T cell in vivo. To confirm our observations, we performed Ribo-Seq to analyze the translational efficiency of genes in DCs and performed m6A-seq to locate the m6A sites.

overall_design: BMDCs obtained from WT and YTHDF1 KO mice were used to genetarate ribo-seq (monosome footprints and polysome footprints) and m6a-seq libraries. Two replicates for each conditions.

first: Dali

last: Han

first: Meng

middle: M

last: Xu

first: Chuan

last: He


title: LARP7 is a substrate of BRCA1 that regulats genome instability and tumorigenesis

status: Public on Jan 01 2019

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: Impaired DNA repair leads to cancer, aging and many genetic diseases. However, understanding of the complexity of DNA is far from complete, resulting in the failure of therapies using genotoxic reagents. Here, we found that LARP7, an RNA-binding protein known to stabilize 7SK RNA, was degraded after DNA injury caused by ionizing radiation and chemotherapy. The LARP7 degradation was catalyzed by an E3 ligase complex of BRCA1 and BARD1 that was triggered by ATM-mediated phosphorylation. LARP7 depletion caused transcriptional repression of the cell cycle regulators CCNB1, CCNB2 and CDK1; this repression arrested cells before the G2/M DNA damage checkpoint and reduced BRCA2 phosphorylation, therefore enhancing Rad51 recruitment and ultimately ensuring the homologous repair of damaged DNA. Importantly, the increased DNA damage repair capacity induced by LARP7 depletion caused resistance to ionizing radiation and CDDP treatment in both wild-type and BRCA1-mutant breast cancer cells and in mouse xenografts. Such resistance also contributed to reduced relapse-free survival rates in breast cancer patients with low levels of LARP7 after chemotherapy. Taken together, the results of this study show that LARP7 coordinates cell cycle progression and faithful DNA repair. We suggest that this mechanism could be exploited to prevent tumorigenesis and improve the effectiveness of cancer therapies.

overall_design: RNA-seq on wild-type MEFs, LARP7-/- MEFs, and two breast cancer cell lines (MDA-MB-231 and HCC1937) with or without siLARP7 treatment.

first: Fang

last: Zhang

first: Pengyi

last: Yan

first: Huijing

last: Yu

first: Huangying

last: Le

first: Zixuan

last: li

first: Jiahuan

first: Xiaodong

last: Liang

first: Shiyan

last: Wang

first: Weiting

last: Wei

first: Li

last: Liu

first: Yan

first: Xing

last: Ji

first: Anyong

last: Xie

first: Wantao

first: Zeguang

first: William

last: Pu

first: Sun

first: Yingwei

first: Kun

last: Sun

first: Bing


title: A runaway PRH/HHEX-Notch3 feedback loop drives cholangiocarcinoma (ChIP-seq)

status: Public on Dec 28 2018

city: Birmingham

first: Philip

last: Kitchen

address: IBR Building

institute: University of Birmingham

overall_design: 2 ChIP samples, CCLP1 cells infected with myc-PRH or empty adenovirus (for background). ChIP done with anti-myc-tag antibody.

first: Padma-Sheela

last: Jayaraman

first: Kevin

last: Gaston


title: RNA m6A-Ythdf1 in dendritic cells triggers anti-tumor immunity (MeRIP-Seq, RIP-Seq and Ribo-Seq in Flt3L-DCs)

first: Chuanyuan

last: Chen

overall_design: Flt3L-DCs obtained from WT and YTHDF1 KO mice were used to generate MeRIP-Seq, RIP-Seq and Ribo-Seq libraries. Two replicates for each conditions.

first: Dali

last: Han

first: Meng

last: Xu

first: Chuan

last: He


title: LPS time-course in WT and Stk40 KO BMDMs

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary:
Bone marrow was harvested from Rosa26CreER; Stk40+/+ (WT; n = 3) and Rosa26CreER; Stk40loxp/loxp (Stk40 KO; n = 3) mice and differentiated for 6 days in the presence of 100 nM 4-OHT to generate WT and Stk40 KO bone-marrow derived macrophages (BMDMs).
2. On day 7 following differentiation BMDMs were treated with 100 ng x ml-1 LPS and harvested at 0 hrs, 6 hrs, 16 hrs, and 32 hrs following LPS exposure.
3. The cells were snap-frozen at the time of harvest. RNA was extracted using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion.
Groups: There are cells from 3 mice x 2 genotypes x 4 time points
G1: WT 0 hr LPS
G2: WT 6 hr LPS
G3: WT 16 hr LPS
G4: WT 32 hr LPS
G5: Stk40 KO 0 hr LPS
G6: Stk40 KO 6 hr LPS
G7: Stk40 KO 16 hr LPS
G8: Stk40 KO 32 hr LPS

overall_design: RNA from BMDMs following LPS treatment at different time points from mice that are Stk40-wt ot Stk40-ko


title: Global increase in DNA Methylation during ripening of sweet orange

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress  Biology

institute: Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Colonization of the Ovary and Metastasis of Fallopian Tube Derived Cancer

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary: This experiment was designed to compare changes in the transcriptome of fallopian tube epithelial cells plated on two-dimensional and three-dimensional collagen.

overall_design: Murine oviductal epithelial (MOE, oviduct is equivalent to the fallopian tube were plated on two- or three-dimensional collagen for 6 hours.

