title: Organoid modeling of the tumor immune microenvironment

city: Stanford

first: Calvin

last: Kuo

address: 265 Campus Dr.

department: Department of Medicine, Division of Hematology

institute: Stanford University

summary: The interaction of neoplastic cells with their tumor microenvironment (TME) is required for cancer progression. However, in vitro cancer models, including recent in vitro 3-dimensional (3D) organoid cultures of primary human tumors, are typically comprised exclusively of neoplastic epithelium, with stromal and/or immune interactions requiring artificial reconstitution. As relevant to cancer immunotherapy, the unified co-culture of primary tumor epithelia with their endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has remained particularly elusive. Here, we used a single 3D air-liquid interface (ALI) methodology to successfully propagate 3D Patient-Derived Tumor Organoids (PDOs) as primary tumor epithelia together with native immune and myofibroblast stromal compartments without reconstitution. Derived from >100 diverse human surgically resected tumor samples or from murine tumors in syngeneic immunocompetent mice, PDOs preserved cancer histologic subtypes and mutational spectrum with endogenous T, B, NK cells and macrophages integrally embedded amidst the tumor epithelium. PDO-based TILs accurately recapitulated the T cell receptor (TCR) spectrum of the original tumors, as determined by a robust droplet-based immune profiling solution that links gene expression and immune repertoire in single cells. Anti-PD-1 or anti-PD-L1 treatment of organoids from murine tumors from syngeneic immunocompetent hosts induced activation and cytolytic activity of tumor antigen-specific TILs, indicating successful PDO modeling of immune checkpoint blockade (ICB) and anti-tumor immunity. Crucially, the anti-PD-1 antibody nivolumab activated TILs in PDOs from human lung, renal and melanoma clinical tumor resections. The organoid-based propagation of primary tumor epithelium en bloc with its endogenous immune stroma should facilitate mechanistic investigation of TME-specific local tumor immunity, with applications for functional testing of individualized patient immunotherapy responses.

overall_design: Single cell GEX and VDJ profiling from the same samples

first: Grace

last: Zheng

first: Jason

last: Zhu


title: Chronic inflammation permanently reshapes tissue-resident immunity in celiac disease

status: Public on Dec 12 2018

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: Chronic inflammation driven by persistent antigenic challenge with dietary gluten permanently reshapes the tissue-resident TCRgd+ intraepithelial lymphocyte compartment in patients with celiac disease.

overall_design: Transcriptional profiles of ex vivo sorted Vd1+ IELs from Control, Active CeD, and GFD CeD patients

first: Toufic

last: Mayassi

first: Kristin

last: Ladell

first: Herman

last: Gudjonson

first: James

middle: E

last: McLaren

first: Dustin

middle: G

last: Shaw

first: Mai

last: Tran

first: Jagoda

middle: J

last: Rokicka

first: Ian

last: Lawrence

first: Jean-Christophe

last: Grenier

first: Vincent

last: van Unen

first: Cezary

last: Ciszewski

first: Matthew

last: Dimaano

first: Hoda

last: Sayegh

first: Vinod

last: Kumar

first: Cisca

last: Wijmenga

first: Ranjana

last: Gokhale

first: Hilary

last: Jericho

first: Carol

last: Semrad

first: Stefano

last: Guandalini

first: Aaron

middle: R

last: Dinner

first: Sonia

middle: S

last: Kupfer

first: Hugh

middle: H

last: Reid

middle: B

first: Jamie

last: Rossjohn

first: David

middle: A

last: Price

first: Bana

last: Jabri


title: Next Generation Sequencing Analysis of human hematopoietic stem/progenitor cells (HSPCs) differentiated from pluripotent stem cells

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

summary:
Purpose: global gene expression profiling of H1 and iPSC derived HSPCs.
Methods: SMART-seq2 amplified polyA RNA from differentiation day 8 CD31+CD34+CD43+ and CD31+CD34+CD43- cells, and day 5 CD31+CD34+ cells cultured in medium with or without insulin supplement
Results: Modulation of key cell signaling pathways lead to highly efficient HSPC differentiation from human pluripotent stem cells.
Conclusions: Highly efficient HSPC differentiation from human pluripotent stem cells in a monolayer, chemically defined culture system.

overall_design: Perform RNA-seq of polyA RNA from differentiation day 5 CD31+CD34+ and day 8 CD31+CD34+CD43+ and CD31+CD34+CD43- cells derived from H1 and iPSCs

first: Fuyu

last: Duan


title: RNA polymerase III regulation during mammalian tissue regeneration

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

type: Genome binding/occupancy profiling by high throughput sequencing

summary: There are about 600 loci in the mammalian genome that are annotated as RNA polymerase III genes. These comprise tRNA genes, the genes encoding 5S RNA, the smallest ribosomal RNA, and genes encoding catalytic or structural RNAs involved in processes as diverse as RNA processing or transcription elongation. Most RNA polymerase III genes have similar promoter structures, yet they are transcribed with different efficiencies. Here we have explored how RNA polymerase III occupancy of these genomic loci varies in a normal tissue, the liver, during the transition from a resting state to a proliferating state. We find that after partial hepatectomy, which causes synchronous entry of remaining liver cells into the cell division cycle, there is a tremendous increase in RNA polymerase III occupancy. This increase is, however, not uniform and concerns mostly loci that were lowly occupied by RNA polymerase III in resting liver. The changes in RNA polymerase III occupancy cannot be correlated with changes in RNA polymerase II occupancy around the RNA polymerase III loci nor at nearby RNA polymerase II promoters. RNA polymerase III loci with the largest fold change tend to be located in clusters, with the cluster displaying the largest changes located on chromosome 13. This suggests that increases in RNA polymerase III occupancy during the transition from resting to proliferating state affect mostly genes whose basal rate of transcription is relatively low and which are located in clusters.

overall_design: C57/BL6 12-14 week old male mice were housed and entrained for two weeks on a 12 hrs on/12 hrs off feeding and dark-light cycle with food access between ZT12 and ZT24 (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when the lights are turned off). Negative control, sham control and post-PH liver samples were collected.

first: Cristian

last: Carmeli

first: Dominic

last: Villeneuve

first: Meghdad

last: Yeganeh

first: Leonor

last: Rib

first: Viviane

last: Praz

first: Winship

last: Herr

first: Mauro

last: Delorenzi

first: Nouria

last: Hernandez


title: IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors

status: Public on Dec 11 2018

city: Frankfurt am Main

first: Dmitry

last: Namgaladze

state: Hessen

address: Theodor-Stern-Kai 7, Building 74

department: Faculty of Medicine

country: Germany

institute: Goethe University Frankfurt

summary: Here we explored how cytokines of the tumor milieu, interleukin (IL)-6 and IL-4, interact to influence target gene expression in primary human monocyte-derived macrophages (hMDMs). We show that dual stimulation with IL-4 and IL-6 synergistically modified gene expression. Among the synergistically induced genes are several targets with known pro-tumorigenic properties, such as CC-chemokine ligand 18 (CCL18), transforming growth factor alpha (TGFA) or CD274 (programmed cell death 1 ligand 1 (PD-L1)). We found that transcription factors of the signal transducer and activator of transcription (STAT) family, STAT3 and STAT6 bind regulatory regions of synergistically induced genes in close vicinity. STAT3 and STAT6 co-binding further induces the basic leucine zipper ATF-like transcription factor (BATF), which participates in synergistic induction of target gene expression. Functional analyses revealed increased MCF-7 and MDA-MB 231 tumor cell motility in response to conditioned media from co-treated hMDMs compared to cells incubated with media from single cytokine-treated hMDMs. Flow cytometric analysis of T cell populations upon co-culture with hMDMs polarized by different cytokines indicated that dual stimulation promoted immunosuppressive properties of hMDMs in a PD-L1-dependent manner. Analysis of clinical data revealed increased expression of BATF together with TAM markers in tumor stroma of breast cancer patients as compared to normal breast tissue stroma. Collectively, our findings suggest that IL-4 and IL-6 cooperate to alter the human macrophage transcriptome, endowing hMDMs with pro-tumorigenic properties.

overall_design: We compared synergistically induced genes in IL-4/IL-6 co-stimulation relative to IL-4, IL-6 and untreated monocyte derived human macrophages via RNA sequencing

first: Sahil

last: Gupta


title: DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: We introduce methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) which has the reduced sequencing requirements of RRBS, but significantly expands the coverage of CpG sites in the genome. Here, we compare MREBS to WGBS and RRBS.

overall_design: Examine DNA Methylation in two cell lines using 3 different methods (MREBS, WGBS and RRBS)

first: Matteo

last: Pellegrini


title: Expression data from mouse skeletal muscle

city: kobe

first: Yu

last: Hirata

address: chuo-ku, kusunoki-chou, 7-5-2

country: Japan

institute: Kobe University

summary:
Evidence suggests that diabetes mellitus is a promoting factor of sarcopenia; mechanism of how diabetes mellitus accelerates the development of sarcopenia is not known. We have recently established a model of diabetes-induced skeletal muscle mass loss in mice by using streptozotocin.
We used microarrays to detail the global programme of gene expression underlying skeletal muscle atrophy in STZ treated mice and identified up-regulated  or down-regulated genes during this process.

overall_design: Gastrocnemius muscle were selected at 3 weeks after STZ treatment of wild type or skeletal muscle specific KLF15 knockout mice for RNA extraction and hybridization on Affymetrix microarrays.

first: Wataru

last: Ogawa


title: Phosphorylation of SRSF1 at Tyr-19 promotes cell proliferation in pediatric acute lymphoblastic leukemia

first: Xu

middle: Li

last: ting

address: 56 NanLiShi Road, Xicheng District

institute: Beijing Children’s Hospital

summary: we identified for the first time that the phosphorylation state of SRSF1 is linked to different phases in ALL. Our results underscore the phosphorylation of SRSF1 at the Tyr-19 residue disrupts subcellular localization of SRSF1 and promotes cell proliferation in leukemic cells by accelerating cell-cycle progression. Targeting Tie2 kinase is able to catalyze Tyr-19 phosphorylation of SRSF1, and offer a promising therapeutic target for the treatment of pediatric ALL. These findings undoubtedly add a new layer in understanding of how post-translational mechanism supports leukemia progression.

