title: Differentiation enhances Zika virus infection in neuronal brain cells

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Zika virus (ZIKV) is an emerging, mosquito-borne pathogen associated with a widespread 2015–2016 epidemic in the Western Hemisphere and a proven cause of microcephaly and other fetal brain defects in infants born to infected mothers. ZIKV infections have been also linked to other neurological illnesses in infected adults and children, including Guillain-Barré syndrome (GBS), acute flaccid paralysis (AFP) and meningoencephalitis, but the viral pathophysiology behind those conditions remains poorly understood. Here we investigated ZIKV infectivity in neuroblastoma SH-SY5Y cells, both undifferentiated and following differentiation with retinoic acid. We perform RNA seq, and global trancriptome analysis to corroborate the effect of retinoic acid in SH-SY5Y cells. Then we analyze the virus infection in differentiated and undifferntiated cells. We found that multiple ZIKV strains, representing both the prototype African and contemporary Asian epidemic lineages, were able to replicate in SH-SY5Y cells. Differentiation with resultant expression of mature neuron markers increased infectivity in these cells, and the extent of infectivity correlated with degree of differentiation.  Enhanced ZIKV infectivity in a neural cell line following differentiation may contribute to viral neuropathogenesis in the developing or mature central nervous system.

overall_design: Analysis of Zika virus infection in one neuroblastoma cell line differentiated, or not with retinoic acid.

first: Claudia

last: Sánchez San Martín

first: Tony

first: Jerome

last: Bouquet

first: Jessica

last: Streithorst

first: Guixia

last: Yu

first: Aditi

last: Paranjpe


title: RNA-seq analysis of diet-driven obesity and anti-obesity effects of Quercetin glucoside or Epigallocatechin gallate in Drosophila adults.

status: Public on Oct 20 2018

city: Soraku-gun

first: Mikiko

last: Yamanaka

state: Kyoto

address: 8-1-1, Seikadai, Seika-cho

department: research institute

country: Japan

institute: Suntory Global Innovation Center

type: Expression profiling by high throughput sequencing

summary: The High Fat Diet (HFD)-feeding significantly stimulated fat accumulation in Drosophila adults. Simultaneous feeding of known anti-obesity drugs that having the effect on rat and mouse, Quercetin Glycosides (QG) and Epigallocatechin gallate (EGCG) also suppressed fat accumulation in Drosophila at an equivalent concentration. Therefore, we have established a convenient model system to study on diet-induced fat accumulation and to evaluate effects of anti-obesity drugs using Drosophila. To understand overview of alterations of gene expression due to diet-induced fat accumulation and its suppression by the known anti-obesity drugs, we performed the RNA seq analyses. Consequently, mRNA levels of several genes involved in lipid metabolism, glycolysis/gluconeogenesis and anti-oxidative stress have changed in adults fed the HFD. Moreover, the levels altered in those fed on HFD supplemented with QG or EGCG. Our qRT-PCR further confirmed the RNA-seq data suggesting that expression of five genes essential for lipid metabolism was changed in HFD-fed animals and further altered in the animals treated with anti-obesity drugs. Among them, the most remarkable alteration was observed in dHSL gene encoding a lipase involved in lipid-storage after HFD feeding and the HFD supplemented with QG or EGCG. These changes are consistent with HFD-induced fat accumulation as well as the anti-obesity effects of those two drugs in mammals, suggesting that these genes play an important role in the anti-obesity effects of the drugs. These are the first evidences that whole profiles of altered gene expression under a condition of a diet-induced obesity and its suppression by anti-obesity drugs in Drosophila.

overall_design: mRNA profiles of Drosophila fed on Normal diet (ND), high fat diet (HFD), HFD supplemented with QG or EGCG were generated by RNA sequencing, 1 replicate performed per group.

first: Maho

last: Azuma

first: Tuan

middle: D

last: Le

first: Yuko

last: Yoshimoto

first: Natsumi

last: Hiraki

first: Fumihiko

last: Ohmura

first: Masaaki

last: Uchida

first: Norihito

last: Murayama

first: Yoshihiro

middle: H

last: Inoue


title: Affinity capture of polyribosomes followed by RNAseq (ACAPseq),  a discovery platform for protein-protein interactions

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

country: USA

institute: Johns Hopkins University

summary: Defining protein-protein interactions (PPIs) is central to the biological sciences.  Here, we present a novel platform - Affinity Capture of Polyribosomes followed by RNA sequencing (ACAPseq) - for identifying PPIs.  ACAPseq harnesses the power of massively parallel RNA sequencing (RNAseq) to quantify the enrichment of polyribosomes based on the affinity of their associated nascent polypeptides for an immobilized protein “bait”.  This method was developed and tested using neonatal mouse brain polyribosomes and a variety of extracellular domains as baits.  Of 92 baits tested, 25 identified one or more binding partners that appear to be biologically relevant; additional candidate partners remain to be validated.  ACAPseq can detect binding to targets that are present at less than 1 part in 100,000 in the starting polyribosome preparation.  One of the observed PPIs wes analyzed in detail, revealing the mode of homophilic binding for Protocadherin-9 (PCDH9), a non-clustered Protocadherin family member.

overall_design: ACAP-seq for 92 baits and 3 input samples.

first: Xi

last: Peng

first: Francesco

last: Emiliani

first: Philip

middle: M

last: Smallwood

first: Hong

last: Lei

first: Mark

middle: F

last: Sabbagh

first: Jeremy

last: Nathans


title: Identification of biomarkers for amyotrophic lateral sclerosis by comprehensive analysis of exosomal mRNAs in human cerebrospinal fluid.

city: Fujisawa

first: Kentaro

last: Otake

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Neuroscience Drug Discovery Unit

institute: Takeda Pharmaceutical Company Limited

summary: In comparison with exosomal mRNAs in CSF from four patients with amyotrophic lateral sclerosis, 543 genes were significantly changed, as represented by CUEDC2.

overall_design: Signatures of CSF exosomal mRNAs were then compared between four normal healthy donors and four sporadic amyotrophic lateral sclerosis patients to identify disease-related biomarkers.

first: Hidenori

last: Kamiguchi

first: Yoshihiko

last: Hirozane


title: Genome-wide expression analysis of human hTert immortalized fibroblasts after downregulation of MCM2

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formation in human cells and zebrafish that is uncoupled from replication. Zebrafish depleted of MCM2 develop ciliopathy-phenotypes including microcephaly and aberrant heart looping due to malformed cilia. In non-cycling human fibroblasts, loss of MCM2 promotes transcription of a subset of genes, which cause cilia shortening and centriole overduplication. Chromatin immunoprecipitation experiments show that MCM2 binds to transcription start sites of cilia inhibiting genes. We propose that such binding may block RNA polymerase II-mediated transcription. Depletion of a second MCM (MCM7), which functions in complex with MCM2 during its canonical functions, reveals an overlapping cilia-deficiency phenotype likely unconnected to replication, although MCM7 appears to regulate a distinct subset of genes and pathways. Our data suggests that MCM2 and 7 exert a role in ciliogenesis in post-mitotic tissues.

overall_design: 6 samples in total: 3 control, 3 siRNA MCM2

first: Melanie

last: Philipps

first: Martin

last: Burkhalter

first: Teresa

last: Casar Tena


title: Genome-wide expression analysis of human hTert immortalized fibroblasts after donwregulation of MCM7

overall_design: 6 samples in total: 3 control, 3 siRNA MCM7


title: RNA-seq profiling of plasmacytoid and conventional dendritic cells from wildtype and PU.1 knockout mice

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Dendritic cells (DCs) are can be broadly divided into conventional (cDC) and plasmacytoid (pDC) subsets. Despite the importance of this lineage diversity, its genetic basis is not fully understood. RNA-seq gene expression analysis of wild type (WT) and PU.1 transgenic mice revealed a key role for PU.1 in maintaining cDC identity.

overall_design: Itgax-Cre mice were crossed to Spi1(fl/fl) mice allowing Spi1 (PU.1) inactivation in CD11c expressing cells. Dendritic cells (DCs) were enriched from the spleen using CD11c magnetic beads.Conventional DCs (CD11c+MHCII+NK1.1-CD19-SiglecH-) and plasmacytoid DCs (CD11c+Bst2+SiglecH+ NK1.1-CD19-) were isolated from the spleens of wild type (WT), PU.1+/- heterozygous and PU.1-/- homozygous knockout mice. RNA was isolated independently from 2 biological replicates for each genotype and cell subset. Transcription was profiled by RNA-seq for all 12 samples on a HiSeq 2500 at the Australian Genomic Research Facility to generate 100 base-pair single-end reads.


title: Transcriptomics analysis of human jejunal enteroendocrine cells after vertical sleeve gastrectomy

status: Public on Oct 19 2018

city: Cambridge

first: Pierre

last: Larraufie

address: Box 289, Addenbrooke's Site

department: WT-MRC Institute of Metabolic Science

country: United Kingdom

institute: Metabolic Research Laboratories and MRC Metabolic Diseases Unit

summary: We report here the transcriptome of a population enriched in enteroendocrine cells from human jejunum from patients before or after gastrectomy. We analyze the effect of surgery on  gene expression and found very little effect on EEC transcriptome

overall_design: 2 conditions: pre operative and post operative

first: P

first: G

last: Roberts

first: F

last: Reimann

last: Gribble


title: Transcriptomics analysis of enteroendocrine cells after vertical sleeve gastrectomy

summary: We report here the transcriptome of sorted enteroendocrine cells from duodenum, ileum and colon from mice after vertical sleeve gastrectomy or sham operation, weight matched or not. We analyze the effect of region of origin and surgery and gene expression and found that only region of origin had an impact on EEC transcriptome

overall_design: 3 conditions (VSG, sham-adlibitum and sham-weightmatched) from 3 regions (duodenum, ileum and colon) with 6 replicates for each


title: Transcriptomics analysis of enteroendocrine cells following vertical sleeve gastrectomy

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide expression analysis of human hTert immortalized fibroblasts after downregulation of MCM2 & MCM7


title: Competitive repopulation of an empty microglial niche gives rise to functionally distinct subsets of microglia-like cells