first: Matthew

last: Dean

first: Vivian

last: Jin

first: Angela

last: Russo

first: Daniel

middle: D

last: Lanvit


title: Global increase in DNA Methylation during ripening of sweet orange [BS-seq]

summary: Using BS-Seq to provide single-base resolution of DNA methylation status in five fruit ripening stages in sweet orange

overall_design: BS-Seq:  five sweet orange fruit ripening stages

first: Huan

last: Huang

first: Ruie

last: Liu

first: Qingfeng

last: Niu

first: Jian-Kang

last: Zhu

first: Zhaobo

last: Lang


title: Transcriptome-wide mapping of host mRNA m6A modification to decipher the role of gut microbiome

first: Tao

last: Pan

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: A recently layer of gene expression regulation is N6-methyladenosine (m6A) mRNA modification. The role of gut microbiota in modulating host m6A epitranscriptomic and gene expression has not been studied. To decipher the role of gut microbiome, we profiled m6A mRNA modification epitranscriptomic mark in conventional mice compared to germ free mice. Transcriptome-wide mapping of host m6A mRNA modifications in four mice tissues allowed us to discover that gut microbiota can greatly impact host m6A mRNA modifications. The expression levels of m6A writers in mice tissues are regulated by gut microbiota. In conclusion, we report transcriptome-wide mapping of host m6A mRNA modifications regulated by gut microbiota. The present study can help better understand the role of the microbiome in host gene expression and host-microbiome interactions.

overall_design: The profiles of mRNA m6A modifications of four tissues from specific pathogen free mice and germ free mice are compared.

first: Xiaoyun

last: Wang

first: Yan

last: Li


title: Global increase in DNA Methylation during ripening of sweet orange [ncRNA-seq]

summary:
Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange
DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.

overall_design: sRNA-Seq: sweet orange fruit ripening stages

last: huang

first: Rui'e


title: Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [BiSulfite-seq]

city: BALTIMORE

first: hari

last: easwaran

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

summary: Abnormal promoter DNA hypermethylation arises early during tumorigenesis and yet its role in cancer initiation has remained underexplored. An important scenario for examining this is, BRAFV600E-mutant colon adenocarcinomas (COAD) which most often arise in the proximal colon and harbor extensive, abnormal gene promoter CpG-island methylation or the methylator phenotype (CIMP). How CIMP and BRAF-mutations specifically interact for COAD initiation has remained unclear. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in wild type cells mimicking “aging like” phenotype. The silenced genes sufficiently activate the Wnt pathway, causing a stem–like state and profound differentiation block. This phenotype renders long-term cultured organoids to be rapidly susceptible to transformation by BRAFV600E with features of typical right-sided COAD. Our studies tightly link epigenetic abnormalities, suggested to arise with aging, to intestinal cell fate changes and define an “epi-driver” role for multiple abnormally silenced genes that predispose to BRAFV600E-driven colon tumorigenesis.

overall_design: Cre-activable BrafV600E and wild type proximal colon organoids were derived from mice carrying heterozygous Cre-activable BrafV600E (termed Braf+/LSL). Lentiviral delivery of Cre with the lentiviral backbone alone serving as control (EV), is used to subsequently activate BrafV600E in the organoids. Expression and methylation analyses were done in organoids 5m after induction of oncogene, and in organoids selected to grow in medium without stem-cell niche factors (Base medium). Two biological replicates of BrafEV  organoids are grown for over 12-14 months which were labled as  BRAF1_EV_12m & BRAF3_EV_14m.

first: Hari

last: Easwaran


title: Global increase in DNA Methylation during ripening of sweet orange [RNA-seq]

first: Huang

last: Huan

summary: Using RNA-Seq to analyse the gene expression pattern in five fruit ripening stages in sweet orange

overall_design: RNA-Seq: five sweet orange fruit ripening stages


title: Transcriptome of  Dmrt3 KO, Dmrt5 KO, Dmrt3;Dmrt5 double KO and wildtype cortical tissue at E12.5.

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Here we generated transcriptomes of dissected cortical tissue of Dmrt3 and Dmrt5 single knockout, of Dmrt3;Dmrt5 double knock-out  and wildtype littermate at embryonic day 12.5.

overall_design: mRNA profiles by RNA-seq of dissected mouse cortex

first: Elodie

last: Desmaris

first: Marc

last: Keruzore

first: Thomas

last: Lingner

first: Kristine

last: Henningfeld

last: Pieler

first: Eric

last: Bellefroid


title: Acne flare-up in treatment process: investigating the difference of gene expression in peripheral blood

status: Public on Dec 27 2018

city: Guangzhou

first: Yuchen

last: Jiang

state: Guangdong

address: 600 Tianhe Road

institute: Third Affiliated Hospital of Sun Yat-sen University

summary:
Objectives: To identify gene expression changes in acne flare-up patients, thereby exploring the mechanisms of acne flare-up after treatment.

Methods: 11 acne patients and 3 healthy people were divided into 4 groups (group1: 4 with flare-up, group2: 4 with improvement, group3: 3 without obvious changes, group4: healthy control). Peripheral blood of patients before and after isotretinoin or minocycline were collected. RNA-seq were used to detect the gene expression. We applied data in self-contrast and intergroup comparisons.

Results: In the self-contrast of group1, 22 upregulated genes were involved in Toll-like receptor signaling pathway and inflammatory response. Comparing group1 and group3 before treatment, 1778 upregulated genes enriched in Th17 cell differentiation, while 57 downregulated genes enriched in defensive response to organism.

