title: Predicting drug-free remission in rheumatoid arthritis: the Biomarkers of Remission in Rheumatoid Arthritis (BioRRA) Study

city: Newcastle upon Tyne

first: Kenneth

middle: Frank

last: Baker

address: Framlington Place

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

summary:
Sustained remission is now an achievable goal in rheumatoid arthritis (RA) using modern treat-to-target regimens of disease-modifying anti-rheumatic drugs (DMARDs). Recent studies have demonstrated that up to half of patients in remission can discontinue DMARDs and maintain drug-free remission (DFR), with consequent benefits of avoidance of drug toxicity and the need for regular and expensive safety monitoring. However, there are currently no reliable biomarkers that can predict DFR prior to withdrawal of DMARDs.
Aim: As part of a wider study of DMARD withdrawal (the BioRRA study), we aimed to identify predictors of time-to-flare following DMARD cessation using whole-genome bulk RNA sequencing data from circulating CD4+ T cells.

overall_design: Circulating CD4+ T cells were isolated from whole blood at baseline in 44 patients with RA in remission immediately prior to conventional synthetic DMARD cessation. Following total RNA extraction and poly-A selection, mRNA was sequenced using an Illumina NextSeq 500.

middle: F

first: John

middle: D

last: Isaacs


title: RNA-seq (H3K9ac and H3K4me3) analysis on Arabidopsis Col-0, hac1-1 (SALK_080380), and hac1-2 (SALK_136314)

status: Public on Jul 12 2019

city: Lakewood

first: Will

middle: E

last: Hinckley

state: CA

address: 4440 Gondar Ave

department: Biology

country: USA

institute: CSULB

type: Expression profiling by high throughput sequencing

summary: Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our lab is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 44 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.

overall_design: Leaves 12-14 from 49 day old Arabidopsis thaliana plants were harvested from one biological replicate and used for RNA-seq and ChIP-seq to identify potential HAC1 targets.

first: Judy

last: Brusslan

first: Keykhosrow

last: Keymanesh

first: Jaime

last: Cordova


title: Genome-wide analysis of liver gene expression in prenatally undernourished male rat offspring under high-fat diet

city: Villeneuve d'Ascq

first: christophe

last: breton

address: Cité Scientifique

country: France

institute: University of Lille 1

summary: Based on the developmental origin of health of disease hypothesis, we previously showed that prenatal 70% maternal food restriction (FR30) predisposes the offspring to development of pathologies in adulthood. In the present study, we focused on the liver gene expression profile of standard and high fat (HF)-fed FR30 adult offspring.

overall_design: Total RNA obtained from isolated liver of control standard and high-fat-fed adult offspring compared to prenatally undernourished (FR30) counterparts.

first: D

last: Vieau

first: C

last: Breton

first: S

last: Lecoutre


title: Genome-wide analysis of impact of culture conditions on gene expression of primary leukemic cells from chronic lymphocytic leukemia (CLL)

status: Public on Jul 14 2019

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital Ulm

summary: Proliferation and survival of CLL cells is highly dependent on the interaction of the tumor cells with different populations of accessory cells, incl. mesenchymal bone marrow stromal cells. In this project interactions between CLL cells and transformed bone-marrow derived fibroblast cell lines were studied. Gene expression was analyzed in CLL cells that were cocultured for different time periods with human (HS-5) or murine (M2-10B4) transformed fibroblasts, as compared to CLL cells from the same patient sample that were cultured in DMEM medium or conditioned medium in which HS-5 cells had been growing.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Total RNA obtained from primary CLL cells, right after CD19 sorting (control) or after being cultured for 30 min, 1 h, 2, h, 3 h, 4 h, 6 h, 8h, 24 h or 48 h in DMEM, in conditioned medium from HS-5 cells, or co-cultured with HS-5 or M2-10B4 cells. In addition, total RNA was extracted from CLL cells that were cultured in DMEM (control) or cocultured with HS-5 or M2-10B4 cells for 24 h, then washed and cultured in DMEM for further 24 h. Total RNA was also also extracted for reference from M2-10B4 cells, as well as from HS-5 cells that were cultured alone, or after they had been cocultured with patient CLL cells for 6 or 24 h.

first: Irina

last: Idler

middle: Y

first: Nupur

last: Bhattacharya

first: Michaela

last: Reichenzeller

first: Viola

last: Meyer-Pannwitt

first: Daria

last: Ezerina

first: Annika

last: Scheffold

first: Sabrina

last: Kugler

first: Anja

last: Weigel

first: Hauke

last: Busch

first: Peter

last: Lichter

first: Hartmut

last: Döhner

first: Tobias

last: Dick

first: Stephan

last: Stilgenbauer

first: Daniel

last: Mertens


title: Identification and validation of GPD1 as an essential cancer stem cell specific target in glioblastoma (RNA-seq: Gpd1 KO)

status: Public on Jul 15 2019

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

summary: Cancer stem cells (CSCs) are attractive targets for cancer therapy, however, little is known about how to target CSCs without affecting the normal stem cell population. Here we report the ribosome-profiling analysis of mouse neural stem cells and brain tumour stem cells (BTSCs), which leads to the identification of glycerol-3-phosphate dehydrogenase 1 (GPD1) as a CSC- specific determinant.  We confirmed that GPD1 is expressed in BTSCs but not in neural stem cells. Intriguingly, expression of GPD1 is only found in the infiltrating dormant BTSCs in vivo and these cells start to divide and drive tumour relapse after chemotherapy. Most importantly, inhibition of GPD1 expression in tumour-bearing mice leads to prolonged survival. Further analysis shows that loss of GPD1 results in widespread changes in important pathways affecting BTSC maintenance. Human patient data analysis suggests that GPD1 is expressed in the dormant infiltrating tumour cells in human glioblastoma and the expression level is associated with a worse prognosis. This study provides an attractive therapeutic target for treating brain tumours and a novel aspect of regulation of CSC dormancy.

overall_design: Two sgRNAs guided Gpd1 knock out in mouse brain tumor stem cells

first: Patricia

last: Rusu

first: Chunxuan

last: Shao


title: Gene expression changes of tumor microenvironment (TME) after STING activation

city: Seongnam-si

first: Hannah

last: Yang

address: CHA Bundang Medical Center

country: South Korea

institute: CHA Bundang Medical Center

summary: The results revealed dramatic differences between the STING-activated and STING-deficient TMEs.

overall_design: To elucidate the transcriptional changes upon STING activation, we used the Nanostring PanCancer panel to compare 750 immune microenvironment-related genes in cGAMP-treated tumors in WT mice and tumors from KO mice.

first: Won

middle: S

last: Lee

first: Chan

last: Kim

first: Hong

middle: J

last: Chon


title: Single cell analysis of Monolayer and Organoid Primary Prostate Human Epithelial Cells Derived from the same patient

status: Public on Jul 11 2019

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: Single human primary prostate epithelial cells grown as a monolayer (2D) or as organoids (3D) were separated, collected and prepped for RNA-seq using the 10x Genomics Chromium Genome Reagent kit v2 Chemistry. 3,500-5,000 cells were collected from each sample and sequenced at a depth of ~45,000 genes per cells on a 2x150nt lane in a HiSeq 4000. CellRanger alignment was performed to produce the RAW data files.

overall_design: Two samples: monolayer cells and organoid cells

first: Tara

last: McCray

last: Moline

first: Donald

last: Vander Griend


title: TLR9 Stimulation of Anergic HCV-Associated Clonal Memory B Cells Triggers Rheumatoid Factor Autoimmunity by the TNF-α Pathway

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

institute: Institut Curie

summary: Transcriptionnal analysis of pathogenic IgM Memory B cells stimulated or not with CpG from 3 differents HCV related Cryoglobulinemia.

overall_design:
We analyzed the transcriptomic profiles of pathogenic IgM Memory B cells stimulated or not with CpG from 3 differents HCV related Cryoglobulinemia.
Microarray analyses were performed 72H after stimulation or not of IgM memory B cells with CpG in 3 differents donors.

first: Cloé

last: Comarmond

first: Valérie

last: Lorin

first: Cindy

last: Marques

first: Anna

last: Maciejewski-Duval

first: Nizar

last: Joher

first: Cyril

last: Planchais

first: Lucie

last: Biard

first: Thierry

last: Hieu

first: Valentin

last: Quiniou

first: Anne-Claire

last: Desbois

first: Michelle

last: Rosenzwajg

first: David

last: Klatzmann

first: Patrice

last: Cacoub

first: Hugo

last: Mouquet

last: Saadoun


title: Prdm16 regulation of Shh-Gli1-Hoxc4 signaling is required for Granule Neuron Progenitor expansion and cerebellar related behavior

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose:To gain a deeper insight into how Prdm16 regulates cerebellar development, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by Prdm16 deletion at P3.
Methods: Total RNA was extracted from P3 cerebellar tissue of Prdm16 cKO and Prdm16fl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately one thousand transcripts showed differential expression between the Prdm16fl/fl and Prdm16 cKO cerebellum, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to regulation of glial cell differentiation and forebrain development, and cerebellum development. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell differentiation. These results reflected the importance of Prdm16 in cerebellar development.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how Prdm16 gene contribute to cerebellar development.

overall_design: Total RNA was extracted from P3 cerebellar tissue of Prdm16 cKO and Prdm16fl/fl mice and generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Xuepei

last: Lei


title: Safeguarding nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis

status: Public on Jul 13 2019

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

institute: Peking university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromobox homolog 4 (CBX4), a component of polycomb repressive complexes 1 (PRC1), plays important roles in the maintenance of cell identity and organism development through epigenetic silencing. However, it remains unclear whether CBX4 regulates the homeostasis of human stem cells. Here, we demonstrate that CBX4 counteracts human mesenchymal stem cell (hMSC) aging via the maintenance of nucleolar homeostasis. CBX4 protein decreases in aged hMSCs, and targeted knockout of CBX4 in young hMSCs destabilizes nucleolar heterochromatin, increases ribosome biogenesis, and accelerates cellular senescence. CBX4 maintains nucleolar homeostasis by recruiting fibrillarin at nucleolar rDNA repeats, limiting excessive expression of rRNAs. Importantly, overexpression of CBX4 expression alleviates physiological hMSC aging as well as attenuates the development of post-traumatic osteoarthritis in mice. Taken together, our study uncovers a novel role of CBX4 in counteracting senescence by maintaining nucleolar homeostasis, providing a potential therapeutic target for aging-associated disorders.

