city: Philadelphia

last: Schiewer

state: Pennsylvania

department: Cancer Biology

institute: Sidney Kimmel Cancer Center at Jefferson

summary: Evaluation of the genome wide impact of PARPi gene expression programs

overall_design: Identification of PARPi sensitive transcripts in prostate cancer cell lines LNCaP and C4-2.

first: Karen

last: Knudsen


title: Transcriptome profiling reveal the effect of Sutent in the mice adipose tissues and livers

status: Public on Dec 26 2018

city: 上海市

first: Yan

last: Qiu

address: 上海岳阳路320号

country: China

institute: University of Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: We administered clinically relevant dose of sutent (a small molecule inhibitor of multi-target receptor tyrosine kinases) to mice daliy for 16 weeks. We then compared the effect of sutent on four tissues(BAT,iWAT,eWAT and liver) transcriptome using RNAseq. We found sutent treatment enhances energy expenditure and improves metabolism in mice under HFD. Results provide insight into the molecular mechanisms of sutent in the treatment of obesity.

overall_design: Four tissues from 8 mice:4 mice were treated with sutent, 4 mice were treated with vehicle.

first: Qiurong

last: Ding

first: Yingming

last: Sun

first: Danqing

last: Xu

first: Yuanyuan

last: Yang

first: Xiaojian

last: Liu

first: Yuda

last: Wei

first: Yanhao

last: Chen

first: Zhuanghui

last: Feng

first: Md

last: Reyad-ul-Ferdous

first: Yongxu

last: Zhao

first: Hongxi

first: Yuanzhi

last: Lao


title: Differential expression profiles of long non-coding RNAs during the mouse pronucleus stage under normal gravity and simulated microgravity

city: guangzhou

first: meiying

last: feng

address: College of Animal Science, South China Agricultural University, 483 Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China.

institute: Zhaoqing University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of lncRNA in mouse cells. By obtaining over 47 million bases of sequence, we identified 3,307 lncRNAs based on single-cell RNA sequencing (RNA-Seq) data, discovered 52 lncRNAs that were significantly differentially expressed, and then selected 10 lncRNAs for qRT-PCR validation. Furthermore, we found that 12 lncRNAs with the target gene Tubb4b or Actn4 might be related to the expression of microtubule and microfilament proteins and the binding relationship was confirmed in a dual-luciferase reporter assay. Finally, Gene Ontology (GO) analysis revealed that the target genes of the differentially expressed lncRNAs participated in cellular processes related to protein transport, binding, catalytic activity, membrane-bounded organelles, protein complexes and the cortical cytoskeleton. We believe the paper will be of particular interest to the readers of your journal as lncRNAs regulated the progress of the mouse early embryo development.

overall_design: LncRNA profiles of two differently gravity during the mouse pronucleus stage were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Meiying

first: Shouquan

last: Zhang


title: Does osteogenic potential of clonal human bone marrow mesenchymal stem/stromal cells correlate with their vascular supportive ability?

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: Headington

country: United Kingdom

institute: University of Oxford

summary: Human bone marrow-derived mesenchymal stem/stromal cells (hBM MSCs) have multiple functions, critical for skeletal formation and function. Their functional heterogeneity, however, represents a major challenge for their isolation and  in developing and potency and release assays to predict their functionality prior to transplantation. Additionally, potency, biomarker profiles and defining mechanisms of action in a particular clinical setting are increasing requirements of Regulatory Agencies for release of hBM MSCs as Advanced Therapy Medicinal Products (ATMPs) for cellular therapies. Since the healing of bone defects in larger bone grafts depends on the coupling of new blood vessel formation with osteogenesis, we hypothesised that a correlation between the osteogenic and vascular supportive potential of individual hBM MSC-derived CFU-F (colony forming unit-fibroblastoid) clones might exist. We tested this by assessing the lineage (i.e. adipogenic {A}, osteogenic {O} and/or chondrogenic {C}) potential of individual hBM MSC-derived CFU-F clones and determining if their osteogenic {O} potential correlated with their vascular supportive profile in vitro using lineage differentiation assays, endothelial-hBM MSC vascular co-culture assays and transcriptomic (RNAseq) analyses. Our results demonstrate that the majority of CFU-F (95%) possessed tri-lineage, bi-lineage or uni-lineage osteogenic capacity, with 64% of the CFU-F exhibiting tri-lineage AOC potential. We found a correlation between the osteogenic and vascular tubule supportive activity of CFU-F clones, with the strength of this association being donor dependent.  RNAseq of individual clones defined gene fingerprints relevant to this correlation.

overall_design: 16 samples from two donors (8 from each donor), possessing high or low osteogenic potential.

first: David

last: Cook

first: Barbara

middle: J

last: Lara

first: Emmanouela

last: Repapi

first: Neil

last: Ashley

first: Yuan

first: Shiang

middle: Y

last: Lim

first: Suzanne

middle: M

last: Watt


title: Next Generation Sequencing Analysis of miRNA profiling in Epithelial Type and Mesenchymal Type Beas-2b Cells

city: Omaha

first: Yaping

last: Tu

state: NE

address: 2500 California Plaza

country: USA

institute: Creighton University

summary: We reported the application of next generation sequencing technology for high-throughput profiling of miRNA expression in bronchile epithelial cell line Beas-2b with epithelial or mesenchymal mophology. By comparation the expression aboundence of known miRNAs between epithelial type and mesenchymal type Beas-2b cells, we found both upregulated and downregulated miRNAs in bronchial epithelial cells during EMT. This study provides a basic condition for further investigation of the roles of the regulated miRNAs during EMT in bronchial epithelial cells.

overall_design: Examination of miRNA profiling in epithelial and mesenchymal subtypes of Beas-2b cells

first: Linjie


title: Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [MBD-Seq]

city: Baltimore

first: Elizabeth

last: Jaffee

state: MD

address: 1650 Orleans St

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

summary: Identification of novel differential DNA methylation sites in human M1 and M2 macrophages using MBD-Seq

overall_design: MBD-Seq was performed using DNA from M1 and M2-polarized macrophages from 4 biological replicates

first: Kimberline

last: Gerrick


title: Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization

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

overall_design: Refer to individual Series


title: Genomic and phenotypic characterization of a refactored xylose utilizing Saccharomyces cerevisiae for lignocellulosic biofuels/biochemicals production

city: Seoul

first: Ja Kyong

last: Ko

address: Seongbuk-gu, Wharang-ro, 14 gil 5

department: Clearn Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

summary: To understand the mechanisms of enhanced xylose metabolism of XUSE, we reported transcriptome analysis of XUS (rationally engineered strain) and XUSE (evolved XUS strain) grown on xylose by performing RNA-sequencing. Compared with XUS, XUSE showed significantly different gene expression landscape with 463 up-regulated and 675 down-regulated genes (>2-fold, p-value<0.05). While the genes involved in non-oxidative pentose phosphate pathway, such as TKL1, TKL2 and TAL1, were down-regulated in XUSE, it shows the decreased transcriptional patterns of a number of genes encoding TCA cycle and respiratory enzymes. Also, the genes involved in the cellular metal ion regulation and sugar transporters showed significantly changed expression levels in XUSE. This study shows the gene expression landscape of XUSE revealing engineering strategies for the enhanced xylose metabolism in S. cerevisiae.

overall_design: Transcriptional landscape of evolved xylose fermenting strains harboring xylose isomerase pathway was generated by RNA-sequencing

first: Sun-Mi

last: Lee

first: Ja

middle: K

first: Phuong

middle: H

last: Tran

first: Youngsoon

last: Um

first: Gyeongtaek

last: Gong


title: Transcriptomic analysis of progenitor marker expression in retinal cells

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: We reported that the cells expressed early RPC markers and late RPC markers at high level.

overall_design: Mouse retinal progenitor cell mRNA profiles and mouse retinal tissue were generated by equencing using HiSeqTM 2500

first: Caixia

last: Jin


title: CARM1 (PRMT4) acts as a transcriptional coactivator during retinoic acid-induced embryonic stem cell differentiation

city: New York

first: Kristian

last: Laursen

state: NY

address: 1300 York Ave.

department: Pharmacology

institute: Weill Cornell Medicine

summary: Our data demonstrate that CARM1 is required for transcriptional activation of a subset of retinoic acid (RA) target genes in J1 murine embryonic stem cells

overall_design: To address CARM1 function during RA-induced differentiation of murine embryonic stem cells (mESCs), we treated WT (wild-type), shCtl (scramble control), and CARM1 knockdown (KD) ESCs with vehicle (EtOH) or 1μM Retinoic Acid (RA) for 48hrs and performed expression profiling by RNA-seq

first: Cynthia

last: Quintero

middle: B

first: Nigel

middle: P

last: Mongan

first: Minkui

last: Luo

first: Lorraine

last: Gudas


title: Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

summary: Identification of novel differentially expressed genes in human M1 and M2 macrophages using RNA-Seq

overall_design: RNA-Seq was performed using RNA from M1 and M2-polarized macrophages from 4 biological replicates


title: Macrophage responses to MDR M.tuberculosis infection

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: The emergence of multidrug resistant (MDR) Mycobacterium tuberculosis (Mtb) strains, resistant to the frontline anti-tubercular drugs rifampicin and isoniazid, forces treatment with less effective and toxic second-line drugs and stands to derail TB control efforts. However, the immune response to MDR Mtb infection remains poorly understood. Here, we determined the RNA transcriptional profile of in vitro generated macrophages to infection with either drug susceptible Mtb HN878 or MDR Mtb W_7642 infection.

overall_design: Bone marrow-derived macrophages (BMDMs) from WT and Il1r1–/– mice were derived in 7 days in GM-CSF supplemented complete DMEM.  Cells were infected with either Mtb HN878 or Mtb W_7642 (multiplicity of infection = 1) and RNA samples collected after 6 days.

