title: Long-term, genome-wide kinetic analysis of the effect of the circadian clock and transcription on the repair of cisplatin-DNA adducts in the mouse liver

first: Yanyan

last: Yang

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

summary: Cisplatin is the most commonly used chemotherapeutic drug for treating solid tumors. However, its toxicity and the innate or acquired resistance of cancer cells to the drug limit its usefulness. Cisplatin kills cells by forming cisplatin-DNA adducts, most commonly in the form of Pt-d(GpG) diadduct. We recently showed that repair of this adduct within 2 hours following injection is controlled by two circadian programs: (1) The circadian clock controls transcription of 2000 genes in mouse liver and thereby controls repair of the transcribed strand of these genes via transcription coupled repair in a rhythmic fashion unique to each gene’s phase of transcription. (2) The basal excision repair activity itself is controlled by the circadian clock with a single phase at which the repair of the non-transcribed strand and the rest of the genome take place. Here, we have followed the repair kinetic for long periods genome-wide both globally and at single nucleotide resolution by the Excision Repair-sequencing (XR-seq) method to gain further insight into cisplatin DNA damage and repair with the aim of improving the therapeutic index of the drug.  Our data show that transcription-driven repair is complete after two days, while completion of basal repair of nontranscribed strands, silent genes and intergenic regions requires weeks.  In rhythmically controlled genes, oscillations of transcribed repair are observed up to 2 days post-injection, and in both constitutively transcribed and rhythmic genes, we see a trend in template strand repair with time from the 5’to 3’ end.  These findings add to the complexity of circadian- and transcription-dependent and -independent control of repair exhibited by this model organism in response to cisplatin.

overall_design: To follow the Pt-d(GpG) repair pattern over a 10-day period, 59 mice were injected with cisplatin (10mg/kg) at ZT20 (3:00AM) on day 1, and for the first two days afterwards 3 mice were sacrificed at 4 hr intervals, their livers were harvested, and Pt-d(GpG) repair was quantified by slot blot and XR-seq. For the remaining mice, six to eight per time point were sacrificed at 4, 8 and 10 days after cisplatin injection and were processed likewise.  An additional 12 mice were injected with cisplatin on day 1, as above, and livers were harvested for slot blot analysis at 5 day intervals from day 15 to day 70.  Insufficient material was available for XR-seq analysis of samples obtained later than 10 days after injection.

first: Zhenxing

last: Liu

first: Christopher

middle: P

last: Selby

first: Aziz

last: Sancar


title: Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

status: Public on Jun 26 2019

city: Davis

first: Gina

middle: Marie

last: Turco

state: CA

address: University of California, Davis

country: USA

institute: UC Davis

type: Expression profiling by high throughput sequencing

summary: Single cell sequencing (DropSeq) from 7 day old Arabidopsis roots with  β-estradiol-VND7, MYB83 and MYB46 induction lines and controls

overall_design: 7 day Arabidopsis roots either treated with β-estradiol and collected after 24 hours or transferred to control MS plates for 24 hours. All experiments where treated at 7am and collected at 7am the next day for protoplasting and DropSeq

first: Siobhan

last: Brady


title: Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene (ChIPseq)

status: Public on Jun 25 2019

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide association studies (GWAS) have identified 100s of loci associated with coronary artery disease (CAD) and blood pressure (BP)/hypertension. Many of these loci are not associated with traditional risk factors, nor include obvious candidate genes, complicating their functional characterization. We hypothesized that many GWAS loci associated with vascular diseases modulate endothelial functions. Endothelial cells play critical roles in regulating vascular homeostasis (e.g. selective barrier, inflammation, hemostasis, vascular tone) and endothelial dysfunction is a hallmark of atherosclerosis and hypertension. We generated an integrated map of gene expression (RNA-sequencing), open chromatin regions (ATAC-sequencing), and 3D interactions (Hi-C) in resting and TNFα-treated human endothelial cells. We showed that genetic variants associated with CAD and BP are enriched in open chromatin regions identified in endothelial cells. We used physical loops identified by Hi-C to link open chromatin peaks that include CAD or BP SNPs with the promoter of genes expressed in endothelial cells. This analysis highlighted 4,548 combinations of regulatory elements-promoters, including 108 pairs that involve a differentially open chromatin site and a differentially expressed gene following TNFα treatment. At a CAD locus, we validated one of these pairs by engineering a deletion of the TNFα-sensitive regulatory element using CRISPR/Cas9 and measuring an effect on the expression of the novel CAD candidate gene AIDA. Our data support an important role played by genetic variants acting in the vascular endothelium to modulate inter-individual risk in CAD or hypertension

overall_design: H3K27ac ChIP-seq of TNF-alpha treated endothelial cells (teloHAEC) for 0, 4h or 24h

first: Simon

last: Lalonde

first: Valérie-Anne

last: Codina-Fauteux

first: Sébastian

last: Méric de Bellefon

first: Francis

last: Leblanc

first: Mélissa

last: Beaudoin

first: Rola

last: Dali

first: Tony

last: Kwan

first: Ken

last: Sin Lo

first: Tomi

last: Pastinen


title: Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene (ATACseq)

overall_design: ATAC-seq of TNF-alpha treated endothelial cells (teloHAEC and HCAEC) for 0, 4h or 24h


title: Therapeutic targets and microenvironment in sequential biopsies of classical Hodgkin lymphoma at diagnosis and relapse

status: Public on Jun 24 2019

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

summary:
BACKGROUND: Classical Hodgkin lymphoma is dominated by the nonneoplastic microenvironment, while the neoplastic Hodgkin-Reed-Sternberg cells compose only a minority of cells in the lymphoma tissue. Both, the Hodgkin-Reed-Sternberg cells due to their expression of CD30 and PD-L1 and the microenvironment with abundant T-cells and expression of PD1 are specifically targeted by new treatment concepts.

AIM: We aimed to understand the dynamics of therapeutic targets in patients treated with conventional chemotherapy.

METHODS: We analyzed sequential biopsy specimens obtained at diagnosis and at relapse from the same patient for morphology, immunophenotype and microenvironmental components.

RESULTS: The morphological subtype changed between primary and relapse biopsy in 20% of cases. The immunophenotype was stable with respect to CD30, CD3 and LMP1 but variable with respect to CD15 and CD20 expression. Gene expression revealed 8 up- and 20 down-regulated genes at relapse (p≤0.05) with a consistent logarithmic fold change direction in at least 75% of all cases. For PD1, we found discrepant results between gene expression analysis (decrease at relapse) and number of PD1 positive cells assessed by immunohistochemistry (unchanged at relapse). PD-L1 in the neoplastic cells appeared unchanged between primary diagnosis and relapse.

CONCLUSION: The expression of the therapeutic targets CD30, PD1 and PD-L1 can reliably be assessed in tumor specimen at first diagnosis and are unchanged under conventional chemotherapy.
We used digital multiplexed gene expression (DMGE) with FFPE derived RNA to analyze sequential biopsy specimens obtained at diagnosis and at relapse from the same patient for morphology, immunophenotype and microenvironmental components.

overall_design: 26 classical Hodgkin lymhoma samples were hybridized to the NanoString nCounter system by using an Immunology Panel of 594 genes.

first: Antje

last: Schnitter

first: Katharina

last: Reddemann

first: Christoph

last: Thorns

first: Falko

last: Fend

first: Birgit

last: Federmann

first: Peter

last: Möller

first: Monika

last: Szczepanowski

first: Rainer

last: Spang

first: Wolfram

last: Klapper


title: Genome-wide mapping of DNA damage hotspots in response to various replication stressors

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

summary: Purpose: The goal of this study is to profile and identify DNA damage hotspots that are sensitive to different replication stressors.

overall_design: Methods: Human lymphoblastoid cell line is treated with aphidicolin, hydroxyurea, or methyl methanesulfonate for 24 hours, and ChIP  with gamma-H2AX were performed. Two independent ChIP experiments for each treated and untreated samples were carried out. ChIP DNA was then subject to Illumina sequencing using Hi-Seq 2500. Sequence reads that passed quality filters were mapped to GRCh38 using Bowtie2. Peaks were then analyzed for enrichment of repetitive sequences, CpG islands, transcription start sites, and histone marks.

first: Megan

last: Chastain


title: An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development (RNA-Seq)

status: Public on Jun 23 2019

city: St. Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology

institute: Washington University School of Medicine

summary: Classical type 1 dendritic cells (cDC1s) are required for anti-viral and anti-tumor immunity, which has motivated a need to understand their development. The development of the cDC1 progentitor requires an E protein–dependent enhancer located 41 kilobases downstream of the transcription start site of the transcription factor IRF8 (+41 kb Irf8 enhancer) but its maturation instead requires the BATF3-dependent +32 kb Irf8 enhancer. To understand this switch, we performed single-cell RNA sequencing of the common dendritic cell progenitor (CDP) and identified a cluster of cells that expressed transcription factors that influence cDC1 development, such as Nfil3, Id2, and Zeb2. Genetic epistasis among these factors revealed that Nfil3 expression is required for the transition from Zeb2hi and Id2lo CDPs to Zeb2lo and Id2hi CDPs, which represent the earliest committed cDC1 progenitors. This genetic circuit blocks E protein activity to exclude plasmacytoid DC potential and explains the switch in Irf8 enhancer usage during cDC1 development.

overall_design: To develop a comprehensive profile of heterogeneity within the CDP, we employed high-throughput single-cell RNA sequencing (scRNA-seq) of 10,000 CDPs.

first: Prachi

last: Bagadia

first: Maximilian

last: Nitschke

first: Zora

last: Modrusan

first: Andrey

middle: S

last: Shaw

middle: M


title: Expression data from cDC2 derived from in vitro culture from Batf3 KO pre-cDC1 and IRF8 +32 KO pre-cDC1 compared to cDC1 derived from in vitro culture of WT pre-cDC1 or cDC2 derived from in vitro culture of WT pre-cDC2

summary: We used gene expression microarrays to determine if Batf3 and the IRF8 +32 kb enhancer are required to sustain IRF8 expression in the pre-cDC1.