overall_design: RNA-Seq and ChIP-Seq

first: Ren

last: Xiaoqing

first: Hu

last: Boqiang


title: Activin A in Combination with ERK1/2 MAPK Pathway Inhibition Sustains Propagation of Mouse Embryonic Stem Cells

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

summary:
Activin/Nodal/TGF-β signaling pathway plays a major role in maintaining mouse epiblast stem cells (mEpiSCs). The mEpiSC medium which contains Activin A and bFGF induces differentiation of mouse embryonic stem cells (mESCs) to mEpiSC. Here we show that Activin A also has an ability to efficiently propagate mESCs without differentiation to mEpiSCs when combined with a MEK inhibitor PD0325901. mESCs cultured in Activin+PD retained high-level expression of naive pluripotency-related transcription factors. Genome-wide analysis revealed that the gene expression profile of mESCs cultured in Activin+PD resembles that of mESCs cultured in 2i. mESCs cultured in Activin+PD also showed features which are related to naive pluripotency of mESCs, including the preferential usage of the Oct4 distal enhancer and the self-renewal response to Wnt pathway activation. Our finding reveals a role of Activin/Nodal/TGF-β signaling in stabilizing self-renewal gene regulatory networks in mESCs.
To compare the gene expression patterns of mESCs cultured in Activin+PD, 2i and LIF+BMP4 and mEpiSCs, we performed genome-wide gene expression analysis by using Affymetrix GeneChip oligonucleotide microarrays

overall_design: Total RNA was isolated with RNeasy Mini kit (Invitrogen). During the isolation, on-column DNaseI digestion was performed. Biotinylated sense-strand DNA was synthesized with GeneChip WT PLUS Reagent kit (Affymetrix), hybridized to Mouse Gene 2.0 ST Array (Affymetrix) and analyzed by GeneChip Scanner 7G System (Affymetrix). The data were analyzed by GeneSpringGX11.5 software (Agilent).

first: Yuhei

last: Ashida

first: May

last: Nakajima-Koyama

first: Akira

last: Hirota

first: Takuya

last: Yamamoto


title: Single cell transcriptome analysis of human fetal pancreas.

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: Organ development is the process in which the mesoderm, endoderm and ectoderm develop into distinct cell types in highly ordered, discrete organs. Although model organisms have been hugely helpful to delineate the specific cell state transformations involved in organogenesis, the considerable differences in time-scale and physiology between human and such model organism can make direct comparisons difficult. Here, we analyze 1982 single cells from all cell lineages in the developing human pancreas, across a wide range of gestational stages (w 12 -22). We find that differentiation of endocrine progenitors into differentiated alpha and delta cells constitute branches in a “default” differentiation path into beta cells, a finding that is corroborated by in vivo reprogramming of alpha cells into beta cell in a mouse model. Further, we find several mesenchymal sub-cell types, the characteristic genes of which suggest specific roles in organ development including rapid cell growth, extracellular matrix reorganization and vascularization. Thus, our data suggests that to understand organ development, we have to chart the supporting mesenchymal cell types, some of which might only exist during organ development.

overall_design: Examination of single cells from primary human pancreas tissue

first: Efsun

last: Arda


title: Epigenome analysis of ascending aorta from normal, aortic dissection and bicuspid aortic valve patients

city: Shanghai

first: Sun

last: Pan

address: Fenglin Road 180

department: Department of Cardiac Surgery

institute: Zhongshan Hospital, Fudan University

summary: Genome wide DNA methylation profiling of ascending aorta tissue samples from normal, aortic dissection and bicuspid aortic valve patients with aortic dilation. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across more than 450,000 CpGs in ascending aorta samples. Samples included 6 normal donors, 12 patients with aortic dissection and 6 patients with bicuspid aortic valve and dilated aorta.

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Individual liver plasmacytoid dendritic cells are capable of producing IFNa and multiple additional cytokines during chronic HCV infection [exp2]

status: Public on Jul 10 2019

city: New York

first: Erin

middle: Heather

last: Doyle

state: New York

address: 1425 Madison Ave

department: Liver

institute: Icahn School of Medicine at Mount Sinai

summary: Plasmacytoid dendritic cells (pDCs) are ÒnaturalÓ interferon _ (IFN_)-producing cells. Despite their importance to antiviral defense, autoimmunity, and ischemic liver graft injury, because DC subsets are rare and heterogeneous, basic questions about liver pDC function and capacity to make cytokines remain unanswered. Previous investigations failed to consistently detect IFN_ mRNA in HCV-infected livers, suggesting that pDCs may be incapable of producing IFN_. We used a combination of molecular, biochemical, cytometric, and high-dimensional techniques to analyze DC frequencies/functions in liver and peripheral blood mononuclear cells (PBMCs) of hepatitis C virus (HCV)-infected patients, to examine correlations between DC function and gene expression of matched whole liver tissue and liver mononuclear cells (LMCs), and to determine if pDCs can produce multiple cytokines. T cells often produce multiple cytokines/chemokines but until recently technical limitations have precluded tests of polyfunctionality in individual pDCs. Mass cytometry (CyTOF) revealed that liver pDCs are the only LMC that produces detectable amounts of IFN_ in response TLR-7/8 stimulation. Liver pDCs secreted large quantities of IFN_ (~2 million molecules of IFN_/cell/hour) and produced more IFN_ than PBMCs after stimulation, p=0.0001. LMCs secreted >14-fold more IFN_ than IFN_ in 4 hours. Liver pDC frequency positively correlated with whole liver expression of ÒIFN_-responseÓ pathway (R2=0.58, p=0.007) and Òmonocyte surfaceÓ signature (R2=0.54, p=0.01). Mass cytometry revealed that IFN_-producing pDCs were highly polyfunctional; >90% also made 2-4 additional cytokines/chemokines of our test set of 10. Liver BDCA1 DCs, but not BDCA3 DCs, were similarly polyfunctional. pDCs from a healthy liver were also polyfunctional. Our data show that liver pDCs retain the ability to make abundant IFN_ during chronic HCV infection and produce many other immune modulators. Polyfunctional liver pDCs are likely to be key drivers of inflammation and immune activation during chronic HCV infection.

overall_design: Total RNA from 11 patient livers isolated from whole liver tissue

middle: H


title: Individual liver plasmacytoid dendritic cells are capable of producing IFNa and multiple additional cytokines during chronic HCV infection [exp1]

overall_design: Total RNA from 55 samples isolated from liver or blood mononuclear cells either ex vivo or stimulated with media, Poly I:C, LPS, or R848


title: Individual liver plasmacytoid dendritic cells are capable of producing IFNa and multiple additional cytokines during chronic HCV infection

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

overall_design: Refer to individual Series


title: A Transcriptomic Model of Postnatal Cardiac Effects of Prenatal Maternal Cortisol Excess In Sheep

city: Gainesville

first: Maureen

last: Keller-Wood

state: Florida

address: 1225 Center Dr

department: Pharmacodynamics

institute: University of Florida

summary: Cortisol administration during late gestation in ewes, modeling maternal stress, resulted in transcriptomic changes suggesting altered maturation and metabolic changes to the offspring heart.   Pregnant ewes were treated with  0.5 mg/kg/day cortisol from 115 days gestation to term lambs were studied over the next 2 weeks. Left ventricular free wall (LV) and intraventricular septum (IVS) were collected at 2 weeks of age (lambs of control, untreated ewes: n=8, lambs of  ewes treated with 0.5 mg/kg/day: n=8).  In this model we found that neonatal plasma glucose was increased and plasma insulin was decreased compared to those in the control group. LV free wall thickness was increased in the 2 week old lamb.  In this study, we have used transcriptomic modeling to better understand the programming effect of this maternal cortisolemia in  the 2 week old hearts. This is a time when both terminal differentiation and a shift in the metabolism of the heart from carbohydrates to lipid oxidation are thought to be complete.  The transcriptomics indicates downregulation of RNA related pathways, but upregulation of ubiquitin-mediated proteolysis and protein targeting to the mitochondria in in the intraventricular septum (IVS) and left ventricle (LV) in lambs of cortisol-infused ewes compared to untreated control ewes. In IVS pathways the AMPK pathway and adipocytokine signaling pathways were also modeled as downregulated in lambs of cortisl-treated ewes   Genes for peroxisomal activity are modeled as decreased in LV and IVS; our previous metabolomic study of the newborn hearts from the 1 mg/kg/d study indicated changes in the plasmogens and phospholipids that are peroxisomal products.  Our results suggest that pathways for  lipid metabolismas well as  cell proliferation and cardiac remodeling have altered activity postnatally after the in utero cortisol exposure.  Together, this model is consistent with the observed increase in cardiac wall thickness at necropys and altered glucose metabolism observed in vivo, and predicts that in utero exposure to excess maternal cortisol causes postnatal cardiac hypertrophy and altered responses to oxidative stress.

overall_design: Left ventricular free wall and intraventricular septum were collected from  2 week old lambs of cortisol treated ewes (0.5mg/kg/day administered from 2100h to 0900h daily from day 115 fo gestation until delivery) (n=8) or untreated ewes (n=8).

first: Andrew

last: Antolic

first: Elaine

last: Sumners

first: Charles

last: Wood


title: Maize transcriptomic responses to Pantoea stewartii vascular infection in B73 and pan1 (R2) lines (experiment B).

city: La Jolla

first: Paula

last: Doblas Ibanez

state: California

address: 9500 Gilman Dr

institute: UCSD

summary: To gain insight into the genetic and molecular mechanisms that underlie the enhanced resistance of pan1 lines to vascular spread of P. stewartii, we used RNA-seq to compare the transcriptomes of B73 and pan1 lines one day after mock or bacterial inoculation of leaf veins, being this the first analysis of maize transcriptional responses to P. stewartii infection.