first: Nicole

last: Howard

first: Alexey

last: Sergushichev

middle: N

first: Shabaana

middle: A

last: Khader


title: Self-associated molecular patterns mediate cancer immune evasion by engagement of Siglec receptors

city: Basel

first: Heinz

last: Läubli

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Cancer immunotherapy targeting inhibitory receptors on T cells has changed the landscape of oncological practice, but most patients do not respond to current approaches. Thus, new targets on T cells for cancer immunotherapy are needed. CD33-related Siglecs are pattern recognition immune receptors binding to a broad range of sialoglycan ligands, which appear to function as self-associated molecular patterns (SAMPs) to dampen unwanted immune responses against self. Naïve T cells in humans have very low levels of inhibitory Siglec expression. Here, we show Siglec-9 in non-small cell lung cancer (NSCLC) are significantly upregulated on tumor-infiltrating T cells. These findings were confirmed in other tumor types including colorectal cancer, and ovarian cancer. Characterization of Siglec-9 expressing T cells showed a co-expression of inhibitory receptors including PD-1 and a distinct phenotype with increased cytokine production upon restimulation, compared to Siglec negative T cells. Functional analysis by reduction of sialoglycan-SAMPs on tumor cells in vitro and in vivo demonstrated an increased tumor cell killing and an inhibition of tumor growth. Overexpression of inhibitory Siglecs on T cells enhanced tumor growth in mice and exchange of inhibitory Siglecs on mouse T cells with an activating Siglec enhanced anti-cancer immunity. Increased T cell expression of Siglec-9 in NSCLC patients also correlated with survival, and analysis of Siglec-9 polymorphisms showed an association with the risk of developing lung and colorectal cancer. Our data identify the sialoglycan-SAMP/Siglec pathway as potential new target to improve T cell activation and cancer immunotherapy.

overall_design: Six non-small cell lung cancer tumor infiltrating CD8+ T cells (CD45+ CD3+ CD8+ CD4-) were sorted by flow cytometry according to their Siglec9 staining into Siglec9+ and Siglec9- samples.

first: Michal

last: Stanczak

first: Marcel

last: Trefny

first: Daniela

last: Thommen

first: Alexander

last: Tzankov

first: Lothar

last: Tietze

first: Didier

last: Lardinois

first: Viola

last: Heinzelmann-Schwarz

first: Alfred

last: Zippelius


title: Role of Neurogenin3 phosphorylation in the reprogramming of pancreatic organoids into endocrine cells

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: During pancreatic development, Neurogenin3 (Ngn3) promotes the differentiation of endocrine cells, including insulin-producing β-cells. Our previous work has shown that Ngn3 phosphorylation on multiple serine-proline (SP) sites increases protein stability and endocrine differentiation (Azzarelli et al., DevCell 2017). Here, we aim to exploit our recent data to investigate whether manipulation of Ngn3 phosphostatus might improve in vitro generation of β-cells for replacement therapies in diabetes. A potential source of β-cells comes from fate conversion of exocrine pancreatic cells into the endocrine lineage, by overexpression of 3 transcription factors, Ngn3, Pdx1 and MafA. Using this approach we show that pancreatic ductal cells grown in vitro as 3D organoids can be reprogrammed to express insulin. The efficiency can be strongly enhanced by substituting wild type Ngn3 with a the un(der)phosphorylated and more active Ngn3 form (6S-A Ngn3). Here we perform transcriptomic analysis of a low number of pancreatic organoid cells expressing wild type or phosphomutant Ngn3, alone or in various combination Pdx1 and/or MafA. The analysis revealed endocrine differentiation and in particular β-like cell gene expression in the conditions where Ngn3 was in combination with both Pdx1 and MafA.

overall_design: RNA-sequencing of pancreatic organoids infected with various combination of transcription factors: WTNgn3-Pdx1, WTNgn3-MafA, WTNgn3-Pdx1-MafA, 6SANgn3-Pdx1, 6SANgn3-MafA, 6SANgn3-Pdx1-MafA, Pdx1 only or MafA only expressing cells, in culture infected with either WTNgn3 or 6SANgn3. Samples are collected 8days after induction: 3 biological replicates and 1-2-3 technical replicates depending on the sample

first: Roberta

last: Azzarelli

first: Sonia

last: Nestorowa

first: Steffen

last: Rulands

first: Berthold

last: Gottgens

first: Anna

last: Philpott


title: Gene expression of 5-azacytidine-treated HCT116 cells

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University Graduate school

summary: DNA methylation plays an important role in regulating gene expression. In this study, a subpopulation with accelerated baseline motility (MG cells) or an immotile one (non-MG cells) from a colon cancer cell line (HCT116) were isolated, and gene expression levels of these cells with 5-azacytidine were measured by microarray analysis.

overall_design: Five μM of 5-azacytidine or vehicle was treated into HCT116 cells for 48 hours and then gene expression was measured by human whole-genome microarray (Agilent Technology).


title: RNA-seq single cells analysis of 2 tumors from KPC (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre) mice

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: We investigated the RNA expression levels of NF-kB ligands and their receptors in epithelial cancer cells and cancer-associated fibroblasts (CAFs) from KPC tumors

overall_design: We analysed 8 samples total (2 biological replicates. Each replicate with 2 conditions: DAPI- sorted cells (all live cells) and DAPI-CD45-CD31-EpCAM-PDPN+ sorted cells (CAFs). Each condition with 2 technical replicates.

first: Giulia

last: Biffi

first: Yuan

last: Hao


title: Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [RNA-Seq]

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Expression profiles of Saline, OVA, and Herb treated mice samples. RNA extracted with the Purelink RNA kit was used for cDNA library preparation with the TruSeq Library Prep Kit (Illumina) and sequenced on the NextSeq500.

overall_design: mRNA profiles of wile type (Saline) , OVA , and Herb treated mice were generated by deep sequencing, using NextSeq 500 (Mus musculus), 76x2 paired end.

first: Chul

last: Kim

first: Sujin


title: Identification of epigenetic recovery factor from medicinal-herb (Descurainia sophia) treated asthma based on multi-omics approach [Methyl-Seq]

summary: Sequencing of bisulfite-converted mouse genomic DNA captured on SureSelect Methyl-Seq

overall_design: Methylation profiles of wild type (Saline) , OVA , and Herb treated mice were generated by deep sequencing, using HiSeq2500 (Mus musculus), 2x101 paired end.


title: Global methylation analysis of highly motility cells

summary: Cell movement is an important character during epithelial-mesenchymal transition. A subpopulation with accelerated baseline motility (MG cells) or an immotile one (non-MG cells) from a colon cancer cell line (HCT116) were isolated. In this study, to investigate changes of global DNA methylation status between these two subpopulations, genomic DNA from these cells were subjected to DNA methylation array.

overall_design: Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Identification of epigenetic recovery factor from medicinal-herb seeds (Descurainia sophia) treated asthma based on multi-omics approach


title: RNA-Seq comparison of pancreatic stellate cells (PSCs) cultured with control media or tumor organoid conditioned media in the presence or absence of JAKi

city: Cold Spring Harbor

address: 1 Bungtown Rd

summary: We investigated the roles of JAK/STAT signaling in PSCs cultured with tumor organoid conditioned media (iCAFs) compared to PSCs cultured with control media (quiescent PSCs)

overall_design: A total of 9 samples (3 biological replicates per cohort) were  sequenced on Illumina NextSeq 500. Each cohort was treated with an independent source of tumor organoid conditioned media.


title: Expression data from tumor samples treated with a tankyrase inhibitor in a mouse xenograft model

city: Tokyo

first: Hiroyuki

last: Seimiya

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

institute: JFCR

summary:
Tankyrase enhances beta-catenin signaling via PARsylation and subsequent degradation of Axin, a negative regulator of beta-catenin. Tankyrase inhibitors stabilize Axin and suppress beta-catenin signaling. We developed a novel tankyrase inhibitor, RK-287107.
We used microarrays to elucidate the gene expression profile of human colorectal cancer cells treated with RK-287107 in a mouse xenograft model.

overall_design: Human colorectal cancer COLO-320DM cells were subcutaneously injected into NOD-SCID mice. After the tumors were established, mice were treated with RK-287107 (treatment group) or vehicle (control group). RNAs were extracted from tumors of two individual mice for each group and subjected to transcriptome analysis with Affymetrix microarrays.

last: Mizutani


title: Determine the role of TXNDC9 in hepatocellular carcinoma progression

city: Jiangyin

first: Dawei

last: Chen

state: Jiangsu

address: No. 163, Shoushan Road

department: Jiangyin People's Hospital

institute: School of Medicine, Southeast University

summary: Thioredoxin Domain Containing 9 (TXNDC9)  is a member of the thioredoxin family. The exact function of this protein is not known. This experiment is a transcriptiome profiling of  TXNDC9 dependent RNA expression in hepatocellular carcinoma cell line HepG2.  By compairing the gene expression profile of WT and TXNDC9 knockout, we identified some genes directly or indirectly regulated by TXNDC9 in hepatocellular carcinoma.

overall_design: RNA-seq analysis of wild Type and TXNDC9 knockout HepG2 cells

first: Shuanghai

last: Liu


title: Mechanism of Telapristone acetate (TPA) on Progesterone receptor (PR) action in T47D breast cancer cells

city: Chicago

first: Julie

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To obtain a global analysis of  the effect of TPA on the Progesterone Receptor (PR) cistrome

overall_design: T47D cells were treated with vehicle (ethanol), R5020 10nM, TPA 1uM, R5020+TPA for 30 mins

first: J

first: Batzaya

last: Davaadelger


title: The Major Surface Glycoprotein of Pneumocystis murina Does not Activate Dendritic Cells

city: Bethesda

first: Joseph

middle: A.

last: Kovacs

address: 10 Center Dr

department: CCMD

institute: NIH

summary: The major surface glycoprotein (Msg) is the most abundant surface protein of Pneumocystis species. Given that Msg is present on both the cyst and trophic form of Pneumocystis, and dendritic cells play a critical role in initiating host immune responses, we undertook studies to examine activation of bone marrow-derived myeloid dendritic cells by Msg purified from P. murina. Incubation of dendritic cells with Msg did not lead to increased expression of CD40, CD80, CD86, or MHCII, or increased secretion of any of 10 cytokines. Microarray analysis identified very few differentially expressed genes. In contrast, LPS activated dendritic cells by all of these assays. However, Msg did bind to mouse mannose macrophage receptor and human DC-SIGN, two C-type lectins expressed by dendritic cells that are important in recognition of pathogen-associated high mannose glycoproteins. Deglycosylation of Msg demonstrated that this binding was dependent on glycosylation. These studies suggest that Pneumocystis has developed a mechanism to avoid activation of dendritic cells, potentially by the previously identified loss of genes that are responsible for the high level of protein mannosylation found in other fungi.

