title: C. elegans establishes germline versus soma by balancing inherited histone methylation [ChIP-seq]

status: Public on Jan 17 2020

city: Atlanta

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

summary: In C. elegans, the H3K4me2 demethylase, SPR-5, and the H3K9 methyltransferase, MET-2, are maternally deposited into the oocyte where they reprogram histone methylation to prevent somatic expression of germline genes. Here, we show that the progeny of spr-5; met-2 mutants display a severe developmental delay that is associated with the ectopic expression of germline genes targeted by the H3K36me2/3 methyltransferase, MES-4. Maternally deposited MES-4 maintains H3K36me2/3 at a subset of germline genes (hereafter referred to as MES-4 germline genes) in a transcription-independent manner, and this is required for germline proliferation in the subsequent generation. By performing ChIP-seq on L1 progeny from spr-5; met-2 mutants, we find that MES-4 germline genes ectopically accumulate H3K36me3 in somatic tissues. Additionally, knocking down MES-4 suppresses the ectopic expression of MES-4 germline genes and rescues the developmental delay. These data suggest a model where SPR-5, MET-2 and MES-4 carefully balance the inheritance of histone methylation from the parental germline to ensure the proper specification of germline versus soma in the progeny. Without SPR-5; MET-2 maternal reprogramming, somatic cells struggle to specify their proper cell fate amongst the background noise of inappropriate germline gene transcription, leading to a severe developmental delay.

overall_design: H3K36me3 ChIP-seq analysis on wild-type (N2) and spr-5; met-2 L1 progeny.

middle: S

first: Teresa

last: Lee

first: Caroline

middle: F

last: Plott

first: Jovan

last: Brockett

first: Dexter

last: Myrick

first: David

last: Katz


title: C. elegans establishes germline versus soma by balancing inherited histone methylation

country: USA

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Deep sequencing identified serum extracellular vesicle delivered miR-181a-5p as an indicator for bone-metastatic prostate cancer

status: Public on Jan 31 2020

city: Shanghai

first: Yanqing

last: Wang

address: NO. 160 Pujian Road

department: Urology

country: China

institute: Shanghai Renji Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to compare the serum extracellular vesicle (EV) delivered miRNA levels of patients with bone-metastatic prostate cancer (PCa),  non-bone -metastatic PCa and benign prostatic hyperplasia (BPH), and to identify EV-delivered microRNAs in patient’s serum as indicators for bone-metastatic PCa.
Methods:Serum extracellular vesicle delivered miRNA profiles of patients with bone-metastatic PCa or non-bone -metastatic PCa or BPH were generated by deep sequencing,  using Illumina HiSeqTM 2500 platform
Results: Using an optimized data analysis method, we mapped about 17 million sequence reads per sample. Differential analysis showed the expressions of 35 EV delivered miRNAs were significantly different between serum of patients with PCa and BPH, with a p value <0.05. the expressions of  5 EV delivered miRNAs were confirmed with qRT–PCR.
Conclusions: Serum EV-delivered miR-181a-5p is a promising diagnostic biomarker for bone-metastatic PCa.

overall_design: Serum extracellular vesicle delivered miRNA profiles of patients with bone-metastatic PCa or non-bone -metastatic PCa or benign prostatic hyperplasia were generated by deep sequencing, and  contrastive analysis.

first: Yuxiang

last: Fang


title: Invasion by diverse fungal pathogens in Arabidopsis thaliana commonly activates both tryptophan-dependent and independent defense pathways exhibiting distinct sensitivity to the bak1-5 mutation

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

summary: Transcriptome analysis to identify genes up- and down-regulated genes in pen2 bak1-5 plants compared with pen2 plants in the case of Alternaria brassicicola (Ab) inoculation .

overall_design: In total 8 samples (four biological replicates of Alternaria brassicicola treated pen2 and pen2 bak1-5 plant samples) were used

first: Ayumi

last: Kosaka

first: Yoshitaka

last: Takano


title: Multi-omics profiling for individualized precision wellness

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University


title: C. elegans establishes germline versus soma by balancing inherited histone methylation [RNA-seq]

overall_design: RNA-seq analysis on spr-5, met-2, and spr-5; met-2 L1 progeny to determine differentially expressed genes compared to wild-type (N2).

middle: W

middle: A

middle: J


title: An agonistic anti-CD137 antibody promotes inflammatory signatures in immune cells that disrupt germinal center formation and T cell-dependent antibody responses

status: Public on Dec 31 2019

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: CD137 is a costimulatory receptor expressed on natural killer cells, T cells, and subsets of dendritic cells. An agonistic monoclonal antibody (mAb) against CD137 has been used to reduce tumor burden or reverse autoimmunity in animal models and clinical trials. When testing the ability of agonistic anti-CD137 mAb to promote clearance of persistent virus infection, we recently reported reduced numbers of germinal center B (GC B) cells and follicular dendritic cells (FDC) in lymphoid tissues. Here, we show that agonistic anti-CD137 agonistic mAb treatment impairs antibody responses with multiple T cell-dependent antigens including virus infection, recombinant viral antigens, and conjugated haptens but not with a T cell-independent antigen or at homeostasis. These effects were not due to enhanced apoptosis or impaired proliferation of B cells but instead correlated with disorganization of the stromal cell compartment of the GC, and were mediated by CD137 signaling in CD4+ and CD8+ T cells. Anti-CD137 treatment in the context of acute infection also resulted in reduced numbers of marginal zone B cells, greater numbers of antibody-secreting plasmablasts, and pro-inflammatory signatures in several myeloid and lymphoid cell populations of the spleen. Our experiments in mice suggest that agonistic anti-CD137 mAbs used in cancer and autoimmunity therapy may alter stromal cell populations to causes GC collapse and impaired long-term antibody and B cell memory responses.

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating single cells from mouse spleen after collagenase digestion, and libraries were prepared using Chromium Single Cell 5′ Reagent Kits in a BSL-3 level laboratory according to manufacturer’s protocol (10x Genomics). For B Cell repertoire libraries, amplified cDNA underwent two rounds of Target Enrichment using nested primer pairs specific for mouse B cell Ig constant regions. The generated scRNAseq libraries were sequenced a NovaSeq S4 flow cell.
Splenocytes from 3 biologically independent mice were pooled per sample.

first: Jun

middle: P

last: Hong

first: Glennys

last: Reynoso

first: Prabhakar

last: Andhey

first: Amanda

last: Swain

first: Jackson

last: Turner

first: Adrianus

middle: C

last: Boon

first: Florian

last: Krammer

first: Ali

last: Ellebedy

first: Fabio

last: Zanini

first: Heather

middle: D

last: Hickman

first: Michael

last: Diamond


title: Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [Saliva RNA-sequencing]

summary:
The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling assessment of saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva were produced at each timepoint (100 timepoints), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling. Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly samples till the end of the investigation.
Omics sample analysis includes: RNA-sequencing of total RNA, small RNA sequencing in saliva extracellular vesicles and saliva mass spectrometry proteomics.
Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24 hour enumeration.

overall_design: Saliva RNA-sequencing summary: Examination of saliva gene expression dynamics in a single individual in saliva over multiple timepoints. 100 total timepoints spanning two 24-hour periods, one without vaccination, and the second with vaccination. 30 daily samples follow and multiple monthly samples over the course of 1 year total.

middle: I

first: Lavida

middle: R

last: Rogers

first: Vikas

middle: V

last: Singh


title: Stress-induced beta cell dedifferentiation prior to immune cell infiltration prevents type 1 diabetes

status: Public on Jan 30 2020

city: Madison

first: Feyza

last: Engin

state: Wisconsin

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison


title: Stress-induced beta cell dedifferentiation prior to immune cell infiltration prevents type 1 diabetes [Single]

summary: Immune-mediated destruction of insulin-producing β-cells causes type 1 diabetes (T1D). However, how β-cells themselves participate in the disease process is poorly understood. Here, we report that modulating the unfolded protein response (UPR) in β-cells of non-obese diabetic (NOD) mice in early stages of disease results in preserved β-cell function, substantially reduced islet immune cell infiltration, and β-cell apoptosis leading to protection from T1D. NOD mice that lack the UPR sensor IRE1α in β-cells show greatly reduced expression of β-cell identity markers, islet autoantigens, and genes involved in antigen presentation. These mice exhibit upregulation of immune inhibitory markers in β-cells and significantly less cytotoxic CD8+ T cells in the pancreas. Our results indicate that triggering transient β-cell dedifferentiation via targeting a specific branch of the UPR in β-cells, prior to insulitis, allow β-cells to escape from immune destruction and may be used as a novel preventive strategy for high-risk individuals.

overall_design: Single cell sequencing of 5-week-old IRE1αfl/fl (WT; n=1) and IRE1αβ-/- (KO; n=2) mice were done.

first: Hugo

last: Lee

first: Yong-Syu

first: Quincy

last: Harenda

first: Stefan

last: Pietrzak

first: Hulya

middle: Z

last: Oktay

first: Sierra

last: Schreiber

first: Yian

last: Liao

first: Shreyash

last: Sonthalia

first: Sunduz

last: Keles

first: Rupa

last: Sridharan


title: An agonistic anti-CD137 antibody promotes inflammatory signatures in immune cells that disrupt germinal center formation and T cell-dependent antibody responses II

first: Maxim

last: Artyomov

first: Jun

last: Hong

first: Glennys

last: Reynoso

first: Prabhakar

last: Andhey

first: Amanda

last: Swain

first: Jackson

last: Turner

first: Adrianus

last: Boon

first: Florian

last: Krammer

first: Ali


title: CRISPR/Cas9-mediated gene correction in newborn rabbits with hereditary tyrosinemia type I [RNA-Seq]