overall_design: The mRNA profiles of stable leukemic cell line overexpressed wild-type SRSF1, mutants (SRSF1-Y19D or SRSF1-Y19F) or the empty vector were generated by deep sequencing using Illumina  HiSeq 4000 platform

first: Liting

last: Xu

first: Huyong

last: Zheng


title: Analysis of the Phosphorylated Estrogen Receptor-α Cistrome Reveals Association with Direct ER-DNA Binding and the Transcription Factor GRHL2

city: Madison

first: Elaine

middle: T

last: Alarid

state: WI

address: 1111 Highland Ave

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin - Madison

summary: Phosphorylation of the estrogen receptor-α (ER) at serine 118 (pS118-ER) is involved in modulating ER-dependent gene transcription and recruitment of ER to certain gene promoters. While the effects of pS118 on ER-DNA interactions have been investigated at specific sites, the genome-wide binding profile (cistrome) of pS118-ER remains to be studied. To characterize the pS118-ER cistrome, ChIP-seq was performed on pS118-ER and pan-ER in MCF-7 cells. A subset of ER sites was occupied by pS118-ER and these sites were associated with the active enhancer mark H3K27ac. Additionally, pS118-ER sites were found to be enriched in the DNA binding motif for GRHL2 as well as the estrogen response element relative to all ER sites. Utilizing a DNA binding microarray, pS118-ER was found to be more commonly associated with direct DNA binding events compared to indirect binding events. These results suggest a role for pS118-ER at active enhancers and as a regulator of direct ER-DNA interactions.

overall_design: MCF-7 cells were treated with 10 nM 17ß-estradiol for 30 min prior to ChIP assay, library creating, and sequencing

first: Kyle

last: Helzer

first: Mary

last: Ozers

first: Mark

last: Meyer

first: Nancy

last: Benkusky

first: Natasha

last: Solodin

first: Rebecca

middle: M

last: Reese

first: Christopher

middle: L

last: Warren

first: J

middle: W

last: Pike


title: RNAseq of fluidically isolated human and mouse motor neuron somas and axons in vitro

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: Spinal motor axons traverse large distances to innervate target muscle, and thus require local control of cellular events for proper functioning of the distal axon. To interrogate axon-specific processes we developed Axon-seq, a refined method incorporating microfluidic devices and stringent bioinformatic quality controls. Axon-seq demonstrates improved sensitivity and accuracy in whole-transcriptome sequencing of axons compared to previously published studies. Importantly, we show that axon transcriptomes are distinct from those of somas, displaying fewer detected genes and no contaminating astrocytic markers. We identified >5,000 transcripts in stem cell-derived spinal motor axons required for local oxidative energy production and ribosome generation. Axons contained unique transcription factor mRNAs, e.g. Ybx1, with implications for local axonal functions. Cross-comparison with existing mouse motor axon datasets, as well as our own human motor axon data identified a common axon transcriptome. As motor axons degenerate in amyotrophic lateral sclerosis (ALS), we investigated their response to the disease-causing SOD1G93A mutation, identifying 121 ALS-dysregulated transcripts. Several of these are implicated in axonal and dendritic outgrowth, including Nrp1, Dbn1, and Nek1, a known ALS-causing gene. In conclusion, Axon-seq proves a robust and improved method for RNA-seq of axons, furthers our understanding of peripheral axon biology, and identifies novel therapeutic targets to maintain neural connectivity in disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A total of 118 samples were analyzed here. Of these, 32 are microfluidic cell culture samples derived from mouse embryonic stem cells differentiated into motor neurons, where axons and somas were separated for RNA isolation. This was performed for 2 cell lines (control and SOD1G93A), resulting in the following 4 groups: control somas (n=13), control axons (n=5), SOD1G93A somas (n=10) and SOD1G93A axons (n=4). An additional 34 single mouse motor neurons were sequenced (n=12 for control, n=22 for SOD1G93A). Human control motor neurons derived from induced pluripotent stem cells were also cultured in microfluidic devices, and separate axon and soma fractions were harvested (n=6 axon, n=7 soma). An additional n=39 human single motor neurons were sequenced.

first: Jik

last: Nijssen


title: Ribosomal protein RPL26 is the principal target of UFMylation

city: Berkeley

first: Celeste

last: Riepe

state: California

address: 1 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: UFM1 is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to ER stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and deUFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.

overall_design: ribosome profiling of membrane and cytosolic fractions of UFM1-KO, UFSP2-KO, and wild-type HEK cells in duplicate (12 samples); mRNA-seq of whole cell lysates of UFM1-KO, UFSP2-KO, and wild-type HEK cells in duplicate (6 samples)

middle: P

last: Walczak

first: Dara

last: Leto

first: Lichao

last: Zhang

first: Ryan

middle: Y

last: Muller

first: Paul

last: DaRosa

first: Nicholas

last: Ingolia

first: Joshua

last: Elias

first: Ron

last: Kopito


title: Brain vascular transcriptomes of mouse hyperglycemia mutants and controls

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary:
Purpose:To take a comprehensive effort in characterizing the brain vasculature gene expression upon hyperglycemia.

Methods: We extracted mRNA from brain microvasculature fragments isolated from a genetic mouse model of hyperglycemia (Ins2-AKITA) and WT mice and analyzed their transcriptome with RNA sequencing The samples were sequenced on an Illumina HiSeq 2500 sequencer at the SNP&SEQ sequencing facility (Science for Life laboratory (SciLifeLab), Uppsala sequencing node). The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1)

Results: Twenty-three genes were significantly regulated in mutant when compared to WT (False Discovery Rate < 0.05)

overall_design: The microvascular RNA from two male heterozygous Ins2-AKITA mice and three littermate wild-type controls were processed and sequenced on the Illumina HiSeq 2500 platform in the sequencing facility in Uppsala University.

first: Maarja

last: Andaloussi Mäe

first: Tian

last: Li

first: Guillem

last: Genové


title: Organ-specific tissue-resident macrophages dynamics during blood stage malaria

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

summary: Blood-stage malaria initiates both innate and adaptive immune responses, inclusive a strong activation of the mononuclear phagocyte network. Here we show that Plasmodium infection results in a transient loss of embryonically established tissue-resident macrophages in spleen, liver and lungs, much before the peak of parasitemia. During acute blood-stage malaria, fate mapping analysis revealed that inflammatory monocytes contribute to the repopulation of the emptied niches of splenic red pulp macrophages and hepatic Kupffer cells, while lung alveolar macrophages refill their niche mainly through self-renewal. Interestingly, the local microenvironment of spleen and liver can “imprint” the molecular characteristics of fetal-derived macrophages in new immigrants from bone marrow including almost identical gene expression profiles and turnover kinetics.

overall_design: Mice were infected with parasitized P. yoelii erythrocytes. Organ samples were collected in triplicates from uninfected mice and from mice infected 35 days before and after parasite clearance.

first: Christiane

last: Ruedl

first: Lai

last: Min


title: Evaluating pre-clinical models for studying NASH driven HCC.

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

country: Australia

institute: Garvan Institute of Medical Research

summary: We sequenced liver biopsy tissue from healthy, patients with NAFLD and patients with NASH

overall_design: 3 patients either healthy, presenting with NAFLD or NASH

first: Mark

last: Febbraio


title: Transcriptome analysis of VMRC-LCD cells following ASCL1 knockdown

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

institute: The University of Tokyo

summary: ASCL1 is a master transcription factor for neuroendocrine differentiation. RNA-sequencing analysis on VMRC-LCD cells following ASCL1 knockdown revealed a subset of genes possibly regulated by ASCL1.

overall_design: VMRC-LCD cells were transfected with siRNAs for ASCL1, and RNA-sequencing was performed using Illumina HiSeq.

first: Naoya

last: Miyashita

first: Masafumi

last: Horie

first: Akira

last: Saito

first: Takahide

last: Nagase


title: Epigenetic control of genes and transposable elements [ATAC-seq]

city: GuangZhou

first: Jiangping

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: Epigenetic control is an elaborate system the cell uses to control aspects of cell type and gene control. Histones and DNA are chemically modified to signal epigenetic information as to whether a gene is active or inactive, and so maintain cell type stability. Whilst epigenetic control of genes has been explored, the control of the rest of the genome is less well explored. The bulk of DNA and chromatin consists of repetitive elements, not genes, and these TEs must be tightly regulated to provide structure and function for nearby genes and, ultimately, cell type control. In this project we explore the intereaction of epigenetic control factors, and inhibitors, and how perturbation of the epigenetic control system disrupts TE regulation inside embryonic stem cells.

overall_design: We analyzed the transcriptome expression profiles (RNA-seq) and chromation accessibility (ATAC-seq) upon specific epigenetic perturbation

first: Andrew

last: Hutchins


title: Drp1 controls an effective T cells' immune-surveillance by regulating their migration, proliferation and cMyc-dependent metabolic reprogramming.

city: Rome

first: Silvia

last: Campello

state: <None>

address: Via della Ricerca Scientifica

department: Department of Biology

country: Italy

institute: University of Rome, Tor Vergata

summary: We performed RNAseq analysis of 3 days in vitro activated control and Drp1 KO T cells to investigate the role of Drp1 in regulating global transcriptional changes upon activation in T cells. Our analysis shows that Drp1 sustains metabolic reprogramming upon TCR stimulation. Indeed, in Drp1 KO T cells most of the genes encoding for glycolytic enzymes are down-regulated, while TCA cycle and oxidative phosphorylation genes, as well as several genes encoding enzymes of fatty acid synthesis and beta-oxidation, are upregulated.

overall_design: RNA sequencing of in vitro activated control and Drp1 KO T cells.

first: Matteo

last: Bordi

first: Luca

last: Simula


title: Epigenetic control of genes and transposable elements [inhibitor RNA-seq]

last: He

overall_design: We analyzed the transcriptome expression profiles(RNA-seq) and chromation accessibility(ATAC-seq) upon specific epigenetic perturbation


title: Nanostring gene expression analysis of splenocytes from 17-β estradiol (E2) and synthetic 17α-ethinyl estradiol (EE) exposed feamle NZB/WF1 lupus mice

status: Public on Dec 10 2018

city: Blacksburg

first: Rujuan

last: Dai

state: VA

address: IDRF 127c,, 245 duck pond drive

department: biomedical science

institute: Virginia Tech

summary: We used the NanoString mouse nCounter immunology panel platform to compare mRNA gene expression profiles of spelnocytes from placebo-, E2, and EE exposed NZB/WF1 mice. With the profling of 548 immunology-related genes, we found that E2 and EE exposure alter  immune-related genes at a similar pattern.

