title: Development and validation of PrOTYPE (Predictor of high-grade-serous Ovarian carcinoma molecular subTYPE)

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

summary:
Gene expression-based molecular subtypes of high grade serous tubo-ovarian cancer (HGSOC) are distinguished by differential immune and stromal infiltration and may provide opportunities for the development of targeted therapies. Integration of molecular subtypes into clinical trials has been hindered by inconsistent subtyping methodology. Adopting two independent approaches, we derived and internally validated algorithms for molecular subtype prediction from gene-expression array data in 1650 tumors. We applied resulting models to assign labels to 3829 HGSOCs from the Ovarian Tumor Tissue Analysis (OTTA) consortium evaluated on NanoString. Using the labeled NanoString data, we developed, confirmed, and validated a clinical-grade test and prediction tool. We also used the OTTA dataset to evaluate associations between molecular subtype, biological, and clinical features.
A gene expression study from the Ovarian Tumor Tissue Analysis (OTTA) consortium

overall_design: 4077 total samples including 3829 unique high-grade serous ovarian cancer specimens plus controls analyzed on a custom NanoString panel including 513 assay genes (housekeeping genes are also present in raw data). Unique clinical samples are denoted as clinical in the specimen title. Biological replicates are denoted as OTTA2014_####_REPB1 where #### matches a clinical sample. Technical replicates are denoted similarly with REPT1 or XSITE in the sample title. XSITE further denotes sample that are technical replicates but run in different laboratories (experimental site). Only a subset of XSITE samples will be replicates of clinical specimens, others are exclusively for control purpose.

first: Aline

last: Talhouk

first: Joshy

last: George

first: Chen

last: Wang

first: Timothy

last: Budden

first: Tuan

middle: Z

last: Tan

first: Derek

last: Chiu

first: Stefan

last: Kommoss

first: Huei

last: Leong

first: Stephanie

last: Chen

first: Maria

middle: P

last: Intermaggio

first: Blake

last: Gilks

first: Tayyebeh

last: Nazeran

first: Mila

last: Volchek

first: Wafaa

last: Elatre

first: Rex

middle: C

last: Bentley

first: Janine

last: Senz

first: Amy

last: Lum

first: Veronica

last: Chow

first: Hanwei

last: Sudderuddin

first: Robertson

last: Mackenzie

first: Samuel

last: Leung

first: Geyi

last: Liu

first: Dustin

last: Johnson

first: Billy

first: Sian

last: Fereday

first: AOCS

last: Group

first: Jennifer

last: Alsop

first: Susana

last: Banerjee

first: Sabine

last: Behrens

first: Clara

last: Bodelon

first: Alison

last: Brand

first: Louise

last: Brinton

last: Carney

first: Yoke-Eng

last: Chiew

first: Kara

last: Cushing-Haugen

first: Cezary

last: Cybulski

first: Darren

last: Ennis

first: Renée

last: Fortner

first: Jesús

last: García-Donas

first: Aleksandra


title: Comparative gene expression analysis of cells derived from rapamycin and PBS-treated mice

status: Public on Jul 21 2020

city: Ulm

first: Jasmin

last: Scheurer

address: Eythstraße 24

country: Germany

institute: Dept of Pediatrics and Adolsecent medicine

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

overall_design: Refer to individual Series


title: Gene expression analysis of intestinal stem cells (ISCs) from polyI:C treated WT mice or Ifnar1-/- mice.

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

country: Japan

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

summary: To explore the influence of IFNR-mediated singnaling in ISCs, we performed microarray analysis of the ISCs from control Lgr5ki mice versus Ifnar1-/-Lgr5ki mice after treating for 1  weeks with low doses of poly(I:C), which potentially induce type I and -III IFNs. The Gene Ontology (GO) analysis indicated that the GO terms overrepresented among the genes upregulated in ISCs from poly(I:C)-treated WT mice compared with those from poly(I:C)-treated Ifnar1−/− mice included “defense response to virus”, “immune system process”, “response to virus”, and “innate immune response”, all from the GOTERM_Biological Processes (BP) category. We compared these results against the Interferome database, which contains genes regulated by type I, II, or III IFN, compiled by analyzing the expression data of IFN-treated cells (http://www.interferome.org), and found that most of the genes found for the GO term “defense response to virus” were IFN-inducible genes, indicating that IFNs act directly on ISCs. The GO analysis also showed an enrichment of defense response to bacteria. In the GOTERM_Cellular Component (CC) category, “extracellular space” and “extracellular region” ranked at the top, indicating a dramatic change in the expression pattern of secretory molecules. Notably, these GO terms included genes encoding antibacterial proteins and endocrine hormones such as angiogenin, defensin, lysozyme, chromogranin, and glucagon, all of which are produced by secretory IECs. Thus, we hypothesized that excess IFN signals force ISCs to lose stemness and differentiate into secretory progenitors.

overall_design: Control Lgr5ki mice or Ifnar1-/-:Lgr5ki mice were injected intraperitoneally with 2 mg/kg BW of poly(I:C) (Sigma) every day for 1 week, then ISCs were isolated by FCM.

first: Toshiaki

last: Ohteki


title: IRF2 ChIP seq in mouse intestinal stem cells (ISCs)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To examine whether IRF2, a negative regulator of IFN signaling, constitutively represses IFN signaling by binding IFN-inducible gene loci in ISCs, we performed a genome-wide chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) analysis of IRF2 in Lgr5 ISCs. We identified 381 binding peaks in these cells, including well-known IFN-inducible genes. Motif analysis showed significant enrichment of consensus-binding motifs for IRF transcription factors within these peaks. Within IRF2-occupied genes in ISCs, we identified 204 of experimentally validated IFN-inducible genes from Interferome database, and 10.8% of them were overlapped with the genes upregulated by type I IFN stimulation in ISCs. These findings indicated for the first time that IRF2 constitutively bound and repressed the sterile IFN signaling at the level of ISCs.

overall_design: Lgr5 ISCs prepared from five Lgr5ki mice were snap-frozen and shipped to Active Motif. Active Motif performed ChIP-seq according to their procedures using an anti-IRF2 antibody.


title: Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [RNA-Seq]

status: Public on Jul 22 2020

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: Somatic cells can be reprogrammed to pluripotent stem cells through the addition of just four transcription factors, OCT4, SOX2, KLF4 and c-MYC (OSKM). Although OSKM initiates reprogramming it is clear that extensive epigenetic remodeling is required to complete reprogramming. Critically, OSKM do not directly activate gene expression but instead recruit co-activators and co-repressors that remodel the local chromatin and in some way make the cells permissive for reprogramming. Consequently understanding how epigenetic co-repressors and co-activators are involved in reprogramming is a critical step in understanding the reprogramming process in detail. In this study we explored the role of the lysine-specific demethylase Kdm6b/Jmjd3 and its role in the reprogramming of somatic cells to pluripotent cells.

overall_design: RNA-seq data consists of MEFs at passage 2 or 4, with or withour JMJD3 overexpression, and reprogrammed cells with the ectopic expression of OSKM (Oct4, Sox2, Klf4, c-Myc), along with either control transfections (FLAG, shLuc) or JMJD3 overexpression or Jmjd3 or Utx knockdown. Two time points in the reprogramming time course were profiled: Day 4 (early) and Day 8 (late)

first: Baoming

last: Qin

first: Huang

last: Yinghua


title: Plasma-derived exosomal circular RNA hsa_circ_0005540 as a novel diagnostic biomarker for coronary artery disease

status: Public on Jul 20 2020

city: Dongguan

first: weipeng

last: Wu

state: Guangdong

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

summary: Aims: Exosomes exist in almost all body fluid and contain diverse biological contents which may be reflective of disease state. Circular RNAs (CircRNAs) are stable in structure and have a long half-life in exosomes without degradation, thus making them reliable biomarkers. However, the potential of exosomal circRNAs as biomarkers of coronary artery disease (CAD) remains to be established. Here we aimed to investigate the expression levels and the potential use of exosomal circRNAs as diagnostic biomarkers of CAD. Main methods: CircRNAs expression levels in exosomes obtained from three plasma samples from CAD patients and three paired controls were analyzed using RNA sequencing. Exosomal circRNAs obtained in the profiling phase were then verified in two-center validation cohorts. Finally, the ability of exosomal circRNAs, adjusting for Framingham Heart Study (FHS) risk factors, was determined to discriminate between CAD patients and non-CAD controls. Key findings: 355 circRNAs were differentially expressed between these two groups: 164 were upregulated, and 191 were downregulated. Here we selected potential circRNAs (fold change > 4, P < 0.05) as candidate biomarkers for further validation. Our data showed that only hsa_circ_0005540 was significantly associated with CAD (P < 0.0001). After adjustment for risk factors, hsa_circ_0005540 showed a high discriminatory power for CAD in ROC analyses (AUC = 0.853; 95% confidence interval [CI] = 0.799 - 0.906, P < 0.001). Significance: Our results suggest that plasma exosomal hsa_circ_0005540 can be used as a promising diagnostic biomarker of CAD.

overall_design: circRNA sequencing on ribosomal RNA-depleted total RNA from  CAD patients and non-CAD controls

first: Xing-dong

last: Xiong

first: Wei-peng

first: Yan-hong

last: Pan

first: Meng-yun

last: Cai


title: Detection of RNAs binding to Vg1 RNP

city: Notre Dame

first: Chao

last: Yang

state: IN

address: 437 Stepan Chemistry Hall

department: Chemistry and Biochemistry

country: USA

institute: University of Notre Dame

summary: We report the application of NGS for high-throughput profiling of transcripts assoicated with the ribonuleoprotein (RNP) formed on Vg1 mRNA  in oocytes of Xenopus Laevis.