overall_design: 16 samples were analyzed (2 genotypes x 2 treatments x 4 replicates). Genotyopes: B73 and pan1-Mu/pan1-Mu (R2). Treatments: P. stewartii-GFP infection and Mock inoculation (serving as wounding control). Four biological replicates were analyzed.

last: Doblas-Ibanez

first: Laurie

last: Smith


title: Maize transcriptomic responses to Pantoea stewartii vascular infection in B73 and pan1 (R1) lines (experiment A).

overall_design: 24 samples were analyzed (3 genotypes x 2 treatments x 4 replicates). Genotyopes: B73, pan1-ems/pan1-ems (R1) and pan1-ems/+ (R1/B73). Treatments: P. stewartii-GFP infection and Mock inoculation (serving as wounding control). Four biological replicates were analyzed.


title: Budding yeast centromeric DNA and A+T rich bacterial DNA can function as centromeres in the fission yeast Schizosaccharomyces pombe

city: Nottingham

first: William

last: Brown

address: Queens Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary: We established a two-step approach to centromere-replacement (Figure 1A in outline, and Supplementary data in detail). FiC31 integrase was used to place a candidate sequence or an empty vector adjacent to the native centromere of chromosome 2 of CBS2777, and Bxb1 integrase was subsequently used to delete the native centromere.

overall_design: Examination of CENP-A binding on the S. pombe centromere 2 in 20 different strains

middle: R

first: Anne

middle: C

last: Barbosa


title: Maize transcriptomic responses to Pantoea stewartii vascular infection in B73 and pan1 lines


title: Defining Housekeeping Genes Suitable for RNA-seq Analysis of the Human Allograft Kidney Biopsy Tissue

city: Pittsburgh

first: Parmjeet

last: Randhawa

state: Pennsylvania

address: E737 UPMC Montefiore Hospital, 3459 Fifth Ave

institute: University of Pittsburgh

summary: This study has used nine different normalization methods to derive housekeeping genes from a RNA-seq data set of 47611 transcripts derived from 30 biopsies.

overall_design: The biopsies were collected in a variety of clinical settings, with 5 replicates each of the following clinicla settings: normal function, acute tubular injury, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy and polyomavirus nephropathy. Transcripts with coefficient of variation below the 2nd percentile were designated as housekeeping genes, and validated by showing their virtual absence in diseased allograft derived transcriptomic data sets available in the Gene Expression Omnibus.

first: Zijie

last: Wang


title: RNA sequencing of CRISPR/Cas9-generated A20 DUB-inative and A20 knock-out U937 cells to elucidate the role of human A20 DUB-domain

city: Mölndal

first: Lisa

last: Öberg

address: Pepparedleden 1

department: Translational Science and Experimental Medicine

institute: Research and Early Development, Respiratory Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden

summary:
Objectives: Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of systemic lupus erythematosus (SLE) and rheumatoid arthritis. A20 is a negative regulator of NF-κB but the role of its DUB domain and related genetic variants remain unclear. We aimed to study the functional effects of A20 DUB-domain alterations in immune cells and understand its link to SLE pathogenesis.
Methods: CRISPR/Cas9 was used to generate human U937 monocytes with A20 DUB-inactivating C103A knock-in mutation. Whole genome RNA-sequencing was used to identify differentially expressed genes between WT and C103A knock-in cells. Functional studies were performed in A20 C103A U937 cells and in immune cells from A20 C103A mice and genotyped healthy individuals with A20 DUB polymorphism rs2230926. Neutrophil extracellular trap (NET) formation was adressed ex vivo in neutrophils from A20 C103A mice and SLE-patients with rs2230926.
Results: Genetic disruption of A20 DUB domain in human and murine myeoloid cells did not give rise to enhanced NF-κB signaling. Instead, cells with C103A mutation or rs2230926 polymorphism presented an upregulated expression of PADI4, an enzyme regulating protein citrullination and NET formation, two key mechanisms in autoimmune pathology. A20 C103A cells exhibited enhanced protein citrullination and extracellular trap formation, which could be suppressed by selective PAD4 inhibition. Moreover, SLE-patients with rs2230926 showed increased NETs and increased frequency of autoantibodies to citrullinated epitopes.
Conclusions: We propose that genetic alterations disrupting the A20 DUB domain mediate increased susceptibility to SLE through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation.

overall_design: We have performed RNA sequencing on U937 cells with different genotypes generated by CRISPR-Cas9. Three U937 clones with homozygote A20 C103A knock-in (KI) mutation (A20 DUB-inactive) were generated (KI1-KI3), as well as four A20 knock-out clones.  Control cells (wt) were grown in parallel and underwent the same processes as the targeted cells but in absence of CRISPR/Cas9 plasmids. Cells where differentiated to macrophages and stimulated with LPS or vehicle and after 6 hours, RNA was extracted and RNA-sequencing was performed with the aim of analyzing differentially expressed genes between the genotypes.

first: Lina

last: Odqvist

first: Kristofer

last: Thörn

first: Outi

last: Vaarala

first: Barry

last: Collins


title: Characteristics of impaired dendritic cell function in patients with hepatitis B virus infection

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary:
Dendritic cells are antigen-presenting cells with a central role in host immune response. This study analyzed gene expression and dendritic cell function in hepatitis B virus (HBV) patients and functions impaired due to HBV, and identified the genes related to these functions.
Peripheral blood mononuclear cells from 23 HBV patients and 9 healthy controls were utilized. Mononuclear cells were isolated from side-scatter and forward-scatter gating using fluorescence-activated cell sorting (FACS), the lineage-negative HLA-DR-positive fraction was extracted, and was further divided into CD123-positive plasmacytoid DCs (pDCs) and CD11c-positive myeloid DCs (mDCs). Cell sorting was performed, and the number of DCs was measured and surface markers were analyzed. After cell sorting, CD11c and CD11b expression levels in the pDC and mDC fractions were confirmed using real-time PCR. RNA was extracted from sorted pDCs and subjected to gene expression analysis using Affymetrix Human 133U Plus 2.0 gene chip.

overall_design: In chronic HBV infection, many abnormalities in immune function, such as decline in cytotoxic T lymphocyte (CTL) function, increase in regulatory T cells, abnormal dendritic cell DC function, and abnormal natural killer cell function have been reported. However, other causes of DC functional decline in HBV infection, and molecules involved in the decline remain unclear. The present study aimed to analyze gene expression and DC function in HBV patients, and to identify the functions that are reduced compared with healthy individuals, as well as the molecules associated with these reduced functions.

first: Atsushi

last: Yonejima

first: Eishiro

last: Mizukoshi

first: Katsutoshi

last: Tamai

first: Hidetoshi

last: Nakagawa

first: Masaaki

last: Kitahara

first: Tatsuya

last: Yamashita

first: Kuniaki

last: Arai

first: Takeshi

last: Terashima

first: Noriho

last: Iida

first: Kazumi

last: Fushimi

first: Hikari

last: Okada

first: Taro

first: Yoshio

last: Sakai

first: Shuichi

last: Kaneko


title: scSLAM-seq reveals core features of transcription dynamics in single cells

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Single cell RNA sequencing so far only depicts cellular transcriptomes at a single time point with low temporal resolution for kinetic changes. Here, we present a single-cell approach based on metabolic RNA labelling for combined sequencing of total and newly transcribed RNA as well as computational analysis of the RNA present prior to labelling. We apply it to cytomegalovirus infection of fibroblasts and reveal its potential for delineating alterations in transcriptional activity and decay in single cells under perturbed experimental conditions.

sample_organism:
Homo sapiens
Mus musculus
Murid betaherpesvirus 1

overall_design: We performed scSLAM-seq on 107 single cells across two biological replicates and analyzed global transcriptional changes of matched bulk cells using SLAM-seq.

first: Florian

last: Erhard

first: Marisa

middle: A

last: Baptista

first: Tobias

last: Krammer

first: Thomas

last: Hennig

first: Marius

last: Lange

first: Panagiota

last: Arampatzi

first: Christopher

last: Jürges

first: Fabian

last: Theis

first: Antoine

first: Lars

last: Dölken


title: Real-time quantitative PCR analysis of human cell-free circulating miRNAs expression in early rheumatoid arthritis

city: Hong Kong

first: Lai-Shan

last: TAM

state: Hong Kong

address: 30-32 Silver City Street, Shatin

department: Department of Medicine and Therapeutics, Prince of wales hospital

country: Hong Kong

institute: The Chinese University of Hongkong

summary:
The second metacarpal head (MCP2) of the 20 ERA patients and 6 sex- and age- matched healthy controls were scanned by HR-pQCT. Then the 20 ERA patients were devided into two sub-groups: bone erosion group and non-erosion group detected by HR-pQCT.
Peripheral blood samples were collected using Ethylenediaminetetraacetic acid (EDTA) at the day of fasting status of ERA patients as well as HCs and were centrifuged at 3000×g for 10 minutes at room temperature. Then, the plasma samples were aliquoted and centrifuged at 3000×g for an additional 10 minutes at 4oC to remove any remaining cellular debris. The plasma was immediately stored at –80oC until analysis.

overall_design: miRNA were extracted from peripheral blood samples using EDTA in ten treatment-naïve ERA patients with maximal erosion volume at MCP2 detected by HR-pQCT, another ten treatment-naïve ERA patients without erosion and six age- and sex-matched healthy controls (HCs) as indicated in the summary. miRNA profiling was performed by TaqMan RT-qPCR (Life Technologies) according to the manufacturer’s instructions. This method allows the simultaneous analysis of 377 unique miRNAs (Human Pools A V2.1) using 384-well Cards.