overall_design: Pre-cDC1s and pre-cDC2s were sorted from WT, Batf3 KO, and IRF8 +32 KO mice and cultured in vitro for 5 days. Mature cDC1 or cDC2 were sorted for RNA extraction and hybridization on Affymetrix microarrays.


title: ATAC-seq of dendritic cell progenitors

city: Saint Louis

first: Vivek

last: Durai

address: 4940 Parkview Place, Dock at CSRB, Murphy Lab 7766

department: Pathology and Immunology

institute: Washington University in St. Louis School of Medicine

summary: Induction of the transcription factor Irf8 in the common dendritic cell progenitor (CDP) is required for classical type 1 dendritic cell (cDC1) fate specification, but the mechanisms controlling this induction are unclear. Here we identified Irf8 enhancers and used CRISPR/Cas9 genome editing to assess their roles in Irf8 regulation. An enhancer 32 kilobases downstream  of the Irf8 transcriptional start site (+32 kb Irf8) that was active in mature cDC1s was required for the development of this lineage, but not for its specification. Instead, a +41 kb Irf8 enhancer previously thought to be active only in plasmacytoid DCs (pDCs) was found to also be transiently accessible in cDC1 progenitors. Deletion of this enhancer reduced Irf8 expression in pDCs as expected, but also surprisingly prevented the induction of Irf8 in CDPs and abolished cDC1 specification. Thus, cryptic activation of the +41 kb Irf8 enhancer in DC progenitors is responsible for cDC1 fate specification.

overall_design: ATAC-seq of three different dendritic cell progenitors (MDP, CDP, pre-cDC1) with three biological replicates of each progenitor

first: Jeffrey

last: Granja

first: Ansuman

middle: T

last: Satpathy


title: Expression data from WT, Batf3, and Id2 KO CDPs or Zbtb46-GFP+ cKit intermediate cells in the bone marrow.

summary: We used microarrays to detail the programme of gene expression underlying CDP commitment to cDC1 lineage and identify differentially regulated genes during this process.

overall_design: DC progenitors were sorted from bone marrow for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression signatures for various DC progenitors and their temperal sequences along developmental axis.


title: Histone ChIP-seq and ATAC-seq of dendritic cell progenitors

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

overall_design: Refer to individual Series


title: Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene (Hi-C)

first: Guillaume

last: Lettre

overall_design: Hi-C of TNF-alpha treated endothelial cells (teloHAEC) for 0h or 4h

first: Simon

last: Lalonde

first: Valérie-Anne

last: Codina-Fauteux

first: Sébastian

last: Méric de Bellefon

first: Francis

last: Leblanc

first: Mélissa

last: Beaudoin

first: Rola

last: Dali

first: Tony

last: Kwan

first: Ken

last: Sin Lo

first: Tomi

last: Pastinen


title: Histone ChIP-seq of dendritic cell progenitors

summary: Induction of the transcription factor Irf8 in the common dendritic cell progenitor (CDP) is required for classical type 1 dendritic cell (cDC1) fate specification, but the mechanisms controlling this induction are unclear. Here we identified Irf8 enhancers and used CRISPR/Cas9 genome editing to assess their roles in Irf8 regulation. An enhancer 32 kilobases downstream of the Irf8 transcriptional start site (+32 kb Irf8) that was active in mature cDC1s was required for the development of this lineage, but not for its specification. Instead, a +41 kb Irf8 enhancer previously thought to be active only in plasmacytoid DCs (pDCs) was found to also be transiently accessible in cDC1 progenitors. Deletion of this enhancer reduced Irf8 expression in pDCs as expected, but also surprisingly prevented the induction of Irf8 in CDPs and abolished cDC1 specification. Thus, cryptic activation of the +41 kb Irf8 enhancer in DC progenitors is responsible for cDC1 fate specification.

overall_design: Examination of two different histone marks (H3K27ac and H3K4me1) in three different dendritic cell progenitor populations

first: Arifumi

last: Iwata

first: Kenneth

last: Murphy


title: Expression data from WT cDC1s, Zeb2 KO cDC1s, Nfil3 Zeb2 DKO cDC1s and Zeb2 Id2 DKO cDC1s

summary: We used microarrays to determine whether cDC1s from the two double KO are bona fide cDC1s, and what are the transcriptional changes within these cDC1s.

overall_design: cDC1 were sorted from mouse spleen for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression signatures for cDC1s from various genotypes.

first: Xiao

last: Huang


title: Expression data from Id2-GFP- CDPs, Id2-GFP+ CDPs, Id2-GFP- pre-CD8, and Id2-GFP+ pre-CD8.

first: Prachi

last: Bagadia


title: JMJD6 and NMYC binding examined by ChIP-seq in NMYC overexpressing CHP134 human neuroblastoma cells

city: Sydney

first: matthew

middle: kwok kei

last: wong

state: New South Wales

address: Lowy cancer centre, University of New South Wales

department: histone modification group

country: Australia

institute: Children's Cancer Institute

summary:
JMJD6 (also known as PTDSR) is an important oncogene that is upregulated in 17q21-ter gained neuroblastoma.It plays a role in E2F and N-Myc-regulated gene pathways and neuroblastoma tumorigenesis
Using ChIP-Seq, we profiled JMJD6 and NMYC binding in the NMYC overexpressing neuroblastoma cell line.
We identified the genomic location of JMJD6 and NMYC binding peaks across the human genome.

overall_design: Identification of JMJD6 and NMYC protein binding locations on a genomic scale in CHP-134 neuroblastoma cells.

first: Matthew

last: Wong

first: Rebecca

last: Poulos

first: Jason

first: Tao

last: Liu


title: Expression data from Zbtb46- CDPs, Zbtb46+ CDPs, and pre-CD8 DCs

first: Tiantian


title: An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development


title: Expression data from WT and Id2 KO splenic cDC2

summary: We used microarrays to detail the genes regulating cDC2 development in the absense of the transcription factor Id2.

overall_design: Splenic cDC2 were sorted from bone marrow for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression signatures for WT and Id2 KO cDC2.


title: Expression data from Zeb2hi CDPs, Zeb2low CDPs, and pre-CD8 DCs


title: H3K27ac, H3K4me and H3K4me3 binding examined by ChIP-seq in the CHP-134 neuroblastoma cell line

summary:
Super-enhancers are defined by peaks in H3K27 acetylation and H3K4 mono-methylation, and the lack of H3K4 tri-methylation. They have been found to play a role in oncogene transcription and tumour maintenance.
Using ChIP-Seq, we profiled H3K27ac, H3K4me and H3K4me3 binding in CHP-134 neuroblastoma cells.
We identified H3K27ac, H3K4me and H3K4me3 binding sites in the CHP-134 neuroblastoma cell line.

overall_design: Identification of potential enhancer and super-enhancer sites in the CHP-134 neuroblastoma cell line.


title: A Stromal Cell Niche Sustains ILC2-Mediated Type-2 Conditioning in Adipose Tissue

city: Cambridge

first: Noe

last: Rodriguez Rodriguez

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: Group-2 innate lymphoid cells (ILC2), type-2 cytokines and eosinophils, have all been implicated in sustaining adipose tissue homeostasis. However, the interplay between the stroma and adipose-resident immune cells is less well understood. We identify that white adipose tissue-resident multipotent stromal cells (WAT-MSCs) can act as a reservoir for IL-33, especially after cell stress, but also provide additional signals for sustaining ILC2.  Indeed, we demonstrate that WAT-MSCs also support ICAM-1-mediated proliferation and activation of LFA-1-expressing ILC2s. Consequently, ILC2-derived IL-4 and IL-13 feed-back to induce eotaxin secretion from WAT-MSCs supporting eosinophil recruitment. Thus, MSCs provide a niche for multifaceted dialogue with ILC2 to sustain a type-2 immune environment in WAT.

overall_design: White adipose tissue from IL-33-critine heterozygous reporter mice was mechanically dissociated in RPMI-1640, and digested with collagenase I (Life Technologies), DNase I (Roche) at 37oC whilst shaking. Lin-CD45-Epcam-CD31-CD24-PDGFRα+CD34+Sca1+Podoplanin+ IL-33-citrine+ or IL-33-citrine- WAT-MSCs, Lin-CD45-Epcam+ and Lin-CD45-Epcam-CD31+ were sorted by flow cytometry using Sony iCyt Synergy (Sony) to >95% purity. Three replicates from independent experiments were obtained and sequenced for RNA-seq.

first: Batika

last: Rana

first: Eric

last: Jou

first: Jillian

middle: L

last: Barlow

last: Rodriguez-Rodriguez

first: Jennifer

middle: A

last: Walker

first: Claire

last: Knox

first: Helen

middle: E

last: Jolin

first: Clare

last: Hardman

first: Meera

last: Sivasubramaniam

first: Ayda

last: Stezo

first: E

last: Cohen

first: Ian

middle: C

last: Scott

last: Sleeman

first: Chiamaka

middle: I

last: Chidomere

first: Sara

last: Cruz Migoni

first: Jorge

last: Caamano

first: Helle

middle: F

last: Jorgensen

first: Stefania

last: Carobbio

first: Antoni

last: Vidal-Puig

first: Andrew

middle: N

last: McKenzie


title: Long-Term Kinetic Analysis of the Effect of the Circadian Clock and Transcription on Repair of Cisplatin-DNA Adducts in Mouse Liver

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

overall_design: To follow the Pt-d(GpG) repair pattern over a 10-day period, 59 mice were injected with cisplatin (10mg/kg) at ZT20 (3:00AM) on day 1, and for the first two days afterwards 3 mice were sacrificed at 4 hr intervals, their livers were harvested, and Pt-d(GpG) repair was quantified by slot blot and XR-seq. For the remaining mice, six to eight per time point were sacrificed at 4, 8 and 10 days after cisplatin injection and were processed likewise.  An additional 12 mice were injected with cisplatin on day 1, as above, and livers were harvested for slot blot analysis at 5 day intervals from day 15 to day 70.  Insufficient material was available for XR-seq analysis of samples obtained later than 10 days after injection.

