title: Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

summary: Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states.

overall_design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2

first: Stefania

last: Dell’Orso

first: Aster

last: Juan

first: Kyung-Dae

last: Ko

first: Faiza

last: Naz

first: Gustavo

last: Gutierrez-Cruz

first: Xuesong

last: Feng


title: Phosphatase inhibitor PPP1R11 modulates resistance of human T cells towards Treg-mediated suppression of TCR signaling

status: Public on Mar 08 2019

city: Stockholm

first: Sunjay

middle: Jude

last: Fernandes

address: Karolinska University Sjukhuset, CMM L8:05, Solna

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: We have performed RNAseq analysis of human T cells upon PPP1R11 siRNA silencing. We have explored the role of PPP1R11 for the first time in primary human T cells and discovered that PPP1R11 is a novel negative mediator of T cell activation.

overall_design: CD4+ T cells from 3 donors were treated with either control or PPP1R11 siRNA for 4.5 days and either stimulated with cross linked CD3/CD28 for 6h or left unstimulated for RNAseq analysis

middle: J

first: Rubin

middle: N

last: Joshi

first: Angelika

last: Schmidt


title: Transcriptome-wide analysis of long and short RNAs in mouse embryonic stem cells (ESC) and differentiated cells depleted of a functional Htt gene

status: Public on Mar 07 2019

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

type: Non-coding RNA profiling by high throughput sequencing

summary:
The HTT gene mutated in Huntington’s Disease (HD) has essential roles during normal development. However, still not fully understood are the functional consequences of its partial inactivation. Our genetic study provides a comprehensive description of the effects of progressively more severe decreases in expression of Htt, the murine HTT counterpart. The most severe Htt decrease leads to lethality of early embryos, while intermediate but still severely reduced Htt dosages yield a variety of recessively inherited developmental abnormalities affecting body size, skin, skeletal and ear formation, and hematopoiesis. Comparative molecular analysis of differentiating wild-type cells and cells lacking Htt function further elucidate genes networks dysregulated during organ development. These nominate chromatin regulators and short non-coding RNAs as key molecular mediators. Together these findings demonstrate that Htt is required from conception to support normal embryonic and fetal development.
Keywords: Huntingtin, Htt, Hypomorphic mice, Pleiotropy, Mouse Embryo Development, Hematopoiesis, Skeletal - Skin - Ear Development, embryonic stem cells, neuronal progenitors, RNA and miRNA sequencing, transcriptome profiling, RNA-Seq, small RNA-Seq

overall_design: In this study, we performed transcriptome-wide gene expression analyses of long and short RNAs, by RNA-Seq and small RNA-Seq respectively. Data were generated from murine wild-type parental ESC, huntingtin-null Hdhex4/5/ex4/5 ESC and from wild-type and huntingtin-null Hdhex4/5/ex4/5 EB differentiated cells.

first: Vidya

last: Murthy

first: Toshimi

last: Yoshida

first: Serkan

last: Erdin

first: Teresa

last: Calzonetti

first: Ravi

last: Vijayvargia

first: Takshashila

last: Tripathi

first: Emanuela

last: Kerschbamer

first: Ihn

middle: S

last: Seong

first: Alessandro

last: Quattrone

first: Michael

middle: E

last: Talkowski

first: James

middle: F

last: Gusella

first: Katia

last: Georgopoulos

first: Marcy

last: MacDonald

first: Marta

last: Biagioli


title: miR-27a is a pivotal regulator of the breast cancer stem cell state

status: Public on Mar 06 2019

city: Shinjyuku-ku

first: Shinobu

last: Ueda

address: 6-1-1, Shinjyuku

country: Japan

institute: Tokyo Medical University

summary:
Comparison af adherent growing breast cancer cell lines versus mammospheres under serum-free conditions
Background:
In patients with breast cancer, subsets of long-lived cells tolerate chemotherapies. These chemoresistant cells can remain dormant at secondary sites, such as bone and lung, for years and decades. Cancer cells endowed with drug resistance are maintained in vivo in a quiescent slow-growing state that preserves them from anti-proliferative cancer drugs. The mechanism of conversion from dormancy to growth remains poorly understood. We aimed to identify microRNAs (miRNAs) as master regulators of cancer stem cells (CSCs) maintainance, because one of the characteristics of CSCs is their slow proliferation or dormancy. MiRNA targeting CSCs may be an effective therapy to improve the prognosis of breast cancer patients.
Methods:
We performed miRNA array analysis to identify differences miRNA expression profiles between adherent cells and mammospheres that contain higher number of breast cancer stem cells (BCSCs). In this approach, we focused on expression of hsa-miR-27a. Further, roles of hsa-miR-27a target genes in maintaining BCSC properties were analysed .
Results:
Here, we showed that hsa-miR-27a was downregulated in mammosphere cells. The formation of BCSCs was attenuated by transfection of hsa-miR-27a. We found that hsa-miR-27a targets F-box and WD-40 domain protein 7 (FBW7), a tumor suppressor gene, thereby inducing tumor dormancy. Additionally, we found that hsa-miR-27a targets genes involved in GSH synthesis, including xCT (encoded by SLC7A11), a heterodimeric protein of a transporter subunit of the xC(-) system, cystathionine gamma-lyase (CTH/CSE), and nuclear factor-erythroid 2-related factor 2 (Nrf2/NFE2L2), thereby increasing intracellular reactive oxygen species (ROS) levels. Upregulation of these genes by antisense (as)-miR-27a induced autophagy.
Conclusions:
Previous studies showed that expression of hsa-miR-27a is elevated in breast cancer. Here, we showed that expression of hsa-miR-27a was reduced in BCSC. CSCs in the dormant state are resistant to chemotherapy due to inhibition of ROS accumulation in these cells. These results demonstrate that hsa-miR-27a plays an essential role in maintaining the BCSCs phenotype via regulation of FBW7, ROS related genes and the Nrf2 pathway, as well as in the dormant-to-proliferative switch of breast cancer cells. Thus, hsa-miR-27a represents a novel strategy for various type of breast cancer.