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary:
Although most tissue macrophages are embryonically derived it is evident that circulating monocytes can compete for virtually any macrophage niche. Monocytes can thus become long-lived replacements of tissue macrophages that are indistinguishable from their embryonic counterparts, but the factors regulating this process are incompletely understood. To study niche competition in the CNS we depleted microglia with >95% efficiency using CX3CR1CreER/+R26DTA/+ mice and monitored long-term repopulation. The microglial niche was repopulated within weeks by a combination of local microglia proliferation giving rise to CX3CR1+F4/80lowClec12a– microglia, as well as infiltration of CX3CR1+F4/80hiClec12a+ macrophages. Adoptive transfer experiments demonstrated that peripherally-derived macrophages arose directly from Ly6Chi monocytes without contribution from hematopoietic progenitors and was independent of BBB breakdown. After repopulation we sorted microglia and monocyte-derived macrophages and performed transcriptional, epigenetic (DNA methylation) and ex vivo functional profiling. This revealed that Ly6Chi monocytes upregulated microglia gene expression and adopted microglia DNA methylation signatures. However, in contrast to proliferating microglia, which rapidly regained their homeostatic gene signature, monocyte-derived macrophages retained a distinct gene signature associated with antigen presentation, interferon signaling and chemotaxis. This translated into functional changes in monocyte-derived macrophages, as demonstrated by differences in surface marker expression, phagocytosis and cytokine production. Our results demonstrate that monocytes are imprinted by the CNS microenvironment but remain transcriptionally, epigenetically and functionally distinct. This may have implications for neuroinflammatory disease states and direct design of novel therapies.
Data was processed using the mEPIC tool PMID:29141580

overall_design: 25 sorted samples from mice on C57BL/6 background

first: Harald

last: Lund


title: RNA-Seq of osteosarcoma cell lines

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary: The Alternative Lengthening of Telomeres (ALT) pathway stimulates telomere elongation and prevents cellular senescence in approximately 60% of osteosarcoma.  While the precise mechanisms underlying the ALT pathway are unclear, mutations in the chromatin remodeling protein ATRX, histone chaperone DAXX, and the histone variant H3.3, correlate with ALT status. ATRX and DAXX facilitate deposition of the histone variant H3.3 within heterochromatic regions including the telomere suggesting that loss of ATRX, DAXX, and/or H3.3 lead to defects in heterochromatin maintenance at telomeres, ultimately contributing to ALT activity.  Previous studies have detected genetic mutations in ATRX, DAXX, and H3.3 in ALT cell lines and tumor samples. However, a subset of ALT samples show loss of ATRX or DAXX protein expression or localization without evidence of genetic alterations, indicating a role for other defects in ATRX/DAXX/H3.3 function. Here, using Next Generation Sequencing, we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, which leads to the translation of a chimeric DAXX-KIFC3 fusion protein.  Here, we demonstrate that the fusion of KIFC3 to DAXX leads to defects in DAXX function and likely perpetuates ALT activity.  These data highlight a previously unrecognized mechanism of DAXX inactivation in ALT positive osteosarcoma and provide rationale for thorough and comprehensive analyses of ATRX/DAXX/H3.3 proteins in ALT positive cancers.

overall_design: 13 cell lines sequenced in triplicate, totaling 39 sequencing samples

first: Rachel

middle: L

last: Flynn

first: Emily

last: Mason-Osann

first: Anqi

last: Dai


title: Transcriptome analysis of murine B cell and CLL samples

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

summary: Transcriptional profiling revealed that murine VH11 and non-VH11 CLL differed in the upregulation of specific pathways implicated in cell signaling and metabolism. We identified a gene expression signature (including Ccdc88a, Clip3, Zcchc18, Chd3 and Itm2a) that was significantly upregulated in T cell-dependent non-VH11 CLL compared with T cell-independent VH11/Vk14 or mutated IgH.TEμ CLL.

overall_design:
biological replicate (n=3-4) RNA-Seq experiments

Please note that the 'countTable_exons_def_norm_rpkm_all.txt' contains the 'FPKM' column headers (as a default output setting for the HOMER software package). However, the .txt file contains RPKM value as described in the sample data processing field.

first: Rudi

middle: W

last: Hendriks


title: An environmental code tunes the intracellular signaling network activity to shape cellular responses

first: Dmitry

last: Kuchenov

state: CA

address: 1700 4th Street

institute: Gladstone Institutes

summary: Cells constantly survey a complex set of inputs that is processed by the intracellular signaling network, but little is known of how cells integrate input information from more than one cue. We employed a FRET biosensor-based imaging platform to study the effect of combinatorial growth factor levels on the signaling network in human cells. We found that pairwise stimuli caused distinct concentration- and ratio-dependent signaling states through signaling signatures such as antagonism, additivity, and synergy. The unique signaling states correlated with differential gene expression and non-additive transcription patterns. We further elucidated how a signal-rich environment can fine-tune the signaling network and adjust physiological outcomes, by kinase and phosphatase activity profiling. We describe how complex extracellular conditions affect phospho-turnover and the basal phosphorylation status. Thus, we provide mechanistic insights into cellular processing of multiple cues and explain part of the complexity of cellular adaptation to changes in the extracellular environment.

overall_design: Examination of mRNA abundance upon individual or combinatorial growth factor treatments (EGF, IGF-1, EGF + IGF-1) at 4 hours after stimulation

first: Carsten

last: Schultz


title: Single-cell RNA sequencing reveals novel markers of pituitary stem cells and hormone-producing cell-types

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

state: New York

address: 101 Nicolls Road

institute: Stony Brook University

summary: Transcription factors and signaling pathways that regulate stem cells and specialized hormone-producing cells in the pituitary gland have been the subject of intense study and have yielded a mechanistic understanding of pituitary organogenesis and disease.  Yet, the regulation of stem cell proliferation and differentiation, the heterogeneity among specialized hormone-producing cells, and the role of non-endocrine cells in the gland remain important, unanswered questions.  Recent advances in single-cell RNA sequencing (scRNAseq) technologies provide new avenues to address these questions.  We  performed scRNAseq on approximately 13,663 cells pooled from six whole pituitary glands of 7-week-old C57BL/6 male mice.  We identified pituitary endocrine and stem cells in silico, as well as other support cell-types such as endothelia, connective tissue, and red and white blood cells.  Differential gene expression analyses identify known and novel markers of pituitary endocrine and stem cell populations.  We demonstrate the value of scRNAseq by in vivo validation of a novel gonadotrope-enriched marker, Foxp2.  We present novel scRNAseq data of in vivo pituitary tissue, including data from agnostic clustering algorithms which suggest the presence of a somatotrope subpopulation enriched in sterol/cholesterol synthesis genes.  At the same time, we show that incomplete transcriptome annotation can cause false negatives on some scRNAseq platforms that only generate 3’ transcript end sequences, and use in vivo data to recover reads of the pituitary transcription factor Prop1.  Ultimately, scRNAseq technologies represent a significant opportunity to address longstanding questions regarding the development and function of the different populations of the pituitary gland throughout life.

overall_design: 10x Chromium single-cell RNAseq of cells from pituitary glands of 7-week-old male C57BL/6 mice

first: L

middle: Y

first: A

middle: S

last: George

first: S

middle: R

last: McGee

middle: Z

last: Daly

first: M

last: Brinkmeier

first: B

last: Ellsworth

middle: A

last: Camper


title: Different Erythrocyte MicroRNA Profiles in Low- and High-Altitude Individuals

city: Beijing

first: Liping

last: Sun

address: No. 28, Fuxing Rd

country: China

institute: Chinese PLA General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: The number of red blood cells (RBCs) increases significantly in response to high-altitude hypoxic environments, and the RBC microRNA (miRNA) expression pattern is similar to that in whole blood. Studies have shown that miRNA in plasma can act as a circulating hypoxia-associated marker, but the effect of a high-altitude hypoxic environment on RBC-derived miRNAs has not yet been reported.
Methods: Blood samples were collected from 20 Han Chinese individuals residing at 500 m (Sichuan Han), 10 migrant Han Chinese citizens residing at 3658 m (Tibet Han) and 12 native Tibetans, and RBC indices measurements and miRNA sequencing analyses were performed for the three sample groups. The levels of some markedly altered miRNAs at high altitude were subsequently measured from 5 randomly selected samples of each group by real-time PCR. Bioinformatic analyses was performed to determine the potential target genes of selected hypoxia-associated miRNAs.
Results: Marked changes of several RBC indices were observed among the Tibet Han population, the Tibetan population and the Sichuan Han population. A total of 516 miRNAs derived from RBCs were initially identified by miRNA sequencing in the three sample groups. Compared with the Sichuan Han population, 49 miRNAs were differentially expressed in the Tibet Han population (17 upregulated and 32 downregulated). 12 upregulated and 21 downregulated miRNAs were observed in the Tibetan population compared with the Sichuan Han population. A total of 40 RBC miRNAs were differentially expressed in the Tibetan population (15 upregulated and 25 downregulated) compared with the Tibet Han population. Two significantly altered miRNAs with the highest expression levels (miRNA-144-5p and miR-30b-5p) were selected for real-time PCR analysis, and the results were consistent with those of miRNA sequencing. Furthermore, bioinformatic analyses showed that some potential target genes of miR-144-5p and miR-30b-5p are involved in the erythroid- hypoxia-, and nitric oxide (NO)-related signaling pathways in response to hypoxia.
Conclusion: Our findings provide clear evidence, for the first time, that a high-altitude hypoxic environment significantly affects human RBC miRNA profiles.

overall_design: The RBC samples were separately pooled to produce three sample pools of the Sichuan Han, Tibet Han and Tibetan populations. We globally analyzed RBC miRNA expression profiles from the three RBC samples using miRNA sequencing.

first: Deqing

last: Wang


title: Impact of cecal ligation and puncture (CLP) on splenic NK1.1+CD3- gene expression [RNA-seq]

city: Iowa City

first: Isaac

middle: J

last: Jensen

state: IA

institute: University of Iowa

summary: NK cell transcriptome comparison of Day 2 Sham and Days 1,2 CLP

overall_design: Mice underwent either Sham (control) or cecal ligation and puncture (CLP) surgery. Splenic NK cells (NK1.1+CD3-) were sorted from Sham hosts 2 days after surgery and from CLP hosts 1 and 2 days after surgery. Sorted cells were used for RNAseq analysis

first: Vladimir

middle: P

last: Badovinac


title: Antioxidant metabolism in activated CD8+ T cells regulates stem-like human memory T cell formation and anti-tumor immunity