first: Zhenxing

last: Liu

first: Christopher

last: Selby

first: Aziz

last: Sancar


title: JMJD6 gene gain is a tumorigenic factor and therapeutic target in neuroblastoma

first: matthew

last: wong


title: Pol2 binding examined by ChIP-seq in inducible JMJD6 knockdown neuroblastoma cells

summary:
JMJD6 is an important oncogene that is upregulated in 17q21-ter gained neuroblastoma.It plays a role in E2F and N-Myc-regulated gene pathways and neuroblastoma tumorigenesis
Using ChIP-Seq, We profiled RNA polymerase 2  binding in doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells, treated with either doxycycline or vehicle control.
We identified a list of genes with reduced RNA Pol II binding peaks at their gene promoters as a result of the JMJD6 knockdown. GSEA analysis showed that the top four gene sets, with most considerable reduction in RNA Pol II binding peaks at gene promoters, were E2F target genes, G2M checkpoint genes, mitotic spindle genes, and Myc target genes.

overall_design: Identification of changes on RNA polymerase 2 binding in doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells,  treated with either doxycycline or vehicle control.

first: Tao

first: Matthew

last: Wong

first: Rebecca

last: Poulos

first: Jason


title: Single-cell RNAseq Reveals Developmental Origins and Ontogenetic Stability of Neurexin Alternative Splicing Profiles

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Neurexins are key synaptic organizers which exist in thousands of alternatively spliced isoforms. Because trans-synaptic neurexin interactions with different post-synaptic molecules are largely isoform dependent, a cell type-level census of different neurexin isoforms could predict molecular interactions relating to synapse identity and function. Using single-cell transcriptomics to study the origin of neurexin diversity in multiple murine hippocampal and cortical cell types, we have discovered shared expression patterns in developmentally-related cell types. By comparing neurexin profiles in immature embryonic neurons, we show that neurexin profiles are specified during early development and remain unchanged throughout neuronal maturation. In contrast to this, we find that expression of other cell-adhesion molecules is modulated throughout circuit maturation. Thus, our findings reveal that ontogenetic stability of neurexin expression is unique among the broader landscape of cell-adhesion molecules, whose coordinated expression progressively governs the emergence of cell type identity.

overall_design: mRNA profiles of 162 Embryonic cells (122 Htr3a line, 18 Nex line, 22 Lhx6 line)

first: David

last: Lukacsovich

first: Jochen

last: Winterer

first: Lin

last: Que

first: Wenshu

last: Luo

first: Tamas


title: RNAseq on developmental endoreplicating (salivary glands) cells in Drosophila melanogaster

status: Public on Jun 22 2019

city: Bloomington

first: Brian

middle: R

last: Calvi

state: IN

department: Biology

institute: Indiana University Bloomington

summary: In order to evaluate the global transcriptomic changes in endoreplicating cells in Drosophila melanogaster we performed RNA-Seq. Endoreplicating cells (salivary glands) and mitotic cycling cells (brains and imaginal discs) were harvested from feeding 3rd instar larvae and mRNA levels were compared. Consistent with our previous results, we found that endoreplicating cells repress genes regulated by the E2F1 transcription factor as well as genes regulated by the Myb-MuvB (MMB) transcription factor complex.

overall_design: Brains and imaginal discs (BD) and Salivary Glands (SG) were dissected from feeding 3rd instar y1 w67c23 larvae and total RNA was isolated. After RNA isolation, poly-A tailed RNA was enriched and cDNA libraries were generated. RNAseq was done on three biological replicates using an Illumina NextSeq 500.

first: Michael

middle: D

last: Rotelli


title: Alu RNA modulates the expression of cell cycle genes in human fibroblasts

status: Public on Jun 21 2019

city: PARMA

first: Giorgio

last: Dieci

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression regulators, might be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblast and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-Sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry, including increased expression of the key cell cycle transcriptional regulator FOXM1 and several FOXM1-regulated genes. Overall, the results of our analysis suggest that increased Alu RNA favors cell cycle progression thus contributing to enable sustained cell proliferation which is an important factor of cancer development and progression.

overall_design: mRNA profiles of human fibroblasts (IMR90) and HeLa cells that overexpress the Alu retrotransposons AluSq2 and AluSx. The experiments were performed in duplicate using Illumina HiSeq4000


title: Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells

city: Stockholm

first: Mikael

last: Ringh

state: Choose state (US & Canada)

address: Medical Epigenetics, CMM L8:00, Karolinska University Hospital Solna

country: Sweden

institute: Karolinska Institutet

summary:
Background  While smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL).   Methods  We profiled changes in DNA methylation (5mC) and its oxidized form hydroxymethylation (5hmC) using conventional bisulfite (BS) treatment and oxidative bisulfite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers.   Findings  We identified 1,667 BS methyl (5mC+5hmC), 1,756 5mC and 67 5hmC differentially methylated positions (DMPs) between smokers and nonsmokers (FDR <0.05, absolute Δβ >0.15). Both 5mC DMPs and to a lesser extent BS methyl (5mC+5hmC) were predominantly hypomethylated. In contrast, almost all 5hmC DMPs were hypermethylated, supporting the hypothesis that smoking-associated oxidative stress can lead to DNA demethylation, via the established sequential oxidation of which 5hmC is the first step. While we confirmed differential methylation of previously reported smoking-associated BS methyl CpGs using former generations of BeadChips in alveolar macrophages, the large majority of identified DMPs, BS methyl (1,639/1,667), 5mC (1,738/1,756), and 5hmC (67/67), have not been previously reported.  Most of these novel smoking-associating sites are specific to the EPIC BeadChip and, interestingly, many of them are associated to FANTOM5 enhancers. Transcriptional changes affecting 633 transcripts were consistent with DNA methylation profiles and converged to alteration of genes involved in migration, signaling and inflammatory response of immune cells.   Interpretation  Collectively, these findings suggest that tobacco smoke exposure epigenetically modifies BAL cells, possibly involving a continuous active demethylation and subsequent increased activity of inflammatory processes in the lungs.
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overall_design: 35 bronchoalveolar lavage samples (mainly alveolar macrophages) from healthy individuals; smokers (S) and nonsmokers (NS). Includes both BS-treated and oxBS-treated samples for 5mC and 5hmC interrogation.

first: Tomas

last: Ekström


title: Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression

summary:
JMJD6 oncoprotein induces neuroblastoma and exerts its biological effects through modulation of downstream target genes.
We identified that JMJD6 knockdown reduces neuroblastoma cell proliferation, so we investigated which downstream signaling pathways were regulated by JMJD6.

overall_design: We performed Affymetrix Clariom S microarray experiments in stable Doxycycline inducible Control shRNA, and 2 independent JMJD6 shRNA CHP134  neuroblastoma cells after Doxycyline treatment for 40 hours. The Control shRNA, JMJD6 shRNA-1 (repeats A, B, C and D) and JMJD6 shRNA-2 samples (repeats A, B, E and F)were run four times. Differential expression analysis (DOXJ2 - NTJ2)-(DOXscr - NTscr) was done for each independent JMJD6 shRNA. The following are identical CEL file pairs: CHP_NT_shSCR_A_(Clariom_S_Human).CEL and CHP_NT_shSCR_A_dup(Clariom_S_Human).CEL, CHP_DOX_shSCR_A_(Clariom_S_Human).CEL and CHP_DOX_shSCR_A_dup(Clariom_S_Human).CEL, CHP_NT_shSCR_B_(Clariom_S_Human).CEL and CHP_NT_shSCR_B_dup(Clariom_S_Human).CEL, CHP_DOX_shSCR_B_(Clariom_S_Human).CEL and CHP_DOX_shSCR_B_dup(Clariom_S_Human).CEL.  Affymetrix Clariom S microarray experiments were also performed in stable Doxycycline inducible Control shRNA, and JMJD6 shRNA-2  SKNAS  neuroblastoma cells after Doxycyline treatment for 40 hours.

first: Nicholas

last: Ho

first: Chelsea

last: Mayoh


title: Expression data from WT CD24+CD172a+ cDC2s, WT CD24–CD172+ cDC2s, and WT CD24+CD172a– cDC1s

first: Kenneth

last: Murphy

summary: We used gene expression microarrays to determine if WT CD24+CD17a+ cDC2 are transcriptionally similar to WT CD172a+ cDC2

overall_design: Splenic WT CD24+CD17a+ cDC2, WT CD24+ cDC1, and WT CD24-CD172a+ cDC2 were sorted for RNA extraction and hybridization on Affymetrix microarrays.

first: Prachi

last: Bagadia


title: Lats1/2 suppress NFkB and aberrant EMT initiation to permit pancreas progenitor differentiation

city: Dallas

first: Ondine

last: Cleaver

state: TX

address: 6000 Harry Hines Boulevard, MC9148

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: The Hippo pathway directs cell differentiation during organogenesis, in part by restricting proliferation. How Hippo signaling maintains a proliferation-differentiation balance in developing tissues and its underlying molecular targets are poorly understood. Our study shows that Hippo suppresses NFκB signaling in pancreatic progenitors to permit cell differentiation and developmental progression. We found that pancreas-specific Lats1/2 kinase deletion (Lats1/2PanKO) from mouse progenitor epithelia results in failure to differentiate 3 key pancreatic lineages: acinar, ductal, and endocrine. We performed an unbiased transcriptome analysis to query the differentiation defects in Lats1/2PanKO. This analysis revealed increased NFκB activator expression, including the pantetheinase Vanin1 (Vnn1). Through in vivo and ex vivo studies, we show that VNN1 activates a detrimental cascade of processes in Lats1/2PanKO epithelium, whereby 1) NFκB activation and 2) initiation of epithelial-to-mesenchymal transition (EMT) together override normal differentiation. We show that exogenous stimulation of VNN1 or NFκB can also trigger this cascade in WT pancreatic progenitors. These findings show that pancreas development requires active suppression of NFκB by LATS1/2 kinases to restrain a cell-autonomous transcriptional program and thereby allow for differentiation.