overall_design: Biriefly, Biotinylated-Vg1 RNA was microinjected into Xenopus  oocyte to allow formation of RNP complex in vivo. Next, streptavidin beads were added to the oocyte extract to specificly pull down the biotin-Vg1 RNP. After extensive washes, biotin-Vg1 RNP were eluted off by incubating the beads with free biotin and the associted RNAs were extracted by phenol and precipitated by ethanol.For RNA sequencing strategy, a single RNA library was prepared and sequenced on an Illumina MiSeq nano 300 cycle reagent kit.

first: Paul

middle: W

last: Huber


title: Exosomal microRNA landscape in human ovarian follicular fluid

city: Shanghai

first: Di

last: Zhang

state: Shanghai

address: 301 Yanchangzhonglu

institute: Center for Reproductive medicine, Shanghai Tenth People’s Hospital of Tongji University

type: Non-coding RNA profiling by high throughput sequencing

summary: We collected ovarian follicle fluids from 68 patients and assigned them to good group or bad group according to their oocyte quality. The exosomes were isolated and characterized. Exosomal microRNAs were extracted, the library was constructed and sequenced by Illumina hiseq platform. The exosomal microRNA expression was analyzed and profiled, the target genes were predicted, GO terms were enriched by GOSeq and KEGG pathway was analyzed using miranda.A total of 47 differential microRNAs was expressed significantly between good and bad group, of which 9 microRNAs were known microRNAs and 7 of them was upregulated in the bad group. In-silico analysis indicated that several of these exosomal microRNAs were involved in pathways implicated in oocyte quality.Our study suggests that exosomal microRNAs in ovarian follicle fluid are critical in maintaining the oocyte quality. Our study greatly improve our understanding of exosomal microRNAs in human ovarian follicular fluid, paving the way for further investigation on the microRNA functions in the ovarian microenvironment and the mechanism behind it.

overall_design: 68 patients samples were collected and assigned them to good group or bad group according to their oocyte quality. Defferent expressed genes were analyzed between these two groups. The samples were pooled in two groups so we have one fastq file for each group.

first: Jia

last: Lv

first: Rongxin

last: Tang

first: Ying

last: Feng


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging [DS3]

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

type: Methylation profiling by genome tiling array

summary: In the present study, we developed a highly accurate Skin-Specific DNAm age predictor, using DNAm data obtained from 508 human skin samples. Based on the analysis of 2,266 CpG sites, we accurately calculated the DNAm age of cultured skin cells, and human skin biopsies. Age estimation was sensitive to the biological age of the donor, cell passage, skin disease status, as well as treatment with senotherapeutic drugs.

overall_design: Analyze the difference in methylation profile on human dermal fibroblasts isolated from a young donor (29 years) and a elderly donor (84 years). Sample 1: human dermal fibrblasts from a 29 years old donor, in triplicate   Sample 2: human dermal fibrblasts from a 84 years old donor, in triplicate

first: Alessandra

last: Zonari


title: Gene expression analysis of intestinal stem cells (ISCs) in Irf2 conditional deletion mice.

first: Taku

last: Sato

summary: To analyze global gene-expression changes caused by IRF2 loss in ISCs, ISCs were prepared from Irf2fl/fl: Lgr5-EGFP-Ires-CreERT2(Irf2fl/fl: Lgr5ki) mice or Irf2fl/fl: Ah-Cre: Lgr5-EGFP-Ires-CreERT2 (Irf2AhcKO: Lgr5ki) mice 1 month after 5 consecutive days of βNF treatment. The Gene Ontology (GO) analysis indicated that the GO terms overrepresented among the genes upregulated in ISCs of βNF treated Irf2AhcKO: Lgr5ki mice compared with those of Irf2fl/fl: Lgr5ki mice included “immune system process”, “immune response”, and “cellular response to Interferon-beta”, all from the GOTERM_Biological Processes (BP) category. Because these GO_term inculded many IFN-inducibl genes, IFN signaling augumented in Irf2 deleted ISCs.

overall_design: ISCs were prepared from Irf2fl/fl: Lgr5-EGFP-Ires-CreERT2(Irf2fl/fl: Lgr5ki) mice or Irf2fl/fl: Ah-Cre: Lgr5-EGFP-Ires-CreERT2 (Irf2AhcKO: Lgr5ki) mice 1 month after 5 consecutive days of βNF treatment. Gene-expression profiles were obtained from the ISCs of four independent Irf2fl/fl or Irf2ΔAh-Cre mice in two biological replicates.

first: Toshiaki


title: Multimodal Single-Cell Analysis Reveals Two Distinct Radioresistant Stem-like and Progenitor Cell Populations in Murine Glioma

city: Seattle

first: Jes

last: Alexander

state: WA

address: 3720 15th Ave NE, Foege Building S-210

department: Genome Sciences

institute: University of Washington

summary: Radiation therapy is part of the standard of care for gliomas and kills a subset of tumor cells, while also altering the tumor microenvironment. Previous work shows that tumor cells with stem-like properties preferentially survive radiation and give rise to glioma recurrence. Various techniques for enriching and quantifying cells with stem-like properties have been used, including the fluorescence activated cell sorting (FACS)-based side population (SP) assay, which is a functional assay that enriches for stem-like tumor cells. In these analyses, mouse models of glioma have been used to understand the biology of this disease and the therapeutic response, including the biology of the radiation response. We present here an analysis of combined SP and single-cell RNA sequencing of genetically-engineered mouse models of glioma to show a time course of cellular response to radiation. We identify and characterize two distinct tumor cell populations that are inherently radioresistant. In addition, we identify and characterize distinct effects of radiation on immune cell populations within the tumor microenvironment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We applied sciRNA-seq to 15 archived, frozen samples, which consisted of normal brain and tumor-containing hemisphere for each of 3 treatment conditions: no IR and 8 ± 2 hours and approximately 72 hours after 10Gy


title: scRNA-seq of electrophysiologically characterized mechanosensetive DRG neurons reveals maturational differences in gene expression

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Cultured dorsal root ganglia neurons of 4 and 12 weeks old C57Bl/6 mice were first characterized as mechanosensitive (showed  rapidly adapting mechanically actived currents in whole-cell votage clamp) and as mechanoreceptors (evoked action potential waveform in whole-cell current clamp). Next, cells were subjected to RNA-seq and sequences were analyzed bioinformatically. We found maturatinal changes comprising age-dependent differential gene expression in these somatosensory mechanoreceptors. The found differences call for tight age-matching of young mice in research and underline found electrophysiological and behavioural maturational changes in somatosensation, see Michel, Niklas and Narayanan, Pratibha and Shomroni, Orr and Schmidt, Manuela, Cutaneous Touch and Piezo2-Mediated Mechanotransduction Decline Throughout Mouse Maturation Until Adulthood. CELL-REPORTS-D-20-00425. Available at SSRN: https://ssrn.com/abstract=3536401 or http://dx.doi.org/10.2139/ssrn.3536401

overall_design: 18 single DRG neuron RNA profiles of 4 and 12 weeks old male WT C57Bl/6J mice, grouped by their electrophysiological profile

first: Michel

last: Niklas

first: Narayanan

last: Pratibha

first: Shomroni

last: Orr

first: Schmidt

last: Manuela


title: Profiling the transcriptome response of Atlantic salmon to formalin-killed Renibacterium salmoninarum

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

institute: Memorial University of Newfoundland

summary: Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify R. salmoninarum bacterin-responsive genes in Atlantic salmon, fish (n=6) were intraperitoneally injected with a high (5×107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control). Head kidney samples were collected at 24 h post-injection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to formalin-killed R. salmoninarum injection.

overall_design:
Twelve Atlantic salmon were injected with a high (5×107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control) and head kidney samples were collected at 24 h post-injection. Test samples were labeled with Cy5, whereas the common reference (i.e. a RNA pool of all 12 samples included in microarray experiment) was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array (i.e. 12 arrays in total).

variable: other: PBS: PBS1, PBS2, PBS3, PBS4, PBS5, PBS6.
variable: other: High_Rs: High_Rs1, High_Rs2, High_Rs3, High_Rs4, High_Rs5, High_Rs6.
repeat: biological replicate: PBS: PBS1, PBS2, PBS3, PBS4, PBS5, PBS6.
repeat: biological replicate: High_Rs: High_Rs1, High_Rs2, High_Rs3, High_Rs4, High_Rs5, High_Rs6.

first: Surendra

last: Kumar

first: Albert

last: Caballero-Solares

first: Hajarooba

last: Gnanagobal

first: Javier

last: Santander

first: Matthew

middle: L

last: Rise


title: Circular RNAs upregulated in medulloblastoma regulate proliferation and growth of tumor cells via host genes

first: tao

last: lv

address: No. 160 Pujian Road,Shanghai 200127, China

department: Department of Neurosurgery

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: It has recently been demonstrated circular RNAs (circRNAs) involve in various biological processes, nevertheless, the function of circRNAs in medulloblastoma is still unknown. The present study aims to investigate the expression profiles of circRNAs in medulloblastoma and related mechanisms for tumorigenesis and progression of medulloblastoma.

overall_design: In this work, we screened circRNAs expression profiles from four normal brain and four medulloblastoma samples. Subsequently, we validated through RT-PCR.

first: Xiaohua

last: Zhang

first: Zilong

last: Qiu

first: Tao


title: Synthetic circular miR-21 RNA decoys enhance tumor suppressor expression and impair tumor growth in mice (small RNA-Seq II)

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: Natural and synthetic circular RNAs effectively impair miRNA function. MiR-21-5p is a potent oncomiR presenting ~33% of all miRNAs across cancers, ~41% in lung adenocarcinoma (LUAD), and ~68% in LUAD-derived cells. We validate and identify five main tumor suppressors targeted by miR-21-5p by deletion of the MIR21 locus in LUAD cells. Synthetic, liposome-delivered circular miR-21-5p decoys enhance expression of these tumor suppressors and severely impair tumor cell vitality at low doses. Decoy efficacy is not increased by bulging of miR-21-5p targeting sites, but associated with substantial cellular decoy stability, indicated by a half-life of ~20h. The intraperitoneal application of nanoparticle-delivered miR-21-5p decoys significantly impairs tumor growth in mouse LUAD tumor models. Decoys are well tolerated and were enriched in lung tissue. However, despite low decoy abundance, tumor suppressor expression was only increased in subcutaneous tumors. These findings suggest nanoparticle-delivered circular miRNA decoys as potent therapeutics in cancer treatment.