Conclusions: The gene expression profiles of acne flare-up patients changed. Inflammatory, immune responses played a prominent role in acne flare-up process and relatively weak defensive response to microbes, comedogenesis might be risk factors.

overall_design: RNA-seq were used to detect the gene expressions in acne flare-up patients and healthy controls.


title: miR205 Regulates Mammary Gland Development and Stem Cell Self-renewal through YAP and Wnt signaling

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary: Mammary gland development is fueled by stem cell self-renewal and differentiation. External cues from the microenvironment coupled with internal cues such as post-transcriptional regulation exerted by miRNAs regulate stem cell behavior and stem cell fate. We have identified a miR205 regulatory network required for mammary gland morphogenesis and stem cell maintenance. In the postnatal mammary gland, miR205 is predominantly expressed in the basal/stem cell enriched population. Conditional deletion of miR205 in mammary epithelial cells severely impaired stem cell self-renewal and mammary repopulating potential both in vitro and in vivo. miR205 null glands displayed significant changes in the basal population, basement membrane and stroma. NKD1 and PP2A-B56, which inhibit the Wnt signaling pathway, and AMOT, which causes YAP cytoplasmic retention and inactivation were identified as miR205 downstream effectors. Collectively these findings reveal an essential role of miR205 in mammary gland development.

overall_design: WT;RosamTmG/mTmG and miR-205fl/fl;RosamTmG/mTmG cells were treated with Ad-cre and transplanted back to 3-wk-old SCID-Beige mice. Mammary epithelial cell (MECs) were isolated from pooled 40 WT;RosamTmG/mTmG cre+ and miR-205fl/fl;RosamTmG/mTmG cre+ outgrowths after 8 weeks. GFP+ basal cells (CD24+CD49fhigh) were further sorted from MECs of each group and RNA-seq were performed on WT and miR205fl/fl cre+ green basal cells to look for differentially expressed genes.

first: Yang

last: Lu

first: Wei

first: Jeffrey

last: Rosen


title: Dysfunctional CD8+ T cells form a proliferative, dynamically regulated compartment within human melanoma [scRNA-seq]

city: Rehovot

first: Yaniv

last: Lubling

address: POB 26

institute: Weizmann Institute of Science

summary: Tumor immune cell compositions play a major role in response to immunotherapy but the heterogeneity and dynamics of immune infiltrates in human cancer lesions remain poorly characterized. Here we identify conserved intratumoral CD4 and CD8 T cell behaviors in  scRNA-seq data from 25 melanoma patients. We discover a large population of CD8 T cells showing continuous progression from an early effector “transitional” into a dysfunctional T cell state. CD8 T cells that express a complete cytotoxic gene set are rare, and TCR sharing data suggest their independence from the transitional and dysfunctional cell states. Notably, we demonstrate that dysfunctional T cells are the major intratumoral proliferating immune cell compartment and that the intensity of the dysfunctional signature is associated with tumor-reactivity. Our data demonstrate that CD8 T cells previously defined as exhausted, are in fact a highly proliferating, clonal and dynamically differentiating cell population within the human tumor microenvironment.

overall_design:
Single-cell transcriptional profiling of immune cells from human melanoma tumors and several matching pbmc samples. See individual samples for details.
Raw sequences are available at the European Genome-Phenome Archive (EGA) under accession number EGAS00001003363.

first: Hanjie

first: Anne

last: van der Leun

first: Ido

last: Yofe

first: Dikla

last: Gelbard Solodkin

first: Alexander

last: van Akkooi

first: Marlous

last: van den Braber

first: Lisette

last: Rozeman

first: John

last: Haanen

first: Christian

last: Blank

first: Hugo

last: Horlings

first: Eyal

last: David

first: Yael

last: Baran

first: Akhiad

last: Bercovich

first: Aviezer

last: Lifshitz

first: Ton

middle: N

last: Schumacher

first: Amos

last: Tanay

last: Amit


title: Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation

city: Toronto

first: Sarah

middle: J.

last: Goodman

state: ON

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

summary: Background: The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts.  In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages. Results: BECs had greater inter-individual DNAm variability compared to PBMCs and highly variable CpGs were more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm co-variation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood. Conclusions: Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNAm profiles in matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages.

first: Sumaiya

last: Islam

first: Julia

last: MacIsaac

first: Jelena

last: Obradović

first: Ronald

middle: G

last: Barr

first: W

last: Boyce

first: Michael

last: Kobor


title: Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent

city: New York

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: Cell fate transitions are essential for specification of stem cells and their niches, but the precise timing and sequence of molecular events during embryonic development are largely unknown. Here, we identify with 3D/4D microscopy unclustered precursors of dermal condensates (DC), signaling niches for epithelial progenitors in hair placodes. With population-based and single-cell transcriptomics, we define a molecular time-lapse from pre-DC fate specification through DC niche formation and establish the developmental trajectory as the DC lineage emerges from fibroblasts. Co-expression of downregulated fibroblast and upregulated DC genes in niche precursors reveals a transitory molecular state following a proliferation shutdown. Waves of transcription factor and signaling molecule expression then coincide with DC formation. Finally, ablation of epidermal Wnt signaling and placode-derived FGF20 demonstrates their requirement for pre-DC specification. These findings uncover a progenitor-dependent niche precursor fate and the transitory molecular events controlling niche formation and function.

overall_design:
Dorsal skins were dissected from E15.0 embryos, dissociated into single cells, and FACS sorted. Single-cell transcriptomics was performed on live cells using an automated version of CEL-seq2 on live, FACS sorted cells. The StemID algorithm was used to identify clusters of cells corresponding to stages of DC development, starting from fibroblasts.

Bulk RNA-sequencing of sorted populations from E15.0 backskin; raw data files contain all transcriptome information for pre-DC, DC1, DC2, fibroblasts, Schwann cells, and negative population, processed data file includes transcriptome information for pre-DC, DC1, DC2, fibroblasts, Schwann cells and negative population used in this study.