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: Adoptive T cell transfer (ACT) immunotherapy benefits from early-differentiated memory stem-like T (TSCM) cells capable to persist in the long term and to generate potent anti-tumor effectors. Due to their paucity ex vivo, TSCM can be derived from less differentiated naïve precursors but the molecular signals at the basis of their generation are ill-defined. We found that less differentiated human circulating CD8+ T cells display substantial antioxidant capacity ex vivo compared to more differentiated central and effector memory T cells. Limiting reactive oxygen species (ROS) metabolism with anti-oxidants during naïve T cell activation hindered terminal differentiation while allowing expansion and generation of TSCM cells. N-acetylcysteine, the most effective in this regard, induced a transcriptional network and a metabolic profile characteristic of self-renewing memory T cells. Upon ACT, the generated TSCM cells established long-term immunity in vivo and exerted more potent anti-tumor immunity in a xenogeneic model when redirected with CD19 CAR, highlighting the translational relevance of NAC as a simple and inexpensive method to improve ACT

overall_design: mRNA profiles of human CD8 T cells after 8 days of cell culture with or without N-acetyl cysteine (NAC)

first: Karolina

last: Pilipow

first: Eloise

last: Scamardella

first: Simone

last: Puccio

first: Emilia

first: Luca

last: Gattinoni

first: Enrico

last: Lugli


title: Promoter-enhancer communication occurs primarily within Gene Unit Sub-TADs (GUSTs)

city: Los Angeles

first: Siavash

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mammalian genome is sequentially partitioned from chromosomes into looped chromatin regions termed Topologically Associating Domains (TADs), and then into numerous smaller sub-TAD loops, each bounded and insulated by CTCF and Cohesin. The sub-TADs encompass enhancers, promoters and often multiple genes but whether promoter-enhancer interactions and gene regulation are broadly restricted to within the sub-TAD loops has not been functionally determined. Here we identify “Gene Unit Sub-TADs” or GUSTs as a class of sub-TADs that confine promoter-enhancer interactions and demarcate functional gene regulatory regions. We depleted Estrogen-related receptor β (Esrrb), which binds to the Mediator co-activator complex, to impair the activity of enhancers controlling 245 mouse embryonic stem cell genes. We find that most Esrrb-responsive enhancers lack significant Cohesin binding but instead correlate with Mediator binding. Esrrb depletion causes reduced Mediator binding, decreased nascent RNA expression and diminished promoter-enhancer looping. In 88% of the cases examined, the effects of Esrrb depletion are restricted to enhancers and target genes within GUSTs. In some GUSTs, active genes lay alongside inactive ones but are distinguished by their proximal promoter chromatin accessibility, explaining further the specificity of enhancer-promoter interactions within GUSTs. Our data indicate that GUSTs represent functional gene regulons in mammalian genomes.

overall_design:
Systematic analysis on how enhancer inactivation by Esrrb knockdown affects gene expression in a GUST. All treatments contain 2 biological replicates except for Smc1 ChIP-seq and Nascent RNA-seq.
Please note that the processed data generated from merged replicates are available as Series supplementary files.

first: Fei

first: Constantinos

last: Chronis

first: Kathrin

last: Plath

first: Michael

last: Carey


title: Age-related loss of innate immune antimicrobial function of dermal fat is mediated by TGFβ

status: Public on Oct 18 2018

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: Dermal fibroblasts (dFB) resist infection by locally differentiating into adipocytes and producing the antimicrobial peptide cathelicidin in response to S. aureus. We found that neonatal dFB were highly adipogenic whereas this adipogenic function was lost during adulthood. To better understand the molecular nature of the change in antimicrobial and adipogenic function of dFB, we profiled the transcriptomes of primary dFB isolated at different ages by RNA-seq. RNA-seq identified the pro-adipogenic to pro-fibrotic gene signature switch in dFB during aging, and identified TGF-beta as the top up-regulated pathway that was activated in 2M dFB compared to neonatal P1 dFB.

overall_design: Examination of differentially expressed genes in cultured primary dermal fibroblasts/pre-adipocytes isolated from mouse skin with various ages.

first: Ling-juan

last: Zhang

first: Richard

last: Gallo

first: Christian

last: Guerrero-Juarez


title: IRE1α-XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Tumors evade immune control by creating hostile microenvironments that perturb T cell metabolism and effector function. However, it remains unclear how intratumoral T cells integrate and interpret metabolic stress signals. Here we report that ovarian cancer (OvCa), an aggressive malignancy refractory to standard treatments and current immunotherapies, induces Endoplasmic Reticulum (ER) stress and activation of the IRE1α-XBP1 arm of the Unfolded Protein Response (UPR)10,11 in T cells to control their mitochondrial respiration and anti-tumor function. XBP1 upregulation in T cells isolated from human OvCa specimens was associated with decreased intratumoral T cell infiltration and reduced IFNG mRNA expression. Malignant ascites fluid obtained from OvCa patients inhibited glucose uptake and caused N-linked protein glycosylation defects in T cells, leading to IRE1α/XBP1-driven suppression of mitochondrial activity and IFN- production. Mechanistically, XBP1 induction limited the influx of glutamine necessary to sustain T cell mitochondrial respiration under glucose-deprived conditions by regulating the abundance of glutamine carriers. Restoring N-linked protein glycosylation, abrogating IRE1α-XBP1 activation or enforcing expression of glutamine transporters enhanced mitochondrial respiration in human T cells exposed to OvCa ascites. XBP1-deficient T cells in the metastatic OvCa milieu exhibited global transcriptional reprogramming and improved effector capacity. Accordingly, OvCa-bearing mice lacking XBP1 selectively in T cells demonstrated superior anti-tumor immunity, delayed malignant progression and increased overall survival. Therefore, controlling ER stress or targeting IRE1α-XBP1 signaling may help restore T cell metabolic fitness and anti-tumor capacity in cancer hosts.

overall_design: RNA-seq in XBP1 WT and KO CD4 tumor infiltrating Tcells

first: Juan

last: Cubillos-Ruiz

first: Minkyung

last: Song


title: Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to ER-directed therapies

first: Ofir

last: Cohen

state: Massachusetts

address: 415 Main St, Cambridge, MA 02142

department: Cancer Program

institute: Broad Institute

summary: Estrogen receptor positive (ER+) breast cancers that develop resistance to therapies that target the ER are the most common cause of breast cancer death. Beyond mutations in ER, which occur in 25-30% of patients treated with aromatase inhibitors (AIs), our understanding of clinical mechanisms of resistance to ER-directed therapies remains incomplete. We identified activating HER2 mutations in metastatic biopsies from eight patients with ER+ metastatic breast cancer who had developed resistance to ER-directed agents, including AIs, tamoxifen, and fulvestrant. Examination of treatment-naïve primary tumors in five patients revealed no evidence of pre-existing mutations in four of five patients, suggesting that these mutations were acquired under the selective pressure of ER-directed therapy. These mutations were mutually exclusive with ER mutations, suggesting a distinct mechanism of acquired resistance to ER-directed therapies. In vitro analysis confirmed that these mutations conferred estrogen independence. In addition, and in contrast to ER mutations, these mutations resulted in resistance to tamoxifen, fulvestrant, and the CDK4/6 inhibitor palbociclib. Resistance was overcome by combining ER-directed therapy with the irreversible HER2 kinase inhibitor neratinib, highlighting an effective treatment strategy in these patients.

overall_design: Examination of the transcriptional output (mRNA) of  the HER2 activating mutations compared with controls under various drugs. Specifically, we expressed the activating mutations S653C, L755S, V777L, and L869R  in ER+/HER2- breast cancer cell line (T47D), and controls (GFP, wild-type HER2, kinase-dead HER2, and ESR1 Y537S). Cell were then treated with DMSO, 1μM fulvestrant, 1μM neratinib, 10μM palbociclib, 1μM fulvestrant + 1μM neratinib, or 1μM fulvestrant + 10μM palbociclib for 24 hours. All experimental conditions were done in 6 replicates, sequenced in 3 replicates

first: Utthara

last: Nayar

first: Wagle

last: Nikhil


title: Epigenetic intersection of BDNF Val66Met genotype with premenstrual dysphoric disorder transcriptome in a cross-species model of estradiol add-back

city: New York

first: Nathan

last: Einhorn

state: NY

address: 1230 York Avenue

department: Laboratory of Neuroendocrinology

institute: The Rockefeller University

summary: Ovariectomized BDNF Val66Met mice, a model that is genetically susceptible to stress, exhibited anxiety- and depression-like behavior when treated with estradiol when compared to wild type mice. Comparing ventral hippocampus of these mice with lymphoblastoid cell line cultures of control women and women with prementrual dysphoric disorder revealed common epigenetic biomarkers that transcend species and cell-type.

overall_design:
Examination of the effects of estradiol and a SNP in the ventral hippocampus of ovariectomized female mice and the translational similarities with healthy women and women diagnosed with PMDD. Human data is sourced from Dubey et al. 2017 (doi: 10.1038/mp.2016.229) and will not be apart of this upload. It can be accessed upon reasonable request to the authors
VV/WT = Wild Type, VM/Het-Met = Heterozygous BDNF Val66Met , E2 = Estradiol, Veh = Vehicle, OVX = Ovariectomized

first: Jordan

last: Marrocco

first: Bruce

last: McEwen


title: A peninsular structure coordinates asynchronous differentiation with morphogenesis to generate pancreatic islets

city: Seattle

first: Raghav

last: Chawla

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: This scRNA-seq data is an integral part of a manuscript with the above title. Using computational methods, we were able to reconstruct a detailed branched trajectory reflecting pancreatic endocrine differentiation in the mouse embryo. Analysis of the transcriptional changes occuring during the differentiation suggested that epithelial-to-mesenchymal transition likely plays no role in this process, contrary to the prevailing dogma. Our findings were corroborated with high-resolution imaging of the developing pancreas, revealing how differentiating endocrine progenitors migrate in cohesion, forming bud-like islet precursors, or "peninsulas", and that spatiotemporal collinearity during differentiation leads to the typical core-mantle architecture of the mature, spherical islet. This work led to a complete overhaul of our understanding of how pancreatic islets are developed, laying the ground for the generation of entire islets in vitro as a potential novel source of islet transplantation.