overall_design: small RNA-Seq of three cancer derived cell lines

first: Simon

last: Müller

first: Alice

last: Wedler

first: Janina

last: Breuer

first: Nadine

last: Bley

first: Marcell

last: Lederer

first: Jacob

last: Haase

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alina

last: Ottmann

first: Tessa

last: Schmachtel

first: Lyudmillya

last: Shalamova

first: Alexander

last: Ewe

first: Achim

last: Aigner

first: Oliver

last: Rossbach

first: Stefan

last: Hüttelmaier


title: Identification of active gene regulatory elements in the human and murine TBX3 locus

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: The human and murine TBX3 locus harbors hundreds of active regulatory elements responding to Smad-/Gata- and Tcf-transcription factors in vitro.

overall_design: STARR-seq with the entire human and murine TBX3 locus as input, transfected in replicate experiments in COS7 cells and co-transfected with pcDNA (ctrl), Smad- and Gata factors (SG4) or Tcf factors (Wnt).

first: Jan

middle: H

last: van Weerd

first: Karel

last: van Duijvenboden

middle: M


title: Plaque gene expression out of the aortic root of wildtype (Con) or myeloid-derived lipin-1 KO mice after high fat diet for 8 or 12 weeks

city: Shreveport

first: Matthew

last: Woolard

state: LA

address: 1501 Kings Hwy

department: Microbiology and Immunology

institute: Louisiana State University Health Science Center Shreveport

summary:
mRNA was isolated from aortic root tissue sections isolated from wild type or myeloid-derived lipin-1 knockout (KO) mice on high fat diet and anlyzed for a myeloid innate immunity panel via Canopy Biosciences Nanostring
In this study, 750 genes of a myeloid innate immunity panel were analyzed within the aortic root plaques of mice on an atherosclerotic diet to analyze the contributions of lipin-1 to gene expression changes

overall_design: Listed here are the results for gene expression analysis between wild type and myeloid-derived lipin-1 knockout mice on atherosclerotic diet for 8 or 12 weeks, n=6

first: Cassidy

last: Blackburn

middle: D


title: Expression profile in WAT from inducible adipocyte specific TFG KO mice

city: Hiroshima

first: Takeshi

last: Yamamotoya

address: 1-2-3, Kasumi, Minami-ku

institute: Hiroshima University

summary:
The expression of Trk-fused gene (TFG) was markedly increased in adipose tissues from ob/ob mice.
To examine the function of TFG in adipocytes, we performed microarray analysis using the Affymetrics Clariom D Array, Mouse.

overall_design: TFG f/f and TFG f/f; Adipoq-ERT2Cre were intraperitoneally injected tamoxifen for 5 days and total RNA isolated from inguinal subcutaneous WAT was subjected to analysis 2 weeks later.

first: Tomoichiro

last: Asano


title: Transcriptomic analysis of transforming growth factor beta (TGF-beta)-responding SCC cells and Fc epsilon receptor I alpha (FceRIa)-positive macrophages

city: Portland

first: Naoki

last: Oshimori

state: OR

address: 2720 S Moody Ave

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: TGF-beta-responding SCC cells, a tumor-initiating cell population, show a unique gene expression signature, including antioxidant gene expression and IL-33 upregulation. IL-33-responding macrophages in SCC, which also express Fc epsilon receptor I alpha, show a gene expression signature that resembles alternatively-activated macrophages

overall_design: To analyze a unique gene expression in TGF-beta-responding SCC cells, we purified TGF-beta signaling reporter (mScarlet) positive and negative tumor basal cells (Rosa-YFP+ CD49f+ CD29+) by FACS. We used RNA-seq analysis to compare the transcriptomes of these FACS-isolated SCC cells and combined the previous RNA-seq data (GSE64867) to obtain higher confidence (p < 0.01). For macrophage analysis, we purified Fc epsilon receptor I alpha positive and negative macrophages (CD45+ F4/80+) from SCC tumor tissues. We also used RNA-seq analysis to compare their transcriptomes.


title: Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition [RNA-seq]

city: Newark

first: Juan

middle: C.

last: Inclan Rico

state: New Jersey

address: 205 South Orange Avenue, Rutgers Cancer Institute of New Jersey at University Hospital

department: Medicine/CII

institute: Rutgers New Jersey Medical School

summary: Type 2 cytokine responses promote parasitic immunity and initiate tissue repair but, can also result in immunopathologies when not properly restricted. Basophilia is recognized as a common feature of type 2 inflammation, however, the roles basophils play in regulating these responses remain unknown. Here, we demonstrate that helminth-induced ILC2 responses are exaggerated in the absence of basophils, resulting in increased inflammation and diminished lung function. Additionally, we show that ILC2s from basophil-depleted mice express reduced levels of the receptor for the neuropeptide, neuromedin B (NMB). Critically, NMB stimulation inhibited ILC2 responses from control but not basophil-depleted mice, and basophils were sufficient to directly enhance NMB receptor (NMBR) expression on ILC2s. These studies suggest that basophils prime ILC2s to respond to neuron-derived signals necessary to maintain tissue integrity. Further, these data provide mechanistic insight into the functions of basophils and identify NMB as a potent inhibitor of type 2 inflammation.

overall_design: Lung-resident ILC2s were sort-purified from WT mice infected with Nippostrongylus brasiliensis 7 days prior and treated with vehicle or recombinant Neuromedin B (NMB) for 24 hours. 3 biological replicates per experimental group were used from ILC2s sort-purified from 5 mice per biological sample.

last: Inclan-Rico

last: Lemenze

first: Mark

last: Siracusa


title: The sensor kinase QseC regulates the unlinked PmrA response regulator and downstream gene expression in Francisella

city: Columbus

first: John

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

summary: The facultative intracellular bacterial pathogen Francisella tularensis is the causative agent of tularemia in humans and animals. Gram negative bacteria utilize two-component regulatory systems (TCS) to sense and respond to their changing environment. No classical, tandemly arranged sensor kinase and response regulator TCS genes exist in the human virulent Francisella tularensis subsp. tularensis, but orphaned members are present. PmrA is an orphan response regulator responsible for intramacrophage growth and virulence; however, the regulation of PmrA activity is not understood. We and others have shown that PmrA represses the expression of priM, described to encode an anti-virulence determinant. By screening a mutant library for increased priM promoter activity, we identified the sensor kinase homolog QseC as an upstream regulator of priM expression, and this regulation is in part, dependent upon the aspartate phosphorylation site of PmrA (D51). PmrA directly binds to the promoter of priM and a PmrAD51A mutation decreases binding. Several examined environmental signals including epinephrine, which is reported to activate QseC in other bacteria, do not affect priM expression in a manner dependent on PmrA. Intramacrophage survival assays also question the finding that PriM is an anti-virulence factor. Thus, these data suggest that the PmrA-regulated gene priM is regulated by an uncoupled TCS QseC-PmrA (QseB) in Francisella.

sample_organism:
Francisella tularensis
Francisella tularensis subsp. novicida

overall_design: To identify the PmrA regulon in Francisella novicida, we compared transcriptional profiles between the wild type strain and its isogenic pmrA mutant. Total RNA from F. novicida and its isogenic mutant at the exponential phase of growth was extracted from four independent experiments and used in the RNAseq. A similar experiment design was performed to identify the PmrA regulon in Francisella tularensis LVS strain.

first: Ky

middle: V

last: Hoang

first: Nrusingh

last: Mohapatra

first: James

last: Fitch

first: White

last: Peter


title: Gene expression analysis of tumors of TN and R clonal pairs in vivo

city: Vienna

first: Anna

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

summary: We previously had generated clonal mouse melanoma cell lines, where each clone was isolated in a RAFi/MEKi-resistant ( R ) or treatment-naïve ( TN ) state using the method CaTCH (clones: 2646TN, 2646R, 14559TN, 14559R, 13TN). We assessed the response to targeted therapy of these clones in in vivo experiments using RAFi/MEKi-treatments. Herey, we saw that, compared to the other treatment-naïve clones, 2646TN exhibited a strongly reduced response to targeted therapy. 2646TN displayed fast growth on drug after only five days, indicating an increased persistence and fast adaption to the treatment, while all other TN clones responded to the treatments and showed tumor regression for weeks before relapsing. To uncover intrinsic programs that might underlie th minimal response of 2646TN, we examined the transcriptome of untreated and short-term treated tumors comprising 2646TN, 2646R, 14559TN, 14559R, or 13TN clones . These clonal cell lines were injected subcutaneously into C57BL/6 mice and tumors were harvested either at tumor engraftment (untreated) or after 3 days of RAFi/MEKi treatment. Lviving cancer cells were sorted from the tumors by FACS and the markers CD45- and the cell line specific marker GFP+. Libraries were prepared using the Lexogen Quantseq 3' mRNA seq kit and sqeuencing was performed on an Illumina HiSeqV4 sequencer (single-read 50 read mode).

overall_design: 5 different mouse melanoma cell lines FACS sorted from subcutaneously injectd tumors, each untreated and RAFi/MEKi treated, 3 tumors per cell line and condition (= 30 samples total)

first: Christian

last: Umkehrer

first: Laura

last: Formenti

first: Felix

last: Holstein

first: Thomas

middle: R

last: Burkard


title: Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome[RNA-Seq]

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

summary: Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

overall_design: RNA-seq data was collected from EBV-transformed lymphocyte cell lines established from 9 different Nomascus leucogenys gibbons

first: Lucia

last: Carbone


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging [DS4]

first: Mariana

last: Boroni

overall_design:
Analyze changes in the methylation profile of human progeria dermal fibroblasts treated for 72 hours with 1.25uM ABT-263, 5uM ABT-263, 100nM Rapamycin compared to no treatment.
Sample 1: human progeria dermal fibroblast, no treatment, in triplicate
Sample 2: human progeria dermal fibroblast, treated with 1.25uM ABT-263, in triplicate
Sample 3: human progeria dermal fibroblast, treated with 5uM ABT-263, in triplicate
Sample 4: human progeria dermal fibroblast, treated with 100nM Rapamycin, in triplicate

first: Alessandra

last: Zonari


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging

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

overall_design: Refer to individual Series


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging [DS5]

overall_design: Analyze changes on the methylation profile of whole skins treated with 100nM Rapamycin compared to no treatment        .Sample 1: human whole skin from a 79 year old donor, control, 5 replicates  Sample 2: human whole skin from a 79 year old donor, treated with 100nM Rapamycin, 5 replicates


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging [DS2]

overall_design: Analyze the effect of cell culture (cell passage) on the methylation profile. Sample 1: human progeria dermal fibroblast at passage 11 in triplicate Sample 2: human progeria dermal fibroblast at passage 19 in triplicate


title: Fc-mediated effector function contributes to the in vivo antiviral effect of an HIV broadly neutralizing antibody.