overall_design: RNA-Seq comparing total RNA from 5 WT samples and 3 Lats1/2-deficient pancreas samples at E11.0.

first: Caitlin

last: Braitsch

first: D

middle: B

last: Azizoglu

first: Yadanar

last: Htike

first: Ulrike

last: Schnell

first: Christopher

last: Chaney

first: Thomas

middle: J

last: Carroll

first: Ben

middle: Z

last: Stanger


title: The oncogenic action of NRF2 depends on de-glycation by Fructosamine-3-kinase (FN3K)

city: New York

first: Viraj

last: Sanghvi

address: 1275 York Ave

department: CABG

institute: MSKCC

summary: We show that NRF2 activation drives hepatocellular carcinoma development in vivo.    Moreover, NRF2 undergoes glucose dependent modification called glycation and requires the de-glycating enzyme FN3K to maintain NRF2' oncogenic functions.

overall_design: Gene expression analysis in MYC-driven murine HCC with and without NRF2 activation.  NRF2 is activated by targeting  its negative regulators Keap1 or Cul3 or targeting NRF2 ETGE motif by sgRNA/Cas9 editing.

first: Hans-Guido

last: Wendel


title: Changes in mitochondrial function and browning markers of subcutaneous and visceral white adipose tissue of C57BL/6j mice from weaning to young adulthood

city: Utrecht

first: Andrea

last: Kodde

address: Uppsalalaan 12

country: Netherlands

institute: Danone Nutricia Research

summary: White adipose tissue (WAT) distribution and WAT mitochondrial function contribute to total body metabolic health throughout life, but little is known about changes following weaning. We therefore assessed changes in mitochondrial density and function in WAT depots of young mice. Inguinal (ING), epididymal (EPI) and retroperitoneal (RP) WAT of 21, 42 and 98 days old C57BL/6j mice was collected. Mitochondrial density (citrate synthase (CS), mtDNA) and function (subunits of oxidative phosphorylation complexes (OXPHOS)) markers were analysed, together with gene expression of browning markers (Ucp1, Cidea). RNA of ING WAT of 21 and 98 old mice was sequenced to further investigate functional changes of the mitochondria and alterations in cell populations. CS levels decreased significantly over time in all depots. ING showed most pronounced changes, including significantly decreased levels of OXPHOS complex I, II and III subunits and gene expression of Ucp1 (PN21-42 and PN42-98) and Cidea (PN42-98). White adipocyte markers were higher at PN98 in ING WAT. The mitochondrial functional profile changed over time from ‘growing’ mitochondria focused on ATP production (and dissipation), to more steady-state mitochondria with more diverse functions and higher biosynthesis. Mitochondrial density and energy metabolism markers declined in all three depots over time after weaning. This was most pronounced in ING WAT where it was associated with reduced browning markers, increased whitening and an altered metabolism. In particular the PN21-42 period may provide a time window to study mitochondrial adaptation and effects of nutritional exposures relevant for later life metabolic health.

overall_design: RNA samples of inguinal white adipose tissue from 21 and 98 days old mice (n = 4 per time point) were used for mRNA sequencing analysis (NXT-Dx, Gent, Belgium). Data analysis included contrast analysis (R package Limma) between PN21 and PN98, omitting transcripts with a FPKM (fragments per kilobase million) of zero in at least one of the samples and including transcripts with an average FPKM >2 at PN21 or PN98.

first: Eefje

last: Engels

first: Annemarie

last: Oosting

first: Kees

last: van Limpt

first: Eline

last: van der Beek

first: Jaap

last: Keijer


title: Determine the genome-wide localization of nmad-1 and top-2 in the transgenic flag tagged strains

city: Boston

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

summary: We report the chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) on flag tagged top-2 and nmad-1 transgeneic strains. We generated over 200 million reads from the IP'd DNA as well as input controls. We found that nmad-1 cobound with top-2 for approximately 80% of regions with p < 0.0001 (Fisher's exact test).  Top-2 localization was also depedent on nmad-1 as  half of the sites were no longer bound by top2 after nmad-1 deletion.

overall_design: Examine the nmad-1 and top-2 in wild type C.elegans thorughout the genome

first: Simon

middle: Y

last: Wang


title: NMAD-1

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

overall_design: Refer to individual Series


title: Transcriptome analysis in the germline of wild-type (WT) n2 worm and nmad-1(ok3133) mutant at 20°C and 25°C.

summary: The goal of RNA-seq is to identify the differential expressed genes in the wild-type worm and nmad-1 mutant worm at 20°C and 25°C respectively. 100 pairs of germlines were  extracted and collected from worm tips. Two biological replicates were assigned for each group and the RNA profiles were generated by deep sequencing, using NEXTseq 500 Illumina. We mapped about 20 - 30 million reads per sample to C. elegans genome (build ce10) with bowtie2 workflow. Differential expression genes were identified through EBSeq in RSEM pipeline with 0.05 p value and 1.2 fold change. Our results showed elevated number of misregulated genes in the nmad-1 mutant groups at 25°C.

overall_design: Germline mRNA profiles of wilde-type (WT) worm and nmad-1 mutant at 20°C and 25°C were generated by deep sequencing, in duplicate, using Nextseq500


title: CUT&RUN comparing occupancy of MAX, MNT, MYC in MAX WT and KO B220+ cells

status: Public on Jun 20 2019

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

summary:
The goal of this study was to genomic occupancy of MAX, MNT, MYC and E2F1 in B cells in the presence and absence of transcription factor MAX
Although MAX is regarded as an obligate dimerization partner for MYC, its function in normal development and neoplasia is poorly defined. We show that B-cell specific deletion of Max has a modest effect on B-cell development but completely abrogates E -Myc driven lymphomagenesis. While Max loss only affects a few hundred genes in normal B cells, it leads to the global downregulation of Myc-activated genes in premalignant E -Myc cells. We show that the balance between MYC-MAX and MNT-MAX interactions in B cells shifts in pre-malignant B cells towards a MYC driven transcriptional program. Moreover, we find that MAX loss leads to a significant reduction in MYC protein levels and downregulation of direct transcriptional targets, including regulators of MYC stability. This phenomenon is also observed in multiple cell lines treated with MYC-MAX dimerization inhibitors. Our work uncovers a layer of Myc autoregulation critical for lymphomagenesis yet partly dispensable for normal development.

overall_design:
Each genotype is represented in duplicate (cells isolated from 2 individual mice for each)
the antibody used in the studies:
anti-MAX (Proteintech catalog no. 10426-1-AP)
anti-MYC (Cell Signaling catalog. No 13987s)
anti-E2F1 (Proteintech catalog no. 12171-1-AP)
anti-MNT (Bethly Labs catalog no. A303-627A)
anti-GFP (IgG control) (Cell Signaling catalog no. 2956S)

first: Robert

last: Eisenman


title: Bcl6 binding sites in in vitro cortical progenitors [ChIP-Seq]

city: Leuven

first: Pierre

last: Vanderhaeghen

address: O&N4 Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Chromatin immunoprecipitation following Bcl6 induction (24h doxycycline) in mouse ES-cell-derived cortical progenitors (differentiation day 12).

overall_design: ChiP-seq screen for Bcl6 target genes in in vitro cortical progenitors (n=3, pooled data for analysis)

first: Jerome

last: Bonnefont

first: Zachary

last: Gaber

first: Xionghui

last: Lin

first: Delphine

last: Potier

first: François

last: Guillemot

first: Stein

last: Aerts


title: Bcl6 neurogenic activity in in vitro cortical progenitors [RNA-Seq]

summary: Transcriptome analysis following Bcl6 induction (24h doxycycline) in mouse ES-cell-derived cortical progenitors (differentiation day 12) shows that Bcl6 promotes a neurogenic transcription program and represses selective genes of the main proliferative pathways.

overall_design: RNA-seq screen for Bcl6-elicited gene expression changes in in vitro cortical progenitors (n=4)

first: Luca

last: Tiberi

first: Anne

last: Lefort

first: Frederick

last: Libert


title: High-Seq porcine granulosa cell

city: Changchun

first: Yun

last: Zhao

state: Jilin

address: Xi'an Road

department: College of Animal Sciences

country: China

institute: Jilin University

summary: To illustrate molecular pathways associated with the effects of RBP4 on GCs, we used high-throughput sequencing to detect differential gene expression in GCs overexpressing RBP4. A total of 113 differentially expressed genes (DEGs) were identified in RBP4-overexpressing GCs, which include 71 upregulated and 42 downregulated genes.

overall_design: mRNA profiles of porcine granulosa cells were generated by high-throughput  sequencing, in triplicate,

first: Chunjin

last: Li


title: Identification of novel regulators of Th2 cells in HDM model (ATAC-Seq)

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

institute: KI

summary: Naïve CD4 T cells differentiate into functionally diverse subsets of T helper (Th) cells. Gene expression profiling has the capacity to pinpoint factors that regulate subset differentiation and function, however obtaining transcriptional profiles of pure populations has been challenging. We performed single cell RNA-Sequencing (scRNA-Seq) of T helper cells from lymph node, lung and airways in a mouse model of asthma. scRNA-Seq resolved transcriptional profiles of naïve CD4 T, Th1, Th2, Treg cells and various activated states including a population responding to type I interferons. A trajectory for Th2 cell differentiation was delineated over time, with Th2 cells acquiring follicular T helper cell characteristics in the lung-draining lymph node before undergoing further modifications in the lung. A feature of airway Th2 cells was their enrichment for genes associated with lipid metabolism and experiments with blockers of key metabolic pathways supported roles for glucose and lipid metabolism in Th2 cell differentiation.