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary: Mutations in the metabolic enzyme fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1) in human. HT1 patients present acute and irreversible liver and kidney damage during infancy. CRISPR/Cas9-medated precise correction of disease-causing mutations in the liver of infant may provide a promising approach for the treatment of monogenetic liver metabolic disorders. However, to date, all previous precise gene therapy studies were conducted in adult HT1 rodent models (mice and rats), which are not able to recover irreversible pathological changes and result in less treatment effectiveness. In addition, rodent animals have very tiny livers comparing with that of humans, and HT1 rodent models do not authentically recapitulate some symptoms of human patients such as kidney damage. Therefore, to achieve the data which could be more translationable to medical practice of HT1 disease treatment by correcting gene mutation of hepatocytes, here, we chose a HT1 rabbit model, owning relatively large livers, and displaying liver and kidney damage as human patients, as the subject to test the gene therapy effectiveness starting from newborn stage. By delivery CRISPR/Cas9 system and donor templates to the livers by ear vein injection of adeno-associated virus (AAV), HT1 rabbits could be rescued the lethal phenotypes and were able to grow up to adult normally without NTBC treatment and give birth to offspring. In the livers of AAV-treated HT1 rabbits, both HDR-mediated and NHEJ-mediated gene corrections were occurred with the efficiencies ranged from 3.30% to 8.58%. Gene corrected HT1 rabbits showed normal structure and function of both livers and kidneys. This study in rabbits provides useful large-animal preclinical data to treat genetic metabolic disorders affecting the liver with gene therapy.

overall_design: 36 samples for RNA sequencing, including 4 sample as WT-L1, 4 sample as WT-L2, 4 sample as WT-L3, 4 sample as FA1-L, 4 sample as FA2-L, 4 sample as FA3-L, 4 sample as FK-L1, 4 sample as FK-L2, and 4 sample as FK-L3.

last: Li

first: Jiaowei

last: Wang

first: Quanjun

last: Zhang

first: Jingke

last: Xie

first: Li

first: Qin

last: Jin

first: Ouyang

last: Zhen

first: Fangbing

last: Chen

first: Weikai

last: Ge

first: Hui

last: Shi

first: Yanhui

last: Liang

first: Huang

last: Xingyun

first: Zhenpeng

last: Zhuang

first: Xiaozhu

last: Zhao

first: Meng

last: Lian

first: Yinghua

last: Ye

first: Longquan

last: Quan

first: Han

last: Wu

first: Kepin

first: Liangxue

last: Lai


title: Saccharomyces cerevisiae deletion collections chemogenomic screen with Triclosan, Methylparaben and Ethylzingerone

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Growth assay in the presence of a toxic chemical that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.

overall_design: Two-condition experiment – growth of a pool of strains in the presence or absence of the drug. Two independent biological replicates for each collection (haploids - homozygous and diploids – heterozigous)


title: The immunoregulatory effects of CD8 T cell-derived perforin on diet-induced nonalcoholic steatohepatitis

city: Beijing

first: Tianqi

last: Wang

address: No. 95 Yong-an Road, Xi-cheng District

institute: Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University

summary:
Method: To better understand the mechanism of perforin in regulating liver CD8 T cell-mediated inflammation during NASH, we sorted CD8 T cells from the livers of WT or Prf1null mice fed the MCD diet for 4 weeks and performed mRNA sequencing of these hepatic CD8 T cells. Total RNA was isolated from FACS-separated hepatic CD8 T cells. Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced bythe University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=2.0 and padj < 0.05 between CD8 T cells from perforin knockout mice or WT mice fed the MCD were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
Result: Gene Ontology categories (biological processes) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the DEGs in hepatic CD8 T cells from MCD-fed Prf1null mice are involved in cell adhesion, apoptotic process, cell migration, T cell proliferation, regulation of cytokine secretion, complement and coagulation cascades, etc. Compared with CD8 T cells from the steatotic livers of WT mice, hepatic CD8 T cells from MCD-fed perforin knockout mice showed significantly upregulated levels of anti-apoptotic genes (Ei24, Tnfrsf22, Tnfrsf23, Maf and Siah2), chemokines (Cxcl3), chemokine receptor (Ccr5), genes linked to cell activation (Sfpq and P2rx7), proinflammatory cytokine secretion (C1qtnf1, C1qtnf6, CD36, and Tek) and proinflammatory signaling pathways (Tnfsf12, Tnfsf14, Ptgs2, Mapk3, Mapk7, Mapk12, Il12rb2 and Grb2), and downregulated levels of apoptosis-promoting genes (Dffb and Tnfrsf21).

overall_design: The hepatic CD8 T cells mRNA profiles of MCD-fed WT mice and perforin konckout mice were generated by deep sequencing in duplicate, using Illumina HiSeq.

first: Dong

last: Zhang


title: CRISPR/Cas9-mediated gene correction in newborn rabbits with hereditary tyrosinemia type I

first: Shixue

last: Gou

type: Genome variation profiling by high throughput sequencing


title: Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [saliva small RNA-seq]

first: George

last: Mias

summary:
The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling assessment of saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva were produced at each timepoint (100 timepoints), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling. Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly sample till the end of the investigation.
Omics sample analysis includes: RNA-sequencing of total RNA, small RNA sequencing in saliva extracellular vesicles and saliva mass spectrometry proteomics.
Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24 hour enumeration.

overall_design: Saliva extracellular vesicle small RNA-sequencing summary: Examination of extra cellular vesicle (EV) gene expression dynamics in a single individual in saliva over multiple timepoints. 104 total timepoints spanning two 24-hour periods, one without vaccination, and the second with vaccination. 30 daily samples follow and multiple monthly samples over the course of 1 year total.

first: Lavida

last: Rogers

first: Vikas

last: Singh


title: Grapevine response to Beauveria bassiana treatment

city: Geisenheim

first: Yvonne

last: Rondot

address: Von-Lade-Str. 1

department: Department of Crop Protection

country: Germany

institute: Geisenheim University

summary:
Fungal entomopathogens like Beauveria bassiana (Bals.) Vuill. (Ascomycota: Hypocreales) are known as antagonist of insects with multiple functional and ecological roles and have attracted increased attention as biocontrol agents in integrated pest management programs. A microarray analysis was performed to work out fundamental aspects of genes involved in the interaction between grapevine and the endophytic fungus B. bassiana.
The results indicate an up-regulation of diverse defense-related genes in grapevine as a response to a treatment with B. bassiana

overall_design: Twelve samples were analysed. Three replicates each were included for each treatment (24 hour and 168 hour after B. bassiana treatment), resulting in six samples. Three control replicates were included for each treatment (24 hour and 168 hour after control treatment), resulting in a further six samples.

first: Annette

last: Reineke


title: Co-expression of long non-coding RNAs and protein-coding genes in pediatric B-cell acute lymphoblastic leukemia

status: Public on Dec 10 2019

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

country: Spain

institute: University of Granada

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

summary: Long non-coding RNAs (lncRNAs) play important roles in numerous diseases and represent an emerging layer of cancer biology. However, the role that lncRNAs play in the pathogenesis of pediatric B-cell leukemia (B-ALL) with t(12;21) (ETV6-RUNX1) translocation is largely unknown. In this study, we assessed the lncRNA expression profiles of 42 pediatric B-ALL (24 with and 18 without the t(12;21) translocation) and 4 bone marrows from healthy donors. We identified 117 lncRNAs that were differentially expressed (fold change> 1.5 and FDR > 0.05) between the B-ALL subgroups (ETV6-RUNX1-positive and ETV6-RUNX1-negative). The most upregulated lncRNAs in ETV6-RUNX1 positive B-ALL were TCL6, RP4-697K14.3, LOC100292680, RP11-345I18.1, LINC00599 and TRAF3IP2-AS1, while the most downregulated were RP11-135F9.1, RP11-561B11.1, AK095221, RP11-463H12.1, AC007283.4 and CCDC26. Coding-non-coding gene co-expression networks were constructed to identify lncRNAs with potential functions in ETV6-RUNX1 translocation. Levels of representative lncRNA-mRNA pairs were further detected by RT-qPCR in patients with pediatric B-ALL. Importantly, pediatric B-ALL patients who expressed low levels of the lncRNA TCL6 had lower disease-free survival than patients with high levels of TCL6. Thus, these findings provide the first detailed description of lncRNA expression profiles related to t(12;21) translocation in pediatric B-ALL. Such lncRNAs profiles might play important roles in driving normal cells to leukemic cells. These lncRNAs may provide novel molecular biomarkers and offer new basis for combating pediatric B-ALL.

overall_design: We assessed the lncRNA expression profiles of 42 pediatric B-ALL (24 with and 18 without the t(12;21) translocation) and 4 bone marrows from healthy donors.