overall_design: Single-cell suspensions were prepared from pancreata of Neurogenin 3-eGFP mouse embryos sacrificed at different days of embryonic development. Single eGFP-positive cells were FACS-sorted into 96-well plates, and single-cell cDNA was prepared using the SMART-seq protocol. Single-cell sequencing libraries were generated using the Nextera XT DNA library preparation kit and sequenced on an Illumina HiSeq sequencer. Reads were aligned to the mouse reference genome build mm10 with TopHat, and single-cell gene expression profiles were computed using Cufflinks.

first: R

first: N

last: Sharon

first: C

last: Trapnell

first: D

last: Melton


title: HP1γ is required for G9a/GLP coactivator function with the glucocorticoid receptor in Nalm6 cells

first: Brian

middle: Hae Kang

last: Lee

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Using a genome-wide analysis, we demonstrated that HP1γ is selectively required for GC-regulated expression of GR target genes that require G9a and GLP, consistent with our previous finding that automethylated G9a and GLP recruit HP1g to specific genomic GR binding sites.

overall_design: We examined whether HP1g is required for GC-induced expression of the genes that require coactivators, G9a and GLP, by depleting HP1g, G9a and GLP in Nalm6 cells using shRNA and examined gene expression changes at 8 hour dexamethasone (dex) treatment compared with ethanol treatment as a control.  shRNA for a nonspecific sequence (shNS) followed by 8h of dex treatment was performed as control.

first: Coralie

last: Poulard

first: Michael

last: Stallcup


title: Splicing and epigenetic factors jointly regulate epidermal differentiation

city: Nijmegen

first: Klaas

last: Mulder

address: Geert Grooteplein 28

institute: RIMLS

summary: We report the effects of silencing SRSF1 or ZMAT2 in human epidermal stem cells on the transcriptome of epidermal stem cells. We found that silencing ZMAT2 or SRSF1 affects global splicing, however, ZMAT2 seems to regulate splicing of a smaller more specific subset of genes.

overall_design: RNA-sequencing data following silencing SRSF1 or ZMAT2

first: Sabine

middle: E

last: Tanis


title: STVI-120 Induction of differentiation in human epidermal stem cells followed by differential splicing analysis

summary: We report the effects of induction of differentiation in human epidermal stem cells on the splicing of the transcriptome.

overall_design: RNA-sequencing data following induction of differentiation in human epidermal stem cells


title: Small RNA sequencing of sessile serrated polyps identifies miRNA profile associated with colon cancer

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: RNA sequencing analysis of small RNA expression in sessile serrated adenoma/polyps, hyperplastic polyps, adenomatous polyps, uninvolved colon and control colon

overall_design: 108 RNA sequencing datasets from RNAlater preserved clinical biopsies (16 sessile serrated adenomoas/polyps, 14 hyperlastic polyps, 14 adenomatous polyps, 34 uninvolved colon and 30 control colon samples)

first: Don

last: Delker

first: Priyanka

last: Kanth


title: Non-coding regions are the main source of tumor-specific antigens [human]

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

country: Canada

institute: Institute for Research in Immunology and Cancer

summary:
Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies.
Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq2000. Using those RNA-Sequencing data to build a global cancer database for each sample, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs.
Results: We identified a total of 30 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, most of these TSAs derived from non-mutated yet cancer-restricted transcripts that can be shared by multiple tumors.
Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

overall_design: Transcriptomic analysis of 7 human primary tumor samples using the Illumina HiSeq 2000.

first: Céline

last: Laumont

first: Claude

last: Perreault


title: Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

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

overall_design: Refer to individual Series


title: Non-coding regions are the main source of tumor-specific antigens


title: Mechanosensitive ion channel regulates tissue stiffening to promote glioma aggression

city: Toronto

first: Xi

last: Huang

address: 686 Bay Street,

institute: SickKids

summary: Tissue stiffening is a physical hallmark of solid tumor. In our study, we found that the mechanosensitive ion channel PIEZO1 can be tumor cells force sensor and transducer that regulate the altered tissue mechanics. We examined the transcriptional changes modulated by depletion of PIEZO1 in two human GBM cell lines. We found that with PIEZO1 KD, the components involved in ECM organization, focal adhesion formation, cytoskeleton, and mitosis, which contribute to tissue stiffness, are down-regulated.

overall_design: RNA-Seq of G508 and G532 human GBM cell lines treated with scrambled shRNA, PIEZO1 shRNA #1, PIEZO1 shRNA #2, in triplicates.

first: Xin

last: Chen

first: Wen-Chi

last: Yin


title: ChIP-sequencing to investigate occupancy of wild-type and fusion ZNF384 proteins in murine pre-B cells

summary: We report the changes in chromatin occupancy between HA-tagged wild-type ZNF384 and the two leukemogenic fusion proteins, TAF15-ZNF384, and TCF3-ZNF384, in Arf-/- pre-B cells. Using ChIP-sequencing we found that 2298 peaks have new or increased binding while 495 peaks have decreased or lost binding of the fusion proteins compared to wild-type ZNF384.

overall_design: 2 technical replicates of 3 genetically-modified cells lines

first: Charles

middle: G

last: Mullighan

first: Kirsten

last: Dickerson


title: Comparing the effects of low protein, high carbohydrate diets and caloric restriction on brain aging in mice.

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

summary: Calorie restriction (CR) increases lifespan and improves brain health in mice. Ad libitum low protein, high carbohydrate (LPHC) diets also extend lifespan, but it is not known whether they are beneficial for brain health. We compared hippocampus biology and memory in mice subjected to 20% CR or provided ad libitum access to one of three LPHC diets, or to a control diet. At age 15 months, patterns of RNA expression in the hippocampus were similar between CR and LPHC diets for genes associated with longevity, cytokines and dendrite morphogenesis. Nutrient sensing proteins including SIRT1, mTOR and PGC1α were also influenced by diet, however the effects varied by sex. CR and LPHC diets were associated with increased dendritic spines in dentate gyrus neurons. CR and LPHC diets led to modest improvements in the Barnes Maze and Novel Object Recognition. LPHC diets recapitulate some of the benefits of CR on brain aging.

overall_design: 30 samples, 6 biological replicates in each group.


title: Patient iPSC-derived neural stem cells display progressive enlargement of lysosomes and disruptions of glycosaminoglycan pathway and autophagy in concordance with clinical severity of Mucopolysaccharidosis I

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Mucopolysaccharidosis type I (MPS I) is caused by genetic defects in alpha-L-iduronidase (IDUA), a lysosomal enzyme involved in the breakdown and recycling of glycosaminoglycans (GAGs). Although an enzyme replacement therapy is available, the efficacy for the treatment of neuropathic symptoms is limited. To facilitate drug discovery and model disease pathophysiology, we have generated neural stem cells (NSCs) from MPS I patient-derived iPSCs. NSCs exhibited characteristic disease phenotypes with deficiency of alpha-L-iduronidase (IDUA), accumulation of glycosaminoglycans (GAGs) and enlargement of lysosomes, correlating with the severity of clinical symptoms. Transcriptome profiling of NSCs revealed differential expression of 429 genes that changed more extensively in the more severe Hurler syndrome subgroup compared to the Hurler-Scheie (median severe) and Scheie (less severe) subgroups. Clustering and pathway analyses demonstrated high concordance of the severity of neurological defects with marked dysregulation of GAG biosynthesis and degradation, lysosomal function and extracellular matrix. Gene Ontology (GO) analysis identified a dramatic upregulation of autophagy pathway, especially in the Hurler syndrome. Thus, GAG accumulation in the patient cells disrupts lysosomal homeostasis affecting multiple related cellular pathways which compensates for IDUA deficiency. These dysregulated process likely lead to enhanced autophagy and more severe disease states. Our studies provide useful tools for clinical biomarker development and potential targets for drug development.

overall_design: Patient iPSC-derived and control neural stem cells from Scheie, Hurler-Scheie, and Hurler disease were expression profiled in triplicate using RNA-seq.

first: Manju

last: Swaroop

first: Linn

last: Gieser

first: Anand

first: Wei

last: Zheng


title: Chd2 is necessary for neural circuit development and long-term memory

first: Robert

last: Hunt

address: 110 Irvine Hall

summary: Considerable evidence suggests loss of function mutations in the chromatin remodeler, CHD2, contribute to a broad spectrum of human neurodevelopmental disorders. However, it is unknown how CHD2 mutations lead to impaired brain function. Here we report mice with heterozygous mutations in Chd2 exhibit deficits in neuron proliferation and a shift in neuronal excitability that included divergent changes in excitatory and inhibitory synaptic function. Further in vivo experiments show Chd2+/- mice displayed aberrant cortical rhythmogenesis and severe deficits in long-term memory, consistent with phenotypes observed in humans. We identified broad, age-dependent transcriptional changes in Chd2+/- mice, including alterations in neurogenesis, synaptic transmission and disease-related genes. Deficits in interneuron density and memory caused by Chd2+/- were reproduced by Chd2 mutation restricted to a subset of inhibitory neurons and corrected by interneuron transplantation. Our results provide initial insight into how Chd2 haploinsufficiency leads to aberrant cortical network function and impaired memory.

overall_design: We examined RNA expression levels between Chd2+/- and WT from E13.5 MGE, E13.5 cortex, and P45 Hippocampus.

first: Young

last: Kim

first: Sattar

last: Khoshkhoo

first: Jan

middle: C

last: Frankowski

first: Bingyao

last: Zhu

first: Saad

last: Abbasi

first: Sunyoung

last: Lee

first: Ye

last: Wu


title: Chromatin association sites of KSHV and RRV PAN RNA

status: Public on Oct 17 2018

city: New Haven

first: Johanna

middle: B

last: Withers

state: CT

address: 295 Congress Ave

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: During lytic replication of Kaposi’s sarcoma-associated herpesvirus (KSHV), a nuclear viral long noncoding RNA known as PAN RNA becomes the most abundant polyadenylated transcript in the cell. Knockout or knockdown of KSHV PAN RNA results in loss of late lytic viral gene expression and, consequently, reduction of progeny virion release from the cell. We studied KSHV and RRV PAN RNA homologs using capture hybridization analysis of RNA targets (CHART) and observed their reproducible associations with host chromatin, but the loci differ between PAN RNA homologs.

overall_design: Examination of the binding sites of viral PAN RNA in KSHV-infected BCBL-1 cells and RRV-infected BJAB-RRV cells. Latent samples, as well as three timepoints of lytic viral induction were analyzed for each cell type (BCBL-1: 16 hr, 24 hr and 48 hr; BJAB-RRV: 18 hr, 24 hr, 36 hr).