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: Treatment of HIV infection with either anti-retroviral therapy (ART) or neutralizing monoclonal antibodies (NAbs) leads to a reduction in HIV plasma virus. Both ART and NAbs prevent new rounds of viral infection but NAbs may have the additional capacity to accelerate the loss of virus-infected cells through Fc gamma receptor (FcgR) mediated effector functions, which should affect the kinetics of plasma virus decline. Here we formally test this premise in vivo by comparing the plasma virus response to a single dose treatment with either unmodified NAb or those with either reduced or augmented Fc function. When infused into viremic SHIV-infected rhesus macaques, there was a 21% difference in slope of plasma virus decline between wt NAb and NAb with reduced Fc function. NAb engineered to increase FcgRIII binding and improve ADCC in vitro resulted in arming of effector cells in vivo yet led to viral decay kinetics similar to NAbs with reduced Fc function. These studies show that the predominant mechanism of antiviral activity of HIV NAbs is through inhibition of viral entry, but that Fc function does contribute to the overall antiviral activity, making them unique from standard ART. However, these data also show that increased FcgRIII engagement is insufficient to improve in vivo virus clearance.

overall_design: Fifteen rhesus macaques, infected with simian HIV, were treated with the wild-type neutralizing monoclonal antibody VRC07-523LS (n=5), antibody with the LALA mutations (n=5) or the antibody with the DEL mutations (n=5). Peripheral blood mononuclear cells were collected pre-infusion (-48h or –30min), 1h and 3 days after antibodies infusion. NK cells were flow-sorted from the peripheral blood mononuclear cells. RNA was extracted from 5000 NK cells and sequenced to determine their transcriptomic profiles. Samples from one animal (from the LALA group) were excluded for technical reason (sequenced on a different machine). In total, the dataset comprises of 42 samples.

first: Jianfei

last: Hu

first: Daniel

last: Douek

first: Mangaiarkarasi

last: Asokan

first: Richard

middle: A

last: Koup

first: Rafick

last: Sekaly


title: Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging [DS1]

summary: In the present study, we developed a highly accurate Skin-Specific DNAm age predictor, using DNAm data obtained from 508 human skin samples. Based on the analysis of 2,266 CpG sites, we accurately calculated the DNAm age of cultured skin cells, and human skin biopsies. Age estimation was sensitive to the biological age of the donor, cell passage, skin disease status, as well as treatment with senotherapeutic drugs.

overall_design: Samples were used to estimate algorithm's performance


title: RNA-sequencing of specific peripheral blood mononuclear cells in sepsis

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

institute: Amsterdam UMC Locatie AMC

summary: We here sought to better understand the transcriptomic alterations in sorted monocytes (CD14+), CD4+, CD8+ T cells and B cells (CD19+) of sepsis patients (n=6) relative to healthy subjects (n=4).

overall_design: RNA-Seq data of purified CD14+ monocytes, CD4+, CD8+ T cells and CD19+ B cells from six critically ill patients with sepsis due to community-acquired pneumonia and four healthy subjects.


title: S-allylmercaptocysteine Improves NAFLD by Enhancing AhR/Nrf2-mediated Drug Metabolising Enzymes and Reducing NF-κB/IκBα and NLRP3/6-mediated Inflammation

city: Hong Kong

first: Qian

last: Yu

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: Hong Kong University

summary: We investigated the novel molecular mechanisms of the antioxidant and anti-inflammatory properties of S-allylmercaptocysteine (SAMC) based on a transcriptomic study in a non-alcoholic fatty liver disease (NAFLD) rat model. NAFLD was induced in Sprague-Dawley rats by feeding with a high fat diet (HFD) for 12 weeks. 200mg/kg SAMC was fed by oral gavage for 4 weeks from 9-12 week. We found that SAMC co-administration attenuated HFD-induced liver injury, including the increased serum ALT, hepatic oxidative stress and inflammation. Transcriptomic analysis revealed that SAMC dramatically induced the XRE- and ARE-driven drug metabolising enzymes (DMEs) including Akr7a3, Akr1b8, and NQO1. The nuclear translocation of the upstream regulator of xenobiotics metabolism, AhR, and regulator of antioxidant responses, Nrf2, were significantly increased by SAMC treatment. Furthermore, SAMC counteracted the effects of HFD on NF-κB/IκB and NLRP3/6 pathways with decreasing protein levels of ASC, cleaved caspase-1, IL-18 and IL-1β. These results were further verified in another mice NASH model induced by an MCD diet with SAMC co-administration. Conclusion: we propose that SAMC triggers AhR/Nrf2-mediated antioxidant responses which may further suppress the NLRP3/6 inflammasome pathway and NF-κB activation, contributing to the improvement of NAFLD/NASH.

overall_design: mRNA profiles of rat livers in four groups including 1) Control; 2) Control+SAMC; 3) HFD; 4) HFD+SAMC. (n=3)

first: Yann-yin

last: Lee

first: Zheng-yun

last: Xia

first: Emily

last: Liong

first: Geroge

last: Tipoe

first: Jia

last: Xiao


title: Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition [bulk RNA-seq]

first: Juan

last: Inclan Rico

overall_design: Lung-resident ILC2s were sort-purified 5 days post Nb infection from wildtype mice or mice depleted of basophils. 6 biological replicates per group (WT vs. Baso) were sort-purified and pooled into 2 samples per group prior to RNA-extraction.

last: Inclan-Rico

first: Alexander

last: Lemenze

first: Mark

last: Siracusa


title: Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumour microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7,581 malignant cells and 40,285 immune cells from 15 primary NPC tumours and one normal sample. We revealed malignant signatures capturing intratumoural transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell-cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for the precision therapies in NPC.

overall_design:
Fifteen patients who were pathologically diagnosed with non-keratinizing or keratinizing NPC were enrolled in this study; normal nasopharyngeal epithelial tissue from one patient with chronic nasopharyngitis was also collected as a control.  The samples were all fresh-processed for 10x genomics V2  3' single cell RNA sequencing.
Raw data access provided at: NGB Nucleotide Sequence Archive (accession code: CNP0000428)

last: Liu

first: Yupei

last: Chen


title: The ERG-regulated LINC00920 promotes prostate cancer cell survival via the 14-3-3ε- FOXO pathway

city: Heidelberg

first: Arlou Kristina

last: Angeles

state: BW

address: Im Neuenheimer Feld 460

institute: DKFZ/NCT

summary: LINC00920 is a tumor-associated lncRNA identified in the transcriptome dataset of the International Cancer Genome Consortium-Early Onset Prostate Cancer (ICGC-EOPC) cohort. SiRNA-mediated knockdown of LINC00920 negatively affected proliferation, colony formation, and migration of PC-3 prostate cancer cells. Genome-wide expression profiling was performed to identify cellular pathways affected by LINC00920.

overall_design: The effect of LINC00920 knockdown was determined in PC-3 prostate cancer cells. Two independent siRNAs were used to silence LINC00920, alongside a scrambled, non-targeting control. All transfection reactions were perfomed in 3 biological replicates. RNA isolation was performed 48 h post transfection.

first: Arlou

middle: K

first: Doreen

last: Heckmann

first: Holger

last: Sültmann


title: Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition [scRNA-seq]

overall_design: 10,000 lung-resident ILC2s were sort-purified 5 days post Nb infection from wildtype mice or mice depleted of basophils. 6 biological replicates per group (WT vs. Baso) were sort-purified and pooled into 2 samples per group.


title: Transcriptomic alterations of stromal cells during ageing

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: The hematopoietic microenviroment plays a pivotal role in erythropoiesis. Here we compare the transcriptome profiles of the bone marrow niche. in young and aged mice

overall_design: Examine the gene expression profile of different stromal populations in the bone marrow for young (8-12 weeks) and aged (24-25 months) mice by bulk RNA-seq (100 cells)

first: Simona

last: Valletta

first: Alex

last: Thomas


title: Effect of TGFbeta inibition on the transcriptional profile of aged hematopoietic stem and progenitor cells

summary: The TGFbeta signalling pathway was found to be enriched in aged bone marrow. Here we treated aged mice (24-25 months) with TGFbeta inhibitor to investigate the gene expression of hematopoietic stem and progenitor cells while TGFbeta signalling is inhibited.