Single Cell RNA-sequencing of E15.0 mouse backskin; raw data files contain all single cell transcriptome information, processed data file includes mesenchymal transcriptome information used in this study.

first: Ka-Wai

last: Mok

first: Nivedita

last: Saxena

first: Nicholas

last: Heitman

first: Laura

last: Grisanti

first: Devika

last: Srivastava

first: Mauro

last: Muraro

first: Tina

last: Jacob

first: Rachel

last: Sennett

first: Zichen

last: Wang

first: Yutao

last: Su

first: Lu

last: Yang

first: Avi

last: Ma'ayan

first: David

last: Ornitz

first: Maria

last: Kasper


title: A runaway PRH/HHEX-Notch3 feedback loop drives cholangiocarcinoma (RNA-Seq)

first: Philip

last: Kitchen

overall_design: 16 samples total. 3 experiments: (i) PRH shRNA knockdown vs scrambled control. 2 independent clones expressing each shRNA (4 samples total). (ii) PRH overexpression using myc-PRH adenovirus vs empty adenovirus. 2 independent infections with each virus (4 samples total). (iii) Overexpression of PRH in Notch3 KD and control shRNA cell lines using myc-PRH adenovirus. (8 samples total - 2 independent infections each for all combinations of Notch3/control shRNA and myc-PRH/empty adenovirus)

first: Padma-Sheela

last: Jayaraman

first: Kevin

last: Gaston


title: RNA_seq analysis on Tfh and Treg before and after abatacept treatment

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

summary: Analysis of transcriptome data identified 96, 64 and 3 genes that were differentially expressed  (DE,  adj.  P  value < 0.05) following  abatacept  treatment in Tfh, Treg and CD4+CD45RO+PD1+CXCR5- T cells, respectively. We determined if abatacept treatment altered the core transcriptional profiles of Tfh and Treg lineages by comparing gene expression of bulk sorted Treg and Tfh cells from cryopreserved PBMCs at baseline, week 24, and after abatacept withdrawal.  Analysis of differentially expressed (DE) genes in Tfh was performed using Gene Ontology (GO) term enrichment analysis.  This analysis revealed 9 significantly enriched GO categories, which were related to processes involved in cell division and proliferation. DE genes in the enriched GO categories showed a highly significant correlation in Tfh and Treg cells, further highlighting the similarity in the response of these two populations to abatacept. In contrast to Tfh and Treg, acatacept had a minimal impact on CD4+CD45RO+PD1+CXCR5- T cells.

overall_design:
Tfh, Treg and CD4+CD45RO+PD1+CXCR5- T cells populations were sorted from 30 different donors from blood draws at 3 different visits weeks 0, 24, and 52. 500 cells of each subset were sorted directly into SMARTseq v4 (Takara) lysis buffer to release RNA, and RT-PCR then used to generate cDNA. Sequencing libraries were constructed using a modified protocol of the NexteraXT DNA sample preparation kit (Illumina).  Libraries were pooled and quantified by Qubit® Fluorometer (Life Technologies).
For the Abatacept group, visit 0 was used as baseline and visit 7 represents the timepoint after abatacept treatment. The placebo group received placebo treatment first and then crossed over to abatacept treatment., hence we used v7 as baseline and visit 15 as the timepoint after abatacept treatment.

first: E

last: Bettelli

first: D

last: Campbell

first: B

last: Hoellbacher

first: S

last: Glatigny

last: Motley

first: C

last: Tan

first: M

last: Rosasco


title: Comparative gene expression profiling of the three main types of mouse dendritic cells isolated ex vivo from the spleen versus generated in vitro in bone marrow FLT3-L cultures

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

type:
Expression profiling by array
Third-party reanalysis

summary: The goal of this experiment was to use global gene expression profiling to compare the transcriptomic profiles between the three major types of dendritic cells (DCs) directly isolated ex vivo from the spleen versus derived in vitro from bone marrow FLT3-L cultures. The three DC types analyzed in each condition were type 1 classical DCs (cDC1s), type 2 cDCs (cDC2s) and plasmacytoid DCs (pDCs). The gene expression profiles of the samples of the in vitro derived DCs used here were not reported before. We have previously reported the gene expression profiles of the samples used here for the DCs directly isolated ex vivo from the spleen. They correspond to a reanalysis of the following records: cDC1: GSM1828801 and GSM1828802, cDC2: GSM3178486 and GSM3178487, pDC: GSM2882708 and GSM2882709.

overall_design: DCs were generated in vitro from mouse bone marrow FLT3-L cultures and sorted by flow cytometry to over 98% purity, as live, singlet, CD11c+ cells that were SiglecH(+) for eq-pDCs, SIRPα(-/low)CD24(high) for eq-cDC1s and SIRPα(high)CD24(-/low) for eq-cDC2s.

first: Cindy

last: Sanchez

first: Marc

last: Dalod


title: Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity [ATAC-seq]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: TH17 cells in autoimmune disease are functionally and metabolically heterogeneous and contain a subset with stemness-associated features but lower anabolic metabolism and a reciprocal subset with higher metabolic activity that supports the transdifferentiation into TH1 cells.

overall_design: ATAC seq of TCRb+YFP+ cells from spleen and draining lymph node in Rptor deficient and wild type cells.

first: Peer

last: Karmaus

first: Xiang

last: Chen

first: Yogesh

last: Dhungana


title: The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Human primordial germ cells (hPGCs) are the first embryonic progenitors in the germ cell lineage, yet the molecular mechanisms required for hPGC formation are not well characterized. To identify regulatory regions in hPGC development, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to systematically characterize regions of open chromatin in hPGCs and hPGC-like cells (hPGCLCs) differentiated from human embryonic stem cells (hESCs). We discovered regions of open chromatin unique to hPGCs and hPGCLCs that significantly overlap with TFAP2C-bound enhancers identified in the naive ground state of pluripotency. Using CRISPR/Cas9, we show that deleting the TFAP2C-bound naive enhancer at the OCT4 locus (also called POU5F1) results in impaired OCT4 expression and a negative effect on hPGCLC identity.