first: Eric

last: Li

first: Tenaya

last: Vallery

first: Therese

last: Yario

first: Joan

last: Steitz


title: Crebbp loss drives small cell lung cancer and increases sensitivity to HDAC inhibition [thyroid]

first: David

last: MacPherson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: This study assessed tumor suppressor roles of CREBBP in SCLC and other neuroendocrine tumors. Genetically engineered mouse models were used to determine the tumor suppressor role of Crebbp in SCLC and other neuroendocrine tumors.

overall_design: Identification of differentially expressed genes regulated by Crebbp using primary thyroid tumors derived from genetically engineered mouse model.

first: Deshui

last: Jia


title: Crebbp loss drives small cell lung cancer and increases sensitivity to HDAC inhibition [preSC cell line]

overall_design: Identification of differentially expressed genes regulated by Crebbp using preSC cells with lentivral shRNA expression.


title: Crebbp loss drives small cell lung cancer and increases sensitivity to HDAC inhibition [SCLC]

overall_design: Identification of differentially expressed genes regulated by Crebbp using primary SCLC tumors derived from genetically engineered mouse model.


title: RNA-Seq of juvenile and early adolescent muscle

status: Public on Oct 16 2018

city: Rochester

first: Joe

last: Chakkalakal

address: 601 Elmwood Avenue, Box 711

institute: University of Rochester

summary: We report significant differences in muscle gene expression during postnatal development (4-8 weeks), especially in regards to ECM content, AMPK signalling, and calcium handling.

overall_design: RNA was isolated from gastrocnemius muscle of 4, 6, and 8- week mice. RNA Seq was performed to look at differences in gene expression.

first: John

middle: F

last: Bachman


title: Targeting of Hematologic Malignancies with PTC299, A Novel Potent Inhibitor of Dihydroorotate Dehydrogenase with Favorable Pharmaceutical Properties

city: Bridgewater

first: Wencheng

state: NJ - New Jersey

institute: PTC Therapeutics

summary: PTC299 was identified as an inhibitor of VEGFA mRNA translation in a phenotypic screen and evaluated in the clinic for treatment of solid tumors. To guide precision cancer treatment, we performed extensive biological characterization of the activity of PTC299 and demonstrated that inhibition of VEGF production and cell proliferation by PTC299 is linked to a decrease in uridine nucleotides by targeting dihydroorotate dehydrogenase (DHODH), a rate limiting enzyme for de novo pyrimidine nucleotide synthesis. Unlike previously reported DHODH inhibitors that were identified using in vitro enzyme assays, PTC299 is a more potent inhibitor of DHODH in isolated mitochondria suggesting that mitochondrial membrane lipid engagement in the DHODH conformation in situ is required for its optimal activity. PTC299 has broad and potent activity against hematological cancer cells in preclinical models, reflecting a reduced pyrimidine nucleotide salvage pathway in leukemia cells. Archived serum samples from patients treated with PTC299 demonstrated increased levels of dihydroorotate, the substrate of DHODH, indicating target engagement in patients. PTC299 has advantages over previously reported DHODH inhibitors, including greater potency, good oral bioavailability and lack of off-target kinase inhibition and myelosuppression, and thus may be useful for the targeted treatment of hematologic malignancies.

overall_design: Transcriptome profiling of PTC299-resistant and parent HT1080 cells using Affymetrix Human Genome U133 plus 2.0 Array. Four replicates of cells for each cell type were performed.

first: Liangxian

last: Cao

first: Marla

last: Weetall

first: Christopher

last: Trotta

first: Katherine

last: Cintron

first: Jiyuan

last: Ma

first: Min

first: Bansri

last: Furia

first: Charles

last: Romfo

first: Jason

middle: D

last: Graci

first: Joshua

last: Du

first: Josephine

last: Sheedy

first: Jean

last: Hedrick

first: Nicole

last: Risher

first: Shirley

last: Yeh

first: Hongyan

last: Qi

first: Tamil

last: Arasu

first: Seongwoo

last: Hwang

first: William

last: Lennox

first: Ronald

last: Kong

first: Janet

last: Petruska

first: Young-Choon

last: Moon

last: Babiak

first: Thomas

last: Davis

first: Allan

last: Jacobson

first: Neil

last: Almstead

first: Art

last: Branstrom

first: Joseph

middle: M

last: Colacino

first: Stuart

last: Peltz


title: Non-coding regions are the main source of tumor-specific antigens [mouse]

first: Krystel

last: Vincent

summary:
Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in two murine cell lines, namely EL4 and CT26 cells.
Methods: We performed RNA-Sequencing on both tumor cell lines (unreplicated) as well as on the syngeneic mature medullary thymic epithelial cells (mTEChi, in triplicate), using either the Illumina HiSeq200 or the Illumina NextSeq 500. Using those RNA-Sequencing data to build a global cancer database for each tumor cell line, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs.
Results: We identified a total of 21 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, about 70% of these TSAs derived from non-mutated yet cancer-restricted transcripts (e.g., endogenous retroelements) that can be shared by multiple tumors.
Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

overall_design: Transcriptomic analysis of EL4 and CT26 tumor cell lines (unreplicated) using the Illumina HiSeq 2000. C57BL/6 mTEChi were extracted from the thymi of 2 female and 2 male 5-8 week-old C57BL/6 mice and sequenced in triplicate using the Illumina HiSeq2000. Finally, Balb/c mTEChi were extracted from the thymi of 2 female and 2 male 5-8 week-old Balb/c mice and sequenced (in triplicate) on an Illumina NextSeq 500.

first: Céline

last: Laumont

first: Claude

last: Perreault


title: Crebbp loss drives small cell lung cancer and increases sensitivity to HDAC inhibition [pituitary tumor]

first: David

last: MacPherson

overall_design: Identification of differentially expressed genes regulated by Crebbp using primary pituitary tumors derived from genetically engineered mouse model.

first: Deshui

last: Jia


title: Expression data of extracellular vesicles from kaposi's sarcoma associated herpesvirus- or mock- infected human endothelial cells treated human endothelial cell

city: Daejeon

first: Hyungtaek

last: Jeon

address: 77 GYERYONG-RO 771BEON-GIL, JUNG-GU

department: school of medicine, Dept. of microbiology and immunology

country: South Korea

institute: Eulji University

summary:
Kaposi’s Sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma, which is the most common cancer in acquired immune deficiency syndrome patients. Because KSHV has many viral proteins modulate many response, However, various effects by extracellular vesicles (EVs) during de novo KSHV infection has not been investigated to our best knowledge.
We used microarrays to detail of gene expression underlying EV treatment and identified the up-regulated genes during treatment.

overall_design: Human umbilical vein endothelial cells were cultured for RNA extraction and hybridization on Affymetrix microarrays.

first: Myung-Shin

last: Lee


title: Unraveling the transcriptional regulation of TWIST1 in limb development

status: Public on Oct 15 2018

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary: 4C-seq on mouse  E11.5  limb and branchial arches

overall_design: We used 4C-seq to characterize active enhancers in the TWIST1-HDAC9 locus in the developing limb and branchial arches.

first: Ramon

last: Birnbaum

first: Naama

last: Hirsch

first: Fania

last: Shemuluvich

first: Darío

last: Lupiáñez

first: Noam

last: Levaot

first: Reut

last: Eshel

last: Bar Yaacov


title: Transcriptome measurements after knocking out the UMLILO lncRNA

city: Cape Town

first: Musa

last: Mhlanga

address: Anzio Road

department: Faculty of Health Sciences

country: South Africa

institute: University of Cape Town

summary:
Purpose: Assess whether knocking out the UMLILO lncRNA altered the expression of genes transcribed within the CXCL chemokine TAD
Outcome:  To confirm whether the effect of UMLILO was limited to the CXCL TAD. Adeno-associated viral vectors (AAVs) were constructed that contain CRISPR/Cas9 and guides targeting UMLILO to delete the full length UMLILO transcript. RNAseq was performed on a transduced THP-1 population to verify genome-wide effects of UMLILO depletion. This revealed that IL8, CXCL1, 2, 3 transcription was abrogated, but a similar effect was not seen for genes located outside of the CXCL TAD boundary

overall_design: AAVs were constructed that contain CRISPRs that harness non homologous end joining (NHEJ) to target UMLILO by deleting the genomic region encoding UMLILO, but not its promoter. The THP-1 monocytic cell line was transduced with the AAVs containing the CRISPRs for 1.5 weeks. Controls were transduced with AAV vector plasmids expressing SpCas9.

first: Stephanie

last: Fanucchi


title: Transciptomic profiling of human fetal lung samples

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

summary: Fibroblast Growth Factor (FGF) signaling plays an important role in lung organogenesis. Over recent decades, FGF signaling in lung development has been extensively studied in animal models. However, little is known about the expression, localization and functional roles of FGF ligands during human fetal lung development. Therefore, we aimed to determine the expression and function of several FGF ligands and receptors in human lung development. Using in situ hybridization (ISH) and RNA-sequencing, we assessed their expression and distribution in native human fetal lung. Human fetal lung explants were treated with recombinant FGF7, FGF9 or FGF10 in air-liquid interface culture. Explants were analyzed grossly, to observe differences in branching pattern, as well as at the cellular and molecular level. ISH demonstrated that FGF7 is expressed in both the epithelium and mesenchyme; FGF9 is mainly localized in the distal epithelium, whereas FGF10 demonstrated diffuse expression throughout the parenchyma with some expression in the smooth muscle cells (SMCs). FGFR2 expression was high in both proximal and distal epithelial cells as well as the SMCs. FGFR3 was expressed mostly in the epithelial cells, with lower expression in the mesenchyme, while FGFR4 was highly expressed throughout the mesenchyme and in the distal epithelium. Using recombinant FGFs, we demonstrated that FGF7 and FGF9 had similar effects on human fetal lung as on mouse; however, FGF10 caused the human explants to expand and form cysts as opposed to inducing epithelial branching as seen in the mouse. In conjunction with decreased branching, treatment with recombinant FGF7, FGF9 and FGF10 also resulted in decreased double-positive SOX2/SOX9 progenitor cells, which are exclusively present in the distal epithelial tips in early human fetal lung. Although FGF ligand localization may be somewhat comparable between developing mouse and human lungs, their functional roles may differ substantially.