overall_design: Female NZB/WF1 lupus mice received E2, EE, or empty (placebo control) implant  treatment  at 6-7 weeks of age.  After 9 wks of treatment, the mice were terminated and splenocytes were isolated and collected. Total RNAs were extracted from splenocytes with miRNeasy Mini Kit and sent to NanoString Technologies for gene profiling analysis with nCounter GX mouse immunology kit.

first: S

last: Ahmed


title: Epigenetic control of genes and transposable elements [Knockdown RNA-seq]


title: Nanostring miRNA exprssion profiling analysis of splenocytes from 17-β estradiol (E2) and synthetic 17α-ethinyl estradiol (EE) exposed feamle NZB/WF1 lupus mice

summary: We used the NanoString mouse nCounter miRNA expression platform to compare the miRNA expression profiles of spelnocytes from placebo-, E2, and EE exposed NZB/WF1 mice. We found that EE exposure has a more profound effect than E2 on miRNA genes expression in splenocytes

overall_design: Female NZB/WF1 lupus mice received E2, EE, or empty (placebo control) implant  treatment  at 6-7 weeks of age.  After 9 wks of treatment, the mice were terminated and splenocytes were isolated and collected. Total RNAs were extracted from splenocytes with miRNeasy Mini Kit and sent to NanoString Technologies for gene profiling analysis with nCounter mouse miRNA V1.5 Assay kit.


title: Epigenetic control of genes and transposable elements

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

overall_design: Refer to individual Series


title: BRCA1 Represses DNA Replication Fork Firing and Prevents Mitotic Catastrophe through Antagonizing Estrogen Signaling during Pregnancy

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The mammary gland at early stages of pregnancy undergoes fast cell proliferation, yet the mechanism to ensure its genome integrity is largely unknown. Here we show that pregnancy enhances expression of genes involved in numerous pathways, including most genes encoding replisomes. In mouse mammary glands, replisome genes are positively regulated by estrogen/ERa signaling but negatively regulated by BRCA1. Upon DNA damage, BRCA1 deficiency markedly enhances DNA replication initiation.  BRCA1 deficiency also preferably impairs DNA replication checkpoints mediated by ATR and CHK1 but not by WEE1, which inhibits DNA replication initiation through CDC7-MCM2 pathway and enables BRCA1-deficient cells to avoid further genomic instability. Thus, BRCA1 and WEE1 inhibit DNA replication initiation in a parallel manner to ensure genome stability for mammary gland development during pregnancy.

overall_design: Identification of genes expressed in WT vs. Mutants with four stage pregnancy (v=0, 10 12, 18 mounths) with three replications per group.

first: Xiaoling

last: Xu

first: Eric

first: Weiping

first: Haiqing

last: Fu

first: Mirit

middle: I

last: Aladjem

first: Chu-Xia

last: Deng


title: Development of potent and selective KDM5 covalent inhibitors

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Histone lysine demethylase (KDMs) are involved in the dynamic regulation of gene expression by reversible regulation of the methylation levels on lysine residues in histone tails. Among the KDMs, the jumonji (JmjC)-domain-containing KDMs (KDM2-7) are Fe(II), 2- OG (α-ketoglutarate) and molecular oxygen-dependent enzymes that employ an oxygenase mechanism to demethylate specific methylation states at various histone sites. KDMs play a critical role in several biological processes such as cell differentiation, inflammation, cancer progression and resistance. Achieving selectivity over the different families of KDMs has been a major challenge. Here we report potent and selective KDM5 covalent inhibitors designed to target a cysteine residue only present in the KDM5 sub-family. In vitro assays show that compounds are selective for the KDM5 sub-family, showing potencies in the low nanomolar range, with higher affinity for KDM5A/B. The covalent binding to the targeted proteins was proved by MS. A kinetic approach was studied in order to describe the components of overall inhibitor potency (reversible binding and chemical reactivity), showing a time-dependent decrease of IC50 values for irreversible inhibition. Additional 2-OG competition assays show that compounds were non 2-OG competitive and target engagement and ChIPs-seq assays showed that the compounds inhibited the KDM5 members in cells in the low micromolar and they induce a global increase of the H3K4Me3 mark.

overall_design: HEK293 cells were clustured for 72 hours in the presence of KDM5 covalent inhibitors, KDOPZ-25, KDOPZ-32, KDOPZ-34, KDOPZ-55, KDOPZ-36, plus DMSO control. Cells were harvested and SF9 cells were spiked at 15%. ChIP-seq was then performed on these samples using H3K4me3 antibody.

first: Paul

last: Brennan


title: A gene regulatory network driven by LIM homeobox 1 (LHX1) for embryonic head development

city: WESTMEAD

first: PIERRE

last: OSTEIL

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI


title: A gene regulatory network driven by LIM homeobox 1 (LHX1) for embryonic head development (RNA-seq)

summary: Development of the embryonic head is driven by the activity of gene regulatory networks of transcription factors. LHX1 is a homeobox transcription factor that plays an essential role in the formation of the embryonic head. The loss of Lhx1 function results in anterior truncation of the embryo caused by the disruption of morphogenetic movement of tissue precursors and the dysregulation of WNT signaling activity. Profiling the gene expression pattern in the Lhx1 mutant embryo revealed that tissues in anterior germ layers acquire posterior tissue characteristics, suggesting Lhx1 activity is required for the allocation and patterning of head precursor tissues. Here, we used LHX1 as an entry point to delineate its transcriptional targets and interactors and construct a LHX1-anchored gene regulatory network. Using a gain-of-function approach, we identified genes that immediately respond to Lhx1 activation. Meta-analysis of the datasets of LHX1-responsive genes and genes expressed in the anterior tissues of mouse embryos at head-fold stage, in conjunction with published Xenopus embryonic LHX1 (Xlim1) ChIP-seq data, has pinpointed the putative transcriptional targets of LHX1 and an array of genetic determinants functioning together in the formation of the mouse embryonic head.

overall_design: Total RNA obtained from FLAG-Lhx1 and FLAG-Lhx1 mutant embryoid bodies differentiated over 2 days with or without doxycycline treatment for 16 hours. There are three replicates per condition.

first: Tennille

last: Sibbritt

first: Chi

middle: K

last: Ip

first: Pierre

last: Osteil

first: Patrick

last: Tam

first: Nicolas

last: Fossat


title: Transcriptome-wide view of endosomal mRNP transport

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg


title: Transcriptome-wide view of endosomal mRNP transport [iCLIP ]

summary: Spatiotemporal protein expression is mediated by active transport and local translation of mRNAs. Key factors of the transport machinery are RNA-binding proteins (RBPs) that recognise mRNAs as cargo for motor-based transport. However, a global view of transported mRNAs with cognate RBP binding sites is missing. Here, we cast a transcriptome-wide view on endosomal mRNP transport in Ustilago maydis by studying the newly identified endosomal RBP Grp1 and the key transport RBP Rrm4 in a comparative iCLIP approach. This uncovered thousand of cargo mRNAs bound by both RBPs.

overall_design: in vivo iCLIP data to study the RNA binding of components of the mRNA transport machinery in hyphae of the phytopathogenic fungus Ustilago maydis

first: Lilli

last: Olgeiser


title: Transcriptome-wide view of endosomal mRNP transport [RNA-Seq]

overall_design: RNA-Seq experiment to analyze the transcriptome of hyphae of the phytopathogenic fungus Ustilago maydis


title: tRFs quantification in HaCaT cell culture

status: Public on Dec 09 2018

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: Detection of tRNA-derived fragments (tRFs) in HaCaT cells under normal growth conditions without treatment

overall_design: Isolation of small RNA fraction using miRVANA isolation kit according to the manufacturer's protocol. Library construction was performed using total RNA-Seq Kit v2 (Ion Torrent) according to the manufacturer's protocol

first: Constantinos

last: Stathopoulos

first: Katerina

last: Grafanaki

first: Dimitrios

last: Anastasakis

first: George

last: Kyriakopoulos

first: Ilias

last: Skeparnias

first: Sophia

last: Georgiou


title: Gene expression profiling in the white matter with oligodendroglial stage-specfic activation or inhibition of ErbB receptors

status: Public on Dec 08 2018

city: Hangzhou

first: Yanmei

last: Tao

state: Zhejiang

address: 16 Xuelin Street, Xiasha

institute: Hangzhou Normal University

summary: To gain insight of how ErbB signaling in oligodendroglial progenitor cell to newly-formed oligodendrocyte stages (OPC-NFOs) regulated adolescent oligodendroglial development, we did RNA-seq analyses of subcortical white matter tissues isolated from Sox10-ErbB2V664E mice or Sox10-dnEGFR mice and their littermate controls after doxycycline treatment, respectively. Both mice were revealed hypomyelination although OPC proliferation or survival were differently altered in them. For each group we sequenced three pairs of samples, and revealed 2298 genes that had altered expression in the white matter of Sox10-ErbB2V664E mice, as well as 1184 genes that had altered expression in that of Sox10-dnEGFR mice. By comparing the two groups of genes, we identified 50 genes which had opposite expression tendency in the two mouse lines which was potentially involved in ErbB signaling and contributed to regulation of OPC proliferation and survival. Meanwhile, we identified 68 genes which exhibited similar expression tendency in Sox10-ErbB2V664E and Sox10-dnEGFR mice which had potential in the regulation of central myelination.

overall_design: Subcortical white matter isolated from Sox10-dnEGFR and littermate TRE-dnEGFR controls with doxycycline treatment from P21-P35, or Sox10-ErbB2V664E mice and littermate TRE-ErbB2V664E controls with doxycycline treatment from P21-P30, were used for global transcriptome analysis by lc-bio Co (Hangzhou, China). After the ﬁnal transcriptome was generated,StringTie was used to perform expression level for mRNAs by calculating FPKM.

first: Xu

last: Hu


title: The RGD sequence in fibrillin-1 regulates mRNA expression

city: Montreal

first: Dieter

middle: P.