overall_design: Gene expression microarrays from 9 samples of mouse immature dentritic cells exposed to endotoxin (LPS) or Msg purified with two methods (Lyticase, SDS) compared with 3 samples of media alone (unexposed control).

first: Monica

last: Sassi

first: Geetha

last: Kutty

first: Gabriela

last: Ferreyra

first: Lisa

middle: R

last: Bishop

first: Yueqin

first: Ju

last: Qiu

first: Da

middle: W

last: Huang


title: Identification of genes associated resistance of everolimus in cutaneous squamous cell carcinoma

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

institute: Konyang university

summary: Metastatic squamous cell carcinoma suggest mTOR inhibitor as therapeutic agent because of activation of the PI3K/AKT/mTOR pathway. However, many therapeutic agents about cancer show resistance. Here, we investigated resistance network about mTOR inhibitor in skin squamous cell carcinoma using microarray. Our study identified that CCND1 overexpression increase resistance about mTOR inhibitor. The molecular mechanism may improve in therapeutic effects of mTOR inhibitor in cutaneous SCC.

overall_design: Total RNA obtained  from cells A431 and HSC-1 treated with DMSO or 100nM everolimus for 72h

first: Dong

middle: C

last: Lee

first: Seung

last: Paik

first: Do

last: Cho

first: Jong

middle: G

last: Choi

first: Jae

last: Kang


title: ChIPseq and RNAseq analysis of T47D cells with/without  silencing TRPS1/CHD4

city: Nanjing

first: liming

last: chen

address: Qixiaqu wenyuanlu 1hao

department: college of life science

institute: Nanjing Normal University

summary: We reported the transcriptional regulation function and mechanism of TRPS1-CHD4/NuRD.

overall_design: Examination of transcription repression role of TRPS1 in breast cancer cells by ChIP and RNA-seq in duplicates using illumina hiseq2500.

first: Liming


title: Limitations of current in vitro models for testing the clinical potential of epigenetic inhibitors for treatment of pediatric ependymoma

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

type: Methylation profiling by genome tiling array

summary:
Background: Epigenetic modifications have been shown to play an important role in the classification and pathogenesis of the pediatric brain tumor ependymoma, suggesting they are a potential therapeutic target.
Methods: The effects of agents targeting epigenetic modifications on the growth and death of a panel of ependymoma cell lines was investigated, as well as toxicity to normal fetal neural stem cells. The ependymoma cell lines were characterized using DNA methylation profiling.
Results: Agents targeting epigenetic modifications inhibited the growth and induced the death of ependymoma cells with variable efficiency. However, this was often not at clinically achievable doses. Additionally, DNA methylation profiling revealed a lack of similarity to primary ependymomas suggesting alterations were induced during culture. Toxicity to fetal neural stem cells was also seen at similar drug concentrations
Conclusions: Agents targeting epigenetic modifications were able to inhibit the growth and induced the death of ependymoma cells grown in vitro. However, many agents were only active at high doses, outside clinical ranges, and also resulted in toxicity to normal brain cells. The lack of similarity in DNA methylation profiles between cultured cells and primary ependymomas questions the validity of using in vitro cultured cells for pre-clinical analysis of agents targeting epigenetic mechanisms and suggests further investigation using models that are more appropriate should be undertaken before agents are taken forward for clinical testing.

overall_design: The Illumina Infinium HumanMethylation450 array and IlluminaHumanMethylationEPIC (Illumina, San Diego, USA) data from n=16 brain tumor cell lines were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Pajtler et al. Cancer Cell. 2015; 27 (5), 728-743)

first: Hazel

last: Rogers


title: The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN

city: Kansas City

first: Peter

last: Baumann

institute: Stowers Institute for Medical Research

summary: Human telomerase RNA (hTR) is transcribed as a precursor that is then posttranscriptionally modified and processed.  A fraction of the transcripts is oligoadenylated by TRAMP and either processed into the mature hTR or degraded by the exosome.  Here, we characterize the processing of 3’ extended forms of varying length by PARN and RRP6. We show that tertiary RNA interactions unique to the longer precursor forms favor RNA degradation, whereas H/ACA RNP assembly stimulates productive processing. Interestingly, the H/ACA complex actively promotes processing in addition to protecting the mature 3’ end.  Processing occurs in two steps with longer forms being trimmed by RRP6 and shorter forms being preferentially processed by PARN.  These results reveal how RNA structure and RNP assembly affect the kinetics of processing and degradation and ultimately determine the amount of functional telomerase produced in cells.

overall_design: We cloned and sequenced 3’ ends by 3' RACE coupled with high-throughput sequencing to gain further insights into hTR processing.

first: Chi-Kang

last: Tseng

first: Hui-Fang

last: Wang

first: Morgan

last: Schroeder


title: Shroom3-Fyn interaction determines nephrin phosphorylation and Albuminuria in allografts

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Glomerular RNA-sequencing: Shroom3 knockdown adult mice vs controls

overall_design: 4 control mice vs. 3 knockdown animals

first: Madhav

last: Menon

first: Zhengzi

last: Yi


title: Heterogeneous maintenance of human tissue resident memory T cells based on efflux capacities

city: new york

first: Brahma

last: Kumar

state: New York

address: 50 haven ave

institute: Columbia University

summary: Tissue-resident memory T cells (TRM) accelerate pathogen clearance through rapid and enhanced functional responses in situ. In humans, TRM cells are prevalent in diverse anatomic sites throughout the human lifespan, yet mechanisms for long-term maintenance are unknown. Here, we identify subpopulations of human TRM in mucosal and lymphoid sites based on differential efflux of mitochondrial dyes, with distinct transcriptional profiles, turnover, and functional capacities. TRM are enriched in efflux(+) populations compared with circulating memory CD8+T cells. Compared to efflux- TRM, efflux(+) TRM showed transcriptional and phenotypic features of quiescence including reduced turnover, decreased expression of exhaustion markers, and increased proliferative capacity and signaling to homeostatic cytokines. Moreover, efflux(+) and efflux(-) TRM subsets both maintain TRM characteristics when activated, while efflux(+) TRM produce IL-17 and efflux(-) produce higher levels of IFN-γ and IL-2. Our results suggest a model for cooperative maintenance of T cell immunity in tissues through interplay of subsets with complementary capacities for longevity and effector function.

overall_design: mRNA profiling of efflux(+) and efflux(-) tissue resident memory T cells (CCR7-CD45RA- CD69+), but unstimulated and stimulated (anti CD3/28/2 beads for 12 hours). All samples are CD8+ T cells. 3 biological replicates for each group for a total of 12 samples.

middle: V

first: Radomir

last: Kratchmarov

first: Michelle

last: Miron

first: Steven

middle: L

last: Reiner

first: Donna

last: Farber


title: T cells activated in the presence or absence of TLR agonists

city: Madison

first: Douglas

last: McNeel

state: Wisconsin

address: 111 Highland Ave., Rm 7007

institute: University of Wisconsin

summary: We report the gene expression differences between OT-1 T cells activated alone or in the presence of TLR1/2 (Pam3CSK4) or TLR7 (Gardiquimod). By activating OT-1 splenocytes in the presence or absence of the TLR agonists, isolating RNA from purified CD8+ T cells we show that cells activated in the presence of either TLR1/2 or TLR7 agonists had similar transcriptional profiles demonstrating an increase in Th1 cytokine expression over cells that were activated alone. This study provides a key piece of information for those designing T cell mediated therapies.

overall_design: Examintation of T cells activated in the presnece or absence of TLR agonists

first: Sean

middle: J

last: McIlwain

first: Christopher

middle: D

last: Zahm

first: Irene

last: Ong


title: Transcriptome analysis of VCaP xenografts resistant to dual therapy with abiraterone and enzalutamide

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 99 Brookline Ave

institute: BIDMC

summary: We report RNA sequencing data on serial biopsies of prostate cancer VCaP xenografts as the tumors pass from androgen-sensitivity (Pre-Cx), to castration resistance (CRPC, castration resistant prostate cancer), onto resistance to dual therapy with abiraterone plus enzalutamide (AER). From comparison of these RNAseq data sets, we were able to determine differentially expressed genes between the AER/CRPC and Pre-Cx states that could mediate resistance to androgen deprivation therapies.

overall_design: RNA sequencing of the transcriptome of serial biopsies (Pre-Cx, CRPC, and Abi/Enza resistant) of 4 VCaP xenograft tumors.

first: Joshua

last: Russo


title: Gene expression profile for B6 wild-type and B6 Bgn gene knockout mice (Bgn0/-) with and without fructose treatment by RNA-Seq

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

summary: To investigate the effects of fructose on affecting the gene expressions in the hippocampus of male B6 wild-type and Bgn gene knockout (Bgn0/-) mice by RNA-Seq.

overall_design: At 3 months of age, the mice were divided into groups of similar mass and body composition within genotype as follows: wild type with regular drinking water, wild type with fructose (15% w/v) in the drinking water, Bgn0/- with regular drinking water, and Bgn0/- with fructose (15% w/v) in the drinking water for 6 weeks. After collecting phenotypic data, mice were sacrificed and the fresh hippocampus tissues were dissected out, flash frozen, and stored at -70°C for later transcriptome sequencing experiments. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng


title: Expression data from primary murine osteoblasts stimulated with C5a

city: Ulm

first: Anita

last: Ignatius

address: Helmholtzstraße 14

department: Institute of Orthopaedic Research and Biomechanics

institute: University of Ulm

summary: The anaphylatoxin C5a is a potent mediator of innate immunity and promotes inflammation via its receptor C5aR1 upon complement system activation danger-associated molecular patterns. Both C5a and C5aR1 are thought to be contributing factors in inflammatory and infectious conditions of the bone. Bone fracture healing, for example, was significantly improved when applying a C5aR1-antagonist in a rodent model of severe systemic inflammation and osteoblasts were found to be target cells for C5a in this setting.  Interestingly, osteoblasts up-regulate C5aR1 during osteogenic differentiation and after bone injury. Further, C5a induces inflammatory cytokines, such as IL-6, and the osteoclastogenic mediator RANKL in osteoblasts. However, the molecular mechanisms underlying C5a-C5aR1 signaling axis in osteoblasts remain unclear, and further targets of C5a are still elusive. Using microarray analysis, we analyzed intracellular events following C5aR1 activation in osteoblasts and defined up- or down-regulated genes and their belonging biological pathways.