overall_design: Mice were sentized and challanged with HDM extract intranasally. scRNA-Seq was performed in 384-well format. The relevant organs (either BAL, lung or mLN) were isolated, rapidly processed, stained for a panel of surface markers and single cell sorted within approximately 90 minutes of organ harvest. In total 764 memory T helper cells (CD3+CD4+CD44+) were sorted directly into lysis buffer using a BD Influx from two independent mice 15 days after sensitization and challenge with HDM as described above. In addition, 50 naïve T Helper cells (CD3+CD4+CD62LhiCD44lo), 50 Treg cells (CD3+CD4+CD25hi) from mLN of a mouse not exposed to HDM; 200 ST2+ mLN and 82 ST2+ lung T helper cells (CD3+CD4+CD44+ST2+CD25-) were sort purified at day 10 of the HDM model. SMART-Seq2 libraries were prepared using the method described in Picelli et al. (Nature Methods 2013) by the Eukaryotic Single Cell Genomics national facility at SciLife Laboratory, Stockholm.

first: Jonathan

last: Coquet


title: Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (RNA-Seq)

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

summary: Atypical teratoid/rhabdoid tumor (AT/RT), which harbors INI1 mutation and exhibits a characteristic histology of rhabdoid cells, has a poor prognosis because of the lack of effective treatments. Here we established human INI1-deficient pluripotent stem cells (hPSCs), which developed AT/RT formation in vivo. We revealed that the activation of ESC-like signature leads to rhabdoid phenotype in tumor by OSKM or c-MYC induction. Finally, we performed CRISPR/Cas9 knockout screening to inhibit activation of ESC-like signature in AT/RT. Our effort identified candidate genes including RAD21 that encodes a key component within the cohesin complex. Notably, chemical inhibition of HDAC8 that indirectly targets the function of cohesin with simultaneous inhibition of EZH2 efficiently suppressed the activation of ESC-like signature and inhibited the growth of AT/RT cells both in vitro and in vivo.

overall_design: Analyzing transcriptional profiles in PSA-NCAM positive NPC INI1-/-; TP53-/- (NPC), GFP-NPC, OSKM-NPC, MYC-NPC and hiPSC INI1-/-; TP53-/--derived tumor cell line treated by DMSO, EZH2 inhibitor, HDAC8 inhibitor or combination of EZH2 and HDAC8 inhibitors.

first: Yukinori

last: Terada

first: Takuya

last: Yamamoto


title: Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (microarray)

summary: Atypical teratoid/rhabdoid tumor (AT/RT), which harbors INI1 mutation and exhibits a characteristic histology of rhabdoid cells, has a poor prognosis because of the lack of effective treatments. Here we established human INI1-deficient pluripotent stem cells (hPSCs), which developed AT/RT formation in vivo. However, INI1-deficient hPSC-derived neural progenitor cell (NPC) gave rise to mostly medulloblastoma-like tumors when transplanted into the mouse brain.

overall_design: Analyzing gene expression profiles in hiPSC INI1-/-; TP53-/-, NPC INI1-/-; TP53-/-, hiPSC INI1-/-; TP53-/--derived tumor and NPC INI1-/-; TP53-/--derived tumor.


title: IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [RNA-seq II]

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

summary: Complete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requires combined action of IFN-γ and LPS. Synergistic activation of canonical inflammatory NF-κB target genes by IFN-γ and LPS is well appreciated, but less is known about whether IFN-γ negatively regulates components of the LPS response, and how this affects polarization. A combined transcriptomic and epigenomic approach revealed that IFN-γ selectively abrogates LPS-induced feedback and select metabolic pathways by suppressing TLR4-mediated activation of gene enhancers. In contrast to superinduction of inflammatory genes via enhancers that harbor IRF sequences and bind STAT1, IFN-γ-mediated repression targeted enhancers with STAT sequences that bound STAT3. TLR4-activated IFN-γ-suppressed enhancers comprised two subsets distinguished by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin, and were functionally inactivated by IFN-γ. These findings reveal that IFN-γ suppresses feedback inhibitory and metabolic components of the TLR response to achieve full M1 polarization, and provide insights into mechanisms by which IFN-γ selectively inhibits TLR4-induced transcription.

overall_design: RNA-seq analysis of transcriptional changes in human macrophages (M-CSF/GM-CSF) that were cultured with or without IFN-γ and then stimulated with LPS or vice versa

first: L

last: Ivashkiv


title: Tumor Infiltrating Lymphocytes and Immune-Related Genes as Predictors of Outcome in Pancreatic Adenocarcinoma

status: Public on Jun 19 2019

city: Bath

first: Alberto

last: D'Angelo

address: Claverton Down

department: Biology and Biochemistry

institute: University of Bath

summary: Background. We investigated the correlation of pancreatic ductal adenocarcinoma patient prognosis with the presence of tumor infiltrating lymphocytes and expression of 521 immune system genes. Methods. Intratumoral CD3+, CD8+, and CD20+ lymphocytes were examined by immunohistochemistry in 12 PDAC patients with different outcomes who underwent pancreaticoduodenectomy. The results were correlated with the gene expression profile using the digital multiplexed NanoString nCounter analysis system (NanoString Technologies, Seattle, WA, USA).  Results. Twenty immune system genes were significantly differentially expressed in patients with a good prognosis relative to patients with a worse prognosis: TLR2 and TLR7 (Toll-like receptor superfamily); CD4, CD37, FOXP3, PTPRC (B cell and T cell signalling); IRF5, IRF8, STAT1, TFE3 (transcription factors); ANP32B, CCND3 (cell cycle); BTK (B cell development); TNF, TNFRF1A (TNF superfamily); HCK (leukocyte function); C1QA (complement system); BAX, PNMA1 (apoptosis); IKBKE (NFB pathway). Differential expression was more than twice log 2 for TLR7, TNF, C1QA, FOXP3, and CD37.    Discussion. Tumor infiltrating lymphocytes were present at higher levels in samples from patients with better prognosis. Our findings indicate that tumor infiltrating lymphocyte levels and expression level of the genes listed above influence pancreatic ductal adenocarcinoma prognosis. This information could be used to improve selection of best responders to immune inhibitors.

overall_design: In this study, we analyzed a total of 12 patients affected by pancreatic tumor split into two different groups based on their outcomes (6 good vs 6 worse prognoses). After the IHC of different populations within cancer, we randomly selected 3 patients for each group and performed a gene expression analysis with Nanostring human PanCancer immune module.

first: Navid

last: Sobhnai

first: Giandomenico

last: Roviello

first: Stefan

last: Bagby

first: Deborah

last: Bonazza

first: Cristina

last: Bottin

first: Fabiola

last: Giudici

first: Fabrizio

last: Zanconati

first: Nicolò

last: De Manzini

first: Alessandra

last: Guglielmi

first: Daniele

last: Generali


title: Identification of novel regulators of Th2 cells in HDM model (RNA-Seq)

first: Chris

last: Tibbitt

first: Jonathan

middle: M

last: Coquet


title: RNAseq on induced endoreplicating S2 cells

first: Brian

last: Calvi

summary: RNA-Seq was used In order to evaluate the global transcriptomic changes of CycA dsRNA and Myb dsRNA induced endoreplicating cells (iECs) in DrosophilaS2-DGRC cells. CycA dsRNA and Myb dsRNA iECs mRNA levels were compared to control mitotic cycling cells treated in parallel with GFP dsRNA, in three biological replicates. The RNA-Seq results indicated that a switch from mitotic cycles to endoreplication is associated with up and down regulation of thousands of genes. Comparison of the CycA dsRNA and Myb dsRNA iEC transcriptomes revealed that they shared a total of 966 genes that were differentially expressed compared to mitotic cycling controls

overall_design: S2 cells treated with either GFP, CycA or Myb dsRNA were harvested 96 hours after dsRNA addition. After RNA isolation, poly-A tailed RNA was enriched and cDNA libraries were generated. RNAseq was done on three biological replicates using an Illumina NextSeq 500. CycA dsRNA and Myb dsRNA data sets were compared to GFP dsRNA control cells.

first: Michael

last: Rotelli

first: Mary

last: Lilly


title: Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: To study the developmental process of human podocytes and compare to the in vitro counterpart, we dissociated cells from the inner and outer kidney cortex as well as kidney organoids, and performed 10X Genomics single-cell RNA sequencing.

overall_design: Identifying cell types and studying human podocyte developmental process in human kidney and in organoids

last: Ransick

first: Tracy

middle: T

last: Tran

first: Nils

middle: O

last: Lindstrom

first: Guilherme

last: De Sena Brandine


title: SETMAR functions in illegitimate DNA recombination and non-homologous end joining repair

city: Leicester

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: RNA-seq in duplicates of a control cell line, TO, and three cell lines expressing full-length SETMAR, SM1, SM2 and SM3

overall_design: Examination of the effect of SETMAR expression on U2OS transcriptome

first: Ronald

last: Chalmers


title: Single-cell profiling guided combinatorial immunotherapy for breast cancer resistance to Her2/neu and CDK4/6 targeted therapy

city: South Bend

first: Qingfei

last: Wang

address: 1234 N Notre Dame Ave, Harper Hall A121

department: Harper Cancer Research Institute

institute: University of Notre Dame

summary: Trastuzumab (Herceptin™), a humanized monoclonal antibody targeting the extracellular domain of human epidermal growth factor receptor-2 (HER2), is one of the most successful examples of targeted therapies for HER2-positive breast cancer. However, drug resistance remains daunting challenges. New combinatorial regimen of CDK4/6 inhibitors plus trastuzumab is currently under active clinical investigations. In this study, we seek to prospectively model the in vivo response to CDK4/6 inhibitor Palbociclib (Pal) plus trastuzumab (Ab) using transgenic Her2/Neu mouse model in parallel with the current clinical trial scenario. We performed single cell RNA-seqencing (Drop-seq) to profile and compare tumor cells and infiltrated immune cells derived from control, Ab+Pal sensitive/residual (APS) and resistant/progressive (APR) tumors. We revealed that although Ab+Pal treatment enhanced antigen processing, presentation and interferon signaling on tumor cells, a distinct immunosuppressive immature myeloid cells (IMCs) infiltrated in the resistant tumor microenvironment to promote resistant phenotype. Based on single cell gene set enrichment analysis (profiling) guided drug screening, we identified and evaluated a combinatorial immunotherapy regimen. We found that combinatorial immunotherapy with receptor tyrosine kinase inhibitor Cabozantinib and immune checkpoint blockades overcome Ab+Pal resistance by inhibiting IMCs and enhancing anti-tumor immunity. Moreover, our rationally designed sequential combinatorial regimens enabled durable response and sustained controlling of the emergence of acquired resistance, thus significantly improved outcomes of rapidly evolving Her2/Neu positive breast cancers. Our results implicate that single-cell RNA sequencing profiling guided combinatorial immunotherapy as a strategy to mitigate the emergence of resistance and to achieve long-term therapeutic benefit merits clinical translation.