last: Reinhardt

state: Quebec

address: 3640 University Street

country: Canada

institute: McGill University

summary: Fibrillins are the major components of microfibrils in the extracellular matrix of elastic and non-elastic tissues. Fibrillin-1 contains one evolutionarily conserved Arg-Gly-Asp (RGD) sequence which mediates cell-matrix interactions through cell-surface integrins. Mutations in close vicinity to the RDG sequence lead to heritable disorders, including Marfan syndrome and stiff skin syndrome.  Two recombinant fibrillin-1 fragments were produced, one wild-type RGD-containing fragment and one fragment containing a mutant RGA sequence, which has been previously shown to abolish interactions with integrins. To determine the differential regulation of signaling pathways, microarray analysis of mRNA expression was conducted using Affymetrix Human Gene 2.0 ST chips. The mRNA expression levels were compared after 24 hours of interaction between human skin fibroblasts (HSFs) and the RGD- and RGA-containing fibrillin-1 fragments.

overall_design: Microarray analysis of HSFs was conducted for mRNAs in biological quadruplicates for each condition using Human Gene 2.0 ST chips (Affymetrix). Values are expressed as rF1M-RGA versus rF1M-WT.

first: Karina

last: Zeyer


title: The RGD sequence in fibrillin-1 regulates miRNA expression

summary: Fibrillins are the major components of microfibrils in the extracellular matrix of elastic and non-elastic tissues. Fibrillin-1 contains one evolutionarily conserved Arg-Gly-Asp (RGD) sequence which mediates cell-matrix interactions through cell-surface integrins. Mutations in close vicinity to the RDG sequence lead to heritable disorders, including Marfan syndrome and stiff skin syndrome.  Two recombinant fibrillin-1 fragments were produced, one wild-type RGD-containing fragment and one fragment containing a mutant RGA sequence, which has been previously shown to abolish interactions with integrins. To determine the differential regulation of signaling pathways, microarray analysis of microRNA expression was conducted using Affymetrix miRNA3.0 chips. The microRNA expression levels were compared after 24 hours of interaction between human skin fibroblasts (HSFs) and the RGD- and RGA-containing fibrillin-1 fragments.

overall_design: Microarray analysis of HSFs was conducted for miRNAs in biological quadruplicates for each condition using miRNA 3.0 chips (Affymetrix). Values are expressed as rF1M-RGA versus rF1M-WT.


title: The RGD sequence in fibrillin-1 regulates mRNA and miRNA expression

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

platform_organism:
Homo sapiens
synthetic construct


title: Analysis of transcrptomes of Danon patient derived hiPSC-cardiomyocytes by RNA-deep Sequencing

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta University

summary: Control and Danon patients derived hiPSCs were differentiated into cardiomyocytes. RNA-seq was performed to analyze the gene expression differences between control and Danon lines.

overall_design: hiPSC-CMs with over 90% purity were cultured in RPMI1640/B27 medium for about 50 days. Total RNAs were prepared from different hiPSC-CM lines and sequenced on a HiSeq 4000 sequencing system (Illumina).

first: Congwu

last: Chi

first: Kunhua

last: Song


title: Nanostring expression analysis of splenocytes from 17-β estradiol (E2) and synthetic 17α-ethinyl estradiol (EE) exposed feamle NZB/WF1 lupus mice

first: Rujuan

last: Dai

platform_organism:
Mus musculus
Mus musculus domesticus


title: Transciptome analysis of acute myocardial infarction

city: Beijing

first: Yan

last: Li

address: An Zhen Road 2, An Ding Men Wai Street, Chaoyang District

institute: Beijing Institute of Heart, Lung and Blood Vessel Diseases

summary:
Analysis of peripheral blood specimens from patients with acute myocardial infarction (AMI).
Results provide insight into molecular mechanisms associated with AMI.

overall_design: The peripheral venous blood specimens from 4 non-ST-segment elevation AMI patients.


title: GR mutation in mice changes the genome-wide epigenome of frontal cortex in a highly sex-specific manner

status: Public on Dec 07 2018

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

summary: We found that the GR mutation leads to a changes of the DNA methylation landscape in frontal cortex of c57/bl6n male mice

overall_design: Frontal cortex  tissue of  GR+/+ vs. glucocorticoid receptor-impaired (GR-i)  mice was analyzed fro DNA methylation state on GR peaks genome-wide by GR-ChIP-bisulfite-sequencing

first: M

last: Schmidt

first: E

first: R

last: Zhou

first: A

last: Ruder

last: Ludiro

first: F

last: Lapert

last: Macedo da Cruz

first: P

last: Sandrini

first: T

last: Calzoni

last: Luoni

last: Massart

first: MA

last: Riva

last: Gass

last: Szyf


title: Temporal gene expression patterns (Next Generation Sequencing) in liver tumourigenesis of hepatocyte-specific deletion of shp2 and/or pten

city: SAN DIEGO

first: gaowei

last: wang

state: CALIFORNIA

address: 3393 Lebon DR, APT 202

institute: University of California San Diego

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to reveal dynamics of liver tumourigenesis in different mouse model and identify some key regulators that control HCC initiation or progression. We also try to define a index based on transcriptome of samples to quantify tumor development stage.
Methods: mRNA profiles of wild-type (WT),  hepatocyte-specific shp2 deletion (Shp2−/−) mice (SKO), hepatocyte-specific pten deletion (Pten−/−) mice (PKO), and hepatocyte-specific shp2 and pten deletion mice (DKO) were generated by deep sequencing. The sequence reads that passed quality filters were mapped to Mouse genome using STAR, and mRNA profiles were obtained using cuffdiff.
Results: quanlity control of mRNA profiles showed that the data captured key features of phenotypes. Significantly changed genes, pathways, biolgocial processes, ligand and receptor, epigenetic regulators et al of SKO, PKO, DKO mice at differnet age were obtaiend. Temporal gene expression patterns during liver tumorigenesis in SKO, PKO and DKO mice were obtained.
Conclusions: Our study represents the first detailed analysis of temporal transcriptomes during liver tumourigenesis, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comprehensive investigations of expression profiles.

overall_design: mRNA profiles of wild-type (WT),  hepatocyte-specific shp2 deletion (Shp2−/−) mice (SKO), hepatocyte-specific pten deletion (Pten−/−) mice (PKO), and hepatocyte-specific shp2 and pten deletion mice (DKO) were generated by deep sequencing, with replicates, using Illumina.

first: Gaowei

last: Wang

first: Xiaolin

last: Luo

first: Gen-sheng

last: Feng


title: Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

city: Indianapolis

first: Yupeng

last: Li

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary:
Background: Activation of microglia, the resident immune cells of the central nervous system, is a prominent pathological hallmark of Alzheimer’s disease (AD). However, the gene expression changes underlying microglia activation in response to tau pathology remain elusive. Furthermore, it is not clear how murine gene expression changes relate to human gene expression networks.

Methods: Microglia cells were isolated from rTg4510 tau transgenic mice and gene expression was profiled using RNA sequencing. Four age groups of mice (2-, 4-, 6-, and 8-months) were analyzed to capture longitudinal gene expression changes that correspond to varying levels of pathology, from minimal tau accumulation to massive neuronal loss. Statistical and system biology approaches were used to analyze the genes and pathways that underlie microglia activation. Differentially expressed genes were compared to human brain co-expression networks.

Results:Statistical analysis of RNAseq data indicated that more than 4000 genes were differentially expressed in rTg4510 microglia compared to wild type microglia, with the majority of gene expression changes occurring between 2- and 4-months of age. These genes belong to four major clusters based on their temporal expression pattern. Genes involved in innate immunity were continuously up-regulated, whereas genes involved in the glutamatergic synapse were down-regulated. Up-regulated innate inflammatory pathways included NF-κB signaling, cytokine-cytokine receptor interaction, lysosome, oxidative phosphorylation, and phagosome. NF-κB and cytokine signaling were among the earliest pathways activated, likely driven by the RELA, STAT1 and STAT6 transcription factors. The expression of many AD associated genes such as APOE and TREM2 was also altered in rTg4510 microglia cells. Differentially expressed genes in rTg4510 microglia were enriched in human neurodegenerative disease associated pathways, including Alzheimer’s, Parkinson’s, and Huntington’s diseases, and highly overlapped with the microglia and endothelial modules of human brain transcriptional co-expression networks.

Conclusion: This study revealed temporal transcriptome alterations in microglia cells in response to pathological tau perturbation and provides insights into the molecular changes underlying microglia activation during tau mediated neurodegeneration.

overall_design:
Compare the microglial cell gene expression changes in rTg4510 tau transgenic mice and wild type at four age groups (2-, 4-, 6-, and 8-months)

The rTg4510 mouse is a tauopathy model providing researchers with temporal control over mutant tau transgene expression. The mice express a repressible form of human tau containing the P301L mutation that has been linked with familial frontotemporal dementia. More information can be found here, https://www.alzforum.org/research-models/rtgtaup301l4510

first: Hong


title: Uncovering a new role for MexMN-OprM in efflux of β-lactams and a novel regulatory circuit (MmnRS) controlling MexMN expression

city: Emeryville

first: Charles

last: Dean

address: 5300 Chiron Way

institute: Novartis Institutes for Biomedical Research

summary:
Target (MexB) and efflux based mechanisms decreasing the effectiveness of the efflux pump inhibitor D13-9001 in P. aeruginosa PAO1: uncovering a new role for MexMN-OprM in efflux of β-lactams and a novel regulatory circuit (MmnRS) controlling MexMN expression
Efflux pumps contribute to antibiotic resistance in Gram-negative pathogens. Correspondingly, efflux pump inhibitors (EPIs) may reverse this resistance. D13-9001 specifically inhibits MexAB-OprM in P. aeruginosa. Mutants with decreased susceptibility to MexAB-OprM inhibition by D13-9001 were identified and these fell into two categories; those having alterations in the target MexB (F628L and ΔV177) and those with mutations in PA1438 (L172P substitution) which encoded a putative sensor kinase of unknown function. The alterations in MexB were consistent with reported structural studies of D13-9001 interaction with MexB. The PA1438L172P alteration mediated a >150-fold upregulation of MexMN pump gene expression and >50-fold upregulation of PA1438 and the neighboring response regulator gene PA1437. We propose that these be renamed as mmnR/mmnS for MexMN Regulator and Sensor. MexMN was shown to partner with the outer membrane channel protein OprM and to pump several β-lactams, monobactams and tazobactam. Upregulated MexMN functionally replaced MexAB-OprM to efflux these compounds but was insusceptible to inhibition by D13-9001. MmnSL172P also mediated a decrease in susceptibility to imipenem / biapenem that was independent of MexMN-OprM. Expression of oprD, encoding the uptake channel for these compounds was downregulated, suggesting that this channel is also part of the MmnSR regulon. RNA-seq of cells encoding MmnSL172P revealed among other things an interrelationships between regulation of mexMN and genes involved in heavy metal resistance.