overall_design: Primary osteoblasts were derived from three different male WT mice (C57BL6, aged 8-12 weeks). Those cells were osteogenically differentiated for 14 days and then each cell pool derived from a specific mouse was either left untreated (n = 3) or treated with recomninant murine C5a  for 4h.

first: Yvonne

last: Mödinger

first: Karlheinz

last: Holzmann


title: Small RNA-seq of human neural stem cells in empty vector and Zika Virus E protein transfected cells

city: Gurugram

first: Reshma

last: Bhagat

state: Haryana

address: Near Nainwal mode,Manesar

department: Cellular and molecular neuroscience

country: India

institute: National Brain Research Centre

summary: We report the Zika Virus E protein causes alterations in human fetal neural stem cells by dysregulation miRNome of fNSCs. We screened four ZV proteins (three non-structural and the E protein) and demonstrated that ZV E protein induces quiescence in human fNSCs and hampers growth of neurospheres. Further employing small RNA NGS we investigate that Zika Virus E protein causes differential expression of 25 miRNAs 24 hours post ectopic expression. Bioinformatic analysis using GO annotation for the targets of differentially expressed miRNAs revealed that upregulated miRNAs are involved in biological processes, including metabolic processes whereas downregulated miRNAs regulate cell cycle and its processes along with metabolic processes. This supports our findings that E protein alters cell cycle dynamics. Our study provides evidence and mechanisms of involvement of ZV E protein and potential miRNAs in Zika Virus induced microcephaly.

overall_design: Examination of miRNA in two empty vector and two Zika Virus E protein transfected samples of human neural stem cells 24 hours post transfection.

first: Pankaj

last: Seth


title: IL-1beta activates IL-17 via calcium

status: Public on Dec 25 2018

city: Suwon

first: Seungyeop

last: Lee

address: Seobu-ro 2066

department: School of Pharmacy

institute: Sungkyunkwan University

summary: IL-17A production via NLRP3 inflammasome-dependent IL-1β secretion aginst Pneumococcal inflammation in mice

overall_design: mice infected with 2x10^8 CFU of  S. pneumoniae

first: seungyeop


title: A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis

city: Wuhan

first: Mingqiu

last: Dai

state: Hubei

address: No.1,Shizishan Street · Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agriculture University

summary: Drought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large scale circRNA profiling identified 2174 and 1354 high-confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought-associated circRNA hosting genes were involved in conserved or species-specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA-hosting genes were enriched for SNPs associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought-tolerant maize. Additionally, the expression levels of circRNAs derived from drought-responsible genes encoding calcium-dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward-rectifying K+-channel) were hypersensitive to ABA, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidences highlighting the universal molecular mechanisms involved in plant drought tolerance.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design: RNA-seq and CircRNA-seq (RNaseR+) to Arabidopsis and maize plants under well-watered condition (WW) and drought treatments at various levels (DT2,DT3,DT4 and DT5 for Arabidopsis; DT2, DT3 and DT4 for Maize). Each treatment has 2 biological replicates


title: Overexpression of Crumbs3/CRB3 in human mammary epithelial line MCF-10A

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Our data demonstrate that overexpression of the polarity protein Crb3 elicits changes in MCF-10A cells that culminate in an increase in the release of amphiregulin (AR) and the subsequent activation of EGFR signaling to drive proliferation. Microarray analysis was performed to define global changes in the transcriptional landscape induced by Crb3. Results provide insight into a FERM domain protein (EBP41L4B) required for Crb3 mediated induction of proliferation.

overall_design: Total RNA was isolated from MCF-10A cells infected with pNG vector control or pNG-Crb3 retrovirus.

first: Stephanie

last: Walker

first: Laura

middle: M

last: Selfors

first: Ben

last: Margolis

middle: S


title: Molecular analysis of the midbrain dopaminergic niche during neurogenesis

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Midbrain dopaminergic (mDA) neurons degenerate in Parkinson's disease and are one of the main targets for cell replacement therapies. A comprehensive view of the signals and cell types contributing to mDA neurogenesis is not yet available. By analyzing the transcriptome of the mouse ventral midbrain at tissue and single-cell level during mDA neurogenesis we found that three recently identified radial glia types (Rgl 1-3) contribute to different key aspects of mDA neurogenesis. While Rgl3 expressed most extracellular matrix components and multiple ligands for various pathways controlling mDA neuron development, such as Wnt and Shh,  Rgl1-2 expressed most receptors. Moreover, we found that specific transcription factor networks explain the transcriptome expression profiles and suggest a function for each individual radial glia type.

overall_design: Triplicate tissue samples from each combination of embryonic day E11.5, E12.5, E13.5, and E14.5 with brain region alar plate, dorsal midbrain, ventral forebrain, ventral hindbrain, and ventral midbrain.

first: Enrique

last: Toledo

first: Ernest

last: Arenas


title: Micronome profiling in 3 pairs of salivary adenoid cystic carcinoma(SACC)  and the corresponding nomal salivary gland tissues

city: shanghai

first: wang

last: yu

address: zhizaoju Road NO.639

institute: Shanghai Ninth People’s Hospital

summary: To screen miRNAs for potential NDRG2 regulation, we performed micronome profiling in 3 pairs of SACC samples and the corresponding normal salivary glands. The sequencing analysis generated approximately 1,000,000 clean reads per sample. All reads were mapped to annotated miRNAs in the miRBase database (version 22), whereas approximately 45% of the clean reads were mapped to mature miRNAs in the database. After applying a stringent filtering criterion to compare the results from SACC tumor tissue and the adjacent normal salivary glands (log2 fold change >1, FDR<0.05), we identified 176 dysregulated miRNAs.

first: Jiang

last: Li

first: Yu

last: Wang

first: Ronghui

last: Xia


title: Comparison between a mouse line selected for high voluntary wheel running and control line in two brain regions, cerebellum and striatum

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: The goals of this study were: 1) to compare the transcriptome of a mouse line selected for high voluntary wheel running and a control line, and 2) evaluate the differences in the cerebellum and in the striatum.

overall_design: At approximately 6 weeks of age, male mice from the selected and control lines were individually place in cages including a running wheel. Brain samples were collected after 7 days. Paired-end RNA sequencing was used to profile individual cerebellum and striatum samples.


title: Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer [RNA-Seq]

city: Columbus

first: Matthew

last: Ringel

state: Oh

address: 565 McCampbell Hal

department: Division of Endocrinology, Diabetes, and Metabolism

institute: The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center

summary: Metastatic medullary thyroid cancer (MTC) is a currently incurable disease. FDA approved therapies that target RET, a commonly mutated receptor tyrosine kinase in MTC, and other receptor tyrosine kinases, do not result in complete responses and acquired resistance is universal due to “gatekeeper” mutation in Ret or overactivation of alternative signaling pathways. Based on data from human MTCs and a number of murine models, the CDK/RB cell cycle pathway is a potential alternative target for MTC. The objective of this study was to determine if CDKs represent therapeutic targets for MTC and to define mechanisms of activity. We demonstrate that targeting the CDK/RB pathway with Palbociclib (CDK4/6 inhibitor) is not cytotoxic to MTC cells but that Dinaciclib (CDK1/2/5/9 inhibitor) remarkably reduced cell viability and proliferation at low doses in two MTC cell lines accompanied by loss of CDK9 and RET protein and mRNA levels. In human tumors, CDK9 protein was highly expressed and array CGH demonstrated copy number gain in 11/30 analyzed tumors. RNA sequencing demonstrated that RNA polymerase II-dependent transcription was markedly reduced by Dinaciclib, consistent with transcriptional mode of action. Subsequent studies using the CDK7 inhibitor, THZ1, demonstrated high potency vs. the MTC cell lines and marked loss of RET mRNA and protein. In silico analysis, and CHIP-Sequencing using H3K27Ac antibody confirmed that RET is associated with a super-enhancer in RET-mutated MTC cells. In summary, this study reveals a novel mechanism of RET transcription regulation that represents a potentially translatable finding for new therapeutic approaches for RET-mutated MTC.

overall_design: mRNA profiles of TT and MZ-CRC-1 cells treated with Dinaciclib or vehicle control for 12h and 24h were generated

first: Anisley

last: Valenciaga

first: Lianbo

last: Yu

first: Ayse

last: Yilmaz


title: Cutaneous T effector transcriptomic responses triggered by early colonization of Staphylococcus species in new-born mice

city: San Francisco

first: Hsin-Wen

last: Chang

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

summary: We used the next generation sequencing method to profile gene expression changes in cutaneous T effectors isolated from mice with early colonization with Staphylococcus aureus or Staphylococcus epidermidis

overall_design: Whole transcriptomic RNAseq profile of cutaneous CD4+ T effector cells isolated from specific pathogen free (SPF) mice with early colonization of S. aureus(SA+SPF), S. epidermidis(SE+SPF) or no additional colonization(SPF).

first: Tiffany

last: Scharschmidt

first: Kimberly

last: Vasquez


title: Medial prefrontal cortex (mPFC) transcriptome analysis of Shank3-overexpressing mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

summary: Shank3 is a core excitatory postsynaptic protein expressed in multiple brain regions including the medial prefrontal cortex, striatum, and hippocampus. We have previously generated and characterized Shank3-overexpressing transgenic mice, and found that these mice exhibited manic-like behavioral phenotypes. To understand molecular mechanisms underlying the behavioral changes, we performed transcriptome (RNA-sequencing) analysis of the mPFC tissues from 10 to 12-week-old wild-type and Shank3 transgenic mice.

overall_design: Medial prefrontal cortex (mPFC) transcriptome of 10 to 12-week-old wild-type and Shank3 transgenic (TG) mice.

first: Jin

last: Chunmei

first: Hyojin

last: Kang


title: Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer

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

overall_design: Refer to individual Series


title: Exploratory analysis of the human breast DNA methylation profile upon soymilk

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary: Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17β-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5 day soymilk treatment, no epigenetic reprogramming in breast tissue could be found in this exploratory study.

overall_design:
This study was a randomized dietary intervention trial with a run-in phase of at least 4 days and a supplementation phase of 5 days before breast surgery. Following eligibility assessment, volunteers were randomly allocated to the soymilk (n = 10) or control (n = 20, of which 10 included in the epigenomics study) group.