overall_design: Examine the gene expression profile of hematopoietic stem and progenitor cells (LSK population) in the bone marrow of aged (24-25 months) mice treated with either vehicle or Tgfb1 inhibitor (SB) by single cell RNA-seq


title: RNA-binding protein Syncrip regulates Starvation-Induced Hyperactivity in adult Drosophila

first: Wanhao

last: Chi

state: IL

address: 947 E. 58th Street

department: Neurobiology

institute: University of Chicago

summary: How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in regulating fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 27 significant loci, corresponding to 18 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of Syp in regulating SIH. Syp encodes Syncrip, an RBP. While ubiquitous knockdown of Syp led to lethality during development, adult flies with neuron specific Syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. Lastly, RNA-seq analyses revealed that Syp was alternatively spliced under starvation while its expression level was unchanged. Together, this study not only demonstrates genetic contributions to SIH as an important behavioral trait but also highlights the significance of RBPs and post-transcriptional processes in regulating SIH.

overall_design: Total RNA was extracted from a group of male w^1118 flies that were maintained on either food or starvation conditions for one day. Four biological replicates for each condition. RNA libraries from each sample were multiplexed and sequenced using two flow-cells.

first: Xiaoxi

last: Zhuang


title: Synthetic circular miR-21 RNA decoys enhance tumor suppressor expression and impair tumor growth in mice

first: Markus

last: Glaß


title: Synthetic circular miR-21 RNA decoys enhance tumor suppressor expression and impair tumor growth in mice (small RNA-Seq I)

summary: Natural and synthetic circular RNAs effectively impair miRNA function. MiR-21-5p is a potent oncomiR presenting ~33% of all miRNAs across cancers, ~41% in lung adenocarcinoma (LUAD), and ~68% in LUAD-derived cells. We validate and identify five main tumor suppressors targeted by miR-21-5p by deletion of the MIR21 locus in LUAD cells. Synthetic, liposome-delivered circular miR-21-5p decoys enhance expression of these tumor suppressors and severely impair tumor cell vitality at low doses. Decoy efficacy is not increased by bulging of miR-21-5p targeting sites, but associated with substantial cellular decoy stability, indicated by a half-life of ~20h. The intraperitoneal application of nanoparticle-delivered miR-21-5p decoys significantly impairs tumor growth in mouse LUAD tumor models. Decoys are well tolerated and were enriched in lung tissue. However, despite low decoy abundance, tumor suppressor expression was only increased in subcutaneous tumors. These findings suggest nanoparticle-delivered circular miRNA decoys as potent therapeutics in cancer treatment.

overall_design: small RNA-Seq of parental or MIR21 deleted A549 cells. Deletion of MIR21 was generated by using Crispr/Cas9.

first: Simon

last: Müller

first: Alice

last: Wedler

first: Janina

last: Breuer

first: Nadine

last: Bley

first: Marcell

last: Lederer

first: Jacob

last: Haase

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alina

last: Ottmann

first: Tessa

last: Schmachtel

first: Lyudmillya

last: Shalamova

last: Ewe

first: Achim

last: Aigner

first: Oliver

last: Rossbach

first: Stefan

last: Hüttelmaier


title: Genome-wide profiling of RNA Polymerase II, MITF and DDX21 occupancy in human A375 cells stably expressing either empty vector or HA-tagged PRL3.

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: To determine the role of PRL3 in gene regulation, empty vector or HA-tagged PRL3 was stably expressed in cultured human melanoma A375 cells. ChIP-seq was used to determine the impact of increased PRL3 expression on the genome-wide distribution of RNA Polymerase II (Total/Ser5-Phosphorylated/Ser2-Phosphorylated), MITF and DDX21. In combination with transcriptional analysis (4sU-seq; GEO accession - GSE127855), this study demonstrated that PRL3 overexpression leads to reduced RNA polymerase processivity at a subset of so called 'restricted' genes which are enriched for endolysosomal functions.

overall_design: ChIP-seq for RNAPII (RNAPII - Total/Ser5-Phospho/Ser2-Phospho), MITF and DDX21 was performed on A375 cells that stably express either PRL3 or an empty vector control. Two independent replicate experiments were prepared for each sample.

first: Jeanette

last: Johansson

first: Robert

first: E

middle: E

last: Patton


title: Only hematopoietic stem and progenitor cells from cord blood are susceptible to malignant transformation by MLL-AF4 translocations

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

institute: University Hospital Tuebingen

summary: MLL rearrangements (MLLr) play a crucial role in leukemogenesis. Dependent on age, major differences exist regarding disease frequency, main fusion partners and prognosis. In infants, up to 80% of acute lymphoid leukemia (ALL) bear t(4;11) resulting in a poor prognosis. In contrast, in adults only 10% of acute myeloid leukemia (AML) bear t(9;11) with an intermediate prognosis. The reasons for these differences are only poorly understood. Recently, we established an efficient human patient-specific CRISPR/Cas9-based MLLr model in hematopoietic stem and progenitor cells (HSPCs) derived from human cord blood (huCB) faithfully mimicking the underlying biology of the disease. Here, we transfer this model into an adult system using HSPCs from adult bone marrow (huBM) allowing us to investigate the impact of the cell of origin and fusion partner on disease development. RNA-Seq uncovered an absent downregulation of FFAR2 in t(4;11) huBM, an epigenetic tumor suppressor, potentially responsible for the inability of MLL-AF4 to immortalize adult cells under myeloid conditions.

overall_design: huCB and huBM CD34+ cells were engineered to bear endogenous MLL-AF4 or MLL-AF9 translocations. Generated cells were cultured to a purity of 100 translocated cells. Control cells were maintained in culture for an equal period of time. RNA sequencing was performed using NextSeq mRNA Stranded Sequencing (Illumina) of two biological replicates comparing tranlocated and control cells in regard to translocation partners and cell of origin.

first: Kathy-Ann

last: Secker


title: Identification of miR-29a-mediated target transcriptome in human pancreatic stellate cells (hPSCs) using RNAseq approach

city: Indianapolis

first: Janaiah

last: Kota

state: Indiana

address: 975 W. Walnut Street, IB 244C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

summary: In this study, we aim to understand the role of miR-29a in in regulating hPSCs. Identification of the differentially expressed  direct and indirect miR-29a targets and the associated pathways from the RNASeq data delineates gene interactions and networks essential for activated PSCs in pancreatic ductal adenocarcinoma (PDAC) in regulating desmoplasia and tumor-stomal crosstalk, which are crucial mechanisms for PDAC progression.

overall_design: Comparison of control vs. miR-29a overexpressing hPSCs identifies differentially expressed genes in the dataset. These genes are further analyzed to identify miR-29a direct and indirect targets, and comprehend their pathways and network interactions in association with PDAC pathogenesis.

first: Jun

last: Wan


title: EPIC analysis of Brazilian babies born with congenital microcephaly

city: North Coogee

first: Denise

last: Anderson

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

summary: Genome-wide DNA methylation profiling of over 850,000 methylation sites carried out using the Illumina MethylationEPIC BeadChip was used to compare 18 babies born  with congenital Zika virus microcephaly, 7 babies exposed to Zika virus in utero but born without clinical signs, and 20 control unexposed unaffected babies

overall_design: Includes 18 babies with congenital Zika virus microcephly, 7 babies exposed to Zika virus in utero but born without clinical signs and 20 control babies


title: Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos (DELP-seq)

status: Public on Jul 19 2020

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

country: South Korea

institute: KRIBB

summary: Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidence of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA-adenine methylase identification (DamID) method, we identified Dnmt1-binding regions in 4-cell and 8-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refute the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the long interspersed nuclear elements (LINE1) and endogenous retrovirus type-K (ERVK) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding-domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.

overall_design: For DamID experiment, 50 of each Dnmt1-V5-Dam or Dam-only injected mouse embryos were harvested at 4~8 stage, and gDNAs from the embryos were used to identify Dnmt1 binding sites.

first: Yong-Kook

last: Kang


title: Vitamin C supplementation reduces expression of circulating miR-451a in poorly controlled type 2 diabetes mellitus

status: Public on Jul 18 2020

city: mueang khon kaen

first: Laongthip

last: Ruknarong

state: Khon Kaen

address: 123 moo 16 mittraphap rd, nai mueang

department: Blood transfusion and clinical immunology

country: Thailand

institute: Faculty of Associated Medical Sciences

summary: Four miRNAs showed significantly different expression post-vitamin C supplementation including the down-regulation of miR-451a, and up-regulation of miR-1253, miR-1290 and miR-644a. Subsequent validation study showed only miR-451a expression was significantly different with supplementation.

overall_design: Pre- and post-vitamin C supplementation samples from five participants who had increased vitamin C levels, improved oxidative status and polymorphonuclear (PMN) function after receiving 1,000 mg vitamin C daily for six weeks were screened for miRNA expression using the NanoString miRNA assay. Differences in miRNA expression identified from the miRNA screen were validated by qRT-PCR

first: Chanvit

last: Leelayuwat


title: SERRATE recruits the NEXT complex to control the levels of miRNA precursors in Arabidopsis

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: total RNA from plant tissues was performed followed by sequencing of NGS libraries

overall_design:
total RNA extraction and NGS library preparation
Total RNA isolation, libraries preparation, single-reads (50 cycles) sequencing, Illumina technology, HiSeq 4000, sequencing performed at Fasteris SA (Switzerland).

first: Dawid

last: Bielewicz

first: Mateusz

last: Bajczyk

first: Artur

last: Jarmolowski


title: Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [PU.1 ChIP-seq]

first: Mariam

last: Okhovat

summary: Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

overall_design: PU.1 ChIP-seq was performed on EBV transformed LCL from two gibbon individuals (biological replicates)

first: Lucia

last: Carbone


title: Expression data from day of isolation and day 4 suspension cultured human pancreatic exocrine cells

city: Jette

first: Jonathan

last: Baldan

address: Laerbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

summary: Donor pancreata were obtained from the Beta Cell Bank of the JDRF Centre for Beta Cell Therapy in Diabetes (Brussels, Belgium), from Pancreatic Islet Processing (ECIT center) of Diabetes Research Institute at the IRCCS San Raffaele Scientific Institute (Milan, Italy) and from the DRWF Human Islet Isolation Facility (Oxford, England). Full written consent for use of donor material for research was obtained according to Belgian, Italian and English laws. This project was approved by the Medical Ethical Committee of all institutions. Cells were cultured in 3D suspension culture for four days in Advanced RPMI supplemented with 5% FBS.