first: Marta

last: Cuadros

first: Alvaro

last: Andrades

first: Isabel

last: Coira

first: Carlos

last: Baliñas

first: María

last: Rodríguez

first: Juan

last: Álvarez-Pérez

first: Paola

last: Peinado

first: Alberto

middle: M

last: Arenas

first: Daniel

last: García

first: Pilar

last: Jiménez

first: Mireia

last: Camós

first: Antonio

last: Jiménez-Velasco

last: Medina


title: Adipocyte serine uptake curbs ROS generation and visceral adiposity

status: Public on Jan 19 2020

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens


title: Large 1p36 deletions affecting Arid1a locus facilitate Mycn-driven oncogenesis in a new neuroblastoma model

status: Public on Dec 01 2019

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Loss of heterozygosity (LOH) at 1p36 is a frequent chromosomal event in a broad range of human cancers with increased incidence observed in nervous system malignancies, including neuroblastoma (NBL). MYCN amplification and 1p36 deletions are highly correlated markers of tumor aggressiveness in NBL. While short distal 1p36 losses are associated with single copy MYCN tumors, larger hemizygous 1p deletions correlate with MYCN amplification, suggesting that two tumor suppressor regions exist in 1p36, a distal and proximal region, which have MYCN-independent and dependent roles. To interrogate this, we genome-edited a proximal candidate, Arid1a, a distal candidate, Chd5, and engineered a syntenic 1p36 LOH deletion in primary mouse NCCs, the likely cell of origin for NBL. Chd5 deletions were found to confer most of the pro-tumorigenic functions of 1p36 LOH in cells expressing endogenous Mycn levels. In contrast, reduced tumor latency in Mycn-driven oncogenesis significantly correlated with the loss of Arid1a. Gene expression analysis found that tumors presenting early onset display a Polycomb Repressive Complex 2 (PRC2) signature and an impaired Trp53 signaling pathway signature. Our findings delineate the tumor suppressor functions of 1p36 LOH in NBL and potentially provide critical insights for the constellation of cancers with 1p36 deletion.

overall_design: comparing normal RNA and RNA from NBL tumor models in mice

first: Jesus

last: Garcia-Lopez

first: Kirby

last: Wallace

first: Joel

last: Otero

first: Rachel

last: Olsen

first: Yong

last: Wang

first: Jerold

last: Rehg

first: Andrew

last: Davidoff

first: Kevin

last: Freeman


title: Antiviral potential of human IFN-α subtypes against influenza H3N2 infection in human lung explants

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Determining the role of interferons in the host defence against influenza A virus
Methods: Tumor-free human lung explants were obtained from patients undergoing lung surgery at the University Hospital Muenster on the day of surgery. Tissue blocks were individually placed in a 12-well plate in RPMI medium. Virus infection of human lung tissue was performed with seasonal IV H3N2 strain A/Panama/2007/1999. RNA was prepared from tissue homogenates.
Results: RNA sequencing revealed significant transcriptional upregulation of genes encoding IFN-α subtypes α1, α2, α8, α14 and α17, which we identified to possess only low to intermediate antiviral activity. In contrast, our experiments provide evidence that subtypes α16, α5 and α4 suppress H3N2 replication 40 – 231 fold more efficiently compared to clinically approved IFN-α2. We detected significantly higher induction of IV restriction factors MxA, RIG-I, OAS1 and PKR by these subtypes compared to the non-active IFN-α1 but correlation of antiviral activity with the expression levels of these restriction factors was not observed.
Conclusions: Our results show that IFN-α subtypes differ in their ability to repress H3N2 replication in human lung tissue and emphasize that IFN-α subtypes α16, α5 and α4 have high therapeutic potential and should be further investigated for the prevention and treatment of severe infections with seasonal H3N2.

overall_design: Design: Lung mRNA profiles of infected lung tissues from five donors after influenza virus infection were compared to mock treated controls. RNA was sequenced on Illumina NovaSeq 6000 with an average of 7.9 x107 reads per sample.

first: Klaus

last: Schughart


title: Interaction with WDR5 recruits MYC to a small cohort of genes required for tumor onset and maintenance

status: Public on Nov 08 2019

city: Nashville

first: Jing

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: The oncoprotein transcription factor MYC is overexpressed in the majority of human cancers. Key to its oncogenic activity is the ability of MYC to bind chromatin and regulate broad gene expression patterns that drive and maintain the tumorigenic state. The interaction of MYC with chromatin is absolutely dependent on interaction with MAX, but may also be facilitated by additional chromatin-resident proteins such as WDR5. If the role of these additional proteins can be understood, they could serve as novel focal points for therapeutically targeting MYC. To stringently challenge the role of WDR5 in MYC function, we developed a Burkitt's Lymphoma system that allows inducible and quantitative exchange of wild-type for mutant forms of MYC defective for interaction with WDR5 or MAX. Using this system, we show that WDR5 recruits MYC to a small cohort of genes, enriched in those encoding ribosome protein subunits, and demonstrate that disrupting the MYC-WDR5 interaction is as effective as disrupting interaction with MAX at preventing tumor initiation and promoting tumor regression in vivo. These findings show that WDR5 is connected to a central tumorigenic function of MYC and forecast that small molecule WDR5 inhibitors could be broadly effective anti-cancer agents.

overall_design: ChIPseq and RNAseq in Ramos cells with engineered Myc mutations

first: William

last: Tansey

first: Lance

last: Thomas

first: Qi

last: Liu


title: Epigenetic signature of human induced pluripotent stem cells identified with the linear machine learning model

status: Public on Dec 06 2019

city: Miyazaki

first: Koichiro

last: Nishino

state: Miyazaki

address: 1-1 Gakuen-Kibanadai-Nishi

department: Veterinary Medicine

institute: University of Miyazaki

summary: Human induced pluripotent stem cells (iPSCs) were established as an artificial embryonic stem cells (ESCs) to avoid immune rejection, for ethical issues in regenerative medicine, and for biological research. Comparison analyses in previous studies revealed that there is no hot spot that distinguishes iPSCs from ESCs. We herewith established a learning model using Jubatus, as a machine learning platform, with linear model for classification to distinguish human iPSCs from ESCs based on DNA methylation profiles. We found that the linear model classification is most suitable for the analysis of human iPSCs whose line number is practically 10 to 100. The learning models discriminated ESCs and iPSCs with an accuracy of ≥ 85.71 % and ≥ 90.91 %, respectively. In addition, the epigenetic signature of iPSCs was identified by component analysis of the learning models. The iPSC-specific fluctuated methylation regions were abundant at chromosome 7, 8, 12, and 22. The method can be utilized with comprehensive data and can also be widely applied to many aspects of molecular biology research.

overall_design: Bisulfite converted DNA were hybridised to the Illumina Infinium Human Methylation450K Beadchip or Infunium MethylationEPIC

first: Ken

last: Takasawa

first: Kohji

last: Okamura

first: Yoshikazu

last: Arai

first: Asato

last: Sekiya

first: Hidenori

last: Akutsu

first: Akihiro

last: Umezawa


title: Micro-RNA 150-5p predicts overt heart failure in patients with univentricular hearts

status: Public on Oct 17 2019

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

institute: Univeristy of Saarland

summary: Background: In patients with left heart failure, microRNAs (miRNAs) have been shown to be of diagnostic and prognostic value. The present study aims to identify miRNAs in patients with univentricular heart (UVH) disease that may be predictive of overt heart failure.  Methods: A large panel of human miRNA arrays were used to determine miRNA expression profiles in the blood of 48 UVH patients and 32 age and gender-matched healthy controls. For further selection, the most abundantly expressed miRNA arrays were related to clinical measures of heart failure and selected miRNAs validated by Reverse transcription quantitative polymerase chain reaction (RT-qPCR). These validated miRNAs were used for the prediction of overt heart failure and all-cause mortality.  Results: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-150-5p was best related to heart failure parameters. According to ROC analysis, NT-proBNP levels (AUC 0.940, 95% CI 0.873-1.000; p=0.001), miR-150-5p expression levels (AUC 0.905, 95% CI 0.779-1.000; p=0.001) and a higher NYHA class ≥ III (AUC 0.893, 95% CI 0.713-1.000; p=0.002) were the 3 most significant predictors of overt heart failure. Using a combined biomarker model, AUC increased to 0.980 indicating an additive value of miR-150-5p. Moreover, in the multivariate analysis, a higher NYHA class ≥ III (p=0.005) and miR-150-5p (p=0.006) turned out to be independent predictors of overt heart failure.  Conclusion: In patients with UVH, miR-150-5p has additive value to natriuretic peptides for the prediction of overt heart failure and thus may be used as additional biomarker for risk assessment in these patients.

overall_design: We profiled the miRNA in 48 patients with univentricular heart (UVH) disease that may be predictive of overt heart failure and 32 healthy controls


title: DM-tRNA-seq of mock and MHV68-infected mouse MC57G fibroblasts

status: Public on Dec 20 2019

city: Berkeley

first: Jessica

middle: Mitchell

last: Tucker

state: CA

address: 565 Li Ka Shing Center

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary: We applied a tRNA-specific sequencing pipeline to analyze tRNA expression during infection of MC57G fibroblasts with the gammaherpesvirus MHV68. We find that expression of 14% of tRNA genes is significantly upregulated during infection. By mapping reads to either premature tRNA (pre-tRNA) or mature tRNA sequences, we find that increased expression of tRNA genes is manifested at the level of the pre-tRNA only, indicating a homeostatic mechanism to maintain the size and composition of mature tRNA pools.

overall_design: 4 replicates of DM-tRNA-seq libraries prepared from mock vs MHV68-infected cells

first: Britt

last: Glaunsinger


title: Whole genomic DNA methylation analysis across human polycystic ovary syndrome ovary granulosa cells [MBD-seq]

status: Public on Oct 09 2019

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

type: Methylation profiling by high throughput sequencing

summary:
Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological conditions including polycystic ovarian syndrome PCOS, a common endocrine disorders and leading cause of infertility. The epigenetic interactions between miRNA and DNA methylation remain unexplored in PCOS.
Our study identifies epigenetic alternation in ovarian granulosa cells from PCOS patients and helps to reveal the pathogenesis of PCOS.

overall_design: In this study, we applied MBD sequencing in ovarian granulosa cells of PCOS patients and normal people.