Please note that SB9 is the technical replicate of SB21, and SB17 is the technical replicate of SB22.

first: Louis

last: Coussement

first: Selin

last: Bolca

first: Wim

last: van Criekinge

first: Geert

last: Trooskens

first: Klaas

last: Mensaert

first: Katrien

last: Poels

first: Nathalie

last: Roche

first: Phillip

last: Blondeel

first: Lode

last: Godderis

first: Herman

last: Depypere

first: Tim

last: De Meyer


title: Patterned human microvascular grafts enable rapid vascularization and increase perfusion in infarcted hearts

status: Public on Dec 24 2018

city: Seattle

first: Ying

last: Zheng

state: WA

address: 850 Republican

department: Bioengineering

institute: University of Washington

summary: Vascularization and efficient perfusion are long-standing challenges in cardiac tissue engineering. Here, we engineer perfusable microvascular constructs, wherein human embryonic stem cell-derived endothelial cells (hESC-ECs) are seeded both into patterned microchannels and the surrounding collagen matrix. In vitro, the hESC-ECs lining the luminal walls readily sprout and anastomose with de novo-formed endothelial tubes in the matrix under flow. When implanted on infarcted rat hearts, the perfusable microvessel grafts integrate with coronary vasculature to a greater degree than non-perfusable self-assembled constructs at 5 days post-implantation. Optical microangiography imaging reveal that perfusable grafts have 6-fold greater vascular density, 2.5-fold higher vascular velocities and >20-fold higher volumetric perfusion rates. Implantation of perfusable grafts containing additional hESC-derived cardiomyocytes show higher cardiomyocyte and vascular density. Thus, pre-patterned vascular networks enhance vascular remodeling and accelerate coronary perfusion, potentially supporting cardiac tissues after implantation. These findings should facilitate the next generation of cardiac tissue engineering design.

overall_design: Three groups of constructs (SA only, µV only, and µV + SA) are made and cultured for three days (the same conditions as that prior to graft implantation). These constructs were then lysed for RNA collection for transcript profiling using RNAseq analysis. The microvessels in the µV only and µV + SA constructs are made from a large grid pattern (13 x 13) with lumen diameter of 125 µm to maximize the vascular surface and RNA yield. Each group had duplicate samples.

first: Meredith

last: Redd

first: Nicole

last: Zeinstra

first: Wang

last: Qin

first: Wei

last: Wei

first: Amy

last: Martinson

first: Yuliang

last: Wang

first: Ruikang

middle: K

first: Charles

middle: E

last: Murry


title: Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

summary: High-throughput small RNA sequencing (sRNA-seq) has facilitated many discoveries, but extracellular sRNA (ExRNA) present unique analytical challenges that are not met by current software. Therefore, we developed a novel data analysis pipeline entitled, “TIGER”, which caters to exRNA. To demonstrate the power of this tool, sRNA-seq was performed on high-density lipoproteins (HDL), apolipoprotein B particles (APOB), bile, urine, and liver samples. TIGER was able to characterize approximately 60% of lipoprotein, and >85% of liver, bile, and urine sRNA-seq depth, a significant advance compared to existing software. A key advance for the TIGER pipeline is the ability to analyze host and non-host sRNAs at genomic, parent RNA, and individual fragment levels. Results suggest that the majority of sRNAs on lipoproteins are derived from bacterial sources in the microbiome and environment. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of exRNA.

overall_design:
All samples are from matched mice, of wild-type or SRBIKO genotype: 14 HDL, 14 apoB, 14 Liver, 13 Bile, 11 Urine

Please note that
[1] the count.txt.tar contains multiple count files listing all annotated features (.count.txt) or fragment reads (read.count.txt) or total categorical counts (category.count.txt) for associated with a given category;
[2] The DESeq2.csv.tar contains outputs from differential expression analysis using DeSeq2 comparing Wild-type vs SRBIKO;
[3] The associated processed data files are indicated in the corresponding sample description field (since most of the samples were combined to generate multiple processed data).

first: Shilin

last: Zhao

first: Marisol

last: Ramirez-Solano

first: Danielle

last: Michell

first: Yuhuan

first: Yu

last: Shyr

first: Praveen

last: Sethupathy

first: MacRae

middle: F

last: Linton

first: Greg

last: Graf

first: Quanhu

last: Sheng

first: Kasey

last: Vickers


title: Transcriptional profile of human STAT1-/- fibroblasts expressing LY6E or empty control vector

city: Dallas

first: John

last: Schoggins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwester Medical Center

summary: Detection of viral infection by pattern-recognition receptors triggers production of interferon. Secreted interferon binds to cognate receptors, triggering JAK/STAT signaling, resulting in the transcription and production of hundreds of interferon-stimulated genes (ISGs). Our lab identified lymphocyte antigen 6, locus E (LY6E) as an ISG that enhances infectivity of a subset of enveloped RNA viruses from Flaviviridae, Orthomyxoviridae, and Togaviridae families. To test whether the enhancing effects of LY6E were due to alterations of the global cellular transcriptome, we overexpressed LY6E and a control empty vector and examined global transcription using RNA-Seq.

overall_design: Human STAT1-deficient fibroblasts stably expressing LY6E or empty control vector in biological triplicate.

first: Katrina

middle: B

last: Mar

first: Nicholas

last: Rinkenberger

first: Ian

middle: N

last: Boys

first: Jennifer

last: Eitson

first: Matt

last: McDougal


title: Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer [ChIP-Seq]

first: Matthew

last: Ringel

summary: Metastatic medullary thyroid cancer (MTC) is a currently incurable disease.  FDA approved therapies that target RET, a commonly mutated receptor tyrosine kinase in MTC, and other receptor tyrosine kinases, do not result in complete responses and acquired resistance is universal due to “gatekeeper” mutation in Ret or overactivation of alternative signaling pathways. Based on data from human MTCs and a number of murine models, the CDK/RB cell cycle pathway is a potential alternative target for MTC.  The objective of this study was to determine if CDKs represent therapeutic targets for MTC and to define mechanisms of activity.  We demonstrate that targeting the CDK/RB pathway with Palbociclib (CDK4/6 inhibitor) is not cytotoxic to MTC cells but that Dinaciclib (CDK1/2/5/9 inhibitor) remarkably reduced cell viability and proliferation at low doses in two MTC cell lines accompanied by loss of CDK9 and RET protein and mRNA levels.  In human tumors, CDK9 protein was highly expressed and array CGH demonstrated copy number gain in 11/30 analyzed tumors.  RNA sequencing demonstrated that RNA polymerase II-dependent transcription was markedly reduced by Dinaciclib, consistent with transcriptional mode of action. Subsequent studies using the CDK7 inhibitor, THZ1, demonstrated high potency vs. the MTC cell lines and marked loss of RET mRNA and protein.  In silico analysis, and CHIP-Sequencing using H3K27Ac antibody confirmed that RET is associated with a super-enhancer in RET-mutated MTC cells. In summary, this study reveals a novel mechanism of RET transcription regulation that represents a potentially translatable finding for new therapeutic approaches for RET-mutated MTC.

overall_design: Examination of BRD4 and H3K27Ac peaks in TT cell DNA.

first: Anisley

last: Valenciaga

first: Lianbo

last: Yu

first: Ayse

last: Yilmaz


title: Expression data of subtypes of inflamed synovia from patients with rheumatoid arthritis

city: Dunedin

first: Paul

last: Hessian

address: 362 Leith St, North Dunedin

country: New Zealand

institute: UniDunedin School of Medicine, Health Sciences, University of Otago

summary: Microarrays were used to detail the global program of gene expression underlying differences in the organisation of inflammatory cells classified by the expression of the CD21L and IL-17A genes. Synovia were defined by the expression of the CD21L and IL-17A genes as determined by semi-quantitative PCR.

overall_design: Twelve synovia were obtained from 10 patients during joint replacement surgery for RNA extraction and hybridization on Affymetrix microarrays. Synovia were randomly selected from cohorts classified as CD21L+/IL-17A+ and CD21L-/IL-17A-. Two CD21L+/IL-17A+ synovia (P1-1 and P1-2) from one patient, and one CD21L+/IL-17A+ synovia (P4-1) and one CD21L-/IL-17A- synovia (P4-2) from another patient, were included to assess gene expression profiles in CD21L/IL-17A subtypes vs. individuals.

first: Kelly

last: McKelvey

first: Les

last: McNoe

middle: A


title: Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons

city: Miami

first: Derek

middle: Michael

last: Dykxhoorn

state: FL

address: 1501 NW 10th Ave, BRB 406

department: Human Genetics

institute: University of Miami

summary:
Purpose: The transcriptional differences between iPSC-derived cortical neurons from patients with idiopathic ASD and unaffected controls was examined over a 135-day course of neuronal differentiation using RNAseq analysis
Methods: Induced pluripotent stem cells (5 control iPSC and 6 ASD-specific iPSC) were differentiated into cortical neurons and RNA samples were obtained at two different time points day 35 post differentiation and day 135 post differentiation. RNAseq was performed from the RNA isolated at the different time points and the differentially expressed genes identified. Pathway analysis for gene ontology and biological processes, as well as, weighted gene co-expression network analysis was performed.
Results: The results of this analysis show ASD-specific misregulation of genes involved in neuronal differentiation, axon guidance, cell migration, DNA and RNA metabolism, and neural region patterning. Furthermore, functional analysis revealed defects in neuronal migration and electrophysiological activity, providing compelling support for the transcriptome analysis data.
Conclusions: Transcriptional analyses of the ASD and control neurons showed ASD-specific molecular phenotypes affecting networks involved in neuronal differentiation, the cytoskeletal matrix structure formation, patterning, DNA and RNA metabolism.

overall_design: Transcriptome analysis was performed on cortical neurons derived from induced pluripotent stem cells from individuals with autism and cognitively normal control individuals. Transcriptome analysis was performed by next generation sequencing (RNAseq) and the genes that were differentially expressed between the control iPSC-derived neurons and the Autism-specific iPSC-derived neurons. Transcriptome analysis was performed at day 35 post differentiation and day 135 post differentiation.

first: Brooke

last: DeRosa


title: Immortalized breast epithelial cell lines from normal breast with luminal and intrinsic subtypes – enriched gene expression

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St.,R3 C218C

institute: IU School of Medicine

summary: The cell-type origin has long been suspected to determine molecular features of tumors but has proven difficult to experimentally validate in human breast cancers because of deficiencies in culturing methods that allow propagation of three major cell types of the breast including stem/basal, luminal-progenitor and mature/differentiated cells. We have created immortalized cell lines from core breast biopsies of ancestry-mapped healthy women that are enriched for luminal gene expression including hormonally sensitive ERa-FOXA1-GATA3 transcription factor network. Gene expression pattern followed by intrinsic subtype classification identified these cell lines as “normal” counterpart to luminal A, basal, and normal-like subtypes of breast cancers. We have also created cell lines from CD201+/EpCAM- cells that are likely “normal” counter part of claudin-low subtype of breast cancers. These cell lines serve as good resources as “normal” cell line controls for breast cancer-related studies.

overall_design:
We propagated breast epithelial cells from breast core biopsies of healthy women using the epithelial reprogramming assay (Nakshatri et al., Scientific Reports, 5:13526). Primary cells were immortalized using human telomerase (hTERT). RNA from immortalized cells in triplicates was subjected to RNA-seq and results are included. hTERT immortalized HME cells from Horizon Discovery, MCF10A cells from ATCC and MCF7 breast cancer cells from ATCC were used as controls for comparison. 1505-10B corresponds to immortalized cells with germ line BRCA2 mutation. KTB40 and KTB42 differ from the rest of the cell lines with respect to cell surface markers profiles. These cells are CD201+/EpCAM-, whereas the remaining cells are CD201+/EpCAM+ or CD201-/EpCAM+. KTB40 and KTB42 are phenotypically fibroblastic or display features of epithelial to mesenchymal transition, whereas the remaining KTB (Komen Tissue Bank) cell lines display luminal features.