overall_design:
We used microarray to determine temporal changes in transcriptome of human panreatic exocrine cells at day of isolation and day 4 of suspension culture
RNA of culster was extracted using RNeasy micro kit (Qiagen; 74004)

first: Luc

last: Bouwens


title: Expression data from of FACS separated acinar and duct cell at day 4 of suspension cultured human pancreatic exocrine cells

overall_design:
We used microarray to determine differential expression of genes to human panreatic acinar and duct ells at day 4 of suspension culture
At day 4, human exocrine cell clusters were dissociated using Neurocult™ enzymatic dissociation kit for adult CNS tissue (Stemcell™ Technologies), incubated for 5 minutes at 37°C while resuspending constantly. Cells were resuspended in medium, filtered over a 40μm filter, spun down, and resuspended in 3% FBS buffer. Cell yield was measured through the Countess automated cell counter (ThermoFisher Scientific). Cells were incubated with mouse monoclonal anti-human carbohydrate antigen 19.9 antibody (anti-CA19.9, Dako, Heverlee, Belgium; 2 μl per million cells in 200 μl) or isotype control (IgG1 kappa, Abcam, Cambridge, MA, USA; 2 μl per million cells in 200 μl) for 15 minutes at 4 °C. Cells were washed with FBS buffer (PBS + 3% FBS) and incubated for 15 minutes at 4 °C with secondary antibody Alexa fluor 647 anti-mouse (Jackson Laboratory, Westgrove, PA, USA; 2 μl per million cells in 200 μl). Analysis and cell sorting was performed on a BD FACSAria (BD Biosciences, Erembodegem, Belgium). Viable, single cells were gated based on forward and side scatter. After sort, cells were immediately collected in RLT buffer (Qiagen, Germantown, MD 20874, USA) and kept on ice. RNA extraction was immediately performed after sorting.


title: Granzyme A-producing CD4+ T cells in graft-versus-host disease

city: West Lafayette

first: Matt

last: Olson

address: 201 St University St

institute: Purdue University

summary: RNAseq sequencing of Cytokine treated Mouse CD4+ Cells

overall_design: CD4+ cells were isolated by negative selection and treated with indicated cytokine(s) for set amounts of time. Cells were prepared for RNAseq of poly-adenylated RNA.


title: Fire ant worker brain transcriptomes

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: Transcriptomes of dissected brains from  workers from polygyne fire ants were analyzed. Four replicates were obtained.

overall_design: Fire ant brain mRNA profiles of workers were generated by deep sequencing of three replicates per condition, using Illumina.

first: Chloe

last: Hawkings


title: Transcriptomic alterations of erythroid progenitors during ageing

first: Claus

last: Nerlov

summary: Functional study has revealed that the erythroid differentiation capacity is compromised during ageing. Here we report the transcriptome profiles of erythroid progenitors in the bone marrow of young and aged mice

overall_design: Examine the gene expression of erythroid progenitors within the bone marrow of young (8-12 weeks) and aged (24-25 months) mice by bulk RNA-seq (100 cells)

first: Simona

last: Valletta

first: Roy

last: Drissen

first: Yiran

last: Meng


title: Effect of IL6 inhibition on the gene expression of erythroid progenitors in aged mice

summary: Gene expression analysis has revealed that Interleukin-6 signalling in murine erythroid progenitors is altered during ageing. Here we study the impact of inhibition of IL6 on the transcription profile of progenitors from bone marrow in aged mice

overall_design: Aged mice (24-25 months) were treated with anti-IL6 antibody or IgG control and examine the gene expression of erythorid progenitors by bulk (100 cells) RNA-seq


title: Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [Histone ChIP-seq]

city: Portland

address: 3030 S Moody Ave.

institute: Oregon Health and Science University

overall_design: ChIP-seq of various histone marks was performed on three different gibbon lymphocyte cell lines (biological replicates)


title: Time-resolved DNA methylation profiling of endocrine resistance in the T47D luminal A breast cancer cell line

status: Public on Jul 17 2020

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

summary: Endocrine therapy is the most used treatment for hormone receptor positive breast cancers. Despite the clear benefit of endocrine therapy for patients with ER+ breast cancer, resistance to treatment is a critical clinical issue affecting a large number of patients. While many studies have shown that genetics is an important factor in therapy resistance, recent publications have also reported that epigenetics might play a major role in the acquisition of resistance to endocrine therapies. This role is exploited both at the DNA methylation level, with activation of oncogenes and silencing of tumor suppressor genes, and at the histone modification level, with changes in chromatin accessibility. DNA methylation exerts its role in resistance both by targeting the ER itself, by inducing promoter methylation, and genome wide, by changing the methylation levels of estrogen response elements. To better understand resistance acquisition in an in vitro setting, researchers developed cellular models of endocrine therapy resistance. The prevalent strategy to identify mechanisms of resistance development and novel targets involved in the process has been to study differences between resistant and sensitive cells. Here, we performed time-resolved DNA methylation profiling of development of resistance to tamoxifen treatment and to estrogen deprivation in the T47D luminal A breast cancer cell line with the aim to identify novel drivers.

overall_design: T47D cells were either treated with 100 nM 4-hydroxytamoxifen (TAM), long-term estrogen deprived (LTED; modelling AI treatment) or not treated (wild type (WT)) in two biological replicates cultured for 7 and 5 months, respectively. DNA was extracted after 0, 1, 2, 5 and 7 (only one replicate) months. Methylation profiling was performed using the Illumina MethylationEPIC BeadChip platform at the Genomic and Proteomic Core Facility (DKFZ, Germany). For each sample two technical replicates were measured.

first: Simone

last: Borgoni

first: Maryam

last: Soleimani

first: Stefan

last: Wiemann


title: Gene expression in gamma-glutamylcyclotransferase-overexpressing mouse embryonic fibroblast NIH3T3 cells.

city: Kamigyo-ku, Kyoto

first: Keiko

last: Taniguchi

state: Kyoto

address: Kawaramachi-Hirokoji

department: Drug Discovery Medicine

institute: Kyoto Prefectural University of Medicine

summary: Although hypoxia inducible factor-1a (HIF-1a) was originally identified as a transcriptional factor to adapt hypoxia, HIF-1a has also been shown to regulate metabolic pathways specific for cancer, including aerobic glycolysis, namely “Warburg effect”. However, the mechanisms by which HIF-1a mediates the metabolic pathway under normoxia are not fully understood. Here, we identified gamma-glutamylcyclotransferase (GGCT) as a novel regulator of HIF-1a. GGCT is a highly expressed protein in various cancer tissues. Knockdown of GGCT exerts anticancer effects both in vitro and in vivo; thus, it is considered a promising therapeutic target. In this study, we show that depleting GGCT downregulates the protein and mRNA expressions of HIF-1a in PC3 prostate cancer cells, and that overexpressing GGCT upregulates them in mouse fibroblast NIH3T3 cells. We also show that depleting GGCT downregulates HIF-1a downstream target genes involved in glycolysis, whereas overexpressing GGCT exhibits upregulation pattern in these genes. Furthermore, we suggest that GGCT induces the metabolic switch from citric acid cycle to glycolysis under normoxia. Additionally, we show that GGCT regulates expression of HIF-1a protein via AMPK-mTORC1-4EBP1 pathway in PC3 cells. These results indicate the GGCT plays a regulatory role in the expression of HIF-1a followed by glycolytic switch in cancer cells.

overall_design: To test the effect of overexpression of GGCT on the gene expression, mouse embryonic fibroblast cell line NIH3T3 was transfected with GGCT expression retroviral vector or control vector. Three independent experiments were performed and GGCT-overexpressing NIH3T3 cells were compared to control cells.

first: Susumu

last: Kageyama

first: Chiami

last: Moyama

first: Shota

last: Ando

first: Hiromi

last: Ii

first: Eishi

last: Ashihara

first: Mano

last: Horinaka

first: Toshiyuki

last: Sakai

first: Shigehisa

last: Kubota

first: Akihiro

last: Kawauchi

last: Nakata


title: Adaptation to low parasite abundance affects immune investment and immunopathological responses of cavefish

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Reduced parasitic infection rates in the developed world are suspected to underlie the rising prevalence of autoimmune disorders. However, the long-term evolutionary consequences of decreased parasite exposure on an immune system are not well understood. We used the Mexican tetra Astyanax mexicanus to understand how loss of parasite diversity influences the evolutionary trajectory of the vertebrate immune system, by comparing river with cave morphotypes. Here, we present field data affirming a strong reduction in parasite diversity in the cave ecosystem, and show that cavefish immune cells display a more sensitive pro-inflammatory response towards bacterial endotoxins. Surprisingly, other innate cellular immune responses, such as phagocytosis, are drastically decreased in cavefish. Using two independent single-cell approaches, we identified a shift in the overall immune cell composition in cavefish as the underlying cellular mechanism, indicating strong differences in the immune investment strategy. While surface fish invest evenly into the innate and adaptive immune systems, cavefish shifted immune investment to the adaptive immune system, and here, mainly towards specific T-cell populations that promote homeostasis. Additionally, inflammatory responses and immunopathological phenotypes in visceral adipose tissue are drastically reduced in cavefish. Our data indicate that long-term adaptation to low parasite diversity coincides with a more sensitive immune system in cavefish, which is accompanied by a reduction in the immune cells that play a role in mediating the pro-inflammatory response.