overall_design: Drop-seq of tumor cells and tumor infiltrating immune cells derived from FVB/N MMTV-neu202Mul mice with different treatment/phenotypes (sensitive and resistant tumors).

first: Siyuan

last: Zhang


title: Integrative metabolomic and transcriptomic analysis for the non-invasive study of bladder cancer

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

summary: In this study has been carried out an integrative metabolomic and transcriptomic analysis of tumoral and non-tumoral bladder tissues using exactly the same samples to determine the possible links between metabolism and gene expression in this tumoral context.

overall_design: Gene expression was compared among bladder cancer tissues and non-tumoral tissues.

first: Alba

last: Loras

last: Suárez-Cabrera

first: Carmen

last: Martinez-Bisbal

first: Guillermo

last: Quintás

first: Jesús

last: Paramio

first: Ramón

last: Martinez-Mañez

first: Salvador

last: Gil

first: José

middle: L

last: Ruiz-Cerdá


title: Transcriptomic profile of human embryonic renal corpuscles

last: McMahon

summary: In order to characterize and benchmark the podocytes-like cells generated through human ES cell differentiation, we generated transcriptional profiles of renal corpuscles from embryonic human kidneys using RNA-Seq.  To compare, we also performed RNA-Seq of human immortalized podocyte cell lines before and after thermoswitch.

overall_design: We performed RNA-Seq of poly-A selected RNA from hESC-derived kidney organoids, organoid-derived MAFB-eGFP+ podocytes at different time points, and human immortalized podocytes.

first: T

first: Q

last: Guo

first: A


title: In vivo developmental trajectories of human podocyte development inform in vitro differentiation of pluripotent stem-cell derived podocytes

first: Andrew

summary: To assess in vitro derived podocytes, we examined the transcriptional changes during human podocyte development and applied that knowledge to pinpoint strengths and limitations of hESC-derived podocytes.

overall_design: We performed transcriptionaling profiling of kidney organoids and organoid-derived MAFB-eGFP+ podocytes at various differentiation time points.

first: Tracy

last: Tran

first: Qiuyu


title: Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. pestis and that Hfq also globally binds noncoding small RNAs (sRNAs) encoded by the intergenic, antisense, and 3′ regions of mRNAs. An Hfq U-rich stretch is highly enriched in sRNAs, while motifs partially complementary to AGAAUAA and GGGGAUUA are enriched in both mRNAs and sRNAs. Hfq-binding motifs are enriched at both terminal sites and in the gene body of mRNAs. Surprisingly, a large fraction of the sRNA and mRNA regions bound by Hfq and those downstream are destabilized, likely via a 5′P-activated RNase E degradation pathway, which is consistent with a model in which Hfq facilitates sRNA-mRNA base pairing and the coupled degradation in Y. pestis. These results together have presented a high-quality Hfq-RNA interaction map in Y. pestis, which should be important for further deciphering the regulatory role of Hfq-sRNAs in Y. pestis.

overall_design: Hfq-binding RNA profiles of Y. pestis wild type (WT) and hfq-flag were generated by deep sequencing using Illumina.

first: Ruifu

last: Yang

first: Yi

first: Yanping

last: Han


title: Activation Dynamics and Immunoglobulin Evolution of Pre-existing and Newly Generated Human Memory B-cell Responses to Influenza Hemagglutinin

city: Bethesda

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

summary: Understanding human vaccine-induced memory B cell responses is critical to developing effective vaccines to evolving viruses like Influenza A.  B cell responses to influenza exposure involve activation of pre-existing immunity and generation of new responses.  To characterize these two types of responses, we analyzed the response to H7N9 vaccination in H7N9 naïve adults.  This allowed us to distinguish responses of pre-existing B cells towards conserved epitopes versus newly generated H7-specific epitopes using hemagglutinin (HA) probes by flow cytometry.  The recall response to conserved epitopes on H7 HA involved a transient expansion of memory B cells with little observed adaptation.  However, the B cell response to newly encountered epitopes was phenotypically distinct and generated a sustained memory population that evolved and affinity matured months after vaccination.  These findings establish clear differences between newly generated and pre-existing memory B cells, highlighting the challenges in achieving long-lasting, broad protection against an ever-evolving virus.

overall_design: 34 Samples

first: Sarah

last: Andrews

first: Michael

last: Chambers

first: Jason

last: Plyler

first: Julie

middle: E

last: Raab

first: Masaru

last: Kanekiyo

first: Rebecca

last: Gillespie

first: Amy

last: Ransier

first: Sam

last: Darko

first: Jianfei

last: Hu

first: Xuejun

first: Hadi

last: Yassine

first: Jeffery

last: Boyington

first: Michelle

last: Crank

first: Grace

first: Cemily

last: Coates

first: John

last: Mascola

first: Daniel

last: Douek

first: Barney

middle: S

last: Graham

last: Ledgerwood

first: Adrian

last: McDermott


title: CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis

status: Public on Jun 18 2019

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: In B lymphopoiesis, activation of the pre-B cell antigen receptor (pre-BCR) is associated with both cell cycle exit and Igk recombination. Yet, how the pre-BCR mediates these functions remains unclear. Herein, we demonstrate that the pre-BCR initiates a feed-forward IRF4-CXC Receptor 4 (CXCR4) amplification loop. ERK activation by CXCR4 then directs the development of small and immature B cells including orchestrating cell cycle exit, pre-BCR repression, Igk recombination and BCR expression. In contrast, escape from IL-7 and pre-BCR expression have only modest effects on B cell developmental transcriptional and epigenetic programs. These data demonstrate a direct and central role for CXCR4 in orchestrating late B cell lymphopoiesis. Furthermore, in the context of previous findings, our data provide a three-receptor system sufficient to recapitulate the essential features of B lymphopoiesis in vitro.

overall_design: 26 samples from mouse: 8 ATAC-seq samples; 18 RNA-seq samples

first: Malay

last: Mandal

first: Michael

middle: K

last: Okoreeh

first: Domenick

last: Kennedy

first: Junting

last: Ai

first: Kaitlin

middle: C

last: McLean

first: Natalya

last: Kaverina

first: Iannis

last: Aifantis

first: Fotini

last: Gounari

first: Marcus

last: Clark


title: Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice

city: Lubbock

first: Beverly

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

summary: The helicase-like transcription factor (HLTF) gene – a tumor suppressor in human colorectal cancer (CRC) - is regulated by alternative splicing and promoter hypermethylation. The detection of hypermethylated HLTF DNA in fecal occult blood tests is an indicator of disease recurrence and poor survival. Hltf-deficiency in the ApcMin/+ mouse strain increased the formation of intestinal adenocarcinoma with a high incidence of gross chromosomal instabilities. To investigate Hltf-deletion effects in CRC without cross-breeding into a tumorigenic strain, Hltf-deletion was studied in mice treated with the carcinogen azoxymethane (AOM) and the proinflammatory agent dextran sulfate (DSS). Hltf-deletion resulted in weight loss beginning at treatment week 6, and poor survival (Kaplan-Meier survival plot). Hltf-deletion increased tumor multiplicity compared to controls, and dramatically shifted the topographic distribution of lesions into the rectum. Differential isoform expression analysis of lesions from control mice revealed both the truncated isoform that lacks a DNA-repair domain and the full length isoform capable of DNA damage repair are present (3:1.8 ratio) during adenocarcinoma formation. iPathwayGuide identified 51 dynamically regulated genes of 10,967 total genes with measured expression. Oxidative Phosphorylation (Kegg: 00190), the top biological pathway (p=0.006; p value correction: Bonferroni) perturbed by Hltf-deletion, resulted from increased transcription of Atp5e, Cox7c, Uqcr11, Ndufa4 and Ndufb6 genes, concomitant with increased endogenous levels of ATP (p=0.0176). Upregulation of gene expression, as validated with qRT-PCR, was accompanied by a stable mtDNA/nDNA ratio. This is the first study to show Hltf-deletion in an inflammation-associated CRC model elevates mitochondrial bioenergetics. The distal shift in tumorigenesis indicates the detection of hypermethylated HLTF DNA in human stool samples might be a prognostic biomarker for distal (left-sided) colorectal cancer rather than proximal (right-sided) colon cancer.

overall_design: Individual samples [all tumors from an individual mouse/sample x 3 biological replicates for test and control male mice = 6 total samples] were flash frozen and sent to Otogenetics Corp. (Norcross, GA) for RNA-seq assays

first: Rebecca

last: Helmer

first: Gurvinder

last: Kaur

first: Lisa

last: Smith


title: Microarray data from human cultured ILC3s

city: St. Louis

first: Marco

last: Colonna

address: 425 Euclide Ave

department: Pathology and Immunology

institute: Washington University in St.Louis

summary: Innate lymphoid cells (ILCs) are tissue-resident lymphocytes subdivided into ILC1s, ILC2s and ILC3s based on core regulatory programs and signature cytokines secreted. ILCs exhibit functional plasticity: for instance, human IL-22-producing ILC3s convert into IFN-γ-producing ILC1-like in vitro. Whether this conversion occurs in vivo is unclear. Using flow cytometry, mass cytometry and scRNAseq, here we found that ILC3s and ILC1s occupy opposite ends of a spectrum including discrete subsets in human tonsils. RNA velocity suggested strong directionality toward ILC1s for one ILC3-ILC1 intermediate cluster. Clonal analysis revealed graded ability of ILC3-ILC1 subsets to convert into ILC1-like cells. When examined in humanized mice, ILC3 acquisition of ILC1 features showed tissue-dependency. In chromatin studies, Aiolos emerged as a nuclear factor that cooperates with Tbet to repress evolutionarily conserved regulatory elements active in ILC3s. The human intestine also exhibited an ILC3–ILC1 transitional population. We conclude that conversion of ILC3s to ILC1-like occurs in vivo in human tissues, and that tissue factors and Aiolos are crucial for this process.