last: Tam

first: Jiang

last: Yue


title: Transcriptomic Evidence that Cortisol Alters Perinatal Epicardial Adipose Tissue Maturation

first: Elaine

middle: Mary

last: Richards

state: FL

summary: Cortisol administration during late gestation in ewes, modeling maternal stress, resulted in transcriptomic changes suggesting altered maturation and metabolic changes to the offspring heart.  This study investigates the effects of cortisol on epicardial adipose tissue (EAT), a visceral fat pad associated with adverse cardiovascular conditions in adults. Pregnant ewes were treated with either 1 or 0.5 mg/kg/day cortisol from 115 days gestation to term and EAT collected from term fetuses (control: n=8, maternal cortisol 1 mg/kg/day: n=6) or two-week-old lambs (control: n=7, maternal cortisol 0.5mg/kg/day: n=9). Transcriptomic modeling was used to identify pathways altered by maternal cortisol over-exposure.  Transcriptomic modeling confirmed the brown fat phenotype of EAT at term and a transition towards white fat at two weeks of age in EAT of control fetuses/lambs, and highlighted a role of immune responses, including complement-coagulation, and serotonin in this transition. Maternal cortisol (1mg/kg/day) increased the lipid peroxidation product 4-hydroxynonenal in EAT of term fetuses, but did not affect the number of activated macrophages or size of the lipid droplets in the depot; transcriptomics suggested an earlier metabolic maturation of EAT via, in part, increased immune responses. Conversely the transcriptomics in EAT of two-week-old lambs of ewes treated with a lower dose of cortisol (0.5mg/kg/day) suggested decreased metabolism of several substrates through both mitochondrial and cytosolic actions, and delayed maturation of EAT associated with a longer period of adipogenesis and angiogenesis.

overall_design: Epicardial adipose tissue was collected from untreated term fetuses (n=8) and naturally born 2-week-old lambs (n=7), and from term fetuses of cortisol-treated ewes (1mg/kg/day) (n=6) or 2-week-old lambs of cortisol treated ewes (0.5mg/kg/day) (n=9).

middle: M

first: Emily

last: McElhaney

first: Katelyn

last: Zerengue

first: Serene

last: Joseph

first: Maureen

last: Keller-Wood


title: Gene Expresion in Ausitm Spectrum Disorders (ASD)

city: Sacramento

first: Boryana

last: Stamova

address: 2805 50th Street

department: Neurology; MIND Institute

institute: University of California, Davis Medical Center

summary: We postulated that specific differences in alternative splicing/exon usage in immune blood cells may be present in ASD boys, and this might differ in ASD boys with large total cerebral volumes (ASD_LTCV) versus ASD boys with normal total cerebral volumes (ASD_NTCV). Thus, we compared ASD and ASD sub-groups related to total cerebral volume to typically developing (TD) controls.

overall_design: Blood from young boys with ASD and TD was collected, and the extracted RNA was interrogated on Affymetrix GeneChip ® Human Exon 1.0 ST arrays. In adition, Total Cerebral Volume (TCV), measured by MRI was considered as a subphenotype. 30 boys with ASD (20 with normal TCV and 10 with large TCV) and 20 matched typically developing controls were assayed.

middle: B

first: Yingfang

last: Tian

first: Christine

middle: W

last: Nordahl

first: Mark

last: Shen

first: Sally

last: Rogers

first: David

middle: G

last: Amaral

first: Frank

last: Sharp


title: BCDIN3D regulates tRNAHis 3’ fragment processing

status: Public on Jul 09 2019

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

summary: 5’ ends are important for determining the fate of RNA molecules. BCDIN3D is an RNA phospho-methyltransferase that methylates the 5’ monophosphate of specific RNAs. In order to gain new insights into the molecular function of BCDIN3D, we performed an unbiased analysis of its interacting RNAs by Thermostable Group II Intron Reverse Transcriptase coupled to next generation sequencing (TGIRT-seq). Our analyses showed that BCDIN3D interacts with full-length phospho-methylated tRNAHis and miR-4454. Interestingly, we found that miR-4455 is not synthesized from the annotated genomic locus, which is a primer-binding site for an endogenous retrovirus, but rather by Dicer cleavage of mature tRNAHis.  Sequence analysis revealed that miR-4454 is identical to the 3’ end of tRNAHis. Moreover, we were able to generate this “miRNA” in vitro through incubation of mature tRNAHis with Dicer. As found previously for several pre-miRNAs, a 5’P-tRNAHis appears to be a better substrate for Dicer cleavage than a phospho-methylated tRNAHis. Moreover, tRNAHis 3’-fragment/”miR-4454” levels increase in cells depleted for BCDIN3D. Altogether, our results show that in addition to microRNAs, BCDIN3D regulates tRNAHis 3’-fragment processing without negatively affecting tRNAHis’s canonical function of aminoacylation.

overall_design: In order to purify RNAs interacting with BCDIN3D, we used HeLa-S3-FlpIn cells containing a single insertion at a FRT locus of BCDIN3D tagged with a FLAG tag at its C-terminus (BCDIN3Df). We first purified BCDIN3Df with a protocol that combines FLAG antibody co-immunoprecipitation, followed by FLAG peptide elution. We then extracted RNAs from FLAG eluates of Control and BCDIN3Df cells with a protocol that allows recovery of RNAs of all sizes. Finally, we used a TGIRT-seq protocol that combines template switching to the RNA 3’ end and a highly processive Thermostable Group II Intron Reverse Transcriptase for cDNA synthesis.

first: Calder

last: Reinsborough

first: Hélène

last: Ipas

first: Nathan

last: Abell

first: Ryan

last: Nottingham

first: Jun

last: Yao

first: Sravan

middle: L

last: Devanathan

first: Samantha

last: Shelton

first: Alan

last: Lambowitz


title: Cortical bone RNAseq comparison of WT, Sik2/3 DKO, and col1a1-Pth1r (H223R) mice

city: Boston

first: Marc

last: Wein

state: MA

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

summary: Cortical bone RNA was isolated from mice of the indicated genotypes followed by RNAseq

overall_design: We analyzed n=6 WT, n=8 Sik2/3 DKO, n=11 WT, and n=12 col1a1-Pth1r H223R mutant samples. For long bone RNA isolation from control and SIK2/3 DKO animals, mice were sacrificed and both femurs were rapidly dissected on ice. Soft tissue was removed and epiphyses cut. Bone marrow cells were then removed by serial flushing of the marrow cavity with ice-cold PBS until bone appeared completely white. TRIzol (Life Technologies) was added to remaining bone tissue and samples were frozen at −80 °C and then homogenized. RNA was then extracted per the manufacturer's instructions, and further purified on RNeasy microcolumns (Qiagen). RNA with a A260/280 ratio <1.7 was not used for downstream analysis, this workflow allows us to avoid use of samples with excessive bone matrix protein contamination. For cDNA synthesis, 1 μg RNA was used in synthesis reactions according to the instructions of the manufacturer (Primescript RT, Takara). SYBR Green-based quantitative PCR (qPCR) detection was performed using FastStart Universal SYBR Green (Roche, Basel, Switzerland) on a StepOne Plus (Applied Biosystems, Carlsbad, CA) thermocycler. All PCR primer sequences are listed in Supplemental Table 3. Transcript levels for genes of interest were determined relative to housekeeping gene (ß-actin) using standard methods (84). A similar protocol for cortical bone isolation was used for the comparison of effects of sclerostin antibody treatment versus vehicle. For bone RNA isolation from control and C1HR mice, the same protocol was used with the exception that the marrow flushing step was not performed. Due to overt phenotypic difference between control and experimental (SIK2/3 DKO, C1HR transgenics, Scl-Ab treated) mice, we acknowledge that many differentially expressed genes here may be due to changes in cellular tissue composition. Therefore, we focus on similarities and differences across comparisons (WT/SIK2/3 DKO versus WT/C1HR, WT/SIK2/3 DKO versus control/Scl-Ab, WT/C1HR versus control/Scl-Ab), to determine the overall molecular concordance between the three different models of increased trabecular bone mass.  RNA-seq   RNA sequencing from bone RNA samples for Figure 4 was conducted using a BGISEQ500 platform (BGI, Shenzhen, China) (85). Briefly, RNA samples with RIN values >8.0 were used for downstream library construction. mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library, and validated on bioanalyzer (Agilent 2100) prior to sequencing. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray followed by SE50 sequencing. On average we obtained 20M reads per bone RNA sample.  Sequencing reads were mapped by the STAR aligner (86) to the mm9 reference genome using Ensembl annotation. Gene expression counts (CPM) were calculated using HTSeq v.0.6.0 (87). Differential expression analysis was performed using EgdeR package (88) based on the criteria of more than two-fold change in expression value versus control and false discovery rates (FDR) <0.05.

first: Murat

last: Cetinbas


title: Sequestration of microRNA-mediated target repression by the Ago2-associated RNA binding protein FAM120A

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: Argonaute (Ago) proteins interact with various binding partners and play a pivotal role in microRNA (miRNA)-mediated silencing pathways. By utilizing immunoprecipitation followed by mass spectrometry to determine cytoplasmic Ago2 protein complexes in mouse embryonic stem cells (mESCs), we identified a putative RNA-binding protein FAM120A (also known as OSSA/C9ORF10) as an Ago2 interacting protein. Individual nucleotide resolution Cross-Linking and ImmunoPrecipitation (iCLIP) analysis revealed that FAM120A binds to homopolymeric tracts in 3´ UTRs of about 2,000 mRNAs, particularly poly(G) sequences. Comparison of FAM120A iCLIP and Ago2 iCLIP reveals that greater than one-third of mRNAs bound by Ago2 in mESCs are co-bound by FAM120A. Furthermore, such FAM120A-bound Ago2 target genes are not subject to Ago2-mediated target degradation. Reporter assays suggest that the 3´ UTRs of several FAM120A-bound miRNA target genes are less sensitive to Ago2-mediated target repression than those of FAM120A-unbound miRNA targets and FAM120A modulates them via its G-rich target sites. These findings suggest that Ago2 may exist in multiple protein complexes with varying degrees of functionality.

overall_design: iCLIP in mouse embryonic stem cells expressing either dox-inducible FLAG-HA-Fam120a (TT-FHFam120a) or untagged Fam120a (TT-Fam120a).