first: Masakatsu

last: Takanashi

first: Katsuko

last: Sudo

first: Masahiko

last: Kuroda


title: The transcription factors TFEB and TFE3 link the FLCN-AMPK signaling axis to innate immune response and pathogen resistance

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

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

overall_design: Refer to individual Series


title: Altered migratory trajectories in cerebral organoids derived from individuals with neuronal heterotopia

city: Stanford

first: Sabina

last: Kanton

state: CA

address: 318 Campus Drive

department: Psychiatry and Behavioral Sciences

country: USA

institute: Stanford University

summary: Malformations of the human cortex represent a major cause of disability. Mouse models  with mutations in known causal genes only partially recapitulate the phenotypes and are  therefore not unlimitedly suited for understanding the molecular and cellular mechanisms  responsible for these conditions. Here we study periventricular heterotopia (PH) by analyzing  cerebral organoids derived from induced pluripotent stem cells of patients with mutations in  the cadherin receptor-ligand pair DCHS1 and FAT4 or from isogenic knock-out lines. Our  results show that human cerebral organoids reproduce the cortical heterotopia associated with  PH. Mutations in DCHS1 and FAT4 or knock-down of their expression cause changes in the  morphology of neural progenitor cells and result in defective neuronal migration dynamics  only in a subset of neurons. Single-cell RNA-sequencing data reveal a subpopulation of  mutant neurons with dysregulated genes involved in axon guidance, neuronal migration and  patterning. We suggest that defective neural progenitor cell (NPC) morphology and an altered  navigation system in a subset of neurons underlie this form of periventricular heterotopia.

overall_design: Single cell transcriptomes from human control and mutant organoids were analyzed in this study. Mutant organoids were generated from patient-derived iPSCs and carry mutations in the cadherin receptor-ligand pair DCHS1 and FAT4. Data were generated from dissected regions of 3 organoids per condition and processed using the SmartSeq2 approach. Additionally, 2d cultured neurons differentiated from control and mutant iPS cells were profiled using 10X Genomics 3' single cell transcriptome technology.

first: Barbara

last: Treutlein


title: A Syngeneic ErbB2 Mammary Cancer Model for Preclinical Immunotherapy Trials [RNA-seq]

city: Davis

first: Alexander

middle: D

last: Borowsky

state: California

address: 1 Shields Ave

institute: University of California at Davis

summary: A cell line was derived from a mammary carcinoma in the transgenic FVB/N-Tg(MMTV-ErbB2)NDL2-5Mul mouse.  The line, referred to as “NDL(UCD)” is adapted to standard cell culture and can be transplanted into syngeneic FVB/N mice. The line maintains a stable phenotype over multiple in vitro passages and rounds of in vivo transplantation. The cell line exhibits high expression of ErbB2 and ErbB3 and signaling molecules downstream from ErbB2. The line was previously shown to be reactive to anti-immune checkpoint therapy with responses conducive to immunotherapy studies. Here, using both histology/immunophenotyping and gene expression/microarray analysis, we show that the syngeneic transplant tumors elicit an immune reaction in the adjacent stroma, with additional tumor infiltrating lymphocytes. We also show that this immune activating effect is greater in the syngeneic transplants than in the primary tumors arising in the native transgenic mouse.  We further analyzed the PD-1 and PD-L-1 expression in the model and found PD-L1 expression in the tumors and in vitro. In conclusion these data document the validity and utility of this cell line for in vivo preclinical immunotherapy trials.

overall_design:
Flash frozen NDL(UCD) cell line tumor transplants were sampled and whole-transcriptome analysis was performed by next-generation sequencing (NGS)-based RNA-Sequencing.