overall_design: Excised piece of human fetal lung samples containing proximal and distal compartments

first: Soula

last: Danopoulos

first: Matthew

last: Thornton

first: Denise

last: Al Alam


title: Assaying RNA Structure with LASER-seq

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: structure probing of ribosomes

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Homo sapiens

overall_design: Purified and in-vivo ribosomes are probed with Naz to identify structural features

first: Dalen

last: Chan

first: Whitney

last: England

first: Chao

last: Feng

first: Rachel

last: Green

first: Robert

last: Spitale


title: Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

status: Public on Oct 24 2018

city: San Francisco

first: Leqian

last: Liu

address: 1700 4th street

department: BTS

institute: UCSF

summary: Cell suspensions were prepared from mouse lungs dissociated at baseline or 14 days after intratracheal bleomycin injury, and single cell mRNA-seq libraries were generated with Drop-seq.

overall_design: Drop-seq was performed on single cell suspensions from lungs of 3 bleomycin-treated and 6 control mouse mice.

first: Mallar

last: Bhattacharya

first: Looney

last: Agnieszka

first: Dvir

last: Aran


title: LncRNA-directed Antigenicity Loss Suppresses Immunosurveillance

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: Expression profiles of mouse breast cancer tissues and mammary gland tissues.

overall_design: Expression profiles were generated from mouse breast cancer tissues and mammary gland tissues, isolated from 5 month old female FVB/NJ; MMTV-Tg (LINK-A) and FVB/NJ; Tg(LINK-A) mice.

first: Qingsong

last: Hu


title: Nut is a cell type-specific stimulator of p300 enhancing H4 hyperacetylation during haploid male genome programming

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: NUT, nuclear protein in testis is the universal fusion partner of BRD4 in the highly aggressive NUT Midline Carcinoma (NMC), but its physiological function is unknown. Here we show that Nut is exclusively expressed in post-meiotic spermatogenic cells, at the time of genome-wide histone hyperacetylation. Inactivation of Nut induces a spermatogenesis arrest at the histone-to-protamine replacement stage, leading to male infertility. Subsequent molecular investigations show that Nut sustains global histone H4 hyperacetylation in post-meiotic cells. Additionally, Nut mediates a p300/CBP-dependent gene expression program and, by enhancing acetylation of H4 at both K5 and K8 sites, provides binding sites for the first bromodomain of Brdt, which drives histone removal. Our results bring the first evidence of Nut’s function in spermatogenic cells where it uses the ubiquitous HATs p300/CBP to direct a cell-type specific histone H4 hyperacetylation. The ectopic activity of Nut in NMC recreates a forced p300-induced histone hyperacetylation / bromodomain-binding loop that normally operates in post-meiotic spermatogenic cells.

overall_design: MNase-Seq in round-elongating spermatids from WT and Nut-KO mice

first: Thierry

last: Buchou

last: Barral

first: Guillaume

last: Charbonnier

first: Denis

last: Puthier

first: Florent

last: Chuffart

first: Ekaterina

last: Bourova-Flin

first: Saadi

last: Khochbin


title: RNA-sequencing to investigate transcriptional changes caused by ZNF384 fusion proteins in murine pre-B cells

first: Beisi

last: Xu

summary: RNA-sequencing was performed on Arf-/- pre-B cell expressing either wild-type ZNF384, TAF15-ZNF384, or TCF3-ZNF384. We found that pre-B cells that express ZNF384 fusion proteins have a gene expression profile similar to patients with ZNF384-rearranged leukemia.

overall_design: 2 biological replicates of 3 genetically-modified cells lines

first: Charles

last: Mullighan

first: Kirsten

last: Dickerson


title: Adult Connective Tissue-Resident Mast Cells Originate from Late Erythro-Myeloid Progenitors [development]

city: Hangzhou

first: ZHI

middle: QING

last: LI

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

summary:
Purpose: The purpose is to systemically identify RNA expression changes along mast cell development during embryogenesis.
Methods: We profiled RNA-seq in early EMPs and their progeny.
Results: Fetal MCPs acquire the mast cell-specific gene signature from E11.5 and complete their maturation in peripheral tissues.

overall_design: Early EMP-derived MCPs/mast cells and macrophages during embryogenesis were sorted using Csf1r-iCre fate-mapping model and then subjected to RNA-seq.

first: Xuetao

last: Cao

first: Zhiqing

last: Li


title: Caveolin-1 modulates mechanotransduction responses to substrate stiffness through actin-dependent control of YAP

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: The transcriptional regulator YAP orchestrates important cell functions, determining tissue homeostasis, organ growth control, and tumorigenesis. Mechanical stimuli are a key input to YAP activity, but the mechanisms controlling this regulation remain largely uncharacterized. We show that CAV1 positively modulates the YAP mechanoresponse to substrate stiffness through actin cytoskeleton-dependent and Hippo kinase-independent mechanisms. RHO activity is necessary but not sufficient for CAV1-dependent mechanoregulation of YAP activity. Systematic quantitative interactomic studies and image-based siRNA screenings provide evidence that this actin-dependent regulation is determined by YAP interaction with the 14-3-3 protein YWHAH. Constitutive YAP activation rescued phenotypes associated with CAV1 loss, including defective ECM remodeling. CAV1-mediated control of YAP activity was validated in vivo in a model of pancreatitis-driven acinar-to-ductal metaplasia. We propose that this CAV1-YAP mechanotransduction system controls a significant share of cell programs linked to these two pivotal regulators, with potentially broad physiological and pathological implications.

overall_design: RNA-Seq in WT and Cav1KO mouse embryonic fibroblasts (MEFs) cultured on stiff or soft polyacrylamide hydrogels

first: R

last: Moreno-Vicente

first: DM

last: Pavón

first: I

last: Martín-Padura

first: M

last: Català-Montoro

first: A

last: Díez-Sánchez

last: Quílez-Álvarez

first: JA

last: López

last: Sánchez-Álvarez

first: J

last: Vázquez

last: Strippoli

first: MA

last: del Pozo


title: Rif1 inhibits replication fork progression and controls copy number in Drosophila.

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

summary: Control of DNA copy number is essential to maintain genome stability and ensure proper cell and tissue function. In Drosophila, the SNF2-domain-containing SUUR protein inhibits replication fork progression within specific regions of the genome to promote DNA underreplication. While dissecting the function of SUUR’s SNF2 domain, we identified a physical interaction between SUUR and Rif1. Rif1 has many roles in DNA metabolism and regulates the replication timing program. We demonstrate that repression of DNA replication is dependent on Rif1. Rif1 localizes to active replication forks in an SUUR-dependent manner and directly regulates replication fork progression. Importantly, SUUR associates with replication forks in the absence of Rif1, indicating that Rif1 acts downstream of SUUR to inhibit fork progression. Our findings uncover an unrecognized function of the Rif1 protein as a direct regulator of replication fork progression suggesting developmental regulation of Rif1 activity.

overall_design: Copy number profiles from third instar salivary gland DNA in WT, SuUR, SuUR(deltaSNF) and Rif1 mutants. Once replicate is included for WT, SuUR and SuUR(deltaSNF). Two replicates are included for the Rif1 mutant. Additionally, copy number profile of stage 13 egg chamber DNA. One replicate for WT and SuUR mutant. Two replicates for Rif1 mutant.

middle: T

first: Alex

last: Munden


title: Expression data from Human Pre-implantation embryos

city: manchester

first: Helen

middle: Louise

last: Smith

address: oxford road

institute: The University of Manchester

summary:
Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the preimplantation embryo’s outer trophectoderm (TE) layer, involved in implantation, while maintaining the inner cell mass (ICM) stem cell population.
Using multiple systems biology approaches to compare developmental stages in the early human embryo with single cell transcript data from blastomeres, we have shown that blastomeres considered to be totipotent are not transcriptionally equivalent.  Furthermore we have linked the developmental interactome to individual blastomeres and to later cell lineage.  This new understanding has clinical implications for understanding the impact of fertility treatments and developmental programming of long term health.

overall_design: Human embryos were selected at successive stages of pre-implantation development for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected embryos according to morphological criteria at four time-points: before fertilisation (embryo), at the begining (4-cell stage) and end (8-cell stage) of embryonic zygotic activation (ETA), and unpon the formation of the Inner cell mass and trophectoderm (blastocyst)

middle: L

first: Adam

last: Stevens

first: Ben

last: Minogue

first: Sharron

last: Sneddon

first: Lisa

last: Shaw

first: Lucy

last: Wood

first: Tope

last: Adenyi

first: Hui

last: Xiao

first: Pietro

last: Lio

first: Susan

last: Kimber

first: Daniel

middle: R

last: Brison


title: Targeting individual cells by barcode in pooled sequence libraries

city: Cambridge

first: Navpreet

last: Ranu

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Purpose: Selectively sequence desired single cells from pooled single cell libraries

overall_design:
10X libraries were prepared from two FACs sorted populations (HLA-DR and CD19) followed by enrichment for targeted single cells in triplicate. Enrichment was achieved with multiplex PCR with primers targeting the single cell barcodes that are added through library preparation.