overall_design: RNA-seq profiling of gene expression in Pseudomonas aeruginosa PAO1 and a mutant in gene PA1438 (MmnS), biological triplicates

first: Srijan

last: Ranjitkar

first: Adriana

last: Jones

first: Mina

last: Mostafavi

first: Zachary

last: Zwirko

first: Oleg

last: Iartchouk

first: S

last: Barnes

first: John

last: Walker

first: Thomas

last: Willis

first: Patrick

last: Lee


title: Microarray Data of U87 and HEK293 cells expressing CIC and their respective controls

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

summary:
Gene expression data generated for the purpose of analyzing the effect of CIC over-expression
Affymetrix Gene Chip

overall_design: RNA isolated directly from U87 and HEK293 cells expressing CIC

first: Severa

last: Bunda


title: Single Cell RNA sequence data from a human ovarian cancer sample

city: Minneapolis

first: Timothy

middle: Kaehler

last: Starr

state: MN

address: 420 Delaware St SE

department: Ob-Gyn & Women's Health

institute: University of Minnesota

summary:
Purpose: Investigate cellular heterogeneity in a fresh human ovarian cancer tissue sample
Methods: Enzymatic digestion of fresh tissue sample collected from the operating room to produce single cell suspension. Cells were labelled with fluorescent antibodies to CD3, CD14, CD19, CD20, CD56 and FACS sorted to remove immune cells.  The negative population was used for sequencing. Single cells were processed using the Fluidigm C1 Chip to generate barcoded cDNA for each cell.  Amplifed cDNA was sequenced using an Illumina HiSeq 2500 machine.
Results: Single cell RNA sequence data was obtained for 92 cells and a "bulk" sample of 1000 cells. 26 cells were removed from analysis due to quality control standards. The remaining 66 cells and the bulk sample were analyzed.
Conclusion: Single cell RNA sequence analysis reveals heterogeneity in gene expression in cells harvested from a high grade ovarian serous cancer

overall_design: A single cell suspension generated from a fresh high grade serous ovarian cancer sample was run through two Fluidigm C1 chips to isolate single cells and produce barcoded cDNA. Sequencing was performed in a single lane of an Illumina HiSeq 2500 machine. 92 single cells were sequenced and 1 bulk sample was sequenced, for a total of 93 samples.


title: Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

summary: RNA-seq analysis of BJ cells overexpressing RasV12 and escaping senescence

overall_design: Immortalized BJ-hTERT cells expressing an oncogenic version of Ras under the control of a doxycyclin-inducible promoter were grown for 60 days in the presence of Dox to induce oncogene-induced senescence (OIS). Three individual clones escaping senescence were isolated and were analyzed by RNA-seq.

first: Hélène

last: Tourrière

first: Philippe

last: Pasero


title: RNA-seq of HUVEC ± shRNA knockdown of SENCR

city: Rochester

first: Joseph

last: Miano

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: To assess the transcriptome of HUVEC where the SENCR is knocked down. SENCR is a lncRNA we show stabilizes the endothelial cell adherens junction by binding CKAP4 and indirectly localizing CDH5 at the cell membrane. The RNA-seq study was carried out to ascertain whether the effects of SENCR could be attributed to a function associated with sponging endogenous microRNAs that target proteins of the adgherens junction.

overall_design: HUVEC were cultured in media and transfected with lentivirus containing a short-hairpin RNA to SENCR and a GFP tag. Cells were tracked in the dish until all cells exhibited GFP positivity which would inducate all cells expressed the shRNA SENCR in lentivirus. Sister plates of cells were transduced with a scambled shRNA with GFP and were similarly tracked for 100% GFP expression. At ~3 days post-transduction, all experimental and control replicates were harvested for total RNA isolation.

first: Qing

last: Lyu


title: H3K36me2 occupancy profiling by high throughput sequencing from nsd2 wt and ko germinal center B cells

city: Nanjing

first: jingjing

last: chen

address: 101 Longmian Road

institute: Nanjing Medical University

summary: WHSC1 catalyzes dimethylation of lysine 36 on histone H3, which is upregualted in germinal center B cells. This study aimed to understand the H3K36me2 genome-wide alterations by analysing CHIP-seq data between wt and ko germinal center B cells.

overall_design: 4×10e6 germinal center B cells were sorted from SRBC immunized nsd2 wt and ko mice then flash frozen on dry ice for CHIP.

first: J

last: Chen

first: X

last: Wang


title: RNA-seq data from nsd2 wt and ko germinal center B cells

summary: The goal of this study was to invetigate the mechanisms by which nsd2 regulate germinal center reaction by comparing RNA-seq data between nsd2 wt and ko germinal center B cells

overall_design: 2×10e6 nsd2 wt and ko germinal center B cells were sorted from SRBC immunized mice and extracted in 1mL trizol. Library were then generated with illumina protocol and subject to NGS and bioinformatic analysis.


title: Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Multiple myeloma (MM), a plasma cell (PC) malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity within and between patients is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply single cell RNA-seq to study the heterogeneity of 40 individuals along the MM progression spectrum. We define malignant PC at single cell resolution, demonstrating high inter-patient variability that can be explained by expression of known MM drivers and additional putative factors. Within newly diagnosed patients, we identify extensive sub-clonal structures for 10/29 patients. In asymptomatic patients with early disease and in minimal residual disease post-treatment, we detect tumor PC for a subset of the patients, with the same drivers of active myeloma. Single cell analysis of rare circulating tumor cells (CTC) allows detection of malignant PC, which reflect the BM disease. Our work establishes scRNA-seq for dissecting blood malignancies and devising detailed molecular characterization of tumor cells in symptomatic and asymptomatic patients.

overall_design: The study includes 29 newly diagnosed patients with plasma cell neoplasms and 11 control donors, for which bone marrow plasma cells were single cell sorted by FACS, and their mRNA sequenced. For 11 patients, targeted genomic DNA panel analysis for myeloma was performed.

first: Guy

last: Ledergor

first: Assaf

last: Weiner

first: Elli

last: Papaemmanuil


title: The splicing factor RBM25 controls MYC activity in Acute Myeloid Leukemia

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaløes Vej 5, 4.

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: Cancer sequencing studies have implicated regulators of pre-mRNA splicing as important disease determinants in Acute Myeloid Leukemia (AML), but the underlying mechanisms have remained elusive. We hypothesized that “non-mutated” splicing regulators may also play a role in AML biology and therefore conducted an in vivo shRNA screen in a mouse model of CEBPA mutant AML. This led to the identification of the splicing regulator RBM25 as a novel tumor suppressor, and down-regulation of RBM25 increased proliferation and decreased apoptosis in human leukemic cell lines. Mechanistically, we could show that RBM25 controlled the splicing of key genes, including those encoding the apoptotic regulator BCL-x and the MYC inhibitor BIN1. Specifically, we demonstrated that RBM25 acts as a regulator of MYC activity and sensitizes cells to increased MYC levels. This mechanism also appears to be operative in human AML patients where RBM25 levels correlative inversely with MYC activity and clinical outcome.

overall_design: Examined transcriptome from U937 cells in biological triplicates.

first: Ying

last: Ge


title: Single cell RNA-Seq of four human kidney organoids

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

institute: Murdoch Childrens Research Institute

summary: These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from four biological replicates of iPSC-derived human kidney organoids, in two batches, differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). The aggregated human organoid data contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.

overall_design: Examination of the celular composition of human kidney organoids

first: B

last: Phipson

first: L

first: A

middle: N

last: Combes


title: Characterisation of the secondary effects of sub-inhibitory concentrations of 1-(1-naphthylmethyl)-piperazine (NMP) in Klebsiella pneumoniae

status: Public on Dec 06 2018

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Efflux of antimicrobial compounds from bacterial cells is one of the important mechanisms responsible for multi-drug resistance (MDR). Inhibiting the activity of efflux pumps using chemosensitizers like 1-(1-naphthylmethyl)-piperazine (NMP) is currently considered as a promising strategy to overcome MDR. However, additional effects of NMP other than inhibition are rarely if ever considered. Here, using phenotypic, phenotypic microarray and transcriptomic assays we show that NMP plays a role in membrane destabilization in MDR Klebsiella pneumoniae MGH 78578 strain. The observation of membrane destabilization was supported by RNA-seq data which showed that many up-regulated genes were either directly involved in responses to envelope stress or bacterial repair systems which are essential to maintain viability in an environment containing NMP. Membrane destabilization happens as early as 15 minutes post-NMP treatment. We postulate that the early membrane disruption leads to destabilization of inner membrane potential, impairing ATP production and consequently resulting in efflux pump inhibition.

overall_design: β-Lactamase activity, membrane potential and Transmission Electron Microscopy assays were used to assay the NMP mediated membrane destabilisation in MDR Klebsiella pneumoniae MGH 78578 strain. We further used the Phenotypic Microarray (Biolog) and RNA-seq to elucidate the transcriptional and metabolic signals. Crystal violet-based assays were also used to assay the biofilm formation ability of NMP treated bacterial cells.

first: João

last: Anes

first: Dechamma

last: Muthappa

first: Séamus

last: Fanning

first: Shabarinath

last: Srikumar


title: Epigenome analysis of ependymoma cell lines

city: Nottingham

first: Hazel

middle: Anne

last: Rogers

address: Medical School

department: Clinical Sciences

institute: University of Nottingham

summary: DNA methylation profiling using Illumina Infinium HumanMethylation450 BeadChip arrays was used to assign cell lines to previously defined subgroups.

overall_design: Bisulphite converted DNA from 6 ependymoma cell lines were hybridised to Infinium HumanMethylation450 BeadChip arrays.