overall_design: 26 ATAC-seq libraries: 9 ATAC-seq libraries from primed hESCs, 4 ATAC-seq libraries from iMeLC induced from primed hESCs, 3 ATAC-seq libraries from hPGCLCs induced from primed hESCs, 6 ATAC-seq libraries from sorted hPGCs, 4 ATAC-seq libraries from liver, lung, skin and heart cells from human embryo.

first: Di


title: Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity

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

overall_design: Refer to individual Series


title: Reprogramming of dermal papilla cell intact gene signature with 3D culture and Lef-1 overexpression

first: HASAN

middle: ERBIL

last: ABACI

address: Russ Berrie Medical Science Pavilion  1150 St. Nicholas Avenue

department: DERMATOLOGY

institute: COLUMBIA UNIVERSITY

overall_design: The reference sample is freshly isolated dermal papilla cells. A total of 4 conditions exist: cells cultured on 2D at passage 3 (2D); cells overexpressing Lef1 cultured on 2D at passage 3 (2D-Lef), cells cultured as 3D spheres in hanging drops at passage 3 (3D); cells overexpressing Lef1 cultured as 3D spheres in hanging drops at passage 3 (3D-Lef).

first: Hasan

last: Abaci

first: Angela

last: Christiano


title: Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity [scRNA-seq]

overall_design: Single Cell analysis of TCRb+YFP+ cells from spleen in Rptor deficient and wild type cells.


title: A-485 induce significant decrease in MITF and MITF signature genes in melanoma cell lines.

city: North Chicago

first: Xin

last: Lu

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary:
Differential response to p300 inhibitor A-485 was observed in a panel of melanoma cell lines.
Three melanoma cell lines were treated with A-485 and microarray was used to determine gene expession changes at 6 and 24 hours.

overall_design: Melanoma cell lines, two sensitive and one resistant cell lines, were treated with A-485 to identify genes that are differentially modulated by A-485.

first: Paul

last: Hessler

first: Lloyd

last: Lam


title: Condensin-dependent chromatin condensation represses transcription globally during quiescence

city: Seattle

first: Sarah

middle: G.

last: Swygert

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center


title: Condensin-dependent chromatin condensation represses transcription globally during quiescence [Micro-C XL]

summary: Quiescence is a stress-resistant state in which cells reversibly exit the mitotic cell cycle and suspend most cellular processes.  Quiescence is essential for stem cell maintenance and its misregulation is implicated in tumor formation.  One of the conserved hallmarks of quiescent cells, from Saccharomyces cerevisiae to humans, is highly condensed chromatin.  Here, we use Micro-C XL to map chromatin contacts at single-nucleosome resolution genome-wide to elucidate mechanisms and functions of condensed chromatin in quiescent S. cerevisiae cells.  We describe previously uncharacterized chromatin domains on the order of 10-60 kilobases that in quiescent cells are formed by condensin-mediated chromatin loops.  Conditional depletion of condensin prevents chromatin condensation during quiescence entry and leads to widespread transcriptional de-repression.  We further demonstrate that condensin-dependent chromatin compaction is conserved in quiescent human fibroblasts.  We propose that condensin-dependent condensation of chromatin represses transcription throughout the quiescent cell genome.

overall_design: Examination of log, quiescent, SMC4-off (condensin depleted) quiescent, and SMC4-on (no depletion) quiescent cell chromatin structure by Micro-C XL.


title: The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic  signaling in the intestine

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

summary:
Aim: RNA binding proteins (RBPs) are expressed broadly during both development and malignant transformation, yet their mechanistic roles in epithelial homeostasis or as drivers of tumor initiation and progression are incompletely understood.
Method: Here we describe a novel interplay between RBPsLIN28B and IMP1 in intestinal epithelial cells. Ribosome-profiling and RNA-sequencing identifies IMP1 as a principle nodefor gene expression regulation downstream of LIN28B.
Results: In vitro and in vivo data demonstrate that epithelial IMP1 loss increases expression of WNT target genes and enhances LIN28B-mediated intestinal tumorigenesis, which was reversed when we overexpressed IMP1 independently in vivo. Furthermore, IMP1 loss in wild type or LIN28B-overexpressing mice enhancesthe regenerative response to irradiation.
Conclusions: Together, our data provide new evidence for the opposing effects of the LIN28B-IMP1 axis on post-transcriptional regulation of canonical WNT signaling, with implications in intestinal homeostasis, regeneration and tumorigenesis.

overall_design: Ribosome-footprinting and RNA-seq samples from LIN28B OE SW480 cells and LIN28B OE+IMP1-/- knockout cells

first: P

last: Chatterji

first: K

last: Hamilton

first: S

last: Liang

middle: F

last: Andres

first: H

last: Wijeratne

first: R

last: Mizuno

first: L

middle: A

last: Simon

last: Hicks

middle: W

last: Foley

first: J

last: Pitarresi

first: A

last: Klein-Szanto

last: Mah

last: van Landeghem

first: B

last: Gregory

first: C

last: Lengner

middle: B

last: Madison

middle: K

last: Rustgi


title: Genome Wide Chromatin Mapping of accessibility (ATAC-seq) and H3K27ac histone modifications in CD56bright and CD56dim natural killer cells

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

summary: We report the epigenenetic and transcriptional profile of blood natural killer cells. For chromatin analysis we analyze H3K27ac and accessability in CD56bright, CD56dimCD57minus, CD56dimCD57plus and CD56dim natural killer cells, purified from periphrial blood. We also examine transcription and accessability from tonsil derived ILC3 and ieILC1

overall_design: Examination of 2 different histone modifications and accessability in different cell types

first: E

last: Oltz


title: RNA-seq and ATAC-seq analysis on mesenchymal stem cells

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: Mesenchymal stem cells (MSCs) are known to be heterogeneous; MSCs from different tissues show characteristic phenotypes. However, underlying molecular mechanisms of this MSC heterogeneity have not been clarified yet. In this study, to comprehensively understand transcriptome and epigenome of MSCs, we have analyzed multiple MSCs by RNA-seq and ATAC-seq.