overall_design: singel cell level study to compare cavefish and surfacefish hematopoietic system difference

first: Robert

last: Peuß

first: Andrew

last: Box

first: Yongfu

last: Wang

first: Dai

last: Tsuchiya

first: Jenna

last: Persons

first: Alexander

last: Kenzior

first: Ernesto

last: Maldonado

first: Jaya

last: Krishnan

first: Jörn

last: Scharsack

first: Brian

last: Slaughter

first: Nicolas

last: Rohner


title: RNA-seq results in adipose tissues of fat-specific Mecp2 knockout mice

city: Wuhan

first: Chengyu

last: Liu

address: No.13, Hangkong Road

institute: Huazhong University of Science and Technology

summary: Fat-specific knockout of Mecp2 results in downregulation of adipogenesis genes and upregulation of theromgenesis genes

overall_design: Fat-specific Mecp2 knockout male mice (Mecp2 Adi KO) and their age-, sex- matched control mice were fed with normal chow diet (NCD) and maintained in standard housing conditions. For each experimental group, two biological replicates of RNA samples were sent for RNA-seq. Each sample consists of a pool of RNAs extracted from inguinal adipose tissue or brown adipose tissue of 3 different mice.

first: Ling

last: Zheng

first: Kun

last: Huang


title: p53-inducible long non-coding RNAs encode functional peptides in hepatocellular carcinoma cells [Ribo-seq]

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: To globally analyse the lncRNAs with potential coding ability upon DNA damage, we performed Ribo-seq using ADR-treated HepG2 cells. The HepG2 cells were treated with 500 ng/mL ADR for 24 h, and cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes.Furthermore,we identified the candidate ORFs with the selected RPF reads using the RiboCode software.

overall_design: Ribo-seq profiles of HepG2 p53 wild-type (WT) treated with ADR were generated by deep sequencing, in two independent experiments, using  Xten Illumina sequencing platform. The ribo-seq data of the two biological replicates were integrated.Then,for the analysis of Ribo-seq data, sequenced reads that were trimmed for the adaptor sequence were aligned to the UCSC hg19 reference genome by STAR (version 2.4.2a) with parameters provided by the RiboCode (version 1.2.10) manual.

first: Wen-Li

last: Xu

first: Bing

last: Deng

first: Peng-Hui

last: Lin

first: Chang

first: Bin

last: Li

first: Ke-Ren

last: Zhou

first: Hui

first: Liang-Hu

last: Qu


title: MN1 colocalizes with the BAF complex on enhancer chromatin

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: We show that the overexpression of MN1, but not MN1-∆pQ, stabilizes the porogenitor-specific enhancer landscape

overall_design: ChIP-seq of H3K27ac, H3K4me1, and Smarca4 in MN1 and MN1-∆pQ transduced murine HSPCs. In MN1-driven murine leukemia cells additionally ChIP for MN1.

first: Simone

middle: S

last: Riedel


title: Synthetic circular miR-21 RNA decoys enhance tumor suppressor expression and impair tumor growth in mice (RNA-Seq)

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: Natural and synthetic circular RNAs effectively impair miRNA function. MiR-21-5p is a potent oncomiR presenting ~33% of all miRNAs across cancers, ~41% in lung adenocarcinoma (LUAD), and ~68% in LUAD-derived cells. We validate and identify five main tumor suppressors targeted by miR-21-5p by deletion of the MIR21 locus in LUAD cells. Synthetic, liposome-delivered circular miR-21-5p decoys enhance expression of these tumor suppressors and severely impair tumor cell vitality at low doses. Decoy efficacy is not increased by bulging of miR-21-5p targeting sites, but associated with substantial cellular decoy stability, indicated by a half-life of ~20h. The intraperitoneal application of nanoparticle-delivered miR-21-5p decoys significantly impairs tumor growth in mouse LUAD tumor models. Decoys are well tolerated and were enriched in lung tissue. However, despite low decoy abundance, tumor suppressor expression was only increased in subcutaneous tumors. These findings suggest nanoparticle-delivered circular miRNA decoys as potent therapeutics in cancer treatment.

overall_design: polyA RNA-Seq of parental or MIR21 deleted A549 cells. Deletion of MIR21 was generated by using Crispr/Cas9.

first: Simon

last: Müller

first: Alice

last: Wedler

first: Janina

last: Breuer

first: Nadine

last: Bley

first: Marcell

last: Lederer

first: Jacob

last: Haase

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alina

last: Ottmann

first: Tessa

last: Schmachtel

first: Lyudmillya

last: Shalamova

first: Alexander

last: Ewe

first: Achim

last: Aigner

first: Oliver

last: Rossbach

first: Stefan

last: Hüttelmaier


title: Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos (MBD-seq)

first: Byungkuk

last: Min

type: Methylation profiling by high throughput sequencing

overall_design: Global DNA methyaltion profiles by MBD-seq in Dnmt1 knock-out 4/8-cell embryos using CRISPR/Cas9 system

first: Yong-Kook

last: Kang


title: Gene expression in gamma-glutamylcyclotransferase-depleted human prostate cancer PC3 cells.

first: Keiko

last: Taniguchi

overall_design: To test the effect of depleting GGCT on the gene expression of cancer cells, human prostate cancer cell line PC3 was transfected with siRNA targeting GGCT or non-targeting control siRNA. Three independent experiments were performed and GGCT knockdown PC3 cells were compared to control cells.

first: Susumu

last: Kageyama

first: Chiami

last: Moyama

first: Shota

last: Ando

first: Hiromi

last: Ii

first: Eishi

last: Ashihara

first: Mano

last: Horinaka

first: Toshiyuki

last: Sakai

first: Shigehisa

last: Kubota

first: Akihiro

last: Kawauchi

last: Nakata


title: Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos (ChIP-seq)

overall_design: Comparison of chromatin association between full-length and catalytic domain depleted DNMT1.


title: Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos (RNA-seq)

overall_design: For RNA-seq, 20 of each siDnmt1- or scrambled siRNA-injected mouse embryos were harvested at 4~8 stage, and RNA-seq libraries were prepared using their poly-A tailed mRNAs.

first: Yong


title: High-throughput profiling of human castration-resistant prostate cancer cell lines

city: Seattle

first: John

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

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

overall_design: Refer to individual Series


title: Lack of desmin in mice causes structural and functional disorders of neuromuscular junctions

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Desmin, the major intermediate filament (IF) protein in muscle cells, interlinks neighboring myofibrils and connects the whole myofibrillar apparatus to myonuclei, mitochondria, and the sarcolemma. However, desmin is also known to be enriched at postsynaptic membranes of neuromuscular junctions (NMJs). The pivotal role of the desmin IF cytoskeletal network is underscored by the fact that over 100 mutations of the human DES gene cause hereditary and sporadic myopathies and cardiomyopathies. A subgroup of human desminopathies comprises autosomal recessive cases resulting in complete abolition of desmin protein. In these patients, who display a more severe phenotype than the autosomal dominant cases, it has been reported that some individuals also suffer from a myasthenic syndrome in addition to the classical occurrence of myopathy and cardiomyopathy. Since further studies on the NMJ pathology is hampered by the lack of available human striated muscle biopsy specimens, we exploited homozygous desmin knock-out mice which closely mirror the striated muscle pathology of human patients lacking desmin protein. Here, we report on the impact of the lack of desmin on the structure and function of NMJs and on the transcription of genes coding for postsynaptic proteins. Desmin knock-out mice display a fragmentation of NMJs in soleus, but not in extensor digitorum longus muscle. Moreover, soleus muscle fibers show larger NMJs. Further, transcription levels of acetylcholine receptor (AChR) genes are increased in muscles from desmin knock-out mice, especially of the AChR subunit, which is known as a marker of muscle fiber regeneration. Electrophysiological recordings depicted a pathological decrement of nerve-dependent endplate potentials and a faster rise time of the nerve-independent miniature endplate potentials. The latter is indicating an enhanced opening time of the AChR channels. Our study highlights the essential role of desmin for the structural and functional integrity of mammalian neuromuscular junctions.

overall_design: Differential gene expression analysis of striated muscle in wildtype vs. Desmin knock out mice was performed on 5 biological replicates of each genotype.

first: Christian

middle: T

last: Thiel

first: Arif

middle: B

last: Ekici


title: Genome-wide analysis of long noncoding RNA expression profile in spontaneously hypertensive rat treated by Ganoderma lingzhi oligopeptide

city: Changsha

first: Wu

last: Qiang

address: 498 Shaoshan Road

institute: Central South University of Forestry and Technology

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

summary: Angiotensin I-converting enzyme (ACE) plays a vital role in cardiovascular disease (CVD). Natural ACE inhibitory peptides from Ganoderma lingzhi (G. lingzhi) showed potential vasodilatation in vitro or in vivo. Recent studies have shown that long non-coding (lncRNA) plays critical roles in biological processes and human diseases, since the roles of lncRNA in CVD remain unclear. Our findings indicate that the expression profiles of lncRNAs has changed in spontaneously hypertensive rats (SHRs) treated by the G. lingzhi peptide, compared with untreatedt groups. It is expected to provide novel insight into the underlying molecular mechanism and potential targets for hypertention therapy.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from three SHR thoracic aorta samples administrated by G. lingzhi peptide and three untreated samples.

first: Liu

last: Gao-Qiang

first: Wang

last: Xiao-Ling

first: Luo

last: Feijun


title: De novo transcriptome assembly and functional annotation for Y-organs of the blue crab (Callinectes sapidus), and analysis of differentially expressed genes during pre-molt

city: Bethesda

first: Megan

middle: Elizabeth

last: Roegner

state: MD

address: 10 Center Drive, RM 8N316

department: NIDDK

institute: NIH

summary: We report the de novo assembled transcriptome of Y-organs from two intermolt and two pre-molt blue crabs. Data was obtained from RNAseq, assembled using Trinity, and differential expression was determined using DEseq2 in R.

overall_design: De novo transcriptome assembled and used as baseline to compare gene expression in two intermolt and two pre-molt blue crabs.