first: Rebecca

middle: J

last: Chapman

first: Martin

last: Sill

first: Kristian

last: Pajtler

first: Stefan

last: Pfister

first: Richard

middle: G

last: Grundy


title: RNA-Seq of PreCFU-E and CFU-E progenitors from wild type and Scf mutants

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

institute: University of Texas Southwestern Medical Center

summary: It has been shown previously that endothelial cells and LepR+ stromal cells are the main sources of SCF in vivo in the mouse bone marrow. We tested whether SCF from endothelial cells and/or LepR+ stromal cells is important for the maintenance of hematopoietic progenitors and erythroid progenitors in mouse bone marrow by conditional deletion of Scf from these two cell types. We discovered that Scf deletion from LepR+ stromal cells, but not endothelial cells, reduced the numbers of hematopoietic progenitors and erythroid progenitors in mice. We performed RNA-Seq on PreCFU-E and CFU-E progenitors from control mice and from mice with Scf deletion from LepR+ stromal cells. We discovered that lack of SCF from LepR+ cells induces a premature differentiation of PreCFU-E and CFU-E progenitors.

overall_design: Examination of gene expression profile in 2 cell tyeps from 3 different genetic backgrounds

first: Stefano

last: Comazzetto

first: Malea

last: Murphy

last: Berto

first: Elise

last: Jeffery

first: Sean

last: Morrison


title: Proteogenomic characterization of human early-onset gastric cancer

city: Seoul

first: Sang-Won

last: Lee

address: 145 Anam-ro Seongbuk-gu

department: Chemistry

country: South Korea

institute: korea University

summary: We report proteogenomic analysis of diffuse gastric cancers (GCs) in young population. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.

overall_design: Transcripome profiling of tumor tissues and adjacent normal tissues from 80 patients in the  early-onset gastric cancer(EOGC) cohort.

first: Daehee

last: Hwang


title: 3' droplet-based single cell RNA sequencing of a human small intestinal tissue and human small intestinal organoids

city: Tokyo

first: Masayuki

last: Fujii

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

summary: Using 3' droplet-based single cell sequencing, we profiled single cells derived from a fresh human small intestinal epithelial tissue and human small intestinal organoids cultured with either IGF1/FGF2 or EGF/p38i.

overall_design:
EpCAM+ live single cells from a human intestinal tissue and live cells from human small intestinal organoids were FACS-sorted and subjected to sequencing.

**Raw data not provided because the current study is not approved to release personally identifiable information.**

first: Kohta

last: Toshimitsu


title: XBP1-KLF9 axis acts as a molecular rheostat to control the transition from adaptive to cytotoxic unfolded protein response

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Elevation of ER stress above a critical threshold causes accumulation of XBP1s protein sufficient for binding to the promoter and activation of a gene encoding a transcription factor KLF9. In turn, KLF9 induces expression of two regulators of ER calcium storage, TRIM38B and ITRP1, facilitating additional calcium release from ER, exacerbation of ER stress, and cell death.

overall_design: RNA was isolated from WI38 cells transduced with empty vector, KLF9 cDNA-expressing vector, control shRNA or 2 independent shRNAs to KLF9. RNA samples were subjected to deep sequencing using Illumina instrumentation.

first: Emily

middle: E

last: Fink

first: Mikhail

middle: A

last: Nikiforov


title: Differences in microRNA expression in breast cancer between women of African and European ancestry

city: Buffalo

first: Jie

last: Wang

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

summary: Differences in microRNAs have not been well studied as potential mechanisms underlying the breast cancer disparity. A number of miRNAs were differentially expressed not only by tumor subtype but by ancestry, indicating differences in tumor biology of breast cancer between women of African and European ancestry. Findings may contribute to a better understanding of the biology of breast cancer disparities and help develop more targeted preventative and therapeutic strategies.

overall_design: miRNA expression profile of normal tissue and breast cancer tissue.

first: Zhihong

last: Gong


title: PRMT5 Interacts with the BCL6 Oncoprotein and is Required for Germinal Center Formation and Lymphoma Cell Survival

city: New York

first: Tharu

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

summary: We have found that PRMT5 methylates BCL6 and is needed for its full transcriptional repressor activity. Concomitant inhibition of both BCL6 and PRMT5 exhibits synergistic killing of BCL6-expressing lymphoma cells.

overall_design: SUDHL6 cells were treated with DMSO or the PRMT5 inhibitor, GSK591, for 24 and 96 h. Total RNA was harvested from cells after vehicle or GSK591 treatment and used for expression profiling via mRNA-seq.

first: Ari

last: Melnick


title: Distinct transcriptomic profiles of early-onset atopic dermatitis in blood and skin of pediatric patients

first: Ariel

last: Israel

address: 1425 Madison Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary:
Background: Atopic dermatitis (AD) predominantly affects young children, but our understanding of AD pathogenesis is based on skin and blood samples from longstanding adult AD. Genomic biopsy profiling from early pediatric AD showed significant Th2 and Th17/Th22-skewing, without the characteristic adult Th1 up-regulation. Since obtaining pediatric biopsies is difficult, blood gene expression profiling may provide a surrogate for the pediatric skin signature.

Objective: To define the blood profile and associated biomarkers of early moderate-to-severe pediatric AD.

Methods: We compared microarrays and RT-PCR of blood cells from 28 AD children (<5yrs and within 6 months of disease onset) to healthy control blood cells. Differentially expressed genes/DEGs in blood (fold change/FCH>1.2 and false discovery rate/FDR<0.05) were then compared with skin DEGs.

Results: Eosinophil and Th2 markers (IL5RA, IL1RL1/ST2, HRH4, CCR3, SIGLEC8, PRSS33, CLC from gene arrays; IL13/IL4/CCL22 from RT-PCR) were upregulated in early pediatric AD blood, while IFNG/Th1 was decreased. Th1 markers were negatively correlated with clinical severity (EASI, pruritus, transepidermal water loss/TEWL), whereas Th2/Th17-induced IL19 was positively correlated with SCORAD. While a few RT-PCR-defined immune markers (IL13/CCL22) were increased in blood, as previously also reported for skin, there was minimal overlap based on gene array DEGs.

Conclusion: The whole blood signature of early moderate-to-severe pediatric AD blood cells show predominantly a Th2/eosinophil profile, but markers largely differ from the skin profile. Given their complementarity, pooling of biomarkers from blood and skin may improve profiling and predictions, providing insight regarding disease course allergic comorbidity development, and response to systemic medications.

overall_design: We performed microarray studies in skin from blood in infants and young children (<5yo) with early-onset AD (<6mo), compared to age-matched controls .

first: Patrick

last: Brunner

first: Emma

last: Guttman-Yassky


title: The THO Complex-Dependent Posttranscriptional Control Contributes to Vascular Smooth Muscle Cell Fate Decision

city: Durham

first: Li

address: 111 T.W. Alexander Dr

institute: NIH

summary: We applied RNA-Seq to analyze the effects of silencing of Thoc2 or Thoc5, two components of the THO complex, in cultured VSMC. The result revealed that Thoc5 silencing closely resembled the gene expression changes induced upon PDGF-BB/PDGF-DD treatments in cultured VSMCs. Mechanistically, our RIP-Seq data revealed both Thoc2 and Thoc5 preferentially interacted with VSMC marker gene mRNAs and mediated their expression. Interestingly, mRNAs that lost Thoc2 or Thoc5 binding during VSMC dedifferentiation were enriched for genes important for VSMC identity. In addition, silencing of Thoc2 or Thoc5 led to dedifferentiation of VSMCs in vitro, characterized by decreased VSMC marker gene expression and increased migration and proliferation. Furthermore, we performed immuno-histochemical staining against Thoc2 and Thoc5, and found a dramatic reduction in their expression in human arteries undergoing carotid endarterectomy (CEA) compared to normal internal mammary arteries (IMA). Notably, Thoc5 overexpression in injured rat carotid arteries significantly repressed loss of VSMC marker gene expression and neointima formation. Together, our data introduce dynamic binding of THO to VSMC marker gene mRNAs as a novel mechanism contributing to VSMC fate decisions, and imply Thoc5 as a potential intervention node for vascular diseases.

overall_design: RNA-Seq of Thoc2 or Thoc5 silencing in cultured mVSMC; ChIP-seq of Thoc5 in wild-type cultured mVSMC; RIP-Seq of Thoc2 or Thoc5 in cultured mVSMC.

first: Fang

last: Yao

first: Xinli

last: Yuan


title: The combination of cantharidin and anti-angiogenic therapeutics presents synergistic antitumor effects against pancreatic cancer

city: Suzhou

first: Meng-Dan

last: Xu

address: Shizi Street

institute: the First Affiliated Hospital of Soochow University

summary: Background: Cantharidin, an active constituent of mylabris, is believed to have anti-tumor activity. Cantharidin selectively inhibit protein phosphatase 2A (PP2A), a repressor of oncogenic kinase pathways (ERK, JNK, NF-κB, and PKC). Cantharidin represses the growth and metastasis of pancreatic cancer cells in vitro. In the present study, we investigated the effects of cantharidin on pancreatic cancer xenografts in vivo.   Methods: Cells stably expressing luciferase were used to establish xenograft models. Xenograft growth was evaluated by living imaging. Gene expression was determined using a microarray, real-time PCR, a RayBiotech antibody array, and the Milliplex assay.   Results: Surprisingly, cantharidin significantly accelerated xenograft growth. Living imaging showed a rapid distribution of D-luciferin in cantharidin-treated xenografts, suggesting a rich blood supply. Immunohistochemistry confirmed increased angiogenesis. Microarray and antibody array identified upregulated pro-angiogenic and downregulated anti-angiogenic factors. The Milliplex assay suggested elevated secretion of IL-6, IL-8, TNF-α, and VEGF. ERK, JNK, NF-κB, and PKC pathway inhibitors attenuated the cantharidin-induced changes to pro-angiogenic gene expression. PKC pathway-inhibiting tamoxifen or antiangiogenic therapeutics, including Ginsenoside Rg3, bevacizumab, Apatinib, and Endostar antagonized the pro-angiogenic effect of cantharidin or its derivatives. These regimens presented remarkable synergistic antitumor effects in vivo.   Conclusion: Although cantharidin presents anti-tumor effects in vitro and has been applied in clinical practice, we revealed an unfavorable pro-angiogenic side effect. We recommend that the clinical application of cantharidin should be performed on the premise of anti-vascularization therapy.