overall_design: Mesenchymal stem cells (MSCs) were isolated from bone marrow (femur, vertebra), lung, and adipose tissue. Same procedure was repeated three times to prepare three lines for each tissue type MSC. RNA-seq and ATAC-seq were conducted in triplicates using standard protocols.


title: Condensin-dependent chromatin condensation represses transcription globally during quiescence [ChIP-Seq]

last: Swygert

state: WA

overall_design: Examination of binding of condensin subunit Brn1 and RNA Polymerase II subunit Rpb3 in log and quiescent cells, and additionally of Rpb3 in quiescent cells in which transcription of the condensin subunit Smc4 has been shut down using an inducible tet-off system


title: Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

summary: Sea spray aerosols (SSAs) have profound effects on our climate and ecosystems. They also contain microbiota and biogenic molecules which could affect human health. Yet the exposure and effects of SSAs on human health remain poorly studied. Here, we exposed human lung cancer cells to extracts of a natural sea spray aerosol collected at the seashore in Belgium, a laboratory-generated SSA, the marine algal toxin homoyessotoxin and a chemical inhibitor of the mammalian target of rapamycin (mTOR) pathway. We observed significant increased expression of genes related to the mTOR pathway and Proprotein convertase subtilisin/kexin type 9 (PCSK9) after exposure to homoyessotoxin and the laboratory-generated SSA. In contrast, we observed a significant decrease in gene expression in the mTOR pathway and of PCSK9 after exposure to the natural SSA and the mTOR inhibitor, suggesting induction of apoptosis. Our results indicate that marine biogenics in SSAs interact with PCSK9 and the mTOR pathway and can be used in new potential pharmaceutical applications. Overall, our results provide a substantial molecular evidence base for potential beneficial health effects at environmentally relevant concentrations of natural SSAs.

overall_design: We exposed human epithelial lung cell lines to (1) natural sea spray aerosols (SSA), (2) sea spray aerosols generated from laboratory tanks inoculated with homoyessotoxin producing algae, (3) the pure bioactive molecule homoyessotoxin (hYTX) and (4) a chemical inhibitor of the mTOR pathway (Torkinib).

first: Emmanuel

last: Van Acker

first: Maarten

last: De Rijcke

first: Laurentijn

last: Tilleman

first: Filip

last: Van Nieuwerburgh

first: Jan

last: Mees

first: Karel

last: De Schamphelaere

first: Colin

last: Janssen


title: Expression of the mannose receptor (CD206) defines distinct populations of human colonic macrophages in health and inflammatory bowel disease

status: Public on Dec 26 2018

city: GLASGOW

first: Simon

last: Milling

address: 120 UNIVERSITY PLACE, ROOM B421, Sir Graeme Davies Building

department: Immunobiology

institute: University of Glasgow

summary:
BACKGROUND & AIMS: Intestinal mononuclear phagocytes (MNP) are phenotypically similar, but have different functions. Macrophages contribute to the pathogenesis of inflammatory bowel disease (IBD). To understand this contribution it is necessary to distinguish macrophages from other MNPs, and identify functionally-different macrophage populations. We aimed to accurately identify intestinal macrophage populations, and to ascertain their functions in patients with inflammatory bowel disease (IBD).
METHODS: We developed 12-parameter flow cytometry protocols to identify and characterise human intestinal MNPs. We then used RNA sequencing, qPCR, and flow cytometry to analyse colonic biopsies from patients with CD, UC, or non-inflamed controls, in a cross-sectional study.
RESULTS: We unambiguously differentiate macrophage populations (CD45+CD64+ HLA-DR+) from dendritic cells (CD45+CD64- HLA-DR+ CD11c;). We identify two distinct subsets within the macrophage population, differentiated by their expression of the mannose receptor, CD206. Further examination of these macrophage sub-populations showed that CD206+ macrophages expressed markers consistent with a mature macrophage phenotype: high levels of CD68 and CD163, higher transcription of IL-10 and lower expression of Trem1. On the contrary, CD64+ HLA-DR- CD206- cells appear to be semi-mature intermediaries in the development of mature intestinal macrophages from their monocyte precursors.
CONCLUSIONS: We identified and purified MNP and macrophage populations from human intestinal lamina propria. Thorough characterisation reveals that human colonic macrophages appear to be derived from a monocytic precursor with high CCR2 and low CD206 expression. As these cells mature they lose their proliferative properties and acquire expression of IL-10, CD206, CD63, and CD168. Targeting the newly recruited monocyte-derived cells may represent a fruitful avenue to ameliorate chronic inflammation in IBD.

overall_design: Examination of human colonic macrophages based on their CD206 expression. 15 samples analysed, divided between CD206+ (n=7) and CD206- (n=8)

first: Pamela

last: Wright

first: Elizabeth

last: McDonald

first: Alberto

last: Bravo-Blas

first: Calum

middle: C

last: Bain

first: Allan

last: Mowat

first: Slater

middle: L

last: Clay

first: Elaine

middle: V

last: Robertson

first: Fraser

last: Morton

first: Jagtar

middle: S

last: Nijjar

first: Umer

middle: Z

last: Ijaz

first: Daniel

last: Gaya


title: Genome-wide expression profiling of the perivascular adipose tissue in abdominal aortic aneurysm