title: SFRPs Are Biphasic Modulators of Wnt Signaling-elicited Cancer Stem Cell Properties beyond Extracellular Control

city: Hsinchu

first: Jia-Lin

last: Lee

address: 101, Sec. 2, Kuang Fu Road

country: Taiwan

institute: National Tsing Hua University

summary: Secreted frizzled-related proteins (SFRPs) are mainly known for their role as extracellular modulators and tumor suppressors that down-regulate Wnt signaling. Using the established (CRISPR/Cas9 targeting promoters of SFRPs and targeting SFRPs transcript) system, we find that nuclear SFRPs interact with β-catenin and either promote or suppress TCF4 recruitment. SFRPs bind with β-catenin on both their N and C termini, which the repressive effects caused by SFRP-β-catenin-N-terminus binding overpower the promoting effects of their binding at the C terminus. By high Wnt activity, β-catenin and SFRPs only bind with their C termini, which results in the up-regulation of β-catenin transcriptional activity and cancer stem cell (CSC)-related genes. Furthermore, we identify disulfide bonds of the CRD domain and two threonine phosphorylation events of the NTR domain of SFRPs that are essential for their role as biphasic modulators, suggesting that SFRPs are biphasic modulators of Wnt signaling-elicited CSC properties beyond extracellular control.

overall_design: Total cellular RNA was extracted from HM20 Mock and SFRP1-5-expressing stable clones after treatment with Wnt3a-containing medium for 24 hours.


title: Next generation sequencing allows the comparison between Ectodysplasin knock-out mutant and wild-type murine lacrimal glands

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: We used RNAsequencing to reveal the differential gene expression in Ectodysplasin knock-out lacrimal gland compared to wild-type. We show that the mutant adult lacrimal gland differentially express specific genes, demonstrating a modifed maturation process when the Ectodysplasin gene is mutated.

overall_design: Lacrimal glands were excised from adult mice (13wo). Three biological replicates were used for each condition (wild-type and mutant).

first: Alison

last: Kuony

first: Frederic

last: Michon


title: Epigenetic Silencing of TGFBI Confers Resistance to Trastuzumab in Human Breast Cancer

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Epigenetic silencing of TGFBI confers resistance to trastuzumab in human breast cancer.

overall_design: Bisulphite-converted DNA from trastuzumab-sensitive and -resistant models were hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

first: Teresa

last: Puig


title: The effect of slow and rapid H2S production on the levels of LPS-induced proinflammatory mediators and transcription in different human cell cultures

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: In this study we investigated the effect of two different agents producing hydrogen sulfide (H2S) on LPS-induced inflammatory mediators such as TNFa, NO and ROS. The agents (GYY4137 and sodium hydrosulfide) applied differ significantly by the kinetics of H2S release. In the investigation we compared the effects of H2S release on the LPS-induced inflammation exploring SH-SY5Y human neuroblastoma cell line and human promonocytic cell line, THP-1. Our data clearly show that both hydrogen sulfide producing agents significantly reduced the production of the investigated proinflammatory mediators when applied both before and after LPS administration. Furthermore, transcriptomic studies demonstrated that H2S release ameliorates the expression of multiple proinflammatory genes up-regulated due to LPS administration. However, the pattern of changes observed in transcriptome differs dramatically  depending on the time of H2S release (before or after LPS-challenge).

overall_design: This series contains data only for THP1 cells. Cells were treated with GYY4137 before or after LPS. Additional cells were treated only with GYY4137 or LPS or were untreated.

middle: P


title: Pentoxifylline-induced differentially-expressed genes in hypertrophic scar fibroblasts

city: xi’an

first: fangfang

last: yang

address: No. 127 Changle West Road

institute: xijing hospital

summary: Pentoxifylline attenuated hypertrophic scars by influencing the cell cycles

overall_design: mRNA profiles of control hypertrophic scar fibroblasts and pentoxifylline treated cells were generated by deep sequencing, in triplicate, using Ion  Proton.

first: Fangfang

last: Yang

first: Dahai

last: Hu


title: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (ATAC-seq)

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

summary: Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

overall_design: Whole genome sequencing of the founding and generation 17 of three lines of mice (6 population samples in total). Statistical modelling of the selection response was performed in order to identify candidate regions responsible for the rapid increase in tibia length. One major locus found to show parallel selection response was Nkx3-2 on Chr5 of the mouse genome. Since no coding mutations were found that could be attributable as the target of selection, functional genomic techniques such as ATAC-Seq and 4C-Seq were performed to help identify relevant functional elements for further investigation and functional dissection. 4C-Seq was performed from fore- and hindlimb tissues as well as liver controls from the "viewpoint" of three enhancers (labelled as N1-N3) as identified by a combination of chromatin modification marks from the ENCODE project and ATAC-Seq signals of open chromatin. Proxmity ligation was performed on BglII sites, and religated amplicons from the chosen viewpoints were amplified for sequencing. Chimeric ligation products were interpreted as indicative of potential chromosome contacts.

first: João

first: Michelle

middle: N

last: Yancoskie

first: Marta

last: Marchini

first: Stefanie

last: Belohlavy

first: Marek

last: Kučka

first: William

last: Beluch

first: Ronald

last: Naumann

first: Isabella

last: Skuplik

first: John

last: Cobb

first: Nick

last: Barton

first: Campbell

last: Rolian

first: Yingguang

middle: F


title: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

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

overall_design: Refer to individual Series


title: Transcriptome analysis of mice adipose tissues

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

summary:
We report that the HF/HS-mediated functional enrichment of genes of immunity and inflammation is driven toward normal by the AOF supplementation
Obesity may not constantly associate with metabolic disorders and mortality later in life, raising the challenging concept of healthy obesity. Here, high fat-high sucrose (HF/HS) feeding produces hyperglycaemia and hypercholesterolemia, increases oxidative stress, elevates endotoxemia, expands adipose tissue (with enlarged adipocytes, macrophage infiltration and accumulation of cholesterol and oxysterols), and reduces lifespan of obese mice. Despite persistence of obesity, supplementation with an antioxidant formulation normalizes plasma lipids and endotoxemia, prevents macrophage recruitment in adipose tissue, reduces adipose accumulation of cholesterol and cholesterol oxides, and extends lifespan. The HF/HS-mediated functional enrichment of genes of immunity and inflammation (in particular response to lipopolysaccharides) is driven towards normal by the antioxidant formulation.
It is concluded that the limitation of immune cell infiltration in adipose tissue on the long term by an antioxidant formulation can increase lifespan independently of body weight and fat storage. It constitutes the hallmark of a healthy adiposity trait.

overall_design: Examination of the expression profile of mice adipose tissues fed either standard (Std), High-fat/high-sucrose (HF/HS) or HF/HS + antioxidant formulation (AOF) for 180 days

first: Virginie

last: Aires

first: Laurent

last: Lagrost


title: Novel Race-specific Genetic and Epigenetic Determinants of ADT-Resistance in African American Prostate Cancer

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study is to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant  miRNome  profiling to  Androgen Deprivation Therapy (ADT) sensitive miRNome profile in African American prostate cancer cells  and validate  by reverse transcription polymerase chain reaction (qRT–PCR) methods.
Method: Mirco-RNA were isolated from different CaP cells who were sensitive and resistant to Androgen Deprivation Therapy  (ADT).  Total micro-RNA were subjected to miRNA-Seq.
Results: We performed whole miRNA-Seq analysis through paired-end deep sequencing to systematically investigate the molecular features of different CaP  cell models- RC-77-N, RC-77T/E, RCC7T/E-ADT, RCC7T/E-CD133-plus, E006AA-hT and E006AA-hT-ADT.
Conclusions:  Our study represents the first detailed analysis of African American ADT resistant miRNome, with biologic replicates, generated by miRNA-seq technology.

overall_design: Androgen resistant and Androgen sensitive miRNA profiles from African American prostate cancer  of  were generated by deep sequencing, in duplicate using Illumina

first: Arsheed

last: Ganaie


title: Comprehensive single cell transcriptome lineages of a proto-vertebrate

status: Public on Jul 08 2019

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Studies of ascidian (sea squirt) embryos have highlighted the importance of cell lineages in animal development for over 100 years.  As simple proto-vertebrates, they are also used to explore the evolutionary origins of novel cell types, such as cranial placodes and neural crest in vertebrates.  To build upon these efforts we have determined comprehensive single cell transcriptomes of Ciona intestinalis throughout embryogenesis. More than 90,000 cells from 10 different developmental stages were examined, spanning the entirety of morphogenesis, from the onset of gastrulation at the 110-cell stage to the hatching of swimming tadpoles.  This represents an average of over 12-fold coverage for every cell at every stage of development, owing to the small cell numbers that are a hallmark property of ascidian embryogenesis.  Single cell transcriptome trajectories were used to construct “virtual” cell lineage maps, which confirm and extend those determined by conventional labeling methods.  These datasets were also used to reconstruct regulatory cascades and provisional gene networks for a variety of cell types, including nearly 40 different neuronal subtypes comprising the larval nervous system.  We summarize several applications of these datasets, including the identification of individual transcriptomes within the complete synaptome of swimming tadpoles, visualizing dynamic changes in gene expression during the birth, migration, and axogenesis of defined neurons, and the evolution of novel cell types such as the vertebrate telencephalon.

overall_design: Synchronized embryos from 10 different stages of development were rapidly dissociated in RNase-free calcium-free synthetic seawater, and individual cells were processed in the 10x Genomics Chromium system with at least 2 biological replicates for each developmental stage. The staged embryos span all of the hallmark processes of development, beginning with gastrulation to swimming tadpoles when all larval cell types, tissues and organs are formed. In total, we profiled 90,579 cells, corresponding to an average of over 12-fold coverage for every cell across each of the sampled stages

first: Mike

middle: S

last: Levine


title: Race-specific  transcriptome and Long non-coding RNA  of ADT-resistant African-American prostate cancer cell models.