This series also includes RNA-seq data for non-immortalized cell lines.


title: Acute viral bronchiolitis

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia


title: Acute viral bronchiolitis (NMS)

summary:
Background: A subset of infants are hyper-susceptible to severe/acute viral bronchiolitis (AVB), for reasons unknown.
Purpose: To characterise the cellular/molecular mechanisms underlying infant AVB in circulating cells/local airways tissues.
Methods: PBMC and nasal mucosal scrapings (NMS) were obtained from Infants (<18mths) and children (1.5-5yrs) during AVB and post-convalescence. Immune response patterns were profiled by multiplex analysis of plasma cytokines, flow cytometry, and transcriptomics (RNA-Seq). Molecular profiling of group-level data utilised a combination of upstream regulator and coexpression network analysis, followed by individual subject-level data analysis employing personalised N-of-1-pathways methodology.
Results: Group-level analyses demonstrated that infant PBMC responses were dominated by monocyte-associated hyper-upregulated type I interferon signalling/pro-inflammatory pathways (drivers: TNF, IL6, TREM1, IL1B), versus a combination of inflammation (PTGER2, IL6) plus growth/repair/remodelling pathways (ERBB2, TGFB1, AREG, HGF) coupled with Th2 and NK-cell signalling in children. Age-related differences were not attributable to differential steroid usage or variations in underlying viral pathogens. Nasal mucosal responses were comparable qualitatively in infants/children, dominated by interferon types I-III, but the magnitude of upregulation was higher in infants (range 6-48-fold) than children (5-17-fold). N-of-1-pathways analysis confirmed differential upregulation of innate immunity in infants and NK cell networks in children, and additionally demonstrated covert AVB response sub-phenotypes that were independent of chronological age.
Conclusions: Dysregulated expression of interferon-dependent pathways following respiratory viral infections is a defining immunophenotypic feature of AVB-susceptible infants and a subset of children. Susceptible subjects appear to represent a discrete subgroup who cluster based on (slow) kinetics of postnatal maturation of innate immune competence.

overall_design: The study design consisted of PBMC from infants (<18months, n=15 pairs) and pre-school children (2-5yrs, n=16 pairs) sampled during severe acute viral bronchiolitis (acute visit = AV) and following recovery during convalescence (convalescent visit = CV). RNA-Seq profiles were generated by sequencing llumina HiSeq2500, 50bp single-end reads, v4 chemistry. Samples were sequenced across two lanes and collapsed prior analysis.

first: A

last: Denise

first: S

last: Galbraith

first: E

last: Fantino

first: D

last: Gutierrez

first: J

last: Read

first: M

last: Serralha

first: B

last: Holt

middle: H

last: Strickland

first: P

last: Sly

last: Bosco


title: Fto knockdown in 2-day post-confluent 3T3-L1 preadipocytes

city: Aurora

first: Jayne

last: Martin Carli

state: CO

department: Pediatrics - Neonatology

institute: University of Colorado Anschutz Medical Center

summary: Fto knockdown inhibits in vitro adipogenesis. We performed RNAseq to identify the molecular mechanisms underpinning this effect.

overall_design: Ctr KD (n=4) and Fto KD (n=4) in 3T3-L1 preadipocytes 2 days after confluence


title: Type 1 interferon signaling is crucial from the loss of tolerance nd the development of autoreactive B cells.

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: The transcriptomes of FACS-sorted B220+GL7+CD95+ germinal center B cells and B220+GL7-CD95- non-germinal center B cells from lupus-prone B6.Sle1b were compared to the same cell types in B6.Sle1b mice without the type 1 interferon receptor (B6.Sle1b.IFNaR1-/-).

overall_design: Examination of effect of IFNaR1 signaling on B cell selection in autoimmune-prone germinal centers.

first: Phillip

last: Domeier

first: Sathi

last: Babu Chodisetti

first: Stephanie

last: Schell

first: Melinda

last: Fasnacht

first: Chetna

last: Soni

first: Ziaur

last: Rahman


title: Acute viral bronchiolitis (PBMC)

first: Anya

last: Jones

middle: C

last: Denise

last: Galbraith


title: In vitro modeling of human germ cell development   using pluripotent stem cells

city: New York

first: Robert

last: Roeder

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: In this study, we developed a feeder-, serum-, and animal product-free culture condition, and successfully induced high percentage of SLCs from human PSCs. Genome-wide expression analyses demonstrated a significant upregulation of germ cell specific genes in SLCs derived from PSCs compared to in vivo isolated human CD90+ SSCs. And furthermore, under this optimized feeder-free condition SLCs have went through meiosis and formed putative round spermatids. Our data demonstrated a robust feeder-, serum- and xeno-free protocol to induce differentiation of PSCs to SLCs from which putative haploid spermatids may develop.

overall_design: Examination of genome-wide genes expression  in PSCs, SLCs and putative haploid spermatids types.

first: zhaoyun

last: cheng

first: wang

last: yuan


title: Fubp1 knockdown in BCR-ABL1 induced chronic myeloid leukemia (CML) like myeloproliferative neoplasm mouse model

status: Public on Dec 23 2018

city: Frankfurt

first: Daniela

last: Krause

address: Paul-Ehrlich-Straße 42-44

institute: Georg-Speyer-Haus

summary: We examine the oncogenic function of the Far Upstream Element Binding Protein 1 (FUBP1) in leukemia-initiating cells. For this perpose we performed knockdown of Fubp1 in CML cells in our mouse model. Here, we transduce donor bone marrow cell with the oncogene BCR-ABL1 and Fubp1 or scrambled shRNA and transplanted in recipient mice. Lineage- BCR-ABL1+ shRNA+ cells were then sorted from diseased mice and analyzed by RNA sequencing. We compare the gene expression of the Fubp1 shRNA expressing CML cells versus the control (scrambled shRNA expressing) cells in order to identify the relevant Fubp1 target genes.

overall_design: Mouse donor BM cells that were harvested from 5-fluorouracil-treated mice, cotransduced twice with cryopreserved and thawed retrovirus expressing MSCV-IRES-RFP BCR-ABL1 and pLKO.1-Venus Fubp1- or scrambled shRNA lentivirus. 2.5-3x10^5 transduced cells were transplanted intravenously into sublethally irradiated (900 cGy) recipient mice. Lineage- BCR-ABL1-RFP+ shRNA-Venus+ DAPI- cells from bone marrow of CML mice (4 mice in the Fubp1 and 4 mice in the scrambled shRNA group) were sorted directly into TRIzol. RNA isolation, library preparation and next generation sequencing were performed by Transcriptome and Genome Analysis Laboratory (TAL, Göttingen, Germany), as described previously.24, 25 RNA-Seq data will be deposited in the GEO database upon acceptance of this manuscript. Read counts per gene were statistically analysed in R (version 3.4.3) using ‘RStudio’ (version 1.1.423). Differential analysis was performed using the ‘DESeq2’ tool (version 1.18.1). For annotation of genes with mouse gene names and human orthologue HGNC symbols, the ‘biomaRt’ package (version 2.34.2) was used. Candidate genes were filtered by a padj value < 0.05 and a log2 fold change < -1 or >1 and visualised in a MA-plot. Principal component analysis was computed with the ‘prcomp’ function and results were visualized using the ‘pca3d package’(version 0.10). Gene set enrichment analysis was performed using the ‘GSEAPreranked’ tool from the GSEA software (version 2.2.3; Broad Institute).

first: Van

middle: T

last: Hoang

first: Gabriela

last: Salinas

first: Birgitta

last: Michels

first: Martin

last: Zörnig

first: Pablo

last: Llavona


title: Gata4-dependent differentiation of c-Kit+ derived endothelial cells underlies deceptive cardiomyocyte regeneration in the heart

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Overall goal: To elucidate the endothelial-specific role of Gata4 signaling in endothelial maturation and vascular maintenance.
Purpose of analysis: To generate a transcriptional profile of Gata4-deficient endothelial cells in the adult myocardium under homeostatic conditions.

overall_design: Experimental structure: Transcriptional profile generated using RNAseq and differential gene expression analyses of endothelial cells lacking Gata4 isolated from healthy hearts.

first: Jeff

last: Molkentin

first: Bryan

last: Maliken


title: Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

city: Oxford

first: Gergana

last: Velikova

address: Roosevelt Drive

institute: University of Oxford

summary: We report a new bisulfite-free 5mC and 5hmC base-resolution sequencing method: TET Assisted Pyridine borane Sequencing (TAPS). TAPS relies on mild reactions and detects DNA modifications directly, without affecting unmodified cytosines. We applied this method for the first time to whole genome sequencing in E14 mESC cell line. For comparsion we prepared whole-genome bisulfite sequencing in the same cell line. Compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing cost, enabling more informative and cheaper methylome analyses. We expect TAPS to become the new standard in epigenetic DNA sequencing.

overall_design: 5hmC and 5mC base-resolution sequencing with TAPS method in E14 mESC cell line.