overall_design: ILC3 were sorted from human tonsils, expanded in SCF+IL-7 and stimulated with IL-23+IL-1b+IL-15 overnight.

first: Blanda

last: Di Luccia

first: Marina

last: Cella

first: Stan

last: Huang

first: Colonna

last: Marco


title: Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment [Hi-C]

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: This study demonstrates the relationship between replication timing, transcription and chromatin compartments in human stem cell differenatiation to endoderm lineage (Hi-C).

overall_design: Measuring replication timing, transcription and chromatin organization using Hi-C at different time points during human stem cell differentiation to endoderm lineage.

first: Vishnu

last: Dileep

first: Korey

last: Wilson

first: Claire

last: Marchal

first: Xiaowen

last: Lyu

first: Peiyao

last: Zhao

first: Ben

last: Li

first: Axel

last: Poulet

first: Daniel

last: Bartlett

first: Juan

last: Rivera-Mulia

first: Zhaohui

last: Qin

first: Allan

last: Robins

first: Thomas

last: Schulz

first: Michael

last: Kulik

first: Rachel

last: McCord

first: Job

last: Dekker

first: Stephen

last: Dalton

first: Victor

middle: G

last: Corces


title: UV laser-induced, time-resolved transcriptome resonses of Saccharomyces cerevisiae

city: Knoxville

first: Melinda

last: Hauser

address: 1311 Cumberland Ave

department: Microbiology

institute: The University of Tennessee

summary: We report changes in the S. cerevisiae transcriptome in response to 30s irradiation with a UV laser

overall_design: Cells (3 biological replicates) were irradiated for 30s with a UV laser.  Irradiated and control cells (non-irradiated) were transferred to growth medium, samples for RNASeq analysis were collected at 0, 15, 30 and 60 minutes post-transfer.

first: Paul

last: Abraham

first: Lorenz

last: Barcelona

first: Jeffrey

last: Becker


title: Drosophila FACT Regulates Promoter Proximal Pol II Pausing and Chromatin Architecture [ChIP-seq]

city: KANSAS CITY

first: Joan

middle: W

last: Conaway

state: Missouri

institute: Stowers Institute for Medical Research

summary: The highly conserved histone chaperone FACT (Facilitates Chromatin Transcription) is thought to contribute to the disassembly and reassembly of nucleosomes in the wake of RNA Polymerase II (Pol II) passage through chromatin. However, FACT’s roles in chromatin biology and transcriptional regulation in vivo in higher eukaryotes are not well understood. Here, we report that depletion of FACT leads to a reduction in the duration of promoter-proximal pausing by Pol II in Drosophila S2 cells. In addition, FACT depletion leads to a modest decrease in the occupancy of histone H3,  and to decrease in occupancy of histone H2A.v in promoter-proximal nucleosomes. Finally, we observed a dramatic 5’ to 3’ repositioning of the co-transcriptionally deposited histone modifications H3K4me3 and H3K36me3 in the FACT depleted cells. Taken together, our findings are consistent with the model that FACT contributes to the interplay between chromatin architecture and control of Pol II promoter-proximal pausing.

overall_design: Genome-wide examination of H3K36me3, H3K4me3, H3, H2Av, total RNA, transcriptionally engaged Pol II, and Pol II half-life in Drosophila melanogaster S2 cells depleted of FACT compared to control cells.

first: Theophilus

last: Tettey

first: Xin

last: Gao


title: RNASeq of total RNA isolated from self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV, co-infected with HBV/HDV, or uninfected at 8 and 28 days post-infection

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Here, we examined the host response relative of SACC-PHHs infected with either hepatitis B virus (HBV) alone or both HBV/hepatitis delta virus (HDV) co-infection compared to non-infected controls.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: SACC-PHHs were generated with PHHs from either a single human donor or mixed donors (in total, there were five donors) and co-cultured with 3T3J mouse non-parenchymal cells. These cultures can be persistently infected for up to 1-1.5 months post-challenge and exhibit a transcriptomic profile similar to what's observed in the 3D context of the liver. Note that not all donors and conditions have the same number of replicates.

first: Benjamin

last: Winer

first: Jenna

last: Gaska

first: Gabriel

last: Lipkowitz

first: Yaron

last: Bram

first: Amit

last: Parekh

first: Lance

last: Parsons

first: Robert

last: Leach

first: Rohit

last: Jindal

first: Cheul

middle: H

last: Cho

first: Anil

last: Shrirao

first: Erick

last: Novik


title: Drosophila FACT Regulates Promoter Proximal Pol II Pausing and Chromatin Architecture [RNA-seq]

overall_design: RNA-seq of S2 cells treated with SSRP1 dsRNA and Spt16 dsRNA to knockdown SSRP1 and Spt16 respectively. Two independent dsRNAs targeting non-overlapping regions were used for knockdown. S2 cells were treated with eGFP dsRNA as a non-targeting control.


title: Impact of CAR agonist ligand TCPOBOP on transcription factor binding in adult male mouse liver

status: Public on Jun 17 2019

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Chromatin immunoprecipitation and sequencing for three transcription factors (RXRa, CEBPa, CEBPb) was performed on livers of male mice treated with vehicle or with TCPOBOP for either 3 h or 27 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

overall_design: Chromatin was isolated from frozen livers from 7 or 8 week old wild-type male mice treated with either vehicle or TCPOBOP. Sonicated chromatin from 3-4 individual livers from each group was immunoprecipitated with antibodies to the following transcription factors:  RXRa, CEBPa, CEBPb.

first: Andy

last: Rampersaud

first: Aram

last: Shin

first: Nicholas

last: Lodato

middle: J


title: PRRX2 and HEY2 double knock-down facilitates ASCL1-induced neuron conversion in human dermal fibroblasts.

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

summary: Forced expression of ASCL1, Nurr1, Lmx1a, miRNA-124 and p53shRNA (ANLmp) in fibroblasts reprograms fibroblasts to induced dopaminergic neurons (iDA). While human lung fibroblasts can be converted rapidly and efficiently, iDA of dermal fibroblast is very unefficient and incompleted. To address this issue,  we performed time series RNAseq on both lung and dermal fibroblasts during the first four days of ANLmp induced neuron convertion. Bioinformatics analysis revealed the stable fibroblast gene regulatory network (GRN)  was a potential repressive factor for iDA in human dermal fibroblasts.

overall_design: Time serial comparison of transcriptomes of isogenic human skin fibroblasts and human lung fibroblasts during their transdifferentiation to dopaminergic neuron induced by ANLmp.

first: Hanqin

last: Li

first: Houbo

last: Jiang


title: Time-dependent changes in microglia transcriptional networks following traumatic brain injury

city: Charlestown

first: Michael

last: Whalen

address: 149 13th Street Room 6303

department: Department of Pediatrics

institute: Massachusetts General Hospital

summary: The temporal course of microglial inflammation-related gene expression was defined uding nanostring platform at acute, subacute, and chronic time points in a pre-clinical TBI model.

overall_design: In the study presented here, we analyzed the temporal course of changes in inflammatory genes of microglia isolated from injured brains at 2, 14 and 60 days after controlled cortical impact in mice, a well-established model of focal cerebral contusion.

first: Izzy

last: Saef

first: Elkhoury

last: Joseph


title: Expression data of enterohemorrhagic E. coli (EHEC) dicF mutant

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Avenue

department: Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: sRNAs play important roles in regulating gene expression post-transcriptionally. Here, we used RNA-seq to compare gene expression in a WT strain and a dicF1-4 deletion strain.

overall_design: EHEC strains were grown planktonically in tissue culture medium, RNA was extracted, and Illumina sequencing was used to assess differences in RNA levels.


title: Alligator embryonic scale samples

city: Los Angeles

first: Ping

last: Wu

state: CA

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

summary: Gene expression in alligator scales

overall_design: RNA-seq was performed to study the gene expression profiling in developing alligator overlapping scales


title: Impact of CAR agonist ligand TCPOBOP (3h and 27hr time points) on H3-K27me3 marks in adult male mouse liver

state: MA

summary: This SuperSeries is composed of the SubSeries listed below. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

overall_design: Refer to individual Series


title: Transcriptional profiling of dense and cystic organoids

status: Public on Jun 16 2019

city: Leuven

first: Benoit

last: Cox

address: Herestraat 49

institute: KU Leuven

summary: We performed RNA-seq on RNA samples of dense and cystic organoids derived from mouse pituitary tissue

overall_design: RNA-seq was performed on 2 RNA samples of dense and cystic organoids using the Illumina NextSeq 500


title: Impact of CAR agonist ligand TCPOBOP (27 hr time point) on H3-K27me3 marks in adult male mouse liver

summary: Chromatin immunoprecipitation and sequencing for the H3K27me3 histone mark was performed on livers of male mice either treated with vehicle or with TCPOBOP for 27 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

overall_design: Chromatin was isolated from frozen livers from 7 week old wild-type male mice treated with either vehicle or TCPOBOP. Sonicated chromatin from 3-4 individual livers from each group was immunoprecipitated with the following antibody:  H3K27me3 (Abcam Cat # ab6002, 2 μg antibody per 10 μg of sonicated chromatin). Sequencing data set was generated from 200 bp fragments.