summary:
Purpose: The goals of this study are to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant  transcriptome  to  profiling (RNA-seq) to  Androgen Deprivation Therapy (ADT) sensitive transcriptome in African American prostate cancer cells  and validate  by reverse transcription polymerase chain reaction (qRT–PCR) methods.
Method: Total RNA was extracted from different CaP cell who were ADT sensitive and  ADT resistance.  Total RNA was subjected to whole transcriptome sequencing analysis.  Sequence reads
Results: We performed whole transcriptome RNA-Seq analysis through paired-end deep sequencing to systematically investigate the molecular features of different CaP  cell models- RCC7/N, RCC7T/E, RCC7T/E-ADT, RCC7T/E-CD133, E006AA-hT and E006AA-hT-ADT We obtained an average of 23.85 million reads per sample, ranging from 22.86 to 24.93 million reads, with an average mapping rate of 98.29% to the reference human genome (UCSC version hg20). Next we performed Kal’s Z-test and generated Fold-Change (FC) values, p values and False Discovery Rate (FDR) values for measuring comparative gene expression profile. By applying stringent statistical threshold of greater than or equal to 2 FC, p value < 0.05 and FDR value < 1, we identified genes that were significantly differentially expressed in three different comparative groups.
Conclusions:  "Our study represents the first detailed analysis of African American ADT resistant transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.              "

overall_design: Androgen resistant and Androgen sensitive mRNA profiles from African American prostate cancer  of  were generated by deep sequencing, in duplicate using Illumina HiSeq

first: Badrinath

last: Konety


title: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (4C-seq)

first: Yingguang Frank

last: Chan

first: João

last: Castro

first: Michelle

last: Yancoskie

first: Marta

last: Marchini

first: Stefanie


title: Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons

first: Matthew

last: Rose

address: 3 Blackfan Circle

department: Neurology/Pathology

institute: Boston Children's Hospital

summary: We report the comparative gene expression between embryonic stem cell derived cranial and spinal motor neurons and multiple time points after induction and primary cultured ocular and spinal motor neurons, using single cell RNA sequencing.

overall_design: Single neurons were isolated in 96-well plates and their gene expression profiled using SMART-Seq2 from 8 samples: (1-2) primary cultured oculomotor/trochlear motor neurons and spinal motor neurons collected at embryonic day E11.5 and cultured for 7 days, (3-8) ESC-derived induced cranial and spinal motor neurons at either 2 days, 5 days, or 7 days after plating.

first: Disi

last: An

first: Ryosuke

last: Fujiki

first: Esteban

middle: O

last: Mazzoni

first: Elizabeth

last: Engle


title: Transcriptome regulated by lncRNA Mymsl in aortas

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

summary: To determine the transcriptome regulated by Mymsl in mouse smooth muscle cells

overall_design: Total RNA was extracted from aortas in 3 pairs of Mymsl knockout versus wildtype(WT) control mice and sujected for RNA-seq

first: Mihyun

last: Choi


title: Gene expression of human myoblasts with ectopic DUXB

city: Seattle

first: Guo-Liang

last: Chew

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary: RNA-seq of MB135 myoblasts with inducible DUXB, comparing uninduced and induced myoblasts

overall_design: MB135 human myoblasts were stably-transduced with a codon-altered version of DUXB.

first: Sean

last: Shadle

first: Stephen

middle: J

last: Tapscott

first: Robert

middle: K

last: Bradley


title: Spinal cord RNA-seq

city: Dunedin

first: Megan

last: Wilson

address: 270 Great King St

country: New Zealand

institute: University of Otago

summary: RNA-seq with male and female juvenile and adult spinal cords

overall_design: RNA was isolated from 4 week and 8 week spinal cords for sequencing


title: Genome-wide identification of 5hmCpGs in multiple myeloma

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

institute: University Rennes 1

type: Methylation profiling by high throughput sequencing

summary: We report the genomic localization of 5-hydroxymethylcytosines in multiple myeloma patients through the use of selective chemical labeling (SCL) and exonuclease digestion. Data highlighted super-enhancers and enhancers specifically undergoing active DNA demethylation in multiple myeloma cells.

overall_design: Genomic DNA from multiple myeloma (MM) cells was extracted and submitted to the SCL-exo protocol. After sequencing with a HiSeq 1500 (Illumina), reads were mapped to hg19 and processed to generate a single-CpG signal file (wig file) indicating the relative levels of hydroxymethylation.

first: Stéphane

last: Avner


title: Gene expression profiling of human colon cancer cell lines implanted in colon and liver of mice

city: South San Francisco

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
RNA was isolated from individual macrodissected tumors 4 weeks post implantation.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0019861

overall_design: Gene expression profiling of colorectal cell lines after their orthotopic implantation in the colon through induced rectal prolapse or in the liver through a modified hydrodynamic tail vein injection

first: Felipe

last: de Sousa e Melo


title: Single-cell transcriptome of human epithelial cells reveals novel insights into early innate immune responses to influenza virus and viral antagonism

city: New York

first: Gregory

middle: Robert

last: Smith

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

summary: Despite intense study, the complexity of interactions between viral and host cell mechanisms have ensured that the cellular innate immune response to influenza infection is still not well understood, especially at early time points following infection. Single cell RNA sequencing provides a new approach with which we can not only examine these early time points of cellular response, but also examine the heterogeneity of that response and more intensely examine patterns of expression that are hidden from bulk sample sequencing. As part of a larger study investigating the immune response of lung epithelial cells to influenza infection, we performed single-cell RNA expression profiling on A549 cells, a lung epithelial cell line, undergoing either a mock infection or infection by the influenza strain PR8-NS1-GFP at MOIs of 2.0 and 0.2. We measured single cell RNA expression at 4 hours and 12 hours post infection. We found a MOI-dependent negative correlation between expression of viral genes and cellular genes, suggesting an antagonist effect of the viral proteins in the innate immune response at the transcriptional level. Also, we found an unexpected early induction of some interferon inducible genes at higher levels in infected than bystander cells, consistent with autocrine activation. Finally, IFN lambda 1 showed broad expression among infected and bystander cells, indicating a possible paracrine component to induction.hile the cellular innate immune response to influenza infection has been studied intensely, there are still many unanswered questions, especially relating to the early

overall_design: Single cell RNA sequencing was conducted on six samples of the human epithelial cell line A549. Samples were either MOCK infected or infected by influenza viral strain PR8-NS1-GFP at MOI of 2.0 or 0.2 and measured at 4 or 12 hours post infection..

first: Irene

last: Ramos Lopez

first: Frederique

last: Ruf-zamojski

middle: R

first: Stuart

middle: C

last: Sealfon


title: RNA-seq analysis about Zscan4 knocked down samples and overpressed samples

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

summary: Transcription factor Zscan4 was newly discovered to be a marker of the intermediate state of 2-cell like cells. In addition, the WGCNA discovered a strong positive correlation between the expression of Zscan4 and that of MT2/MERVL .Hence, we examined the possibility for Zscan4 as an activator of MT2/MERVL.

overall_design: We knocked down Zscan4 by shRNA and overexpressed Zscan4 in J1. We performed RNA-seq analysis in order to exam the transcriptome.

first: Ruiqing

last: Chen

first: Fuquan

first: Xinyi

last: Lu


title: Changes in human endometrial gland transcriptome over the window of implantation

status: Public on Jul 07 2019

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

summary: Human endometrial glands from early, mid and late secretory phases were captured using laser microdissection, and analyzed to characterize the gene expression changes during the window of implantation.

overall_design: Laser-captured endometrial glands were analyzed for gene expression changes over time during the window of implantation

first: Flavio

last: Barros

first: Emma

last: Lucas

first: Sascha

last: Ott

first: Pavle

last: Vrljicak


title: A homeostatic Arid1a-dependent permissive chromatin state licenses hepatocyte responsiveness to liver injury-associated YAP signaling

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS


title: Expression data from human macrophage

status: Public on Jul 06 2019

first: Xinxin

last: Hou

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

summary:
In patients with endometriosis,  the abnormal immune microenvironment of the pelvic cavity is associated with a large number of macrophages, which participate in the formation and development of ectopic lesions. Different polarization states of macrophages play different biological roles. However, the molecular mechanisms of macrophage polarization remains far from being elucidated.
We used microarrays to detail the gene expression underlying macropages polarized by rhFGL2 and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: We isolated PBMC  from peripheral blood of healthy volunteer via Ficoll density gradient centrifugation, the CD14 MicroBeads were used for the magnetic positive selection of human CD14+ monocytes from PBMC. Monocytes were further differentiated into macrophage (monocyte-derived macrophage, MDM) by incubation with M-CSF for 6 days.  The macrophages were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Xiaoqiu

last: Wang

first: Wenjie

last: Zhou

first: Dajin

last: Li


title: Potential Antigens Involved In Delayed Xenograft Rejection in a GGTA1/CMAH DKO Pig-To-Monkey Model

city: Shenzhen

first: junfang

last: zhang

address: NO.3002 Sungang Road

institute: Institute of Translational Medicine, Shenzhen Second People's Hospital

summary: When hyperacute rejection is avoided by deletion of Gal expression in the pig, delayed xenograft rejection (DXR) becomes a major immunologic barrier to successful xenotransplantation. This study was to investigate potential antigens involved in DXR. We isolated primary renal microvascular endothelial cells (RMEC) and aortic endothelial cells (AEC) from GGTA1/CMAH double-knockout (DKO) pig and immunized monkeys with both of these cells. After sensitization, monkey serum antibody binding and cytotoxicity to RMEC was significantlyhigher than to AEC,suggesting that RMEC are more immunogenic than AEC. Transcriptome sequencing of DKO pigs indicated that the expression of 1,500 genes was higher in RMEC than in AEC, while 896 genes was lower. The differentially-expressed genes were mainly related to cell and biological adhesion.

sample_organism:
Macaca fascicularis
Homo sapiens
Sus scrofa

overall_design: Four kinds of cells were used for transcriptome sequencing, GGTA1/CMAH DKO pig AECs, GGTA1/CMAH DKO pig RMECs,cynomolgus monkey RMECs and human RMECs (HRGEC). Illumina Sequencing System (HiSeq2000, San Diego, CA, USA), following the manufacturer’s standard workflow. (This work was carried out by Novegene, Beijing, China).