overall_design: Examination of gene expression profiles after treatment with Ginsenoside Rg3 or tamoxifen in PANC-1 cells

first: Wei

last: Li


title: A DNA methylation reader complex that enhances gene transcription

city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

summary: DNA methylation generally functions as a repressive transcriptional signal, but it is also known to activate gene expression. In either case, the downstream factors remain largely unknown. By using comparative interactomics, we isolated proteins in Arabidopsis thaliana that associate with methylated DNA. Two SU(VAR)3-9 homologs, the transcriptional antisilencing factor SUVH1, and SUVH3, were among the methyl reader candidates. SUVH1 and SUVH3 bound methylated DNA in vitro, were associated with euchromatic methylation in vivo, and formed a complex with two DNAJ domain-containing homologs, DNAJ1 and DNAJ2. Ectopic recruitment of DNAJ1 enhanced gene transcription in plants, yeast, and mammals. Thus, the SUVH proteins bind to methylated DNA and recruit the DNAJ proteins to enhance proximal gene expression, thereby counteracting the repressive effects of transposon insertion near genes.

overall_design: This dataset includes: 4 ATAC-seq, 26 ChIP-seq, 14 whole genome bisulfite seq (WGBS) and 45 RNAseq datasets.

first: C


title: CRISPR-Cas9-based editing of histone H3 arginine 17 reveals its methylation-dependent regulation of Yap signaling and early mouse embryo development (genomic DNA-seq data set)

city: Guangzhou

first: Yunbo

last: Qiao

address: Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.

institute: Guangzhou University

summary: we use rAPOBEC-XTEN-Cas9n-UGI (BE3) to introduce a point mutation (R17H) into 8 loci of Hist1H3 by a single sgRNA and a pre-stop codon into Carm1 in early mouse embryo, and both strategies resulted in developmental defects in pre-implantation embryos and fetal stages with smaller or developmental-delayed embryos. Transcriptomic analysis revealed that Yap1 and cell cycle signaling pathways were dysregulated in Carm1 pre-stop and H3R17H embryos, and Yap1 overexpression could rescue the developmental defects. Our results establish the direct regulatory relationship between Carm1-mediated site-specific histone modifications and mouse embryo development, and we also demonstrate that Hippo-Yap1 acts downstream of Carm1-mediated H3R17me2a to regulate the embryonic development and size determination.

overall_design: Examination of on-target and off-target induced by base editing

first: Guang

last: Yang


title: CRISPR-Cas9-based editing of histone H3 arginine 17 reveals its methylation-dependent regulation of Yap signaling and early mouse embryo development (RNA-seq data set)

department: Precise Genome Engineering Center, School of Life Sciences

summary: We use rAPOBEC-XTEN-Cas9n-UGI (BE3) to introduce a point mutation (R17H) into 8 loci of Hist1H3 by a single sgRNA and a pre-stop codon into Carm1 in early mouse embryo, and both strategies resulted in developmental defects in pre-implantation embryos and fetal stages with smaller or developmental-delayed embryos. Transcriptomic analysis revealed that Yap1 and cell cycle signaling pathways were dysregulated in Carm1 pre-stop and H3R17H embryos, and Yap1 overexpression could rescue the developmental defects. Our results establish the direct regulatory relationship between Carm1-mediated site-specific histone modifications and mouse embryo development, and we also demonstrate that Hippo-Yap1 acts downstream of Carm1-mediated H3R17me2a to regulate the embryonic development and size determination.

overall_design: Examination of RNA expression profiles of E4.5 WT/H3R17H/Carm1-/- mouse embryos by deep sequencing.


title: Expression data from iPSCs, iPSC-derived neurons, PBMC-derived Monocytes, PBMC-derived Macrophages, PBMC-derived induced microglia

status: Public on Dec 05 2018

city: Boston

first: Roy

middle: H.

last: Perlis

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

overall_design: 5 cell types each with 2 to 5 replicates

middle: H

first: Steven

middle: D

last: Sheridan


title: RNA-seq and targeted deep sequencing data of base editing-mediated epigenome engineering in mouse embryo

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

overall_design: Refer to individual Series


title: Widespread inter-individual gene expression variability in Arabidopsis thaliana

first: James

last: Locke

address: Bateman St

institute: SLCU

summary: A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.

overall_design: RNA-seq were generated for 14 individual seedlings for each of the 12 following time points: ZT2, ZT4, ZT6, ZT8, ZT10, ZT12 (just before dusk), ZT14, ZT16, ZT18, ZT20, ZT22 and ZT24 (just before dawn).

first: Sandra

last: Cortijo


title: Paired Related Homeobox Protein 1 Regulates Quiescence in Human Oligodendrocyte Progenitors

first: Fraser

middle: James

last: Sim

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

summary: Human oligodendrocyte progenitor cells (hOPCs) persist into adulthood as an abundant precursor population of capable of division and differentiation. The transcriptional mechanisms that regulate hOPC homeostasis remain poorly defined. Herein, we identified paired related homeobox protein 1 (PRRX1) in primary PDGFaR+ hOPCs. We show that enforced PRRX1 expression resulted in reversible G0/1 arrest. While both PRRX1 splice variants reduced hOPC proliferation, only PRRX1a abrogated migration. hOPCs engraftment into hypomyelinated shiverer/rag2 mouse brain was severely impaired by PRRX1a, characterized by reduced cell proliferation and migration. PRRX1 induced a gene expression signature characteristic of stem cell quiescence. Both IFN-g and BMP signaling up-regulated PRRX1 and induced quiescence. Importantly, PRRX1 knockdown modulated IFN-g induced quiescence. In mouse brain, PRRX1 mRNA was detected in non-dividing OPCs and was up-regulated in OPCs following demyelination. Together, these data identify PRRX1 as a regulator of quiescence in hOPCs and as a potential regulator of pathological quiescence.

overall_design: Effect of PRRX1a or PRRX1b over-expression on hOPCs, 3 mCherry control, 3 PRRX1a, 3 PRRX1b

first: Jing

last: Wang

first: Darpan

last: Saraswat

first: Anjali

last: Sinha

first: Jessie

last: Polanco

first: Karen

last: Dietz

first: Melanie

last: O'Bara

first: Suyog

middle: U

last: Pol

first: Hani

last: Shayya


title: Unveiling the Role of the Most Impactful Cardiovascular Risk Locus Through Haplotype Editing at Cell

city: La Jolla

first: Kristin

last: Baldwin

state: California

address: 10550 North Torrey Pines Road

department: Department of Neuroscience

institute: The Scripps Research Institute

summary: The 9p21.3 cardiovascular disease locus is the most influential common genetic risk factor for coronary artery disease, accounting for ~10-15% of disease among non-African populations. The ~60kb risk haplotype is human-specific and lacks coding genes, hindering efforts to decipher its function. Genetic studies implicate the 9p21.3 locus and other risk genes to effects in the vascular wall. Here,  we use genome editing to delete the entire risk on non-risk haplotype from the genomes of human iPSCs and perform genomewide transcriptional profiling along the timecourse of their differentiation into vascular smooth muscle cells (VSMCs). These studies identify a network of ~3000 genes governed by the risk haplotype in VSMCs that predict deficits in cell division, adhesion and contraction, which we confirmufunctionally. Remarkably, deleting the risk haplotype reverts VSMCs to resemble the non-risk VSMCs, suggesting that the risk region drives a cell state transition.  transcriptionally and functionally. . Deleting the risk haplotype reverts these cells to reverted to the non-risk of iPSCs we show that the non-risk haplotype has little effect on locus we produce iPSCs from risk and non-risk individuals, delete each haplotype using genome editing and generate vascular smooth muscle cells (VSMCs). We show that risk VSMCs exhibit aberrant adhesion and contraction, concomitant with dramatically altered global transcriptional changes that are enriched in previously identified cardiovascular disease genes and pathways. Unexpectedly, deleting the risk haplotype rescues VSMC transcriptional identity and function, while expressing the 9p21.3-associated long non-coding RNA ANRIL induces risk phenotypes in non-risk VSMCs. This studies shows that the risk haplotype dominantly predisposes VSMCs to adopt perturbed phenotypes associated with cardiovascular disease and establishes haplotype-edited iPSCs as powerful tools for functionally annotating human-specific variation in non-coding genomic regions.

overall_design: RNA-seq proiles of 3 stages of human SMC differentiation starting from iPSC

first: Ali

last: Torkamani

first: Valentina

last: Lo Sardo

first: Pavel

last: Chubukov


title: Comparison of serum and saliva miRNAs for identification and characterization of mild Traumatic Brain Injury (mTBI) in adult mixed martial arts fighters

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We evaluated the utility of serum and salivary microRNAs (miRNAs) to serve as sensitive and specific peripheral biomarkers of possible mTBI. Levels of miRNAs were obtained stranded small RNA-sequencing. Functional outcomes were evaluated using a computerized assessment system that measured cognitive performance, body sway, and combined cognitive performance and body sway during dual task completion. We identified a subset of salivary and serum miRNAs that showed robust utility at predicting TBI likelihood and demonstrated quantitative associations with head impacts as well as cognitive and balance measures.

overall_design: Small RNA sequencing of serum and saliva in adult human subjects before, during, and after competition in an amateur mixed martial arts competition.


title: The genetic ancestry of modern Indus Valley populations from Northwest India

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

summary: We genotyped 45 new samples from 4 populations of Northwest India and combined it with previously published data to characterize the population structure of modern Northwest Indian populations in the context of their geographic neighbors across South Asia and West Eurasia.

overall_design: 45 samples were analysed with the Illumina HumanOmniExpress-24 Genotyping BeadChip and are described herein.

first: Richard

last: Villems

first: Mait

last: Metspalu

first: Gyaneshwer

last: Chaubey

first: Ajai

last: Pathak

first: Anurag

last: Kadiyan


title: The cytokine environment influence on human skin-derived T cells

city: Vienna

first: Philip

last: Kienzl

state: Vienna

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

summary: Illumina RNA sequencing to study DEGs between freshly isolated and emigrated skin T cells

overall_design: skin T cell RNA profile of freshly isolated T cells and emigrated T cells under IL-2, IL-4, TGF-beta and IL-2, IL-15 cytokine condition

first: Adelheid

last: Elbe-Bürger


title: Development and Validation of a Simplified Method to Generate Human Microglia from Pluripotent Stem Cells

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Rd

country: USA

institute: University of California, Irvine

summary: Comparison of published protocol (Abud et al. Neuron 2016) to simplified method of microglial differentiation which does not require hypoxia or FACS. We show each method produced highly similar microglia.

overall_design: Comparison of two microglia populations to blood monocytes

first: Amanda

last: McQuade


title: DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [CBD Methylation]