NOTE: Submitter states that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.


title: Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

city: TSURUMI WARD YOKOHAMA

first: Aki

last: Minoda

state: KANAGAWA

address: 230-0045, 1 CHOME-7-22 SUEHIROCHO

department: IMS

institute: RIKEN YOKOHAMA

summary: We employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.

overall_design: ATAC-seq libraries are genreated from oLT and iMT region cartilage of 8 OA patients

first: Ye

last: Liu

first: Jen-Chien

last: Chang


title: Gene expression perturbation upon over-expression of a new PPARG isoform

status: Public on Oct 14 2018

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

summary: PPARγ regulates glucose and lipid homeostasis, insulin signaling and adipocyte differentiation. Here we report the skipping of exon 5 as legitimate splicing event generating PPARγΔ5, a new truncated isoform lacking the ligand binding domain. PPARγΔ5 is endogenously expressed in human adipose tissue and during adipocyte differentiation, lacks the ligand-dependent transactivation ability and acts as dominant negative reducing PPARγ activity. Ligand-mediated PPARγ activation induces exon 5 skipping in a negative feedback loop, suggesting alternative splicing as a new mechanism regulating PPARγ activity. PPARγΔ5 over-expression modifies PPARγ-induced transcriptional network, significantly impairing the differentiation ability of adipocyte precursor cells. Additionally, PPARγΔ5 expression in subcutaneous adipose tissue positively correlates with BMI in two independent cohorts of obese and diabetic patients. From a functional perspective, PPARγΔ5 mimics PPARG dominant negative mutated receptors, possibly contributing to adipose tissue dysfunctions. These findings open unexplored scenario in PPARG regulation and PPARγ-related diseases.

overall_design: Three samples analyzed: 1) HEK293 cells treated with troglitazone; 2) HEK293 cells treated with troglitazone and over-expressing PPARG (plasmid vector); 3) HEK293 cells treated with troglitazone and co-expressing canonical PPARG and PPARD5 (plasmid vectors).

first: Marianna

last: Aprile

first: Maria

last: Ambrosio

first: Simona

last: Cataldi

first: Alfredo

last: Ciccodicola


title: Crebbp loss drives small cell lung cancer and increases sensitivity to HDAC inhibition

city: Seattle

first: David

last: MacPherson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

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

overall_design: Refer to individual Series


title: PRC2 Inactivation Induces Primary Chemoresistance by Repressing Mitochondrial Apoptosis in T-ALL

city: Boston

first: Ingrid

last: Aries

address: 1 Blackfan circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: The tendency of mitochondria to undergo or resist BCL2-controlled apoptosis (so-called mitochondrial priming) is a powerful predictor of response to cytotoxic chemotherapy.  To fully exploit this finding, it will be important to understand the molecular genetic contexts responsible for the relative mitochondrial priming of chemotherapy-sensitive versus resistant cell populations.   Here, we report that mitochondrial apoptosis resistance in T-cell acute lymphoblastic leukemia (T-ALL) is mediated by inactivation of polycomb repressive complex 2 (PRC2).  In T-ALL clinical samples from children with T-ALL treated on recent Dana-Farber Cancer Institute or Children’s Oncology Group clinical trials, we found that loss-of-function mutations in any of three core components of PRC2 (EZH2, EED or SUZ12) were associated with resistance to mitochondrial apoptosis.  In human T-ALL cells, PRC2 depletion induced resistance to apoptosis induction by multiple chemotherapeutics with distinct mechanisms of action, including dexamethasone, doxorubicin and vincristine.  PRC2 loss induced apoptosis resistance via transcriptional upregulation of the LIM domain transcription factor CRIP2, and subsequent downstream upregulation of the mitochondrial chaperone TRAP1.  Importantly, TRAP1 overexpression was necessary to induce resistance to chemotherapy-induced apoptosis downstream of PRC2 inactivation, and pharmacologic inhibition of TRAP1 synergized with dexamethasone and doxorubicin.  These findings demonstrate the importance of relative mitochondrial apoptotic priming as a prognostic factor in T-ALL, and implicate mitochondrial chaperone function as a molecular determinant of response to cancer chemotherapy, suggesting a rationale for targeted therapeutic intervention.

overall_design: CCRF-CEM cells transduced with shRNAs targeting control (Luciferase) or EZH2 were cross-linked using formaldehyde, and sonication was performed to fragment chromatin to 200-700 bp size range using a Covaris E220 Focused-ultrasonicator.  Immunoprecipitation was then performed on 5 million cells with anti-H3K27me3 antibody (Active Motif Cat #39155). Protein A/G dynabeads were used to pull down antibody-bound chromatin, followed by washing and elution.  Cross-linking was reversed with proteinase K treatment, and DNA was cleaned up using SPRI beads.  ChIP DNA was quantified using the Qubit system (Invitrogen).  Sequencing libraries for ChIP-seq were prepared according to Illumina’s instructions.  ChIP DNA and input were sequenced with the Illumina NextSeq 500 platfom.

first: Alejandro

last: Gutierrez


title: Rheumatoid arthritis associated DNA methylation sites in peripheral blood mononuclear cells

city: Suzhou

first: Xingbo

last: Mo

address: Renai Road

institute: Soochow University

summary: Genome wide DNA methylation profiling of rheumatoid arthritis (RA) patients and healthy controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles in peripheral blood mononuclear cells (PBMCs). Samples included 25 RA patients and 18 healthy controls.

overall_design: To identify more rheumatoid arthritis (RA) associated DNA methylation sites and comprehensively understand their underlying pathologic mechanism, we compared the Illumina Infinium 450k Human DNA methylation microarray data from PBMCs of 25 RA patients with that of 18 healthy controls.

first: Hong

last: Zhu

first: Long-Fei

last: Wu

first: Xiao-Wei

first: Shu-Feng

last: Lei


title: RNA-seq analysis of BAP1-depleted uveal melanoma cells

city: Saint Louis

first: Michael

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

summary: OCM-1A uveal melanoma cells were infected with lentivirus carrying shRNA expression constructs specific for BAP1 or GFP (control), and placed under selection for 6 days. RNA-seq was performed.

overall_design: Samples represent three independent experiments treated with control or BAP1 shRNA

first: Matthew

last: Yen


title: Gene expression profiling of chronic hepatitis B induced HCC and adjacent-normal tissues

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

summary: Differential gene expression analysis between chronic hepatitis B induced HCC and adjacent Normal tissues using Affymetrix gene arrays.

overall_design: Tissues from chronic hepatitis B induced HCC and their adjacent Normal tissues were isolated and total RNA was extracted for Affymetrix gene microarray analysis.


title: Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes

status: Public on Feb 06 2019

city: Uppsala

first: Holger

last: Weishaupt

address: Dag Hammarskjölds väg 20

institute: Uppsala University

type:
Expression profiling by array
Third-party reanalysis

summary:
Medulloblastoma (MB) is a brain cancer predominantly arising in children. Roughly 70% of patients are cured today, but survivors often suffer from severe sequelae. MB has been extensively studied by molecular profiling, but often in small and scattered cohorts. To improve cure rates and reduce treatment side effects, accurate integration of such data to increase analytical power will be important, if not essential. We have integrated 23 transcription datasets, spanning 1350 MB and 291 normal brain samples. To remove batch effects, we combined the Removal of Unwanted Variation (RUV) method with a novel pipeline for determining empirical negative control genes and a panel of metrics to evaluate normalization performance. The documented approach enabled the removal of a majority of batch effects, producing a large-scale, integrative dataset of MB and cerebellar expression data. The proposed strategy will be broadly applicable for accurate integration of data and incorporation of normal reference samples for studies of various diseases. We hope that the integrated dataset will improve current research in the field of MB by allowing more large-scale gene expression analyses.
For all selected samples, raw CEL files were downloaded from GEO or AE. Subsequently, all raw CEL files from the same platform were processed together using the R/Bioconductor package oligo in conjunction with the RMA algorithm. The Human Gene 1.0 ST and Human Gene 1.1 ST arrays were analysed at the core level, while the Human Exon 1.0 ST arrays were processed at the extended level. Subsequently, we mapped the identifiers of the HG-U133 Plus 2 and Human Exon 1.0 ST to Human Gene 1.0/1.1 ST identifiers using `Best Match' information from Affymetrix (https://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1). In addition, to increase the overlap between the Human Exon 1.0 ST and Human Gene 1.0/1.1 ST data we also inspected and added probe mappings from the `Good Match' and `Complex Match' files, including probes for the genes MYCN, PTCH1, NPR3, UNC5D, DKK2, and GABRA5. After mapping of probe identifiers within each platform, multiple rows mapping to the same identifier were collapsed using the mean value. Subsequently, all platform datasets were merged on probe identifiers, and gene symbols were assigned using the hugene11sttranscriptcluster.db package. Multiple rows mapping to the same gene or multiple columns mapping to the same patient were collapsed using the mean value. Finally, the resulting gene expression matrix was quantile normalized using the respective function in the preprocessCore package.

overall_design: We downloaded a total of 1796 CEL files from previously published GEO or ArrayExpress records: GSE85217(n=763), GSE25219(n=154), GSE60862(n=130), GSE12992(n=40), GSE67850(n=22), GSE10327(n=62), GSE30074(n=30), E-MTAB-292(n=19), GSE74195(n=30), GSE37418(n=76), GSE4036(n=14), GSE62803(n=52), GSE21140(n=103), GSE37382(n=50), GSE22569(n=24), GSE35974(n=50), GSE73038(n=46), GSE50161(n=24), GSE3526(n=9), GSE50765(n=12), GSE49243(n=58), GSE41842(n=19), GSE44971(n=9). After preprocessing of all CEL files, we averaged the expression profiles of samples that mapped to the same patient in a single dataset, producing a final expression array comprising 1641 samples, of which 1350 samples represent primary medulloblastomas and 291 samples represent normal brain (cerebellum/upper rhombic lip).

first: Patrik

last: Johansson

first: Anders

last: Sundström

first: Zelmina

last: Lubovac-Pilav

first: Björn

last: Olsson

first: Sven

last: Nelander

first: Fredrik

middle: J

last: Swartling


title: Long non-coding RNAs are central regulators of the IL-1b-induced inflammatory response in human lung fibroblasts

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

institute: University of Bath

summary: There is accumulating evidence to indicate that long non-coding RNAs (lncRNAs) are important regulators of the inflammatory response. In this report, we have employed next generation sequencing to identify 14 lncRNAs that are differentially expressed in human lung fibroblasts following the induction of inflammation using interleukin-1b (IL-1b). Knockdown of the two most highly expressed lncRNAs, IL7AS and MIR3142HG, showed that IL7AS negatively regulated IL-6 release whilst MIR3142HG was required for IL-8 and CCL2 release.  Parallel studies in fibroblasts derived from patients with idiopathic pulmonary fibrosis showed similar increases in IL7AS levels, that also negatively regulate IL-6 release. In contrast, IL-1b-induced MIR3142HG expression was reduced by 8-fold in IPF fibroblasts, with the consequence being that MIR3142 knockdown showed no effect upon IL-8 and CCL2 release. In summary, we have catalogued those lncRNAs that are differential expression following IL-1b-activation of human lung fibroblasts and shown that these regulate the inflammatory response.

overall_design: Total RNA was extracted from lung fibroblast exposed to either buffer (controls) or 3 ng/ml of IL-1b for 6h and subjected to paired-end and stranded 75bp sequencing using the Illumina HiSeq4000

middle: A


title: Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes

city: Montreal

first: Daniel

last: Sinnett

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

type: Methylation profiling by high throughput sequencing

summary:
Very long intergenic non-coding RNAs (vlincRNAs) are a novel class of long transcripts (~50 kb to 1 Mb) with cell type- or cancer-specific expression. We report the discovery and characterization of 256 vlincRNAs from a cohort of 64 primary childhood pre-B and pre-T acute lymphoblastic leukemia (cALL) samples, of which 61% are novel and specifically expressed in cALL.  Validation was performed in 35 pre-B and pre-T cALL primary samples. We show that their expression is cALL immunophenotype and molecular subtype-specific and correlated with epigenetic modifications on their promoters, much like protein-coding genes. While the biological functions of these vlincRNAs’s are still unknown, our results suggest they could play a role in cALL etiology or progression.