first: Yibin

last: Liu

first: Paulina

last: Siejka-Zielinska

first: Ying

last: Bi

first: Fang

last: Yuan

first: Marketa

last: Tomkova

first: Chunsen

last: Bai

first: Lei

last: Chen

first: Benjamin

last: Schuster-Boeckler

first: Chun-Xiao

last: Song


title: Primary mid-trimester and term human cytotrophoblast, untreated [RNA-Seq]

status: Public on Dec 22 2018

city: New Brunswick

first: Bingbing

last: Wang

state: New Jersey

address: 125 Paterson St Room 2143

institute: Rutgers RWJMS

summary: We detected a genome-wide differential gene enrichment between mid-trimester and term human placenta. Pathway analysis identified that cytokine-cytokine receptor interaction, NF-κB, and TNF are the leading pathways enriched in term placenta.  Our analysis has provided the first-time characterization of the key players of human placental origin with molecular changes across pregnancy, which could drive human labor.

overall_design: Total RNAs were extracted from 4 individual placentas at either mid-trimester or term pregnancy with use of Trizol method.


title: Long-term culture with charcoal-stripped serum effect on the androgen-dependent LNCaP prostate cancer cell line

city: Tianjin

first: Yuanjie

last: Niu

address: Pingjiang Road 23

institute: Tianjin Institute of Urology

summary: To further determine the gene expression in the castration resistant condition for treating PCa, we generated and characterized an androgen-independent LNCaP-AI cell line by long-term culture of androgen-dependent LNCaP cells in RPMI-1640 medium containing charcoal-stripped serum.

overall_design: Three independent experiments were performed using three independent samples for LNCaP and LNCaP-AI cell lines.

first: Zhiqun

last: Shang

first: Qian

last: Dong

first: Libin

last: Sun

first: Jianpeng

last: Yu


title: The Possible Role of Complete Loss of Myostatin in Limiting Excessive Proliferation of Muscle Cells (C2C12) via Activation of MicroRNAs

status: Public on Dec 21 2018

city: Changchun

first: Wenni

last: You

address: No 5333 Xi`an road

institute: Jilin University

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

overall_design: Refer to individual Series


title: The Possible Role of Complete Loss of Myostatin in Limiting Excessive Proliferation of Muscle Cells (C2C12) via Activation of MicroRNAs (miRNA-seq)

summary: Myostatin (MSTN) is a member of the TGF-β superfamily that negatively regulates skeletal muscle growth and differentiation. However, the mechanism by which complete MSTN deletion limits excessive proliferation of muscle cells remains unclear. In this study, we knocked out MSTN in mouse myoblast lines using a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) system and sequenced the mRNA and miRNA transcriptomes. Our study suggests that complete loss of MSTN may limit excessive cell proliferation via activation of miRNAs.

overall_design: miRNA profiles of wild type (WT) and MSTN-knockout (MSTN-KO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000

first: Peixuan

last: Huang

first: Hao


title: Transcriptomic characterization of a human in vitro model of arrhythmogenic cardiomyopathy under topological and mechanical stimuli

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

summary: Cell junctions play an important role in coordinating intercellular communication and intracellular ultrastructures, with desmosomes representing the mechanical component of such intercellular connections. Mutations to desmosomal component proteins compromise both inter- and intracellular signalling and correlate with severe diseases like arrhythmogenic cardiomyopathy (AC), with pathological phenotypes in tissues subjected to intense mechanical stimuli (skin and heart). Here, we explore the consequences of dysfunctional desmosomes in one line of induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs) derived from an AC patient with a homozygous pathogenic mutation in desmosomal component protein plakophilin-2 (PKP2). We specifically aim at investigating the response to mechanical stress in an AC-pathological setting. To this aim, we aligned hiPS-CMs on stretchable patterned substrates to mimic the cardiac functional syncytium and compared transcriptomic profiles of PKP2-mutated hiPS-CMs and healthy controls. AC-CMs display altered transcription towards a pro-fibrotic gene expression program, and concurrent dysregulation of gene sets closely associated with cell-to-cell connections. By integrating the culture substrate with a macroscopic stretching setup able to accurately apply cyclic uniaxial elongation, we show how response to mechanical loads in AC-CMs deviates from the canonical mechanical-stress response observed in healthy-CMs.

overall_design: mRNA profiles of human pluripotent stem cell-derived cardiomyocytes from 4 samples, each analyzed in duplicate: healthy patient's cells under stretched and non-stretched conditions, Arrhythmogenic Cardiomyopathy (AC) patient's cells under stretched and non-stretched conditions.

first: Sebastian

last: Martewicz

first: Elena

last: Serena

first: Piero

last: Pavan

first: Vincent

first: Alessandra

last: Rampazzo

first: Nicola

last: Elvassore


title: The Possible Role of Complete Loss of Myostatin in Limiting Excessive Proliferation of Muscle Cells (C2C12) via Activation of MicroRNAs (mRNA-seq)

overall_design: mRNA profiles of wild type (WT) and MSTN-knockout (MSTN-KO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000


title: Female-biased embryonic death from genomic instability-induced inflammation

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: To identify sex-based differences in gene pathways affected by endgoenous genomic instaiblity resulting in embryonic death, total RNA from E13.5 placentas was isolated for RNAseq. Placentas from male and female embryos from wild-type matings and Mcm4^C3/C3 homozygous matings were used as references. Male and female placentas derived from embryos of the genotype : Mcm4^C3/C3 Mcm2^Gt/+ from either male Mcm4^C3/+ Mcm2^Gt/+ crossed to female Mcm4^C3/C3 or male Mcm4^C3/C3 crossed to female Mcm4^C3/+ Mcm2^Gt/+ were the experimental samples.

overall_design: Total RNA was isolated from E13.5 placentas and subjected to directional RNAseq to identify sex-based transciptome differences.

first: Adrin

last: McNairn

first: John

last: Schimenti


title: A C/EBPα–Wnt connection in gut homeostasis and carcinogenesis

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Str. 10

department: Cancer Research

institute: MDC Berlin

summary: We explored the connection between C/EBPα (CCAAT/enhancer binding protein α) and Wnt signaling in gut homeostasis and carcinogenesis. C/EBPα was expressed in human and murine intestinal epithelia in the transit amplifying region of the crypts and was absent in intestinal stem cells and Paneth cells with activated Wnt signaling. In human colorectal cancer and murine APCMin/+ polyps, C/EBPα was absent from nuclear β-catenin–positive tumor cells. In chemically induced intestinal carcinogenesis, C/EBPα KO in murine gut epithelia increased tumor volume. C/EBPα deletion extended the S-phase cell zone in intestinal organoids and activated typical proliferation gene expression signatures, including that of Wnt target genes. Genetic activation of β-catenin in organoids attenuated C/EBPα expression. Comparing gene expression of wild type and C/EBPα KO organoids by RNA sequencing aimed to identify C/EBPα dependent alterations in gene expression.

overall_design: These data suggest homeostatic and oncogenic suppressor functions of C/EBPα in the gut by restricting Wnt signaling.

first: Julian

last: Heuberger

first: Undine

last: Hill

first: Susann

last: Förster

first: Karin

last: Zimmermann

first: Victoria

last: Malchin

first: Anja

last: Kühl

first: Ulrike

last: Stein

first: Michael

last: Vieth

first: Walter

last: Birchmeier


title: RET-mediated autophagy suppression as targetable co-dependence in acute myeloid leukemia

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Many cases of acute myeloid leukemia (AML) are associated with mutational activation of RTKs such as FLT3. However, RTK inhibitors have limited clinical efficacy as single agents, indicating that AML is driven by concomitant activation of different signaling molecules. We used a functional genomic approach to identify RET, encoding an RTK not previously implicated in AML, as essential gene in different AML subtypes, and observed that RET-dependent AML cells show activation of RET signaling via ARTN/GFRA3 and NRTN/GFRA2 ligand/co-receptor complexes.

overall_design: Gene expression profiling was performed for 260 AML patients using an RNA microarray (Affymetrix HG U133plus2). RET mRNA expression was analyzed with the probe RET 211421_s_at. GSEA was performed on genes that were preranked according to their transcriptional fold change in AML patients high versus low RET mRNA expression, for a manually curated autophagy gene signature.


title: Cell-Cycle Restriction Sustains Therapy-Resistant Pre-Leukemic Stem Cells

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: Pre-leukemic stem cells (pre-LSCs) provide a reservoir of cells that evolve to acute leukemia and cause relapse following chemotherapy. We postulated that quiescence of pre-LSCs is an important mechanism of therapeutic resistance. Using a doxycycline-inducible H2B-GFP transgene in a mouse model of T-cell acute lymphoblastic leukemia, we show that long-term self-renewal, clonal evolution and resistance to chemo-radiation are intrinsically linked to restricted cell cycle. We show that restricted cell cycle of pre-LSCs requires the presence of the CDK inhibitor p21, with absence of p21 leading to chemosensitivity and clonal extinction by loss of asymmetric cell division and terminal differentiation. These results provide a model to identify and test strategies to eradicate an important source of clonal evolution and leukemic relapse.

overall_design: Three pooled replicates from LSC (GFP-High) and non-LSC (GFP-Low) populations. Profiled by mRNA Seq

first: Cedric

last: Tremblay

first: David

last: Curtis


title: Sexual difference of small RNA expression in Tetralogy of Fallot

city: Shanghai

first: Bo

last: Wang

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center

summary: Small RNAs, especially the microRNAs, have been revealed to play great roles in heart development and congenital heart defects. Several studies have shown dysregulated miRNAs in ventricular tissues of Tetralogy of Fallot (TOF) patients. In the present study, we conducted high throughput sequencing to obtain the global profiling of small RNA transcriptome in heart right ventricular samples from 10 age -matched TOF patients. These samples showed dominant composition of miRNA and mitochondrial associated RNAs. By sRNA cluster identification and differential gene expression analysis, significant sexual difference was discovered for sRNA expression in TOF patients. miR-1/miR-133, the first identified miRNA cluster essential for cardiac development, account for the most variance of sRNA expression between sexes. Our results suggested divergent molecular basis between female and male TOF patients.

overall_design: Small RNA expression profile of right heart ventricle samples from 10 age matched TOF patients (5 females vs 5 males) generated by deep sequencing

first: Guocheng

last: Shi

first: Zhongqun

last: Zhu

first: Huiwen

last: Chen

first: Qihua

last: Fu


title: Sequencing of cfDNA derived from the plasma of individuals of different ages