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary: Perivascular adipose tissue (PVAT) is thought to play a role in vascular homeostasis and in the pathogenesis of diseases of large vessels, including abdominal aortic aneurysm (AAA). We tested the hypothesis that locally restricted transcriptional profiles characterize PVAT surrounding AAA. Using a genome-wide approach, we investigated the PVAT transcriptome of AAA in 30 patients with either large (≥55 mm) or small (<55 mm) aneurysm diameter. We performed a data adjustment step using the DaMiRseq R/Bioconductor package, to remove the effect of confounders as produced by high-throughput gene expression techniques. We compared PVAT of AAA with PVAT of not-dilated abdominal aorta of each patient to limit the effect of inter-individual variability, using the limma R/Bioconductor package.  We found highly consistent differences in PVAT gene expression clearly distinguishing PVAT of AAA from PVAT of not-dilated aorta, which increased in number and magnitude with increasing AAA diameter. These changes did not systemically affect other abdominal adipose depots (omental or subcutaneous fat). We dissected putative mechanisms associated with PVAT involvement in AAA through a functional enrichment network analysis: both innate and adaptive immune-response genes along with genes related to cell-death pathways, metabolic processes of collagen, sphingolipids, aminoglycans and extracellular matrix degradation were strongly overrepresented in PVAT of AAA compared with PVAT of not-dilated aorta. Our results provide support to a possible role of PVAT in AAA pathogenesis and suggest that AAA is an immunologic disease with an underlying autoimmune component. These disease-specific expression signatures could help identifying pharmacological targets for preventing AAA progression.

overall_design: A paired-sample study design was used to reduce the problem of inter-individual variations. Thirty male patients with either large (≥55 mm, n=7) or small (<55 mm, n=23) aneurysm diameter were consecutively enrolled. Diverse adipose tissue (AT) depots were safely obtained sequentially, in the following order: subcutaneous abdominal fat, omental-visceral fat, periaortic fat obtained from the aortic neck proximal to the aneurismal sac (non-dilated perivascular adipose tissue, ND-PVAT), and periaortic fat surrounding the aneurysmal sac (dilated perivascular adipose tissue, D-PVAT). RNA was extracted from 50-100 mg of frozen AT samples. RNA samples of poor quality and yield were discarded.

first: Luca

last: Piacentini

first: Josè

middle: P

last: Werba

first: Elisa

last: Bono

first: Mattia

last: Chiesa

first: Claudio

last: Saccu

first: Elena

last: Tremoli

first: Rita

last: Spirito

middle: I


title: Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital


title: ALS/FTD-linked mutation in FUS suppresses intra-axonal protein synthesis and drives disease without nuclear loss-of-function of FUS

city: La Jolla

first: Sandrine

last: Da Cruz

state: Ca

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research-UCSD

summary:
Through the generation of humanized FUS mice expressing full length human FUS, we identify that when expressed at near endogenous murine FUS levels both wild-type or ALS- and frontotemporal dementia (FTD)-causing mutations complement the essential function(s) of murine FUS. Replacement of murine FUS with mutant, but not wild-type, human FUS causes stress-mediated induction of chaperones, decreased expression of ion channels/transporters essential for synaptic function, and reduced synaptic activity, without loss of nuclear FUS or its cytoplasmic aggregation. Most strikingly, accumulation of mutant human FUS is shown to activate an integrated stress response and inhibit local, intra-axonal protein synthesis in hippocampal neurons and sciatic nerves. Collectively, our evidence demonstrates that human ALS/FTD-linked mutations in FUS induce a gain-of-toxicity that includes stress-mediated suppression in intra-axonal translation, synaptic dysfunction, and progressive, age-dependent motor and cognitive disease without cytoplasmic aggregation, altered nuclear localization, or aberrant splicing of FUS-bound pre-mRNAs.

Methods: RNA from mouse spinal cords of 18-month-old mFUS-/-/hgFUS (WT, R521C or R521H) and their Non-Tg control littermates was extracted with TRIzol. RNA quality was measured using the Agilent Bioanalyzer system and processed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to manufacturer’s protocols. mRNA profiles were generated by deep sequencing, with n≥3 biological replicates per group.

Results: We mapped on average 15 million non-redundant reads per sample. Fastq files were aligned to mouse reference genome (mm9 UCSC Genome Browser) using TopHat workfow and the transcript abundance for each annotated protein-coding gene [as fragments per kilobase of transcript per million mapped reads (FPKM)] was estimated by Cufflinks. 13,468 genes which expressed FPKM>=1 were kept for downstream analyses. RNA profiles from normal (Non-Tg) and humanized hgFUSWT mice were almost undistinguishable. Both humanized mutant FUS lines had highly distinct RNA profiles [determined with unsupervised hierarchical clustering and principal component analysis (PCA)], with 709 down and 348 up-regulated genes relative to age-matched Non-Tg or humanized hgFUSWT littermates (P<0.05). These changes uncovered FUS mutant dependent altered pathways that may contribute to ALS/FTD-linked mutant FUS-mediated toxicity. The validation by RT-QPCR of altered expression of 20 genes is shown in Figure 5.

overall_design: RNA expression profile of mouse spinal cords from 18-month-old mFUS-/-/hgFUS (WT, R521C or R521H) and their Non-Tg control littermates was obtained by deep sequencing in n≥3 indendepent animals per genotype using Illumina HiSeq 2000 sequencer.