first: Zhanrui

last: Mao

first: Yani


title: Transcriptional Roles for STAT3 in Leptin Action

status: Public on Dec 17 2019

city: Ann Arbor

first: Martin

last: Myers

state: MI

address: 1000 Wall Street 6317 Brehm Tower

institute: University of Michigan

summary: TRAP-seq from hypothalamic LepRb neurons in either control or mice lacking Stat3 in LepRb cells

overall_design: 3 Control (LepRb-Cre) and 3 Stat3KO (LepRb-Cre; Stat3-flox) samples, consisting of hypothalami from 5-8 mice, were dissected and separated into GFP (bead-bound) and supernatant fractions before RNA-seq

middle: G

first: Alan

last: Rupp


title: Identification of microRNAs involved in polycystic ovary syndrome based on High-throughput sequencing [miRNA-seq]

summary:
Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological conditions including polycystic ovarian syndrome PCOS, a common endocrine disorders and leading cause of infertility. The epigenetic interactions between miRNA and DNA methylation remain unexplored in PCOS.
Few studies have reported that the regulation of miRNAs in polycystic ovary syndrome(PCOS). Our study helps to understand the molecular pathogenesis of PCOS in human ovarian granulosa cells from the perspective of post-transcriptional level.

overall_design: In this study, we applied small RNA sequencing in ovarian granulosa cells of PCOS patients and normal people.


title: Transcriptome Profiling Reveals the key genes and pathways involved in polycystic ovary syndrome [RNA-seq]

status: Public on Oct 08 2019

summary:
Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological conditions including polycystic ovarian syndrome PCOS, a common endocrine disorders and leading cause of infertility. The epigenetic interactions between miRNA and DNA methylation remain unexplored in PCOS.
Few studies have reported that the key genes and pathways involved in polycystic ovary syndrome(PCOS). Our study helps to understand the molecular pathogenesis of PCOS in human ovarian granulosa cells and identifiy genes and pathways that may be potential therapeutic targets for PCOS treatment..

overall_design: In this study, we applied RNA sequencing in ovarian granulosa cells of PCOS patients and normal people.


title: Total RNA sequencing for human induced pluripotent derived cerebral organoids [controls only]

status: Public on Nov 23 2019

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

summary: Total RNA sequencing for human induced pluripotent derived cerebral organoids from healthy controls and schizophrenia (SCZ) patients

overall_design: This series includes data only for healthy controls comparing cerebral organoids and 2D cortical neurons.

first: Rakesh

last: Karmacharya


title: Identification of epigenetic interactions between miRNA and DNA methylation associated with polycystic ovarian syndrome

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

overall_design: Refer to individual Series


title: Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples

status: Public on Nov 16 2019

city: Oxford

first: Fabiola

last: Curion

state: Ox

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: RNA-seq is the standard method for profiling gene expression in many biological systems. Due to the wide dynamic range and complex nature of the transcriptome, RNA-seq provides an incomplete characterisation, especially of lowly expressed genes and transcripts. Targeted RNA sequencing (RNA CaptureSeq) focuses sequencing on genes of interest, providing exquisite sensitivity for transcript detection and quantification. However, uses of CaptureSeq have focused on bulk samples and its performance on very small populations of cells is unknown. Here we show CaptureSeq greatly enhances transcriptomic profiling of target genes in ultra-low-input samples and provides equivalent performance to that on bulk samples. We validate the performance of CaptureSeq using multiple probe sets on samples of iPSC-derived cortical neurons. We demonstrate up to 275-fold enrichment for target genes, the detection of 10% additional genes and a greater than 5-fold increase in identified gene isoforms. Analysis of spike-in controls demonstrated CaptureSeq improved both detection sensitivity and expression quantification. Comparison to the CORTECON database of cerebral cortex development revealed CaptureSeq enhanced the identification of sample differentiation stage. CaptureSeq provides sensitive, reliable and quantitative expression measurements on hundreds-to-thousands of target genes from ultra-low-input samples and has the potential to greatly enhance transcriptomic profiling when samples are limiting.

overall_design: Post-capture libraries. Multicentre bulks 58 replicate each capture panel (TF capture, NF capture). Two sets of oligonucleotide capture probes were designed for synthesis as Roche NimbleGen SeqCap Libraries. The first targeted human neurological disease risk loci and candidate genes (NeuroGWAS) ,while the second targeted human transcription factor gene (hereafter referred to as the NF and TF captures respectively). 24 mini-bulk samples: 8 replicates each for each capture condition (NF panel 850ng, 850ng TF panel, 150ng TF panel). PreCapture libraries: Multicentre bulks: 58 replicates. Minibulks: 8 replicates for each capture panel (TF capture, NF capture).

first: Adam

middle: E

last: Handel

first: Moustafa

last: Attar

first: Giuseppe

last: Gallone

first: Rory

last: Bowden

first: M

last: Cader

first: Michael

middle: B

last: Clark


title: Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [ChIP-Seq]

status: Public on Oct 04 2019

city: Farmington

first: Annabelle

last: Rodriguez

state: CT

address: 263 Famington Ave, MC-3501

department: Center for Vascular Biology

institute: UCONN Health

summary:
Purpose: Using a selected carrier (C) allele of rs10846744 SNP associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele, chromatin immunoprecipitation of a protein of interest, NR2F2, overexpressed and bound to the rs10846744 region in the risk (CC) cells was performed in triplicate.
Methods: Using NR2F2 as the target protein, chromatin was immunoprecipitated from each cell type and subjected to Next-gen sequencing. Input controls for each cell type were also sequenced.
Results: MACS (Zhang et al., 2008) was utilized for analysis. The narrow peak results were visualized using the Washington University EpiGenome Browser (Zhou and Wang, 2013) and bedgraph files were visualized in the Integrative Genomics Viewer (Thorvaldsdóttir et al., 2013) as bigwig files.
Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

overall_design: Reference (GG) cells and risk (CC) cells were examined for differences in NR2F2 binding, in triplicate.

first: Diana

last: Golden

first: Sameet

last: Mehta


title: Trancriptomics of primary human monocytes, Langerhans cells (LC), and monocyte-derived Langerhans cells (moLC)

status: Public on Nov 27 2019

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

institute: Newcastle University

summary: We propose a novel method of generating Langehans cell in culture. This sequencing dataset was produced in order to confirm the authenticity of the monocyte-derived LC produced in culture.

overall_design: Transcriptomics profiling of human blood monocytes, skin LC, and moLC in two biological replicates

first: Paul

last: Milne

first: Matthew

last: Collin


title: Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks

summary:
Increased high density lipoprotein (HDL) cholesterol levels have been associated with mutations in the cholesterol efflux receptor gene SCARB1, contributing to coronary artery disease (CAD). Using chromatin capture techniques (4C-Seq and HiC), ChIP-Seq and RNA-Seq, we identified a potential mechanism between a non-coding SNP (rs10846744) within the first intron of SCARB1 and LAG3, a negative regulator of T cells, both on chromosome 12. We previously demonstrated how loss of LAG3 is associated with inflammation and CAD found in carriers of the rs10846744 risk allele (C) both in our hyperalphalipoproteinemia (HALP) participants and the Multi-Ethnic Study of Atherosclerosis (MESA), increasing the risk of a coronary event by 45% (PMID: 27777974). NR2F2 transcription factor binding, as detected by (yeast 1 hybrid assay, ChIP, and ChIP-Seq) to the rs10846744 risk (C) allele, bridges NR2F2, SCARB1, and LAG3 loci, altering gene networks associated with a CAD proinflammatory signature.

This SuperSeries is composed of the SubSeries listed below.


title: Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [Hi-C]

summary:
Purpose: Utilized Next-generation sequencing (NGS) to profile global chromatin interaction differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele.
Methods: Chromatin was isolated from two subjects, one homozygous for the rs10846744 reference (G) allele and one homozygous for the rs10846744 risk (C) allele, processed for dilution HiC (Lieberman-Aiden, van Berkum et al., 2009) and then subjected next-gen sequencing.
Results: HiC-Pro integrated pipeline (with default parameters) was used for generating the HiC contact probability matrices (Servant et al., 2015). The results were visualized using HiCPlotter (Akdemir and Chin, 2015) and HiTC (Servant et al., 2012) and the Washington University EpiGenome Browser (Zhou and Wang, 2013). Juicebox (Durand et al., 2016) was utilized to extract observed/expected KR (Knight-Ruiz) normalized contacts for chromosome 12.
Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

overall_design: Reference (GG) was compared to Risk (CC)


title: Mouse Klf14matKO Placenta mRNA-seq

status: Public on Oct 01 2019

city: Pittsburgh

first: Erik

last: Koppes

state: PA

address: 204 Craft Ave

department: MWRI

institute: University of Pittsburgh

summary: Bulk, paired-end mRNA seq from matKO and control 17.5dpc placentas

overall_design: 4 matKO and 4 control 17.5dpc male placentas

first: E

first: J

last: Chaillet

first: Y

last: Sadovsky


title: Deep sequencing of GSK-126 treated HER2+ PDX tumours

status: Public on Aug 26 2019

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

country: Canada

institute: McGill University

summary: Monoclonal antibodies (mAbs) targeting the oncogenic receptor tyrosine kinase ERBB2/HER2, such as Trastuzumab, are the standard of care therapy for breast cancers driven by ERBB2 overexpression and activation. However, a substantial proportion of patients exhibits de novo resistance. Here, by comparing matched Trastuzumab-naïve and post-treatment patient samples from a neoadjuvant trial, we link resistance with elevation of H3K27me3, a repressive histone modification catalyzed by Polycomb Repressor Complex 2 (PRC2). In ErbB2+ breast cancer models, PRC2 silences endogenous retroviruses (ERVs) to suppress anti-tumor Type-I interferon (IFN) responses. In patients, elevated H3K27me3 in tumor cells following Trastuzumab treatment correlates with suppression of IFN-driven viral defense gene expression signatures and poor response. Using an immunocompetent model, we provide evidence that EZH2 inhibitors promote IFN-driven immune responses that enhance the efficacy of anti-ErbB2 mAbs, suggesting the potential clinical benefit of epigenomic reprogramming by H3K27me3 depletion in Trastuzumab-resistant disease.