first: Junfang


title: Surface PEGylation Suppresses Pulmonary Effects of CuO in Allergen-Induced Lung Inflammation

city: Helsinki

first: Harri

last: Alenius

address: Haartmaninkatu 3

department: Human Microbiome Research Program

institute: University of Helsinki

summary: The objective of the study was to investigate how pristine CuO modulates allergic lung inflammation and whether surface modifications can influence its reactivity. CuO materials exacerbated the existing allergic airway inflammation by eliciting dramatic pulmonary neutrophilia. Transcriptomic analysis showed that CuO, CuO COOH and CuO NH3 commonly enriched neutrophil-related biological processes in lungs with and without the pre-existing condition. In contrast, CuO PEG had a significantly lower potential in triggering pulmonary changes revealing that surface PEGylation suppresses the effects triggered by the pristine material.

overall_design: Pristine CuO (CuO) and its carboxylated (CuO COOH), methylaminated (CuO NH3) and PEGylated (CuO PEG) derivates were investigated in a murine asthma model. In the used model, each mouse (eight per group) received intraperitoneally a mixture of 50 mg of OVA and 2 mg of aluminum/magnesium hydroxide in 100 ml of PBS on day 1 and 10. After 10-day recovery, mice were exposed to 50 ml of PBS or 50 mg of OVA in 50 ml of PBS with or without dispersed CuO nanomaterials via oropharyngeal aspiration in isoflurane anaesthesia on four consecutive days. CuO materials were tested at three doses – 2.5, 10 and 40 mg/mouse/administration. Bronchoalveolar lavage was collected for cytological analysis and lung tissue samples for histological assessment and Agilent microarrays.

first: Marit

last: Ilves

first: Pia

middle: A

last: Kinaret

first: Joseph

last: Ndika

first: Piia

last: Karisola

first: Veer

last: Marwah

first: Vittorio

last: Fortino

first: Yuri

last: Fedutik

first: Manuel

last: Correia

first: Nicky

last: Ehrlich

first: Katrin

last: Loeschner

first: Alexander

last: Besinis

first: Joanne

last: Vassallo

first: Richard

middle: D

last: Handy

first: Henrik

last: Wolff

first: Kai

last: Savolainen

first: Dario

last: Greco


title: Bulk RNA sequencing of cell specific profile of RIS

city: Nashville

first: Sierra

last: Palumbos

state: TN

address: 2201 West End Ave, Nashville

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: The transcriptome profile of the RIS neuron in L1 C. elegans

overall_design: RIS was isolated using FACS sorting

first: Rebecca

last: McWhirter


title: Identification of known and novel miRNAs in the salt tolerant rice Oryza sativa cv. Pokkali in root and shoots of control and NaCl exposed seedlings

city: Bhubaneswar

first: Birendra

middle: Prasad

last: Shaw

state: Odisha

address: Nalco Square, Besides Kalinga Hospital

country: India

institute: Institute of Life Sciences

summary: The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 21.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ, and on the same logic it is also expected that their expression profile would differ considerably in the plant under contrasting environmental conditions. However, report on comparative study of expression profile of miRNAs in rice cultivars, or in any crop cultivars, contrast for salt tolerance, or tolerance to any abiotic stress is scant. Therefore, the current study was planned to see the expression profile of miRNAs in a salt-tolerant rice (Oryza sativa L. ssp indica) cultivar (cv.) Pokkali in presence and absence of NaCl and to check the response pattern of a few important salt-responsive miRNAs in a salt-sensitive rice cultivar Badami in order to identify the miRNAs and their targets that could be involved in the salt tolerance process

overall_design: The seedlings of Oryza sativa cv. Pokali were  subjected to 1.5 % NaCl stress through root, and sRNAs were isolated from the root and shoot tissues. Known and novel miRnAs were identified bioinformatically, and theie expression was validated by Northern.

first: Shaifaly

last: Parmar

first: Ravichandra

last: Tagirasa

first: Lambodar

last: Behera

first: Sushant

last: Dash


title: RNA-Seq data used to explore transcriptional dynamics in multipartite fungus-plant interactions: Hordeum vulgare, Serendipita vermifera, Bipolaris sorokiniana

city: Cologne

first: Alga

last: Zuccaro

state: NRW

address: Zuelpicher Str. 47b

department: Botanical Institute

institute: University of Cologne

summary: We addressed the question  how the interaction between the beneficial root endophyte Serendipita vermifera (Sv) and the pathogen Bipolaris sorokiniana (Bs) affects fungal behavior and determines barley host responses using a gnotobiotic natural soil-based split-root system for phenotypic and transcriptional analyses.

sample_organism:
Hordeum vulgare
Bipolaris sorokiniana
Serendipita vermifera

overall_design: Fungal and barley (Hv) plant mRNA profiles were  generated by deep sequencing, 33 samples including replicates.

first: Ganga

last: Jeena

first: Debika

last: Sarkar

first: Gregor

last: Langen


title: SETD1A protects from senescence through regulation of the mitotic gene expression program

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

summary: SETD1A, a member of the Set1/COMPASS family maintaining H3K4 methylation in the promoters of transcriptionally active genes, is critical for the execution of developmental gene expression and is overexpressed in multiple cancers including breast cancer1-3. Here we show that SETD1A is essential for supporting cellular mitotic processes and consequentially, its depletion leads to senescence. SETD1A directly regulates the expression of several genes orchestrating mitosis and DNA damage responses and its depletion results in multiple mitotic defects including chromosome misalignment and segregation defects.  Senescence-associated cell cycle arrest in SETD1A knockdown cells is independent of the mutational status of p53, RB and p16, key mediators of this process, instead, is sustained through direct transcriptional suppression of SKP2, the ubiquitin ligase, which degrades p27 and p21. Rare cells escape senescence and re-enter the cell cycle by restoring SKP2 expression but with enhanced genomic instability. In >200 cancer cell lines and in primary circulating tumor cells, expression of SETD1A correlates with genes involved in mitosis and cell cycle suggesting a role in suppressing senescence induced by aberrant mitosis. Thus, SETD1A encodes a chromatin modifier, whose modulation may maintain the balance between senescence and genomic instability in cells.

overall_design: Compare histon H3K4 trimethylation status between groups

first: Toshi

last: Shioda

first: Satoru

last: Matsuda

first: Ken

last: Tajima

first: Shyamala

last: Maheswaran


title: Transcriptome Analysis of a Bovine Mammary Epithelial Cell Model with Different Milk Fat Synthesis Capacity

status: Public on Jul 05 2019

city: Harbin

first: Xiaoming

last: Hou

state: Heilongjiang

address: 600 changjiang road

institute: northeast agricultural university

summary: Synthesis of milk fat is a complex biochemical process regulated by a series of molecular events. To determine gene expression changes during milk fat synthesis in bovine mammary epithelial cells, we established a cell model with a high capacity for milk fat synthesis using stimulation with acetate and β-hydroxybutyrate. RNA sequencing was used to identify differentially expressed genes (DEGs) between the high-milk-fat and control cells. A total of 625 DEGs (358 upregulated, 267 downregulated) were identified. Among the highly expressed genes, there was enrichment for terms associated with fatty acid synthesis, activation, and triacylglycerol synthesis, consistent with active milk fat synthesis. Kyoto Encyclopedia of Genes and Genomes analysis suggested that DEGs were most enriched in the “lipid metabolism” subcategory of the “metabolism” category, and in the “signal transduction” subcategory of the “environmental information processing” category. Although an in vitro cell model cannot completely simulate in vivo lactation, it eliminates interference from other cell types and from the synthesis of other milk components during transcriptome profile analysis. This work provides a profile of gene expression changes that occur during milk fat synthesis in bovine mammary epithelial cells, which furthers our understanding of the molecular regulation of lipid metabolism.

overall_design: 3 from high-milk-fat samples and 3 from control samples

first: Ye

last: Lin


title: Gene responses to LKB1 overexpression in NSCLC cell line A549

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: Differential gene expression analysis of LKB1-deficient and LKB1-reconstituted A549 NSCLC cells

overall_design: RNA from A549 cells expressing the pBabe vector or full length LKB1 was isolated and RNA-seq was performed.

first: Laura

last: Rodón

middle: U

last: Svensson

first: Matthew

middle: H

last: Chun

first: Wen-Wei

last: Tsai

first: Lillian

last: Eichner

first: Reuben

first: Marc

last: Montminy


title: Flagellar mutants have reduced pilus synthesis in Caulobacter crescentus

city: Bloomington

first: Yves

middle: V

last: Brun

state: IN

address: 1001 E Third Street

department: Biology

institute: Indiana University

summary: Surface appendages such as flagella and type IV pili mediate a broad range of bacterial behaviors including motility, attachment, and surface sensing. While many species harbor both flagella and type IV pili, little is known about how or if their synthesis is coupled. Here, we show that deletions of genes encoding different flagellum machinery components result in a reduction of pilus synthesis in Caulobacter crescentus. First, we show that different flagellar mutants exhibit different levels of sensitivity to a pilus-dependent phage and that less cells within populations of flagellar mutants make pili. Furthermore, we find that single cells within flagellar mutant populations produce less pili per cell. We demonstrate that these gene deletions result in reduced transcription of pilus-associated genes and have a broad effect on global transcription profiles. Finally, we show that the decrease in pilus production is due to a reduction in the pool of pilin subunits that are polymerized into pilus fibers. These data demonstrate that mutations in flagella gene components affect not only motility but can also have considerable and unexpected consequences on other aspects of cell biology.

overall_design: Gene expression of two different Caulobacter crescentus NA1000 mutants were compared to wildtype controls; all experiments were carried out in triplicate

first: Courtney

last: Ellison

first: Douglas

middle: B

last: Rusch


title: LKB1-deficient and LKB1-reconstituted A549 NSCLC cells

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

overall_design: Refer to individual Series


title: SMRT regulates metabolic homeostasis and adipose tissue macrophage phenotypes in tandem