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

type: Methylation profiling by genome tiling array

summary:
The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays.
We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. We identified 2,726 differentially methylated CpGs mapping to 1,944 unique genes when comparing CBD patients to beryllium-sensitized (BeS) individuals without disease. 69% of these genes were also differentially expressed in CBD. Sarcoidosis patients exhibited directional consistency at many loci, but genome-wide significance was not achieved, likely due to heterogeneity in the patient population.

overall_design: RNA and DNA were extracted from BAL fluid from 8 CBD, 8 BeS, and 8 Sarcoidosis patients. DNA was bisulfite converted and hybridized to Illumina 450k Human Methylation arrays to profile differential methylation at CpGs genome-wide.

middle: V

first: Iain

middle: R

last: Konigsberg

first: Kristyn

last: MacPhail

first: Li

last: Li

first: Elizabeth

last: Davidson

first: Peggy

middle: M

last: Mroz

first: Nabeel

last: Hamzeh

first: May

last: Gillespie

first: Lori

last: Silveira

first: Tasha

last: Fingerlin

first: Lisa

last: Maier


title: DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [sarcexp]

overall_design: This cohort of 15 remitting and 9 progressive sarcoidosis patients, as defined in part by Scadding scale, were analyzed to detect epigenetic and transcriptomic differences within subsets of the heterogeneous sarcoidosis population. DNA and RNA were extracted from BAL fluid and analyzed on microarrays to define differential methylation and transcription genome-wide.


title: DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [sarcmeth]


title: hnRNP L protects mRNAs from nonsense-mediated mRNA decay

city: Bethesda

first: J. Robert

last: Hogg

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: Identification of RNAs differentially expressed upon treatment with nontargeting siRNA, hnRNP L siRNA, UPF1 siRNA, or hnRNP L and UPF1 siRNAs together.

overall_design: Paired-end high throughput RNA sequencing of total RNA from HEK-293 cells treated with siRNAs against hnRNP L, UPF1, or a non-targeting control (NS).

first: Aparna

last: Kishor

first: J


title: Single-cell transcriptomics confirms heterogeneity of contractile cells in large skin wounds

first: Maksim

last: Plikus

address: 845 Health Sciences Road

department: Developmental and Cell Biology

summary: We report transcriptomes of pre-sorted skin wound dermal cells. Post-wounding day (PWD) 12, 15 and 21 Zombie-neg;tdTomatoHi cells were  FACS sorted from Sm22-Cre;TdTomato mice.

overall_design: Examination of single cell heteregeneity in large skin wounds on PWD 12, 15 and 21

first: Christian

middle: F

last: Guerrero-Juarez


title: In vivo verification of the pathophysiology of lipoid congenital adrenal hyperplasia in the adrenal cortex

status: Public on Dec 04 2018

city: Shinjuku-ku

first: Yusuke

last: Mizuno

state: Tokyo

address: Shinanomachi 35

department: Pediatrics

institute: Keio University

summary: Our study showed that the steroidogenic capacity firstly decreased without tissue change (the first hit) and secondarily declined with tissue change (the second hit) in the adrenal cortex of lipoid congenital adrenal hyperplasia. The key feature of the secondary decline of steroidogenic capacity might be the decreased gene expression related to steroid biosynthesis following the lipid accumulation exacerbated by ACTH hypersecretion.

overall_design: Detection of the genes with significant fluctuation in expression between the mice before and 8 wk after TAM induction to regulate STAR expression.

first: Tomohiro

last: Ishii


title: DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease

first: Ivana

last: Yang


title: Characterization of Wnt-Tcf functions during Ciona heart development

first: wei

last: wang

address: 100 washington square east

department: Biology

institute: New York University

summary: To assay Tcf functions during early cardiopharyngeal specification, bulk RNAseq were performed to profile the FACS-purified cardiopharyngeal lineage cells isolated from 15 and 18hpf Ciona larvae with CRISPR/Cas9-mediated Tcf mutagenesis.

overall_design: Examination of CRISPR/Cas9-mediated Tcf mutagenesis in TVCs from two (15&18hpf) time points.

first: Nicole

last: Kaplan

first: Wei

last: Wang

first: Lionel

last: Christiaen


title: RNA-sequencing and CRISPR/Cas9 Screen of PEO1 cells grown in suspension.

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: RNA-sequencing of PEO1 cells grown in suspension (SUS1 and SUS3) was performed to evaluate transcriptional reprogramming during anokis escape. CRISPR/Cas9 screen of PEO1 cells grown in adherent and suspension culture settings for 5 days or 10 days. GeCKO v2 library transduced in PEO1 cell line and cells were selected with puromycin. PEO1 line was authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G).

overall_design:
PEO1 cells grown in suspension (SUS1 and SUS3) compared to PEO1 cells grown in adherent conditions (PEO1_Adherent_1  and PEO1_Adherent_2). PEO1 cells transduced with GeCKO v2 library were cultured in adherent or suspension settings for 5 or 10 days.

Please note that the two PEO1_Adherent sample records are duplicated sample record of GSM3308399, GSM3308400 for the convenient retrieval of the complete raw data from SRA

first: Benjamin

last: Bitler

first: Aik-Choon

last: Tan

first: Kelly

last: Sullivan


title: DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [CBD exp]

overall_design: RNA was extracted from BAL fluid from 8 CBD, 8 BeS, and 6 Sarcoidosis patients.

first: Iain

last: Konigsberg

first: Kristyn

last: MacPhail

first: Li

last: Li

first: Elizabeth

last: Davidson

first: Peggy

last: Mroz

first: Nabeel

last: Hamzeh

first: May

last: Gillespie

first: Lori

last: Silveira

first: Tasha

last: Fingerlin

first: Lisa


title: mRNA expression in lung tissue

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Previous studies have reported sex differences in the incidence, prognosis and control of respiratory diseases and lung immunity. However, the role of sex hormones in the inflammatory response, and the mechanisms involved are unknown. Here, we explored whether variations in circulating hormone levels in the mouse estrous cycle could alter the inflammatory response to air pollutants such as ozone. To test this, female mice of the C57BL/6 background were exposed to 2ppm of ozone or filtered air (control) for 3 hours at different stages of the estrous cycle. Following exposure, lungs were harvested and total RNA was extracted. We used Inflammatory Response and Autoimmunity PCR Arrays to study differences in gene expression across the estrous cycle. Our results identified differentially expressed mRNA signatures in the lungs of females exposed to ozone at different stages of the estrous cycle. In addition, in silico pathway analyses discovered differences in mRNA expression and predicted regulatory networks in females exposed to ozone at different estrous cycle stages. These results indicate that the effects of ozone exposure in the female lung are affected by hormonal status.

overall_design: Female C57BL/6 mice of 8 weeks of age were exposed to 2ppm ozone (O3) or filtered air (FA) for 3 hours at different stages of the estrous cycle: Metestrus (M), Diestrus (D), proestrus (P), estrus (E). Total RNA was extracted from whole lung homogenates and PCR arrays were used to determine the expression of 84 mRNAs associated with inflammation and immunity (3-6 animals per group).

first: Nathalie

last: Fuentes

first: Noe

last: Cabello

first: Marvin

last: Nicoleau

first: Zissis

last: Chroneos


title: Iron Chelator Deferasirox Reduces Candida albicans Invasion of Oral Epithelial Cells and Infection Levels in Murine Oropharyngeal Candidiasis

city: Buffalo

first: Mira

last: Edgerton

address: 310 Foster Hall, 3435 Main Street

summary: Candida albicans, the causative agent of mucosal infections including oropharyngeal candidiasis (OPC) as well as bloodstream infections is becoming increasingly resistant to existing treatment options. In the absence of novel drug candidates, drug repurposing aimed at using existing drugs to treat off label diseases is a promising strategy. C. albicans requires environmental iron for survival and virulence while host nutritional immunity deploys iron-binding proteins to sequester iron and reduce fungal growth. Here we evaluated the role of iron-limitation using Deferasirox (an FDA approved iron chelator for treatment of patients with iron overload) during murine OPC; and assessed Deferasirox-treated C. albicans for its interaction with human oral epithelial (OE), neutrophils, and antimicrobial peptides. Therapeutic Deferasirox treatment significantly reduced salivary iron levels while a non-significant reduction in fungal burden was observed. Preventive treatment that allowed for two additional days of drug administration in our murine model, resulted in significant reduction of C. albicans colony forming units (CFU)/g of tongue tissue, a significant reduction in salivary iron levels, and significantly reduced neutrophil-mediated inflammation. C. albicans harvested from tongues of animals undergoing preventive treatment had differential expression of 106 genes, including those involved in iron metabolism, adhesion, and response to host innate immunity. Moreover, Deferasirox-treated C. albicans cells had two-fold reduction in survival in neutrophil phagosomes (with greater susceptibility to oxidative stress); and reduced adhesion and invasion of OE cells, in vitro. Thus Deferasirox treatment has the potential to alleviate OPC by affecting C. albicans gene expression and reducing virulence

overall_design: RNA expression profiles of  C. albicans isolated from mice tongue treated with deferasirox or control generated by duplicate analyses using Illumina HiSeq 2500

first: Sumant

last: Puri

first: Rohitashw

last: Kumar

first: Isolde

last: Rojas

first: Ornella

last: Salvatori


title: GR mutation in mice changes the genome-wide epigenome of placental tissue in a highly sex-specific manner

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

institute: Ariel University

summary: We found that the GR mutation leads to a complete change of the DNA methylation landscape in fetal placenta of c57/bl6n mice in a highly sex-specific manner. The genome-wide capture-sequencing analysis revealed enrichments in genes related to a broad range of biological functions associated with basic signaling pathways and neurological development, but also with diseases like diabetes and dementia. Furthermore, we showed that the methylation status of certain genes in fetal placenta tissue predicts/is significantly correlated with anxiety of these animals in adulthood. These possible biomarkers could be used as diagnostic tools in the easily available placental tissue at birth allowing primary prevention for children at high risk at the earliest possible point of time in the future.

overall_design: Fetal placental tissue of both sexes in GR+/+ vs. GR+/- c57/bl6 mice was analyzed genome-wide by capture sequencing

first: M

last: Schmidt

first: E

first: Z

last: Zhou

first: A

last: Ruder

last: Ludiro

first: F

last: Lapert

last: Macedo da Cruz

first: P

last: Sandrini

first: T

last: Calzoni

last: Luoni

first: R

last: Massart

first: MA

last: Riva

last: Gass

last: Szyf