overall_design: Experiments performed in duplicate, controls are vehicle (captisol) treated

first: Alison

last: Hirukawa

first: Willliam

first: Jarey

last: Wang


title: Challenging bovine foot skin fibroblasts with digital dermatitis treponemes: effects on global gene expression

status: Public on Sep 26 2019

city: Woking

first: Kerry

middle: Louise

last: Newbrook

state: Surrey

address: Ash Road, Pirbright, Woking

department: Orbivirus Research

institute: The Pirbright Institute

summary:
Purpose, aims and objectives: Bovine digital dermatitis (BDD) is a painful and ulcerative, inflammatory, infectious disease of digital skin in dairy and beef cattle and is one of the most economically important causes of severe cattle lameness worldwide. A polytreponemal aetiology has been consistently implicated in BDD pathogenesis with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis and Treponema pedis. This study aimed to investigate the hypothesis that the three Treponema phylogroups implement distict mechanisms of pathogenesis within cells of the bovine foot skin tissue during infection. Using a next generation RNA sequencing (RNA-Seq) approach, the dysregulation of global mRNA expression was investigated in primary bovine foot skin fibroblasts following challenge with representative strains of the three predominant BDD Treponema phylogroups (T19, T320A and T3552B respectively). Transcriptome profiles were compared to that of a commensal treponeme, Treponema ruminis strain Ru1, in attempts to identify pathogenic signatures.
Results and conclusions: Here, for the first time, we implicate fibroblasts as a likely source of interleukin-8 dysregulation in BDD lesions. Despite treponemes reportedly having atypical LPS, a strong pro-inflammatory response was elicited by the BDD treponemes in a similar manner to the Gram-negative LPS control, which appeared to be mediated through interleukin-17 signalling. Along with interleukin-17, several interesting gene targets were identified which may help to inform and drive future vaccine development and therapeutic approaches; particularly those of RGS16, GRO1, MAFF and ZC3H12A, which were only stimulated by BDD treponemes. Interestingly, the three BDD treponemes were found to elicit very distinct mechanisms of pathogenesis in fibroblasts. T. phagedenis and T. pedis spirochaetes were found to upregulate several genes associated with apoptosis. Both T. medium and T. pedis spirochaetes, but notably not T. phagedenis, stimulated genes associated with actin rearrangement and a loss of cell adhesion, which may promote their persistence and deeper invasion within host tissues. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. Interestingly, T. medium phylogroup was the least stimulatory and appeared to induce immunosuppression via the dysregulation of genes such as TSC22D3. Together with findings that the commensal, T. ruminis, significantly dysregulated over three times the number of host genes compared to each BDD treponeme; this suggests that, alike the syphilis pathogen (Treponema pallidum), BDD treponemes have evolved to become “stealth pathogens” and avoid triggering a substantial host immune/inflammatory response to promote persistence and facilitate invasion of host tissues. Overall, this study has highlighted the complexities of BDD pathogenesis; three key Treponema phylogroups appear to elicit very distinct mechanisms of pathogenesis in bovine foot skin cells. Several interesting gene targets have been identified from this study which may help to inform and drive future vaccine development and therapeutic approaches.

overall_design:
RNA sequencing analysis was performed on RNA extracted from primary bovine foot skin fibroblast cell cultures following challenge for six hours with either control media (three experimental replicates), lipopolysaccharide from Salmonella enterica serotype Typhimurium (as an inflammatory stimulant control) (three experimental replicates), Treponema medium phylogroup strain T19 (three experimental replicates), Treponema phagedenis phylogroup strain T320A (three experimental replicates plus an extra technical replicate), Treponema pedis strain T3552B (three experimental replicates) or Treponema ruminis strain Ru1 (three experimental replicates plus an extra technical replicate). Following RNA extraction, these 20 samples underwent rRNA depletion and cDNA libraries were  prepared using an Illumina NEBNext Ultra Directional RNA Library Prep Kit. Libraries undewent paired-end clustering and were subsequently sequenced on an Illumina HiSeq 4000 using version 1 chemistry, generating 2x 150 bp paired end reads. On average, we generated approximately 66 million sequenced reads per sample (range 44-102 million). FASTQ sequence files were trimmed to exclude adaptor sequences and poor quality reads using Cutadapt V1.2.1 and Sickle V1.200 respectively. Reference-based assembly was implemented using the Galaxy platform's main public server. Trimmed reads were mapped to the Bos taurus genome (UMD 3.1.1/bosTau8; Genbank assembly accession number: GCA_000003055.5) using TopHat2, with an overall average mapping rate of 86%. Mapped reads were assembled into transcripts using Cufflinks and a master transcriptome generated by Cuffmerge, using the Bos taurus genome as a reference. Differential gene expression profiles of fibroblasts (mean FPKM gene expression) were generated for each challenge group compared to the media control by implementing CuffDiff; using the master transcriptome assembly and mapped read (BAM) files for all corresponding replicates of the challenge and control group comparison. Differentially expressed genes with an adjusted p (q or FDR) value ≤ 0.05 were considered statistically significant, with a further log2 fold change cut-off (≥ 1 and ≤ -1) used to define biological significance; these criteria were used as a cut-off for SDE in all downstream analyses. Ingenuity pathway analysis was used to identify significantly enriched canonical pathways, diseases and biological functions.

Technical replicates were obtained from cell monolayers seeded within different flasks from the same experimental culture.

middle: L

first: Stuart

last: Carter

first: Nicholas

last: Evans


title: Profiling of EMT-associated mitochondrial RNAs in hepatocellular carcinoma cells

status: Public on Aug 27 2019

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

summary: Mitochondria, the powerhouse of the cell, has been recognized as the key players in cancer cell biology, including cancer metabolism, metastasis, and drug resistance. Recent studies have demonstrated a functional interplay between mitochondria and epithelial-mesenchymal transition (EMT) in cancer. To delineate the role of mitochondrial components in this interplay, we induced the EMT in hepatoma HepG2 cells. Mitochondria was isolated from EMT-HepG2 cells, untreated HepG2 cells, and normal hepatic HL7702 cells. Mitochondrial RNAs were isolated for Illumina sequencing. Identification of mitochondrial RNAs that regulate EMT or mitochondria function may serve as potential therapeutic targets for developing new strategies to treat cancers.

overall_design: HepG2 cells were seeded into 6‑well plates, and EMT was induced by 10 ng/ml TGF‑β1 in the medium was used to replace the common medium for 24‑72 h. Cells were characterized by examining the EMT markers using Epithelial-Mesenchymal Transition (EMT) Antibody Sampler Kit (#9782, Cell Signaling Technology). After confirming the EMT, cells were collected and mitochondria was isolated using Qproteome Mitochondria Isolation Kit (Cat.37612, Qiagen). Mitochondrial RNAs were extracted using the miRNeasy Mini Kit (Cat# 217004, Qiagen). Qualified RNAs were further purified by RNAClean XP Kit (Cat.A63987, Beckman Coulter, CA) and were treated with RNase-Free DNase Set (Cat.79254, QIAGEN, CA). Ribosomal RNA was removed by TruSeq Stranded Total RNA LT-(Ribo-Zero Gold rRNA Removal Kit)-Set A/B (#RS-122-2301/2302, Illumina, CA). RNA transcriptome sequencing (RNA-Seq) was performed to identify mitochondrial RNAs that are associated with EMT.

first: Jiuwei

last: Cui

first: Yijing

last: Zhao


title: Microarray analysis of ErbB2-driven mouse mammary tumour cells treated with GSK-126

status: Public on Aug 22 2019

overall_design: We used microarrays to analyze transcriptional responses to the H3K27me3 inhibitor GSK-126 in cells isolated from primary mouse mammary tumours isolated from ErbB2 driven mammary gland tumours (NIC model). DMSO treated cells were used as contols. We extracted total RNA from 2 control cells and 2 drug treated cells lines and subjected the RNA to Affymetrix microarray analysis.

middle: J


title: Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [RNA-Seq]

first: Annabelle

last: Rodriguez

summary:
Purpose: Utilized Next-generation sequencing (NGS) to profile transcriptional differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele.
Methods: RNA was isolated from three subjects homozygous for the rs10846744 reference (G) allele and three subjects homozygous for the rs10846744 risk (C) allele and then subjected to full transcriptome sequencing. Triplicates of one sample from each group were also sequences to overlay with chromatin data from each group. Knockdown of NR2F2 using lentiviral particles assessed differential expression between the treated and untreated risk replicates. The Illumina NextSeq 500 next gen sequencing  platform (UCONN CGI, Storrs, CT) was used for RNA-Seq. HiSeq 2000 was used for biological replicates at Perkin Elmer. RNA targets of interest were validated by qPCR using TaqMan assays and proteins were blotted using standard western methodologies.
Results: We normalized the raw read count by FPKM and using Cufflinks, identified differential transcripts. RNA-seq data confirmed differential expression of NR2F2 and LAG3, validated by qPCR.
Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

overall_design: Transcriptional profiles from 3 carriers of the risk (C) allele and 3 non-carriers of the (G) reference allele, were generated by NGS, in triplicate, using Illumina platform technology. Replicates of one sample from each group and knockdown of NR2F2 in the risk replicate were also sequenced (n=3) to overlay with chromatin interaction data.

first: Diana

last: Golden

first: Sameet


title: Liaison between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion-Negative Rhabdomyosarcoma

status: Public on Dec 25 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Rhabdomyosarcoma (RMS) is a pediatric malignancy of mesenchymal origin.  Fusion Negative-RMS (FN-RMS) tumors are associated with RAS-pathway activation. RMS tumors express pro-differentiation myogenic transcription factors MYOD and MYOG, yet why they are unable to differentiate is poorly understood. Here we show that SNAI2 is highly expressed in FN-RMS, is regulated by MYOD and blocks myogenic differentiation promoting growth. Molecularly, SNAI2 preferentially binds E-Box-associated enhancer elements and represses expression by dampening enhancer function. SNAI2 inhibits MYOD at a subset of myogenic enhancers associated with terminal differentiation. Functional dissection demonstrates SNAI2 suppresses a MYOG, MEF2 and CDKN1A differentiation program.  SNAI2 knockdown transcriptionally mimics a chemical blockade of the mutant RAS signal in FN-RMS, providing new insight connecting the genetic and epigenetic causes of this disease.

overall_design:
Epignome-wide binding profiles of histone modifications and transcription factors, before and after selected disruption of SNAI2 via chemical or genetic means, in FN_RMS cell lines, by ChIP-seq.