first: R

last: Watson


title: Multi-omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma

city: Minneapolis

first: Timothy

last: Starr

state: MN

address: 420 Delaware St SE

department: Department of Obstetrics

institute: University of Minnesota

summary: Multiple studies have identified transcriptome subtypes of high-grade serous ovarian carcinoma (HGSOC), but their interpretation and translation are complicated by tumor evolution and polyclonality accompanied by extensive accumulation of somatic aberrations, varying cell type admixtures, and different tissues of origin. In this study, we examined the chronology of HGSOC subtype evolution in the context of these factors using a novel integrative analysis of absolute copy number analysis and gene expression in The Cancer Genome Atlas complemented by single-cell analysis of six independent tumors. Tumor purity, ploidy, and subclonality were reliably inferred from different genomic platforms, and these characteristics displayed marked differences between subtypes. Genomic lesions associated with HGSOC subtypes tended to be subclonal, implying subtype divergence at later stages of tumor evolution. Subclonality of recurrent HGSOC alterations was evident for proliferative tumors, characterized by extreme genomic instability, absence of immune infiltration, and greater patient age. In contrast, differentiated tumors were characterized by largely intact genome integrity, high immune infiltration, and younger patient age. Single-cell sequencing of 42,000 tumor cells revealed widespread heterogeneity in tumor cell type composition that drove bulk subtypes but demonstrated a lack of intrinsic subtypes among tumor epithelial cells. Our findings prompt the dismissal of discrete transcriptome subtypes for HGSOC and replacement by a more realistic model of continuous tumor development that includes mixtures of subclones, accumulation of somatic aberrations, infiltration of immune and stromal cells in proportions correlated with tumor stage and tissue of origin, and evolution between properties previously associated with discrete subtypes.

overall_design: 10X Genomics single-cell RNA sequencing of five high-grade serous ovarian carcinomas


title: Gene expression and polysome profiling data of Eμ-Myc B-lymphoma cells

city: Melbourne

first: Anna

last: Trigos

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan street

institute: Peter MacCallum Cancer Centre

summary: Acute response to combinatorial ribosome-targeting therapy in vivo is associated with downregulation of the cells' translational activity and energy metabolism. Translational alterations drive therapeutic resistance by promoting elevated metabolic activity and activation of a cAMP-dependent pro-survival mechanism via EPAC1/2.

overall_design: Polysome profiling analysis of lymph node isolated from mice treated with CX-5461 and/or everolimus to investigate acute response(s) to ribosome-targeting therapy. Resistance mechanism to ribosome-targeting therapy was evaluated by polysome profiling of in vivo-derived early-passage cell lines isolated at ethical endpoint upon disease relapse.

first: Eric

middle: P

last: Kusnadi

first: Richard

last: Pearson


title: High-throughput gene expression profiling of human castration-resistant prostate cancer cell lines

summary: We examine the gene expression and chromatin accessibility profiles of four human castration-resistant prostate cancer cell lines including two representative of small-cell neuroendocrine prostate cancer

overall_design: RNA from the human castration-resistant prostate cancer cell lines 22Rv1, LNCaP95, NCI-H660, and MSKCC EF1 were analyzed in replicate on an Illumina HiSeq 2500


title: High-throughput chromatin accessibility profiling of human castration-resistant prostate cancer cell lines

overall_design: ATAC libraries from the human castration-resistant prostate cancer cell lines 22Rv1, LNCaP95, NCI-H660, and MSKCC EF1 were analyzed in replicate on an Illumina HiSeq 2500.


title: Long-read cDNA Sequencing of Transposable Element-Activated Arabidopsis Mutants

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: We have used the genetic resources of Arabidopsis thaliana to generate mutant lines that have reactivated TE expression. We used these lines with long-read Oxford Nanopore sequencing technology to capture Transposable Element (TE) mRNAs for TE transcript annotation.

overall_design: Examination of full-length mRNA using long-read cDNA sequencing. cDNA was PCR amplified.

first: Kaushik

last: Panda


title: E2A regulates neural ectoderm fate specification in human embryonic stem cells

city: Beijing

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

institute: Peking University


title: microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs (Illumina HT12v4 expression arrays)

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

summary: MiR-140 is selectively expressed in cartilage. Deletion of the entire miR-140 locus in mice results in a growth retardation phenotype and an early-onset osteoarthritis-like pathology, however the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified that miR-140-3p was in vast abundance (>10-fold) to miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase [1] annotation at both the 5´ and 3´ end, with >99% of miR-140-3p isomiRs having one of two ‘seed’ sequences (5´ bases 2-8). The most abundant isomiR with each seed were selected for further analysis; miR-140-3p.2 which has an identical seed to the miRBase miR-140-3p (ACCACAG) and miR-140-3p.1 which has an altered seed (CCACAGG), and thus different potential targets. Each isomiR was overexpressed in chondrocytes and whole-genome transcriptomics used to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes respectively (adj.P.Val<0.05), of which only 162 genes were commonly down-regulated by both isomiRs. Targets of both isomiRs were validated using 3´UTR luciferase assays. A significant enrichment of miR-140-3p.1 targets was identified within genes whose expression increase in the rib chondrocytes of Mir140-null mice and within genes whose expression decreased during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene WWP2 in 124 previously published datasets an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than the original consensus miR-140-3p or the isomiR with the same seed, miR-140-3p.2.

overall_design: Total RNA from 9 samples were hybridised to two Illumina HT12v4 expression arrays

first: Kathleen

last: Cheung


title: Genomic comparison of post-radiation versus sporadic sarcomas

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

type: Genome variation profiling by genome tiling array

summary: Post-radiation sarcomas are rare secondary cancers arising from radiation therapies. To date, few genetic specificities have been described for such malignancies and the oncogenesis of sarcomas with complex genetics (both sporadic and post-radiation) remains largely misunderstood. We performed genomic analyses on both sporadic and post-radiation sarcomas to study their copy-number alterations. This analysis is described in Lesluyes et al. 2019 (PMID: 31243333).

overall_design: We used DNA-arrays on 56 sporadic (Affymetrix SNP6 arrays) and 77 post-radiation (Affymetrix CytoScanHD) sarcomas.

first: Tom

last: Lesluyes

first: Jessica

last: Baud


title: IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer [ATAC-Seq]

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Interleukin 6 (IL6) signaling has been associated with an aggressive and metastatic phenotype in multiple solid tumors including breast cancer, but its mechanism of action in mediating tumor progression and treatment response is not clear. By exploiting a clinically relevant intraductal xenograft model of estrogen receptor positive (ER+) breast cancer, we demonstrate that IL6 increases both primary tumor growth and distant metastases. By integrating pre-clinical models and clinical specimens, we show that signal transducer and activator of transcription 3 (STAT3) mediates IL6-induced activation of a metastatic gene program from enhancer-elements shared with ER and its pioneer factor FOXA1. Although IL6 activated STAT3 and ER/FOXA1 share cis-regulatory regions, STAT3 drives transcription independent of ER and FOXA1 function, and the IL6/STAT3 gene program is not influenced by ER-targeted therapies, decoupling these two important pathways. This demonstrates that ER/FOXA1 and IL6/STAT3 are two parallel, but independent actionable pathways controlling breast cancer progression.

overall_design: ATAC-sequencing on T47D cells with FOXA1 siRNA with or without IL6

first: Rasmus

last: Siersbaek

first: Igor

last: Chernukhin


title: DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

summary: The DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor. Naïve B cells undergo class switch recombination (CSR) to generate antibodies with different isotypes by joining two DNA double-strand breaks at different switching regions via the cNHEJ pathway. DNA-PK and the cNHEJ pathway play important roles in the DNA repair phase of CSR. To initiate cNHEJ, KU binds to DNA ends and recruits and activates DNA-PK. Activated DNA-PK phosphorylates DNA-PKcs at the S2056 and T2609 clusters. Loss of T2609 cluster phosphorylation increases radiation sensitivity but whether T2609 phosphorylation has a role in physiological DNA repair remains elusive. Using the DNA-PKcs5A mouse model carrying alanine substitutions at the T2609 cluster, here we show that loss of T2609 phosphorylation of DNA-PKcs does not affect the CSR efficiency. Yet, the CSR junctions recovered from DNA-PKcs5A/5A B cells reveal increased chromosomal translocations, extensive use of distal switch regions (consistent with end-resection), and preferential usage of micro-homology – all signs of the alternative end-joining pathway. Thus, these results uncover a role of DNA-PKcs T2609 phosphorylation in promoting cNHEJ repair pathway choice during CSR.

overall_design: To understand the role of T2609 phosphorylation in CSR and DSB repair specifically, we evaluated the role of T2609 phosphorylation in physiological DSB repair during CSR using germline mouse models. As in the case of V(D)J recombination, T2609A mutation also does not affect CSR efficiency. But CSR junctions from DNA-PKcs5A/5A  B cells revealed a preferential loss of Sμ-Sε junctions, increased MH usage, increased use of downstream switch regions (consistent with excessive end resection) and increased inter-chromosomal translocations ((+) strand preys)– all consistent with cNHEJ deficiency and compensatory Alt-EJ-mediated CSR.  Together these findings support the role of DNA-PKcs T2609 phosphorylation in promoting cNHEJ-mediated CSR. In the absence of T2609 phosphorylation, the increased dependence on the Alt-EJ pathway, together with the extensive length of the Sg1 region (12.5kb in 129SV strain), the dense RGYW/AGCT sequence motifs, and the sequence-independent 3D interactions (synapses) between Sµ-Sg1, lead to robust Alt-EJ-mediated CSR to IgG1 in DNA-PKcs5A/5A  B cells. Thus, our analyses identify a novel role of DNA-PKcs T2609 phosphorylation in repair pathway choice during CSR.

first: Jennifer

middle: L

last: Crowe

first: Zhengping

last: Shao

first: Shan

last: Zha