title: Impact of CAR agonist ligand TCPOBOP (3 hr time point) on H3-K27me3 marks in adult male mouse liver

summary: Chromatin immunoprecipitation and sequencing for the H3K27me3 histone mark was performed on livers of male mice either treated with vehicle or with TCPOBOP for 3 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

overall_design: Chromatin was isolated from frozen livers from 7 week old wild-type male mice treated with either vehicle or TCPOBOP. Sonicated chromatin from 3-4 individual livers from each group was immunoprecipitated with the following antibody:  H3K27me3 (Abcam Cat # ab6002, 2 μg antibody per 10 μg of sonicated chromatin). This sequencing data set was generated from long DNA fragments (between 600 - 1100 bp) which were digested down to a size of 500 bp and then sequenced.


title: Capture of a functionally active Methyl-CpG Binding Domain by an arthropod retrotransposon family

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

type: Methylation profiling by high throughput sequencing

summary: The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Unexpectedly, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD domain. We functionally demonstrate how retrotransposon encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host genome, in the myriapod Strigamia maritima. Consistently, young MBD-encoding Copia retrotransposons (CopiaMBD) accumulate in regions with higher CpG-densities than other LTR-retrotransposons also present in the genome. This would suggest that retrotransposons use MBDs to integrate into heterochromatic regions in Strigamia, avoiding potentially harmful insertions into host genes. In contrast, CopiaMBD insertions in the spider Stegodyphus dumicola genome disproportionately accumulate in methylated gene bodies when compared to other spider LTR-retrotransposons. Given that transposons are not actively targeted by DNA methylation in the spider genome, this distribution bias would also support a role for MBDs in the integration process. Together, these data demonstrate that retrotransposons can co-opt host-derived epigenome readers, potentially harnessing the host epigenome landscape to advantageously tune the retrotransposition process.

overall_design: Profiling of cytosine methylation of Strigamia maritima. DAP-seq and ampDAP-seq of retrotransposon encoded MBDs on Strigamia maritima genomic DNA.

first: Ryan

last: Lister


title: Expression data for  tumor-infiltrating CD45+ cells

status: Public on Jun 15 2019

city: Pittsburgh

first: Chang

middle: of

last: Liu

state: PENNSYLVANIA

address: 200 Lothrop Street, W1028-22A, Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

summary:
Regulatory T (Treg) cells are crucial for immune homeostasis but they also contribute to tumor immune evasion by promoting a suppressive tumor microenvironment (TME). Mice with Treg cell-restricted Neuropilin 1 deficiency show tumor resistance while maintaining peripheral immune homeostasis, thereby providing a controlled system to interrogate the impact of intratumoral Treg cells on the TME. Using this and other genetic models, we showed that Treg cells shaped the transcriptional landscape across multiple tumor-infiltrating immune cell types. Treg cells suppressed CD8+ T cell secretion of interferon- (IFN), which would otherwise block the activation of sterol regulatory element-binding protein 1 (SREBP1)-mediated fatty acid synthesis in immunosuppressive (M2-like) tumor-associated macrophages (TAMs). Thus, Treg cells indirectly but selectively sustained M2-like TAM metabolic fitness, mitochondrial integrity and survival. SREBP1 inhibition augmented the efficacy of immune checkpoint blockade, suggesting that targeting Treg cells or their modulation of lipid metabolism in M2-like TAMs could improve cancer immunotherapy.
Microarray gene expression assay was performed to interogate the impact of fragile (Nrp1–/–) Tregs on the gloabal transcriptome oftumor immune infiltrates (CD45+ cells) at various time points over the course of tumor growth.

overall_design: B16. F10 or MC38 tumor -infiltrating CD45+ cells isolated from the Foxp3Cre-YFP or Nrp1L/LFoxp3Cre-YFP mice on designated days over the course of tumor growth

first: Dario

last: Vignali


title: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [RNA-Seq]

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

summary: Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.

overall_design:
RNA-seq on iPSC-induced excitatory neurons (2 replicates), iPSC-derived hippocampal dentate gyrus (DG)-like neurons (2 replicates), iPSC-induced lower motor neurons (2 replicates), and human primary fetal astrocytes (4 replicates)

Plase note that processed data generated from multiple samples is linked to the corresponding rep1 sample records.

last: Song


title: Transcriptomic profiling of human coronary artery endothelial cells under laminar shear stress (LS), oscillatory shear stress (OS) and static culture (ST)

city: Ann Arbor

first: Jifeng

last: Zhang

state: Michigan

address: 2800 Plymouth Road

department: Internal medicine

institute: University of Michigan

summary:
Aim: To survey the alteration of endothelial transcriptome under different types of shear stress and find novel shear stress-sensitive protein-coding genes as well as non-coding RNAs as potential therapeutic targets for the treatment of atherosclerosis
Method: After exposed to LS, OS and ST for 24 hours (n=4, respectively), ECs were harvested by scraping, and RNA was isolated and purified. Double-stranded cDNA was generated from 100 to 150 ng of total qualified RNA using selective priming and prepared for the final library. Quantitative PCR (qPCR) was performed to quantify the library using a KAPA kit for Illumina sequencing platforms. Twelve samples were then clustered on the cBot and sequenced on a 50-cycle single end on a HiSeq 2000 to generate 50 bp paired-end reads, using TruSeq SBS v3 reagents according to manufacturer’s protocols. RNA-seq fastq files were aligned to the human genome primary assembly (GRCh38) using the Subread package. Read counts on each gene were determined by featureCounts function in the Subread package using GeneCode human GTF file version 23 (http://www.gencodegenes.org/). Differential expression analysis between endothelial cells under different types of shear stress were performed using the limma package with the voom transformation. P values were adjusted by default Benjamini-Hochberg procedure.
Results: RNA-seq data provided a broad view of endothelial transcriptome under shear stress. We mapped about 70 million reads and discovered over 16,000 genes that are well-expressed in human coronary artery endothelial cells. RNA-seq results were consistent with previously reported DNA microarray data and we also confirmed the expression of genes that are previously reported and novel genes with qRT–PCR results. Comparing the endothelial transcriptomes under different types of shear stress, we found that there are approximately 50% genes that are differentially expressed in ECs under ST vs. LS and OS vs. LS while 10% under ST vs. OS.
Conclusion: RNA-seq data provide a framework for investigating endothelial transcriptome under shear stress. We found that endothelial cells under LS condition profoundly differs from those under either ST or OS conditions. The profiling also reveals a large amount of novel shear sensitive genes and lncRNAs that are not reported before. It provides the community with potential targets for anti-atherosclerosis drug development considering the determinant role of shear stress in the distribution of atherosclerotic lesions in the arterial tree.

overall_design: Human coronary artery endothelial transcriptomic profiles under LS, OS and ST were generated by RNA-sequencing, in quadruplicate, using Illumina HiSeq 2000

first: Cong-Zhen

last: Qiao

first: Fan

last: Meng

first: Inhwan

last: Jang

first: Hanjoong

last: Jo

first: Yuqing

last: Chen


title: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [PCHiC]

overall_design: pcHi-C on iPSC-induced excitatory neurons (3 replicates), iPSC-derived hippocampal dentate gyrus (DG)-like neurons (2 replicates), iPSC-induced lower motor neurons (3 replicates), and human primary fetal astrocytes (4 replicates)

first: Michael


title: Transcriptome profile of Theileria infected bovine leucocytes under curcumin treatment

city: Hyderabad

first: Anand

last: Srivastava

state: India

address: Survey No 37/4,  Gowalidoodi  Area ,   Gopanpally

country: India

institute: National Institute of Animal Biotechnology (NIAB)

summary: Using Illumina technology, we aim to identify global change in gene expression of bovine leucocytes and Theileria transcrits upon curcumin treatment

sample_organism:
Theileria annulata
Bos taurus

platform_organism:
Theileria annulata
Bos taurus

overall_design: Theileria infected bovine cells were treated with curcumin and gobal change in transcriptome was compared with untreated samples.

first: Prasanna

middle: B

last: Araveti


title: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [ATAC-seq]

overall_design: ATAC-seq on iPSC-induced excitatory neurons (2 replicates), iPSC-derived hippocampal dentate gyrus (DG)-like neurons (2 replicates), iPSC-induced lower motor neurons (3 replicates), and human primary fetal astrocytes (4 replicates)


title: Genome-Wide Copy Number Variation Analysis of Chinese Patients with Intellectual Disability

city: Wenzhou

first: Xiangnan

address: west load of college 268

institute: Wenzhou Medical University

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

summary: Objective: Intellectual disability (ID) is often sporadic, and its complex etiology can make clinical diagnosis difficult. The aims of this study were to detect genomic copy number variations (CNVs) in Chinese patients with ID, and to analyze the correlation between pathogenic CNVs and clinical phenotypes.  Methods: After excluding cases of ID caused by chromosomal aneuploidy, metabolic dysfunction, or environmental factors, we enrolled 60 patients with moderate to severe ID. We performed karyotype and single-nucleotide polymorphism (SNP) array analyses for all patients. Finally, we analyzed the relationship between CNVs and phenotype using CNV databases and genotype-phenotype comparisons.  Results: Karyotype analysis showed chromosomal terminal abnormalities in five patients and balanced translocations in two patients. Using SNP array analysis for 60 patients, we detected 87 CNVs in 45 patients, which included 16 pathogenic CNVs in 12 patients with a diagnostic yield of 20.0% (12/60). In one patient, we observed 14 regions of homozygosity > 10 Mb to 266 Mb. We detected a large deletion at 16q22.2 or 3q24q25 in each of two patients, in regions that have not previously been associated with specific syndromes. One case carried a 210-kb deletion at 1q21, including only one coding gene, LPPR4, which may be a candidate gene for the ID phenotype.  Conclusions: Use of the genome-wide array screening method can improve the detection rate of CNVs, reveal chromosomal abnormalities that have not been well characterized by cytology, and provide a new way to locate genes for patients with the ID phenotype. However, interpretation of CNVs remains a major challenge, which is why we believe that publicly shared data on CNVs and phenotypes can create a rich database of information.

first: Xueqin

last: Xu

first: Shaohua

last: Tang