RNA-seq in 2 FN-RMS cell lines exposed to either shControl or shSNAI2.

H3K27ac HiChIP of RMS cell line.

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Cyclophosphamide (CTX) Enhances Cancer Antibody Immunotherapy in the Resistant Bone Marrow Niche by Modulating Macrophage FcγR Expression

status: Public on Aug 20 2019

city: Cambridge

first: Guangan

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Purpose: To understand the molecular mechanisms underlying the CTX synergization with antibody therapies in resistant niche-specific organs and BM-resident tumors

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Humanized mice were treated with CTX or PBS. Two days post treatment, mouse and human macrophages in the spleen and bone were sorted and applied to RNAseq.

first: Ali

last: Roghanian


title: A basal specific microRNA promotes tumorigenesis in both basal and luminal cells of murine prostate gland

status: Public on Sep 16 2019

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

summary: Recent studies demonstrate both basal and luminal cells of the prostate gland can initiate tumorigenesis upon oncogenic transformation. However, it remains unclear how molecular mechanisms operating within each cell lineage contribute to the initiation and progression of the prostate cancer. Here we investigate functions of individual miRNAs using genetically engineered mouse models. By both quantitative miR-Seq and in situ hybridization, we identify microRNA-205 (miR-205) as the most highly expressed miRNA and specific to the basal cells in the prostate. MicroRNA-205 expression is further elevated in the basal cells in the well-established Pten null tumorigenic mouse model. To investigate the role of miR-205 in Pten-deletion mediated tumorigenesis, we generated a Pten/miR-205 double knockout mouse model. Concurrent deletion of both miR-205 and Pten significantly compromised tumor progression in both basal and luminal compartments. We observed significantly reduced tumor size and compromised proliferation in both basal and luminal cells. We have previously demonstrated a critical requirement of miR-205 for maintaining the PI(3)K signaling and pAkt levels in skin stem cells. Consistent with this role, we observed strong reduction of pAkt and significantly increased cellular senescence in the basal cells of the dKO, compared to the Pten KO alone. These results suggest that miR-205 is cell-autonomously required for the tumorigenesis of the basal cells. Taken together, we have identified miR-205 as an important regulator in prostate cancer. Our study also reveals an essential and unexpected role of the basal cells for promoting prostate tumorigenesis.

overall_design: microRNA-RNA seq in the basal and luminal cells of wild-type prostate.

first: Glen

middle: A

last: Bjerke

first: Kent

last: Riemondy

first: Li

first: Rui

last: Yi


title: The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

status: Public on Oct 03 2019

city: Boulder

first: John

last: Rinn

address: 3415 Colorado Avenue

institute: University of Colorado Boulder

summary: We used the Functional intergenic repeating RNA element (Firre) locus - a conserved intergenic lncRNA gene that is located on the X chromosome11,12 - as a model to discriminate DNA- and RNA-mediated effects in vivo. Using genetically defined loss-of-function, gain-of-function, and rescue mouse models for Firre, we identify cell-specific defects during hematopoiesis and immune function. This includes impaired survival upon lipopolysaccharide challenge and diminished production of immune cells in Firre knockout mice. We show that these defects can be rescued by induction of Firre RNA from a transgene in the Firre knockout background. Moreover, upon ectopic induction of Firre expression, we observe an in vivo rescue of gene expression programs that were lost in the Firre knockout model. Finally, we show that unlike most regulatory DNA and RNA species, which function locally to regulate the expression of neighboring genes, Firre RNA acts in trans to alter cellular functions.

overall_design: Comparision of WT, KO and rescue by RNA-seq

first: Jordan

middle: P

last: Lewandowski

first: Taeyoung

last: Hwang

first: Abbie

middle: F

last: Groff

first: Chiara

last: Gerhardinger


title: H3K27me3 ChIP-Seq analysis of ErbB2-driven mouse mammary tumour cells treated with GSK-126

status: Public on Aug 23 2019

first: William

last: Muller

overall_design: Examiation of H3K27me3 in mouse mammary tumour cells treated with inhibitors of H3K27me3 or vehicle (DMSO)

first: Alison

last: Hirukawa


title: Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [4C-Seq]

first: Annabelle

last: Rodriguez

summary:
Purpose: Isolating chromatin interactions from a specific viewpoint, we utilized Next-generation sequencing (NGS) to profile specific chromatin interaction differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele.
Methods: Chromatin was isolated from two subjects, one homozygous for the rs10846744 reference (G) allele and one homozygous for the rs10846744 risk (C) allele, processed for 4C-Seq (van de Werken et al., 2012).
Results: 4C-ker (Raviram et al, 2016) analyzed the chromatin interaction data from the specific viewpoint. The results were visualized using the Washington University EpiGenome Browser (Zhou and Wang, 2013).
Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

overall_design: Reference (GG) cells were compared to Risk (CC) cells from the SCARB1 rs10846744 (1A) and LAG3 (2A) viewpoints, in duplicates

first: Diana

first: Sameet

last: Mehta


title: Loss of 9p21 regulatory hub promotes kidney cancer progression by upregulating HOXB13

status: Public on Aug 13 2019

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

overall_design: Refer to individual Series


title: Bone marrow TTP deficeincy significantly increased inflammation while reduced plasma lipid and hepatic steatosis in LDLR knockout mice

status: Public on Aug 12 2019

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: In order to examine the effects of bone marrow TTP deficiency on inflammation and lipid metabolism and determine the driving force during atherosclerosis, 8 week-old female LDLR−/− mice on C57BL/6J background were lethally irradiated  and reconstituted with a wild type (TTP+/+) or TTP knockout (TTP−/−) bone marrow cells and fed a Western diet for 12 weeks. Then mice were sacrificed and tissues were collected for analysis. Liver tissues were collected and gene expression was analysed using a whole genome microarray. Bone marrow TTP−/− recipients displayed a significantly higher systemic and multi-organ inflammation compared to the BM-TTP+/+ recipients. BM-TTP−/− mice displayed a significant reduction of serum lipid levels, attenuated hepatic steatosis, and decreased lipid excretion than the control mice. microarray data showed that BM-TTP deficiency modulate liver genes involved in lipid metabolism and inflammatory response. RT-qPCR was used to confirm the results in several genes from microarray data. BM-TTP deficiency did not further accelerate atherorogenesis process in LDLR−/− mice after a Western diet feeding. TTP promoted VLDL to drive proinflammatory mechanism into proatherogenic mechanism.

overall_design: Two-condition, one-color experiment. LDLR knockout mice were transplanted with wild type or TTP knockout bone marrow cells and gene expression was performed on RNA isolated from liver. 4 biological replicates per each experimental group.

first: Fatma

last: Saaoud

first: Dapin


title: 4C analysis of 9p21 interaction network in HEK TE cells

summary: 4C was performed to identify genomic loci interacting with the 9P21 locus. Subsequently, the effect on cell transformation was furhter investigated upon knockdown/overexpression of the selected candidate targets.

overall_design: HEK TE cells were analyzed using 4C experimental protocol and 5 viewpoints designed specifically on the 9p21 region.

first: Maria

last: Baietti

first: Anna

last: Sablina


title: Gene chip analysis of ASCs with and without cocultured with NPCs

status: Public on Aug 31 2019

city: Shanghai

first: Zhihua Han

last: Han

state: Please select region, state or province

address: Xin Songjiang Road 650

department: Orthopedic Traumatology, Shanghai Trauma and Emergency Center

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University

summary: We used microarrays to detail the global programme of gene expression underlying the coculturing of  ASCs and degenerative NPCs and identified distinct classes of altered genes and ncRNAs during this process.

overall_design: We used 3 samples ( ASCs after coculturing) with 3 control (ASCs without coculturing), then compare the genes and ncRNAs.

first: Zhihua

first: Jianhong

last: Wu


title: Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer

status: Public on Jul 17 2019

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The widespread and long-term use of potent therapies designed to repress androgen receptor (AR) signaling is changing the molecular and phenotypic landscapes of prostate cancer. We conducted molecular profiling of metastatic castration-resistant prostate cancer (mCRPC) patient specimens and patient-derived xenograft models and identified five distinct mCRPC phenotypes. Herein, we characterize an AR-low phenotype that has low AR expression with concomitant decreases in a subset of AR regulated genes, and an amphicrine phenotype that has both AR and neuroendocrine activity in the same cell. Furthermore, our data highlight an emerging squamous cell mCRPC phenotype.

overall_design:
RNA sequencing of human prostate tumor cell lines, patient-derived xenograft (PDX) models, and metastatic castration-resistant prostate cancer (mCRPC) tumors using Illumina TruSeq Library prep and sequenced on Illumina HiSeq 2500.