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

summary: We provide the first in vivo evidence of global and local chromatin changes in human aging by analyzing cfDNA from the blood of individuals of different age groups. Our results show that nucleosome signals inferred from cfDNA are consistent with the redistribution of heterochromatin observed in cellular senescence and aging in other model systems. It also revealed age and deteriorating health status correlate with a low-level enrichment of signals from cells in the thyroid gland. In addition, we detected an overall nucleosome loss at several genomic locations, such as transcription start and termination sites, 5’UTR of L1HS retrotransposons and dimeric AluY elements with age.

overall_design:
We profiled cfDNA extracted from a total of 12 individuals across three different ages: 25 year-old (young), 70 year-old (old), healthy 100 year-old (healthy centenarian) samples and unhealthy 100 year-old (unhealthy centenarian)

Please note that each wig pair (*100kb.Fnor.smooth.wig and *10bp.Fnor.smooth.wig) were generated from triplicates (rep1, rep2, rep3) together and are linked to the corresponding *rep1 sample records.

first: Yee

middle: V

last: Teo


title: RNA Sequencing Analysis of Control and Blnc1 liver specific knockout mice (LKO)  Liver Transcriptomes after 24 weeks NASH diet feeding

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

institute: Life Sciences Institute

summary: Hepatic lipogenesis is a central aspect of the feeding response and is aberrantly induced in the progression of fatty liver disease. Liver X receptors (LXRs) and sterol regulatory element-binding protein 1c (SREBP1c) are potent activators of the lipogenic gene program that promote triglyceride synthesis and hepatic steatosis in the insulin-resistant state. To date, key protein components of the LXR-SREBP1c axis have been uncovered that mediate transcriptional activation of SREBP1c by LXRs and nutrient and hormonal regulation. However, whether this regulatory pathway interfaces with long noncoding RNAs (lncRNAs) remains largely unexplored. Here we show that hepatic expression of Blnc1, a regulator of brown adipocyte development, is strongly associated with adiposity and liver fat content in mice. Blnc1 is required for the induction of SREBP1c and hepatic lipogenic genes in response to LXR activation. CRISPR/Cas9-mediated liver-specific inactivation of Blnc1 abrogates high fat diet-induced hepatic steatosis and insulin resistance. We further observed that liver Blnc1 expression is elevated in a mouse model of nonalcoholic steatohepatitis (NASH). Mice lacking Blnc1 in the liver are protected from diet-induced NASH and exhibit attenuated liver injury, inflammation and liver fibrosis. At the molecular level, proteomic analysis of the Blnc1 ribonucleoprotein complex in the liver identified endothelial differentiation related factor 1 (EDF1) as a component of the LXR transcriptional complex that acts in concert with Blnc1 to stimulate SREBP1c expression. These findings uncover a lncRNA ribonucleoprotein complex that licenses obesity-linked activation of hepatic lipogenesis and NAFLD pathogenesis.

overall_design: Liver mRNA profiles of control and Blnc1 liver specific knockout mice after 24 weeks NASH diet feeding were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Xuyun

last: Zhao

first: Jiandie

last: Lin


title: Genomic, transcriptomic and epigenomic characterization of multifocal breast cancer

city: Brussels

last: Brown

address: Boulevard de Waterloo 127

institute: Institut Jules Bordet

type:
Expression profiling by array
Methylation profiling by array

summary:
A significant proportion of breast cancer patients develop multiple synchronous unilateral breast tumors, also referred to as multifocal tumors, which represent a diagnostic and therapeutic challenge.  Multifocality has been associated with a possible adverse patient outcome, propensity for axillary nodal involvement, and increased risk of local recurrence following breast conserving surgery when compared to unifocal tumors. Previous studies indicate that most lesions from multifocal tumors are concordant with regard to the currently used pathological parameters (histological subtype and grade, hormonal receptors and HER2 status). However, to our knowledge, no study has yet provided a detailed molecular analysis of multifocal breast cancer. Here, we aimed to better define the incidence of multifocal breast cancer using a systematic analysis of pathology reports of primary breast cancers and to compare different foci from 5 multifocal breast cancers in a global analysis using genomic, transcriptomic and epigenomic data. We demonstrate that multifocality is a frequent finding since it concerns 22% (945/4340) of breast cancer patients with primary ductal breast cancer. We find that different lesions from multifocal breast cancer can differ at the (epi)genomic and transcriptomic level even when the foci present similar histology, grading, hormonal and HER2 status despite having a common genetic background. Since the number of (epi)genetic alterations with potential clinical utility is rapidly growing due to increasing numbers of targeted therapies, these findings suggest that it might be necessary to interrogate the different lesions of multifocal breast cancers for adequate treatment management of these tumors.
The biological characterization of multifocal breast cancer here is focused on 5 cancers for which the foci did not differ in terms of histological grade, hormonal receptors and HER2 status. The characterization of multifocal tumors involved the identification of somatic rearrangements in 2 foci from each patient via low-coverage whole genome sequencing. Putative rearrangements were amplified by polymerase chain reaction (PCR) and capillary sequenced in tumor and matching blood-derived germline DNA to validate the somatic rearrangements. For all patients, the presence of a number of validated rearrangements was assessed in different paraffin blocks of tumor-adjacent histologically normal tissue by nested PCR. We also performed transcriptomic and epigenomic profiling in 4 and 5 patients respectively using the HG-U133 Plus 2.0 Chips and Infinium Methylation 450K arrays (RNA was not available for patient E).

overall_design: To investigate the incidence of multifocality in primary breast cancer patients, we systematically queried pathological reports from patients diagnosed between 2000 and 2010 at the Institut Jules Bordet through the Belgian National Cancer Registry. Five patients with multifocal ductal breast cancer, for which a frozen sample of at least 2 lesions with similar ER, HER2 and histological grade was available, were studied. The cellular composition and the immuno-histochemistry staining of ER, PgR, HER2 and Ki67 were centrally reviewed by the same pathologist. All patients gave their written consent for this research project. The molecular characterization of the multifocal tumors involved the identification of somatic rearrangements, transcriptomic and epigenomic profiling in 2 foci from each patient, via low-coverage whole genome sequencing, HG-U133 Plus 2.0 Chips and Infinium Methylation 450K arrays respectively. Genomic rearrangements were validated using an orthogonal sequencing platform. The project has been approved by the ethics committee of the Institut Jules Bordet.

first: Christine

last: Desmedt

first: Serena

last: Nik-Zainal

first: Debora

last: Fumagalli

first: Françoise

last: Rothé

first: Samira

last: Majjaj

first: Sarah

last: Dedeurwaerder

first: Mathieu

last: Defrance

first: Emilie

last: Calonne

first: Marion

last: Maetens

first: Pierre-Yves

last: Adnet

first: Marianne

last: Paesmans

last: O'Meara

first: Stefan

last: Michiels

first: Delphine

last: Vincent

first: Roberto

last: Salgado

first: François

last: Fuks

first: Martine

last: Piccart

first: Denis

last: Larsimont

first: Mike

last: Stratton

first: Peter

last: Campbell

first: Christos

last: Sotiriou


title: Pseudogene repair driven by selection pressure applied in experimental evolution

status: Public on Dec 20 2018

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

institute: UCSD

summary: We performed evolution of ∆menF∆entC strain of Escherichia coli K12 MG1655 to study how the system adapt to the loss of siderophore biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.

overall_design:
Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.
ALE is the acronym for adaptive laboratory evolution. ALE_39.91, ALE_29.82 and ALE_30.83 are the independent biological replicates of ∆menF∆entC which are evolved in our laboratory to study how the strains adapt to the loss of the menF and entC genes. Similarly, ALE_36.86, ALE_37.25 and ALE_38.28 are the independent biological replicates of ∆menF∆entC∆ubiC which are evolved in our laboratory to study how the strains adapt to the loss of the menF, entC and ubiC genes.

first: Anand

last: Sastry


title: Fusion of Human Brain Organoids Assembles Bidirectional Connectivity Between Thalamus and Cortex

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Human brain organoid techniques have rapidly advanced to facilitate investigating human brain development and diseases. Recent reports in generation and fusion of regionally defined brain organoids provide further opportunities to investigate the specific brain domains and their interactions. Focus of brain organoids has been to generate telencephalon due to its direct relevance in a variety of forebrain disorders. Despite its importance as a relay hub between cortex and peripheral tissues, the investigation of three-dimensional (3D) organoid model for the human thalamus has not yet been explored. Here, we describe a method to differentiate human embryonic stem cells (hESCs) to the thalamic organoids (hThOs) that specifically recapitulate the development of thalamus. Single-cell RNA sequencing (scRNA-seq) revealed a formation of distinct thalamic lineage cells, a lineage divergence from telencephalic lineage. Importantly, we developed a 3D system to create the reciprocal projections between thalamus and cortex by fusing the two distinct region-specific organoids representing the developing thalamus or cortex. Our study provides a platform for understanding human thalamic development and modeling circuit organizations and related disorders in the brain.

overall_design: mRNA profiles of human thalamic organoids (hThO) at early and late time point with single-cell level were generated by deep sequencing

first: Yangfei

last: Xiang

first: In-Hyun

last: Park


title: Microglial RNA-sequencing after stress-sensitization by repeated social defeat

city: Columbus

first: Kristina

middle: Grace

last: Witcher

address: 460 Medical Center Dr

institute: Ohio State University

summary: Stress is associated with an increased prevalence of anxiety and depression. Repeated social defeat (RSD) stress in mice increases the release of monocytes from the bone marrow that are recruited to the brain by microglia. These monocytes enhance inflammatory signaling and augment anxiety. Moreover, RSD promotes stress sensitization, in which exposure to acute stress 24 days after cessation of RSD causes anxiety recurrence. The purpose of this study was to determine whether microglia were critical to stress sensitization and exhibited altered gene expression 24 days after RSD.

overall_design: Adult (2mo) C57BL/6 mice were subjected to 6 cycles of repeated social defeat (RSD) or controls (CON). At 24d after the final cycle of RSD, RNA was extracted from FAC-sorted microglia (CD11b+/CD45int). RNA sequencing was performed and sequences were aligned with STAR and normalized counts and differential gene expression were determined using DESeq2 in R.

first: Jonathan

middle: P

last: Godbout