first: Jone

last: López-Erauskin

first: Takahiro

last: Tadokoro

first: Michael

last: Baughn

first: Melissa

last: McAlonis-Downes

first: Carlos

last: Chillon-Marinas

first: Joshua

middle: N

last: Asiaban

first: Jonathan

last: Artates

first: Anh

middle: T

last: Bui

first: Anne

last: Vetto

first: Sandra

last: Lee

first: Ai

last: Le

first: Ying

last: Sun

first: Mélanie

last: Jambeau

first: Jihane

last: Boubaker

first: Deborah

last: Swing

first: Jinsong

last: Qiu

first: Geoffrey

middle: G

last: Hicks

first: Zhengyu

last: Ouyang

first: Xiang-Dong

last: Fu

first: Lino

last: Tessarollo

first: Shuo-Chien

last: Ling

first: Philippe

last: Parone

first: Christopher

middle: E

last: Shaw

first: Martin

last: Marsala

first: Clotilde

last: Lagier-Tourenne

first: Don

last: Cleveland


title: Genome wide expression change in LCC2 and MCF-7 cells

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

summary: We aim to the investigate the role of tamoxifen in breast cancer progression. LCC2 and MCF-7 cells were used as the resistant and sensitive model.

overall_design: The MCF-7 and LCC2 cells were lysed and the total RNA was extracted.

first: Jian

last: Zhu


title: Expression data from Huh7.5 hepatoma cells transfected with 100 nM miR-124 mimic

city: Ottawa

first: John

middle: Paul

last: Pezacki

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

summary:
Our work demonstrated that miR-124 regulates fatty acid and triglyceride homeostasis.
We used microarrays to detail the effect of miR-124 on hepatic gene expression, and, within downregulated genes, identified an enrichment for genes involved in lipid metabolism.

overall_design: Huh7.5 cells were transfected with miR-124 or control mimics (100 nM), and total RNA was isolated 72 hours post-transfection.

first: Tyler

middle: A

first: Ragunath

last: Singaravelu


title: TL1A is a central regulator of group 3 innate lymphoid cell function in colitis

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A in linking tissue homeostasis and intestinal inflammation is not known. Here, using cell-specific genetic deletion models, we report an essential role for CX3CR1+ mononuclear phagocyte (MNP)-derived TL1A, which is induced by adherent IBD-associated microbiota, in regulating group 3 innate lymphoid cell (ILC3) production of IL-22 and mucosal healing in acute colitis. However, in contrast to this protective role in acute colitis, TL1A-dependent expression of OX40L in MHCII+ ILC3 during colitis leads to co-stimulation of antigen-specific T cells and is required for chronic T cell colitis. These results identify a new role for ILC3 in regulating intestinal T cells and reveal a central role for TL1A in regulating ILC3 barrier immunity during colitis.

overall_design: RNA from media- or TL1A-stimulated sorted Lin-CD127+IL23R-GFP+ ILC3s from IL23R-GFP/WT mice

first: Randy

last: Longman


title: STAT2 Signaling Regulates Macrophage Phenotype during Influenza and Bacterial Super-infection

city: Pittsburgh

middle: F

last: Alcorn

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: Children's Hospital of Pittsburgh

summary: Influenza is the common respiratory problem that infects between 5-20% of the US population and results in 30,000 deaths annually. A primary cause of the influenza-associated death is due to secondary bacterial pneumonia. In this study, we investigated the role of STAT2 signaling during influenza and influenza-bacterial super-infection in mice. Herein, we demonstrate that STAT2 signaling is required for viral control, regulation of inflammation, and limiting mortality during influenza single infection. Surprisingly, despite this deficiency in anti-viral immunity, we found increased bacterial control and survival in STAT2 deficient mice during influenza-MRSA super-infection compared to controls. This protection in the absence of STAT2 was associated with accumulation of dual phenotype M1/M2 macrophages, which were required for control of bacterial infection. Together, these results suggest that the STAT2 signaling is involved in suppressing macrophage activation and bacterial control during influenza-bacterial super-infection.

overall_design: We analyzed whole lung RNA from WT and STAT2-/- mice infected with influenza A/PR/8/34 for 6 days followed by MRSA USA300 for one additional day.


title: Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation I

first: Cenny

last: Taslim

summary: The transcriptional profile of A673 parental and SP-2509 Drug resistant cells treated with DMSO and SP-2509 (2uM 48hrs)

first: Kathleen

last: Pishas

first: Stephen

last: Lessnick


title: Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation II

summary: The transcriptional profile of A673 parental,  and SP-2509 drug resistant washout cells (4 and 6 months)

overall_design: Following generation of A673 SP-2509 drug resistant cells (chronic exposure for 7 months), drug was withdrawn with cell pellets collected 4 and 6 months after removal.


title: Carbodiimide reagents for the chemical probing of RNA structure in cells

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of single-stranded nucleotides. The most widely used probes are either selective SHAPE (2'-hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. The constitutively charged carbodiimide N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) is widely used for probing G and U nucleotides, but has not been established for probing RNA in cells. Here, we report the use of a smaller and conditionally charged reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), as a chemical probe of RNA conformation, and the first reagent validated for structure probing of unpaired G and U nucleotides in intact cells. We showed that EDC demonstrates similar reactivity to CMC when probing transcripts in vitro. We found that EDC specifically reacted with accessible nucleotides in the 7SK noncoding RNA in intact cells. We probed structured regions within the Xist lncRNA with EDC and integrated these data with DMS probing data. Together, EDC and DMS allowed us to refine predicted structure models for the 3’ extension of repeat C within Xist. These results highlight how complementing DMS probing experiments with EDC allows the analysis of Watson-Crick base-pairing at all four nucleotides of RNAs in their cellular context.

overall_design: Chemical probing either in vitro or in cells using reagents including CMC and EDC carbodiimides, with structured RNAs 7SK and Xist either IVT or in mouse, with analysis of reverse transcription termination or mutation frequency induced by modification.

first: Peter

middle: Y

last: Wang

first: Alec

last: Sexton

first: William

middle: J

last: Culligan