This series includes re-analyzed samples from GSE118435.

first: Mark

last: Labrecque

first: Lisha

last: Brown

first: Lawrence

middle: D

last: True

first: Lori

last: Kollath

first: Bryce

last: Lakely

first: Holly

last: Nguyen

first: Yu

middle: C

last: Yang

first: Arja

middle: H

last: Kaipainen

first: Roger

middle: T

first: Celestia

middle: S

last: Higano

first: Evan

middle: Y

last: Yu

first: Heather

last: Cheng

first: Elahe

last: Mostaghel

first: Bruce

last: Montgomery

first: Michael

last: Schweizer

first: Andrew

last: Hsieh

first: Daniel

middle: W

last: Lin

first: Eva

last: Corey

first: Peter

last: Nelson

first: Colm

last: Morrissey


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1, H1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation

status: Public on Jul 26 2019

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to verify the dynamic changes of MAGs in H1 derived different population of cells during human early hematopoietic differentian.
Methods: mRNA profiles of hESC samples collected from day 0 to day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions:MAGs showed convincingly dynamic expression during early hematopoietic differentiation of H1 cells

first: Hongtao

last: Wang


title: Development of gene expression signatures for knock down expression of ARL4C

status: Public on Jun 04 2019

city: Chong qing

first: qian

last: chen

address: Gaotanyan street， shapingba

institute: Southwest hospital

summary:
o further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish expression of ARL4C.
Human primay GBM cell was transfected with control or eGFP-Sh-ARL4C lentivirus, 588 gene are down-regulated and 366 gene are down-regulated.

overall_design: knock down expression of ARL4C induced gene expression in human GBM cell was measured. Three independent experiments were performed for each experiment

first: Q

last: Chen

first: X

last: Yao


title: Gene expression changes in astrocytes by pulsed radiofrequency: a possible mechanism of neuropathic pain improvement

status: Public on May 31 2019

city: Gifu

first: Kumiko

last: Tanabe

address: Yanagido 1-1

institute: Gifu University School of Medicine

summary: We investigated genomic effects of pulsed radiofrequency (PRF) on mouse cultured astrocyte cell line, C8D1A cells, using microarray analysis.  PRF increased 2,431 genes and decreased 209 genes.  Among these genes, 435 genes were upregulated with more than 10-fold, 89 genes with more than 30-fold, while there was no gene with 10-fold decrease.  From the gene ontology analysis using the list of 10-fold upregulated genes, PRF treatment activated immune response.  From pathway analysis using Kyoto Encyclopedia of Gene and Genomes using the same list, 7 pathways related with neuropathic pain were detected.

overall_design: Pulsed radiofrequency-induced gene expression in cultured mouse astrocyte cell line (C8D1A) was measured and copared with non-treated cells.  Three independent experiments were performed.

first: Shigeo

last: Takashima

first: Hiroki

last: Iida


title: The impact of TCR affinity on resident memory T cell formation during influenza virus infection

status: Public on Jun 18 2019

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

institute: University of Minnesota

summary: Resident memory T (TRM) cells in the lung are vital for heterologous protection against influenza A virus (IAV). Environmental factors are necessary to establish lung TRM, however the role of T cell intrinsic factors like T cell receptor (TCR) signal strength have not been elucidated. Here we investigated the impact of TCR signal strength on the generation and maintenance of lung TRM cells after IAV infection. We inserted high and low affinity OT-I epitopes into IAV and infected mice after transfer of OT-I T cells. We uncovered a bias in TRM formation in the lung elicited by lower affinity TCR stimulation. TCR affinity did not impact the overall phenotype or long-term maintenance of lung TRM cells. Overall, these findings demonstrate that TRM formation is negatively correlated with increased TCR signal strength. Lower affinity cells may have an advantage in forming TRM to ensure diversity in the antigen-specific repertoire in tissues.

overall_design: OT-I CD8+ T cells were transferred into mice and animals were challenged with 40 PFU of IAV_N4 or IAV_T4. After 34 days, lungs were harvested after CD8-alpha iv staining, and single cell suspensions were sorted for live CD4-B220-F4/80-CD8+iv-CD45.1+CD45.2-Valpha2+CD44hi cells. Cells were FACS sorted directly into cell cysis buffer for RNA extraction. cDNA libraries were prepared using the SMARTer Universal Low Input RNA Kit (Takara Bio). Samples were then profiled by illumina sequencing

first: Jessica

middle: K

last: Fiege

first: Ian

last: Stone

first: Elizabeth

last: Fay

first: Matthew

last: Markman

first: Sathi

last: Wijeyesinghe

first: Marissa

last: Macchietto

first: Steven

last: Shen

first: David

last: Masopust


title: Transcriptome profiling of neonatal heart regeneration

status: Public on Jul 15 2019

city: New York

first: Zhaoning

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary:
Background: The adult mammalian heart has limited capacity for regeneration following injury, whereas the neonatal heart can readily regenerate within a short period after birth. To uncover the molecular mechanisms underlying neonatal heart regeneration, we compared the transcriptomes and epigenomes of regenerative and non-regenerative mouse hearts over a 7-day time period following myocardial infarction.
Methods: RNA-Seq, H3K27ac ChIP-Seq and H3K27me3 ChIP-Seq were performed on ventricular samples from regenerative P1 or non-regenerative P8 mouse hearts at +1.5d, +3d and +7d after MI or Sham surgery to assemble the transcriptome, active chromatin and repressed chromatin landscapes during neonatal heart regeneration. Dynamic enhancer landscapes from mouse hearts during cardiac development were analyzed using data from ENCODE. Effects on cardiomyocyte proliferation and cardiac function from selected factors identified in this study were tested using BrdU/EdU pulse-labeling or mouse models coupled with immunohistochemistry and echocardiography.
Results: By integrating gene expression profiles with histone marks associated with active or repressed chromatin, we identified transcriptional programs underlying neonatal heart regeneration and the blockade to regeneration in later life. Our results reveal a unique immune response in regenerative hearts and an embryonic cardiogenic gene program that remains active during neonatal heart regeneration. Among the unique immune factors and embryonic genes associated with cardiac regeneration, we identified Ccl24, which encodes a cytokine, and Igf2bp3, which encodes an RNA-binding protein, as previously unrecognized regulators of cardiomyocyte proliferation.
Conclusions: Our data provide insights into the molecular basis of neonatal heart regeneration and identify genes that might be modulated to promote heart regeneration.

overall_design: We performed myocardial infarction (MI) or sham surgeries to mouse hearts at postnatal day 1 or day 8. At 1.5d, 3d or 7d post P1 and P8 surgery, ventricle samples below the surgery plane were collected in triplicate for mRNA-Seq.

first: Miao

last: Cui

first: Wei

last: Tan

first: Wenduo

last: Ye

first: Giovanni

last: Botten

first: Eric

middle: N

last: Olson


title: Determinaton the effect of IR-61 on macrophage gene expression

status: Public on May 06 2019

city: Chongqing

first: Yawei

last: Wang

address: 30 gaotanyan center street

institute: Third Millitary Medical University

summary: To  identify the influence of IR-61 on macrophage gene expression , we have employed whole genome microarray expression profiling as a discovery platform to identify genes expression changes. RAW264.7 cell line was treated with additional 10μm IR-61 or vehicle control for 24 h and then conducted further experiments

overall_design: Gene expression of IR-61 or vehicle control -treated RAW264.7 cells for 24 h was measured.

first: Yu


title: Mechanistic basis of neonatal heart regeneration revealed by transcriptome and histone modification profiling

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


title: Transcription Restart Establishes Chromatin Accessibility after DNA Replication

status: Public on May 21 2019

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: CPR

summary: DNA replication is highly disruptive to chromatin, leading to eviction of nucleosomes, RNA polymerase and regulatory factors. When and how transcription resumes on DNA following DNA replication is unknown. Here we develop a replication-coupled Assay for Transposase-Accessible Chromatin, repli-ATAC-seq, to investigate active chromatin restoration post-replication in mouse embryonic stem cells. We find nascent chromatin is inaccessible and transcriptionally silent, with accessibility and RNA polymerase occupancy re-appearing within 30 minutes. Chromatin accessibility restores differentially genome-wide, with super enhancers regaining transcription factor occupancy faster than other genomic features. We also identify opportunistic and transient accessible chromatin within gene bodies after replication. Systematic inhibition of transcription shows that transcription restart is required to re-establish active chromatin states genome-wide and resolve opportunistic binding events resulting from DNA replication. Collectively, this establishes a central role for transcription in overcoming the genome-wide chromatin inaccessibility imposed by DNA replication every cell division.

overall_design: repli-ATAC-seq time series, RNA polymerase ChOR-seq time series, and repli-ATAC-seq with transcription inhibition in mouse embryonic stem cells.

first: Kathleen

middle: R

last: Stewart-Morgan

first: Nazaret

last: Reverón-Gómez


title: Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [ATAC-seq]

status: Public on Apr 30 2019

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. We then found that KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. We finally determined that the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific regulators of gene expression. Thus, by taming the transcriptional impact of TEs during early embryogenesis, KZFPs allow for their genome-wide incorporation into transcriptional networks, thereby contributing to the species-specificity of human genome regulation.

overall_design: ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs

last: Pontis


title: Vitamin D receptor ChIP-Seq in primary prostate epithelial cells

status: Public on Apr 01 2019

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: We investigated the genomic activity of vitamin D in primary prostate epithelial cells (PrE) through vitamin D receptor (VDR)-ChIP-sequencing. PrE cells treated with 50 nM 1,25D showed nuclear localization the VDR within 1 hr, persisting until 4 hr, and a 2 hr treatment was selected for ChIP-seq. Rigorous testing of the ChIP conditions and VDR antibody were performed. Nearly 5,000 VDR binding sites were identified.