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: The Silencing Mediator of Retinoid and Thyroid Hormone Receptors (SMRT) is a nuclear corepressor that regulates the transcriptional activity of many transcription factors critical for metabolic processes. While the importance of SMRT’s role in the adipocyte has been well-established, prior mouse models have yielded contradictory phenotypes, limiting our understanding of its in vivo function in the context of homeostatic maintenance. Multiple models suggest that SMRT deficiency leads to increased adiposity, though the effects of SMRT loss on glucose tolerance and insulin sensitivity have been variable. We therefore generated an adipocyte-specific SMRT knockout (adSMRT-/-) mouse to more clearly define SMRT’s metabolic contributions. In doing so, we found that SMRT deletion in the adipocyte does not, in fact, lead to obesity, despite increased food consumption in knockouts – even when mice are challenged with a high-fat diet. This suggests that prior adiposity phenotypes described in generalized models were due to effects beyond the adipocyte. However, an adipocyte-specific SMRT deficiency still led to dramatic effects on systemic glucose tolerance and adipocyte insulin sensitivity, impairing both. This metabolically deleterious effect was coupled with a surprising immune phenotype, wherein most genes differentially expressed in the adipose tissue of adSMRT-/- mice were upregulated in pro-inflammatory pathways. Flow cytometry and conditioned media experiments demonstrated that secreted factors from knockout adipose tissue strongly informed resident macrophages to develop a pro-inflammatory, MMe (metabolically activated) phenotype. Taken together, these studies suggest a novel role for SMRT as an integrator of metabolic and inflammatory signals to effectively maintain physiological homeostasis.

overall_design: RNA sequencing on 20-week old high-fat diet-fed mice was conducted on a total of 8 mouse perigonadal whole adipose tissue samples, which were collected from either wildtype or knockout age- and weight-matched mice (4 mice/genotype). Following sample homogenization, RNA was collected using a commercially available kit (E.Z.N.A Total RNA Kit, Omega Bio-Tek, GA) per manufacturer’s instructions. Samples were then prepared for RNAseq on the Illumina HiSeq4000 platform, and provided to the University of Chicago’s Center for Research Informatics core for sequencing.

first: Jonathan

last: Kahn

first: Ronald

last: Cohen


title: Divergent Gene Expression through PI3K/Akt Signaling Pathway Cause Different Models of Hypertrophy Growth in Chicken

city: Ahvaz

first: Seyed

middle: Nader

last: Albooshoke

state: khozestan

address: sazeman aab-o-bargh

department: Animal Science

country: Iran

institute: Khuzestan Agricultural and Natural Resources Research and Education Center

summary: RNA-Seq technology was used to investigate differences in the gene expression of pectoralis muscle tissue between two chicken breeds (Ross as commercial (rapidly growing) and Isfahani as Iranian local breed (slow-growing)).

overall_design: Total RNA was isolated from breast muscle samples at end of 4 weeks of age and sequenced by an Illumina Hiseq 2000 sequencer. Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) was applied to align clean reads to chicken reference genome. Then, Cufflinks package was used to assemble transcripts and identify significantly differentially expressed genes (DEGs).

first: S

first: M

last: Bakhtiarizadeh


title: An Lkb1-Sik axis suppresses tumor growth and controls differentiation [RNA-Seq]

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

institute: Stanford University

summary:
Background: LKB1 is among the most frequently altered tumor suppressors in lung adenocarcinoma. Despite being implicated in the regulation of a variety of cellular processes, the mechanisms by which LKB1 constrains lung tumor growth and progression remains an area of intense investigation.
Purpose: To determine the extent of overlap in terms of the transcriptomic states arising from either Lkb1 deletion or Sik-targeting within cancer cells isolated from genetically engineered mouse models of oncogenic Kras-driven lung adenocarcinoma
Approach: Cancer cells sorted from mouse lung tumors of defined genotypes were profiled by RNA-seq.
Results: A strong overlap existed between Lkb1-deficient and Sik-targeted cancer cells both at the gene and pathways levels.
Conclusions: Given the strong transcriptional overlap, loss of either Lkb1 or Sik appear to be functionally related.

overall_design: RNA-seq of WT, Lkb1 deletion or Sik-targeted mouse lung cancer cells.

middle: W

first: Monte

middle: M

last: Winslow


title: An Lkb1-Sik axis suppresses tumor growth and controls differentiation


title: The landscape of mRNA translation in tomato roots

city: East Lansing

first: Polly

last: Hsu

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary: We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. Most of the newly identified ORFs are small and difficult to detect with in silico methods. We also identified over thirteen hundreds of upstream ORFs on annotated genes. This data could facilitate gene annotation. Besides, this data also demonstrated that uORFs, miRNAs and antisense RNAs are regulating the expression of associated genes. This study uncovered mechanisms of translational regulation and gene annotation in tomato.

overall_design: 3 biological replicates of 4-day old tomato roots (about 2~3 cm from root tips) collected and processed for Ribo-seq and RNA-seq sample preparation. The Ribo-seq library was sequenced with illumina single-end 50 sequencing and the RNA-seq library was sequenced with illumina paired-end 100 sequencing.

first: Yingshan

first: Hsin-Yen

last: Wu


title: RNA sequencing for mouse arcuate nucleus in male miR-17-92 knockout mice and female miR-7-sponge mice

first: Yanxia

last: Gao

address: No. 800, Dongchuan Road

institute: Shanghai Jiaotong University

summary: To address the molecular basis of miR-7 and miR-17-92 regulation in the POMC neuron and sex-differential expression of genes in the arcuate nucleus.

overall_design:
To address the molecular basis of miR-7 and miR-17-92 regulation in the POMC neuron, sequencing was performed. 2 samples (17-92-1, 17-92-2) in the male miR-17-92 knockout group and 2 samples (17-92-C1, 17-92-C2) in its control group (male wild type littermates) were sequenced and compared, and 2 samples in the female miR-7-sponge group (7-sp-1, 7-sp-2) and 2 samples (7-sp-C2, 7-sp-C4) in its control group (female wild type littermates) were sequenced and compared. To explore sex-differential expression of genes in the arcuate nucleus, 2 samples in the male wild type group and 2 samples in the female wild type group were compared. Arcuate nucleus from 2 mice were included in each sample.
ARC tissues in the coronal brain sections were accurately cut with syringe needles under the microscope and homogenized immediately in the TRIZOL reagent (Invitrogen). Total RNA was separated using chloroform and precipitated with isopropanol. Whole RNA sequencing was performed at the go beyond RNA arraystar company in the United States using the Illumina HiSeq 4000. The transcript abundances for each sample were estimated with StringTie (Pertea et al., 2015) and the Fragments per kilobase of transcript per million mapped reads (FPKM) (Mortazavi, Williams, McCue, Schaeffer, & Wold, 2008) value for gene and transcript level were calculated with R package Ballgown (Frazee et al., 2015).

first: Tao

last: Sun


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma [sHCC1]

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

institute: IDIBAPS

summary: Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions.    Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. Genes altered in early lesions [31 dysplastic nodules (DNs) and 38 small HCCs (sHCC)] were defined as trunk. The distribution of candidate trunk genes was explored in: a) different regions of large tumors [43 regions of 21 tumors, (2-3 regions/tumor)]; and b) different nodules of the same patient [39 multinodular tumors from 17 patients]. Multinodular lesions were classified as intrahepatic metastases (IMs) or synchronous tumors based on chromosomal aberrations.     Results: TERT promoter mutations (10.5%) and broad copy-number aberrations in chromosomes 1 and 8 (3-7%) were identified as trunk gatekeepers in DNs and were maintained in sHCCs. Trunk drivers identified in sHCCs included TP53 (23%) and CTNNB1 (11%) mutations, and focal amplifications or deletions in known drivers (6%). Overall, TERT, TP53 and CTNNB1 mutations were the most frequent trunk events in early stages. 89% of mutations in these genes were shared between different regions of large tumors. In multinodular HCCs, 35% of patients harbored IMs. 85% of mutations in TERT, TP53 and/or CTNNB1 were retained in primary and metastatic tumors.    Conclusions: Trunk events in early stages (TERT, TP53, CTNNB1 mutations) were ubiquitous across different regions of the same tumor and between primary and metastatic nodules in >85% of cases. This concept supports the knowledge that single biopsies would suffice to capture trunk mutations in HCC.

overall_design: Paraffin-embedded tumors and dysplasias from 19 patients were collected and RNA was extracted. Matched non-tumor cirrrhotic tissue was also collected for all cases. 6 non-tumoral and non-cirrhotic liver tissues were alsco included as controls. Whole-genome trasncriptome analysis was done using HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina) according to manufacturer’s protocols. Raw data were normalized using cubic spline algorithm implemented in the Illumina Normalizer module of the GenePattern analysis toolkit (www.broadinstitute.org/genepattern) as previously described (Sia D et al, Gastroenterology, 2013).

first: Josep

last: Llovet

first: Daniela

last: Sia


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma [sHCC2]

overall_design: Paraffin-embedded tumors or dysplasias from 29 patients were collected and RNA was extracted. Matched non-tumor cirrrhotic tissue was also collected for all cases. Whole-genome trasncriptome analysis was done using HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina) according to manufacturer’s protocols. Raw data were normalized using cubic spline algorithm implemented in the Illumina Normalizer module of the GenePattern analysis toolkit (www.broadinstitute.org/genepattern) as previously described (Sia D et al, Gastroenterology, 2013).


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma [early CNV]

overall_design: Paraffin-embedded  and fresh-frozen samples representing early steps of hepatocarcinogenesis were collected and gDNA was extracted. This cohort comprised: 29 dysplastic nodules (DN) -including low-grade and high-grade dysplasia (LGDN and HGDN)-; and 17 small tumors (sHCCs) -including 6 very-early and 11 early HCCs (veHCC and eHCC). When available matched cirrhotic tissues was also collected and extracted. Comparative Genomic Hybridization analysis was done using HumanOmniExpress-24 v1.1 BeadChip (Illumina) according to manufacturer’s protocols. Previous treatment with the Infinium FFPE restoration kit (Illumina) was performed for FFPE samples. Log R ratio (LRR, reflecting total copy number) and B-allele frequency (BAF) obtained from GenomeStudio were used for CNV detection.

first: Zhongyang

last: Zhang

first: Ke

last: Hao