Please note that the study consists of investigating very long intergenic non coding RNAs (vlincRNAs) in childhood acute lymphoblastic leukemia. The study primarily uses RNA-seq data (GSE89071) with the current additional epigenetic data that is specific to this study (chip-seq and wgb-seq).

overall_design:
Identification and characterization of very long intergenic non-coding RNAs in childhood ALL

Please note that the 'characteristic: cell type' field indicates the cell type of each sample. The cell type is 'Pre-B' cells, and the cALL subtype is also indicated. For the control, CD10+ and CD19+ cord blood cells were used.

first: Maxime

last: Caron

first: Pascal

last: St-Onge

first: Simon

last: Drouin

first: Chantal

last: Richer

first: Thomas

last: Sontag

first: Stephan

last: Busche

first: Guillaume

last: Bourque

first: Tomi

last: Pastinen


title: Regional differences in mRNA and lncRNA expression patterns in the non-failing human heart

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Background: Although chamber specialization is critical for proper cardiac function, a comprehensive, genome-wide analysis of the cardiac transcriptome, including identification of regional differences in mRNA and lncRNA expression patterns for the four chambers and interventricular septum of the non-failing human heart, has not been performed.   Methods and Results: mRNA and long noncoding RNA (lncRNA) transcriptional profiling of the left (LA) and right (RA) atria, left (LV) and right (RV) ventricles, and the interventricular septum (IVS) of non-failing human hearts (N=8) was performed by deep sequencing. Analysis of the mRNA and lncRNA expression profiles revealed that the different regions of the heart are distinct. Differential expression analysis of paired tissue samples identified 5,747 mRNAs and 2,794 lncRNAs with chamber-enriched expression patterns. The largest differences in mRNA and lncRNA expression were evident between atria and ventricular samples, including regional differences in ~20% of all cardiac expressed mRNA and lncRNA transcripts. Regional differences in mRNA and lncRNA expression were also evident, although to a lesser extent, between the LA and RA, and between the LV, RV and IVS. Gene ontology classification of differentially expressed gene sets revealed regional differences in chamber specialization, including differences in signaling, metabolism, and muscle contraction. Sex differences in mRNA and lncRNA gene expression profiles were also identified between male and female LA and RA samples.    Conclusions: There are marked regional differences in the mRNA and lncRNA expression profiles in non-failing adult human heart, and are associated with chamber specialization.

overall_design: 8 human hearts, 5 chambers from each

first: Eric

middle: K

last: Johnson

first: Jeanne

last: Nerbonne


title: Profiling in vivo Bone Lesion (IVBL) and Orthotopic tumors by Next Generation Sequencing

city: Buffalo

first: Hai

last: Wang

state: NY

address: Elm and Carlton Streets, MRC 328

department: Molecular and Cellular Biology

institute: Roswell Park Cancer Institute

summary: Based on RNA-seq, we performed transcriptomic profiling to examine the differences between Orthotopic and IVBL (in vivo bone lesion). We found Calcium signalling is upregulated in IVBL and correlated to the expression of gap junctions.

overall_design: Orthotopic tumors and Bone lesions, all developed by MCF-7, are subject to NGS and then analyzed.

first: Xiang

last: Zhang


title: RNA-sequencing of human tendon after injury

city: Shanghai

first: Wei

last: Zheng

address: 600 Yishan Road

department: department of Orthopedics

institute: Shanghai Jiao Tong University

summary: RNA-sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates


title: Quantifying post-transcriptional regulation in the development of Drosophila melanogaster [s2r]

status: Public on Oct 13 2018

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

summary: Proteome and transcriptome often show poor correlation, hindering the system-wide analysis of post-transcriptional regulation. Here, the authors study proteome and transcriptome dynamics during Drosophila embryogenesis and present basic mathematical models describing the temporal regulation of most protein-RNA pairs.

overall_design: S2R+ drosophila cell lines with Hrb98de knock down

first: Falk

last: Butter

first: Kolja

last: Becker

first: Stefan

last: Legewie


title: Requirement for PRC1 subunit BMI1 in host gene activation by Epstein-Barr virus protein EBNA3C

city: London

first: Martin

last: Allday

state: London

address: Norfolk Place

department: Medicine

institute: Imperial College London

summary: EBV proteins EBNA3A, EBNA3B and EBNA3C control hundreds of host genes after infection. Changes in epigenetic marks around EBNA3-regulated genes suggest they exert transcriptional control in collaboration with epigenetic factors. The roles of PRC2 subunit SUZ12 and of PRC1 subunit BMI1 were assessed for their importance in EBNA3-mediated repression and activation. ChIP-seq experiments for SUZ12 and BMI1 were performed to determine their global localization on chromatin and analysis offered further insight into polycomb protein distribution in differentiated cells. Their localization was compared to that of each EBNA3, to resolve longstanding questions about the EBNA3-polycomb relationship. SUZ12 did not co-localize with any EBNA3, whereas EBNA3C co-localized significantly and co-immunoprecipitated with BMI1. In cells expressing a conditional EBNA3C, BMI1 was sequestered to EBNA3C binding sites after EBNA3C activation. When SUZ12 or BMI1 was knocked down in the same cells, SUZ12 did not contribute to EBNA3C-mediated regulation. Surprisingly, after BMI1 knock down, EBNA3C repressed equally efficiently, but host gene activation by EBNA3C was impaired. This overturns previous assumptions about BMI1/PRC1 functions during EBNA3C-mediated regulation, for the first time identifies directly a host factor involved in EBNA3-mediated activation and provides a new insight of how PRC1 can be involved in gene activation.

overall_design: A lymphoblastoid cell line created by infection of B cells with B95-8 EBV was used to perform ChIP-seq for proteins BMI1 (PCGF4) and SUZ12 to determine their global localization onto the genome

first: Kostas

last: Paschos


title: Quantifying post-transcriptional regulation in the development of Drosophila melanogaster [devel]

overall_design: Whole embryos of Drosophila melanogaster measured at 14 time points during the first 20h of development (0h, 1h, 2h, 3h, 4h, 5h, 6h, 8h, 10h, 12h, 14h, 16h, 18h, 20h). Each sample was measured in biological quadruplicates. RNAseq samples correspond to proteome measurements deposited in ProteomeXchange as PXD005713.


title: Gene expression dataset for whole cochlea of Macaca fascicularis

city: Tokyo

first: Hideki

last: Mutai

address: 2-5-1 Higashigaoka, Meguro-ku

department: National Institute of Sensory Organs Div Hearing and Balance Research

institute: National Hospital Organization Tokyo Medical Center

summary: Macaca fascicularis (long-tailed, cynomolgus, or crab-eating macaque) is a highly advantageous model in which to study human cochlea with regard to both evolutionary proximity and physiological similarity of the auditory system. To better understand the properties of primate cochlear function, we analyzed the genes predominantly expressed in M. fascicularis cochlea.

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Total RNA was extracted from Left and right whole cochleas of an adult male Macaca fascicularis. RNA was hybridized on either macaque array chip or human array chip, both of which have been widely used and therefore comparable with other dataset.

first: Fuyuki

last: Miya

first: Hiroaki

last: Shibata

first: Yasuhiro

last: Yasutomi

first: Tatsuhiko

last: Tsunoda

first: Tatsuo

last: Matsunaga


title: Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: We analyzed single cell transcriptomes over 80,000 cells isolated from 65 organoids differentiated from iPSCs and ESCs using two different protocols. We find that both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios as well as non-renal cell types. We reconstructed lineage relationships during organoid differentiation through pseudotemporal ordering, and identified transcription factor networks associated with fate decisions. When comparing to adult human kidney, we  reveal immaturity of all kidney organoid cell types. These results define impressive kidney organoid cell diversity, identify incomplete differentiation as a major roadblock for current directed differentiation protocols and provide a human adult kidney snRNA-seq dataset against which to benchmark future progress.

overall_design: Dropseq and 10X Chromium were used to profile organoid cells and adult kidney nuclei

first: Benjamin

last: Humphreys


title: Deregulation of neuronal miRNAs induced by amyloid-β or TAU pathology

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

summary: Despite diverging levels of amyloid-β (Aβ) and TAU pathology, different mouse models, as well as sporadic AD patients show predictable patterns of episodic memory loss. MiRNA deregulation is well established in AD brain but it is unclear whether Aβ or Tau pathology drives those alterations and whether miRNA changes contribute to cognitive decline. Therefore miRNAseq was performed on the hippocampus of APPswe/PS1L166P and Thy-TAU22 mice and their respective wild-type littermates when they were cognitively intact (4 months) and impaired (10 months). We found 6 miRNAs that are commonly upregulated between APPtg and TAUtg mice, and four of these were also altered in AD patients. All 6 miRNAs are strongly enriched in neurons as verified by in situ hybridization.

overall_design: miRNAseq on 96 biological samples (mouse hippocampus), n=12 per experimental group, examining APPswe/PSEN1L166P and Thy-TAU22 mice and their respective WT littermates, at 4 and 10 months of age (8 groups in total)

first: Annerieke

last: Sierksma

first: Ashley

last: Lu

first: Evgenia

last: Salta

first: Elke

last: Vanden Eynden

first: Zsuzsanna

last: Callaerts-Vegh

first: Rudi

last: D'Hooge

first: David

last: Blum

first: Luc

last: Buée

first: Mark

last: Fiers


title: Ascorbate Suppresses VEGF Expression in Retinal Pigment Epithelial Cells

status: Public on Oct 12 2018

city: Provo

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show that ascorbate (vitamin C) shifts the hydroxymethylome and transcriptome in RPE cells, and downregulates expression of VEGF.

overall_design: Examination of transcriptome and hydroxymethylome in vitamin C treated or control ARPE-19 cells

first: Gaofeng

last: Wang

middle: W

first: Vladimir

last: Camarena