overall_design: One primary prostate epithelial cell line treated with ethanol (control) or 50 nM 1,25-VitaminD3 for 2 hr

last: Lugli

first: Bethany

last: Baumann


title: Epigenome profiling of neonatal heart regeneration

overall_design: We performed myocardial infarction (MI) or sham surgeries to mouse hearts at postnatal day 1 or day 8. At 1.5d, 3d or 7d post P1 and P8 surgery, ventricle samples below the surgery plane were collected in duplicate for H3K27ac and H3K27me3 ChIP-Seq


title: Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs


title: GeoChip data from fungal community in Alaskan tundra soil

status: Public on Mar 07 2019

city: Biejing

first: Jingmin

last: Cheng

address: NO. 30 Shuangqing Road, Haidian District

department: School of Environment

institute: Tsinghua University

summary:
The effects of two years' winter warming on the overall fungal functional gene structure in Alaskan tundra soil were studies by the GeoChip 4.2
Resuts showed that two years' winter warming changed the overall fungal functional gene structure in Alaskan tundra soil.

overall_design: comparison of overall fungal functional gene structure between control plots and warmed plots in Alaskan tundra

first: Mengting

middle: M

last: Yuan

first: Lei


title: Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2 (single-cell RNA-seq)

status: Public on Feb 27 2019

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: Basic helix-loop-helix (bHLH) proneural transcription factors (TFs) Ascl1 and Neurog2 are integral to the development of the nervous system. Here, we investigated the molecular mechanisms by which Ascl1 and Neurog2 control the acquisition of generic neuronal fate and impose neuronal subtype identity. Using direct neuronal programming of embryonic stem cells, we found that Ascl1 and Neurog2 regulate distinct targets by binding to largely different sets of sites. Their divergent binding pattern is not determined by the previous chromatin state but distinguished by specific E-box enrichments which reflect the DNA sequence preference of the bHLH domain. The divergent Ascl1 and Neurog2 binding patterns result in distinct chromatin accessibility and enhancer activity landscapes that shape the binding and activity of downstream TFs during neuronal specification. Our findings suggest that proneural factors contribute to neuronal diversity by differentially altering the chromatin landscapes that shape the binding of neuronally expressed TFs.

overall_design: Single-cell RNA-seq was used to characterize gene expression in mixed populations of mES cells containing induced expression of either Ascl1 or Neurog2.

first: Begüm

last: Aydin

first: Akshay

last: Kakumanu

first: Mary

middle: G

last: Rossillo

first: Mireia

last: Moreno-Estelles

first: Niels

last: Ringstad

first: Nuria

last: Flames

first: Esteban

middle: O

last: Mazzoni


title: Cohesin-dependent regulation of dynamic gene expression during differentiation is lost in Cohesin-mutated myeloid malignancies

status: Public on Apr 09 2019

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

institute: University Medical Center Mainz

summary: The Cohesin complex critically controls interactions between proximal and distal cis-regulatory elements, while Cohesin disruption causes improper gene activation. This process associates with biased hematopoiesis, and Cohesin mutations are common in myeloid neoplasia. In this study, we initially explore Cohesin-associated dynamics and regulation of hematopoietic stem cell renewal and erythropoiesis. Cohesin binding to chromatin increases during erythroid differentiation at active promoters and enhancers only, with pre-binding of Etv6 predicting the subsequent dynamics of Cohesin binding at these elements. Etv6 also binds with the Cohesin complex at chromatin during haematopoiesis. Perturbation of Cohesin members does not alter hematopoietic self-renewal, but severely impairs erythroid differentiation. As in normal erythroid differentiation, the strongest impairment of gene activation in Cohesin-perturbed erythropoiesis occurs at Etv6-pre-bound loci. Taken together these findings propose a mechanism for how the Cohesin complex regulates the induction of gene expression during differentiation and how this may be perturbed in myeloid malignancies.

overall_design: Integrative analysis of Cohesin-associated cis-regulatory units (ChIP Seq, RNA Seq, promoter Capture HiC in HSPC and Erythroid cells

first: Brian

last: Huntly


title: Expression data from myocardial tissue from Spontaneously hypertensive rat (SHR) and its minimal congenic strain PD5

status: Public on Feb 20 2019

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

summary:
Spontaneously hypertensive rat (SHR; Rat Genome Database (RGD) ID: 631848) is probably the most commonly used rodent model for essential hypertension. Its minimal congenic subline PD5 ( SHR.PD-(D8Rat42-D8Arb23)/Cub; (RGD ID: 1641851)) which differs by a short segment of chromosome 8 (encompassing only 7 genes) displays lower levels of blood pressure and amelioration of cardiac fibrosis compared to SHR.
We used microarray aproach to unravel gene expression differences between SHR and PD5 responsible for the different phenotypes in our rat strains.

overall_design: Both strains were bred in-house. Rats were kept under 12 hours light-dark cycle, fed standard laboratory chow and given access to water ad libitum. After 2 months rats were anesthetized and decapitated. Organs were snap frozen in liquid nitrogen, and left ventricular myocardium was used for RNA extraction and further analysis.

first: L

first: F

last: Liska


title: Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2 (RNA-seq)

overall_design: RNA-seq was used to characterize gene expression upon overexpression of Ascl1 and Neurog2 in mouse embryonic stem cells. t=0 (uninduced) RNA samples were used as controls.


title: Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2 (ATAC-seq)

overall_design: ATAC-seq was used to profile chromatin accessibility upon overexpression of Ascl1 and Neurog2 in mouse embryonic stem cells.  t=0 (uninduced) chromatin was used as a control.


title: microRNA expression profile of exosomes from bone marrow derived macrophage

status: Public on Feb 21 2019

city: shanghai

first: haomin

last: cui

address: 600 Yishan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People’s  Hospital

summary: MicroRNA has the potential for cross-regulation and functional integration of discrete biological processes during complex physiological events. In this study, we found that the highly expressed microRNAs in exosomes from bone marrow derived macrophage appear to control fibrotic healing response in the tendon.  Notably, fibrotic microRNA-21 in mice distributed in the early stage of healing after tendon injury, having the similar expression with mammals. Therefore, we hypothesized the bone marrow derived macrophage secreted miRNAs-containing exosomes play important functions in peritendinous adhesion after tendon injury.

overall_design: we investigated miRNA expression profiles in exosomes from  bone marrow derived macrophages by using high-throughput sequencing technology.

first: Haomin

last: Cui

first: Yu

last: Zheng


title: Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2

overall_design: Refer to individual Series


title: Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [400K]

status: Public on Dec 31 2018

city: Harbin

first: Xueyuan

last: Jia

address: 157 Baojian Road, Nangang District

institute: Harbin Medical University

summary: Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. These amplification regions localized in two populations of DMs. Through a combined analysis on the results of array CGH, high throughput sequencing, multiplex-fluorescence in situ hybridization and chromosome walking results, we constructed molecular structures of the two populations of DMs at nucleotide resolution.

overall_design: Oligonucleotide-based Human Genome Microarrays (Agilent Technologies) containing 60K, 180K, 400K and 1M features were used for hybridization, among which 2×400K format was used to examine genome-wide copy number alteration in a human colorectal adenocarcinoma cell line NCI-H716. The 4×180K format targeting amplified regions was customized microarray that we created by using the Agilent eArray online system (https://earray.chem.agilent.com/) for interrogating the genome of DMs with high-resolution and accuracy.

first: Wenjing

last: Sun

first: Feng

last: Zhang

first: Songbin

last: Fu


title: Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716 [custom 180K]


title: Global transcriptome of Sclerotinia sclerotiorum during in vitro growth and Arabidopsis thaliana infection

status: Public on Jan 24 2019

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

institute: INRAE

summary: Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains however largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram towards division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during A. thaliana colonization compared to in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta. Using a multi-cell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.

overall_design: Border and Center of mycelium colonies grown in vitro or in planta and control samples, three independent replicates

first: Malick

last: Mbengue


title: Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2 (ChIP-seq)

first: Shaun

last: Mahony

overall_design: ChIP-seq was used to characterize transcription factor binding upon overexpression of Ascl1 and Neurog2 in mouse embryonic stem cells. Input (no IP) was used as control.

first: Begüm

last: Aydin

first: Akshay

last: Kakumanu

first: Mary

last: Rossillo

first: Mireia

last: Moreno-Estelles

first: Niels


title: Comparison of single hWJSCs and hBMMSCs

status: Public on Feb 19 2019

city: Singapore

first: WENTING

last: LIU

address: #02-01 GENOME 60 BIOPOLIS STREET

country: Singapore

institute: Genome Institute of Singapore

summary: The Wharton’s jelly of the human umbilical cord contains a population of mesenchymal stem cells that are unique and possess significant clinical utility. Known as human Wharton’s jelly stem cells (hWJSCs), they have broad differentiation potential, are proliferative and available in large numbers from discarded cords thus requiring minimum ex vivo expansion. They are safe and non-tumorigenic and maintain stemness properties for prolonged periods in culture. Besides their potential to produce tissues for cell based therapies, it has been demonstrated that they have anti-cancer and wound healing properties and provide cues for expansion of hematopoietic stem cells for treatment of hematopoietic malignancies. They are thus an attractive alternative source of MSCs of therapeutic value compared to bone marrow MSCs (hBMMSCs). We aimed to characterise the differences in gene expression profiles between these two stem cell types using single cell RNA sequencing to determine which pathways are involved in conferring hWJSCs with their unique properties.

overall_design: One hundred and three hWJSCs and sixty-three hBMMSCs. There are no replicates.

first: Angela

last: Barrett

first: Wenting

last: Liu


title: Identified amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716