This series includes three biological replicates of the same cell line grown in three different (but same strain) mouse.

first: Zsófia

last: Pénzváltó

first: Jane

middle: Q

last: Chen

first: Clifford

middle: G

last: Tepper

first: Ryan

last: Davis

first: Matthew

last: Silvestrini

first: Maxine

last: Umeh-Garcia

first: Colleen

last: Sweeney


title: Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

summary: Embryonic stem cells can self-renew and differentiate, holding great promise for regenerative medicine. They also employ multiple mechanisms to preserve the integrity of their genomes. Nucleotide excision repair, a versatile repair mechanism, removes bulky DNA adducts from the genome. However, the dynamics of the capacity of nucleotide excision repair during stem cell differentiation remain unclear. Here, using immunoslot blot assay, we measured repair rates of UV-induced DNA damage during differentiation of human embryonic carcinoma (NTERA-2) cells into neurons and muscle cells. Our results revealed that the capacity of nucleotide excision repair increases as cell differentiation progresses. We also found that inhibition of the apoptotic signaling pathway has no effect on nucleotide excision repair capacity. Furthermore, RNA-seq-based transcriptomic analysis indicated that expression levels of four core repair factors, xeroderma pigmentosum (XP) complementation group A (XPA), XPC, XPG, and XPF-ERCC1, are progressively up-regulated during differentiation, but not those of replication protein A (RPA) and transcription factor IIH (TFIIH). Together, our findings reveal that increase of nucleotide excision repair capacity accompanies cell differentiation, supported by the up-regulated transcription of genes encoding DNA repair enzymes during differentiation of two distinct cell lineages.

overall_design: Determination of nucleotide excision repair capacity during multi-lineage differentiation of NT2 cells.

first: Wenjie

last: Liu

first: Ayano

last: Kakoki

first: Rujin

last: Wang

first: Ogun

last: Adebali

first: Yuchao

last: Jiang

first: Aziz

last: Sancar


title: Similarity Regression predicts evolution of transcription factor sequence specificity

city: Toronto

first: Samuel

last: Lambert

state: ON

address: 160 College St.

department: Donnelly Centre for Cellular and Biomolecular Research

institute: University of Toronto

summary: Transcription factor (TF) binding specificities (motifs) are essential to the analysis of noncoding DNA and gene regulation. Accurate prediction of TF sequence specificities is critical, because the hundreds of sequenced eukaryotic genomes encompass hundreds of thousands of TFs, and assaying each is currently infeasible. There is ongoing controversy regarding the efficacy of motif prediction methods, as well as the degree of motif diversification among related species. Here, we describe Similarity Regression (SR), a significantly improved method for predicting motifs. We have updated and expanded the Cis-BP database using SR, and validate its predictive capacity with new data from diverse eukaryotic TFs. SR inherently quantifies TF motif evolution, and we show that previous claims of near-complete conservation of motifs between human and Drosophila are grossly inflated, with nearly half the motifs in each species absent from the other. We conclude that diversification in DNA binding motifs is pervasive, and present a new tool and updated resource to study TF diversity and gene regulation across eukaryotes.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 341 diverse eukaryotic transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

middle: A

first: Ally

middle: W

last: Yang

last: Sasse

first: Gwendolyn

last: Cowley

first: Mihai

last: Albu

first: Mark

middle: X

last: Caddick

first: Quaid

last: Morris

middle: T

last: Weirauch

first: Timothy

middle: R

last: Hughes


title: mRNA sequencing of single-cell and 20-cell pools of CD103+CD8+ and CD103-CD8+ T lymphocytes sorted from human ovarian cancer

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

summary: Cytotoxic T cells confer a prognostic benefit in many tumors, including ovarian cancer. We and others have previously identified a subset of CD8+ T cells, namely CD103+CD8+ T cells, that seems to have a better prognostic effect. The aim of this study is to identify how these CD103+ T cells differ from CD103-CD8+ T cells on mRNA level in human samples of ovarian cancer.

overall_design: mRNA profiles of 10 pools of 20 cells CD103+CD8+, 10 pools of 20 cells CD103-CD8+, 20 single-cells CD103+CD8+, 20 single-cells CD103-CD8+ were generated from TILs of 3 ovarian cancers (high-grade serous ovarian cancer) by SMARTseq2

first: Hagma

middle: H

last: Workel


title: A Syngeneic ErbB2 Mammary Cancer Model for Preclinical Immunotherapy Trials [microarray]

first: Alexander

last: Borowsky

summary:
A cell line was derived from a mammary carcinoma in the transgenic FVB/N-Tg(MMTV-ErbB2)NDL2-5Mul mouse.  The line, referred to as “NDL(UCD)” is adapted to standard cell culture and can be transplanted into syngeneic FVB/N mouse. The line maintains stable phenotype over multiple in vitro passages and rounds of in vivo transplantation. The cell line exhibits high expression of ErbB2 and ErbB3 and signaling molecules downstream ErbB2. The line was previously shown to be reactive to anti-immune checkpoint therapy with responses conducive to immunotherapy studies. Here, using both histology/immunophenotyping and gene expression/microarray analysis, we show that the syngeneic transplant tumors elicit an immune reaction in the adjacent stroma, with additional tumor infiltrating lymphocytes. We also show that this immune activating effect is greater in the syngeneic transplants than in the tumors arising in the transgenic mouse.  We further analyzed the PD-1 and PD-L-1 expression in the model and found strong PD-L1 expression in the tumors and in vitro.
Three distinct transplantable syngenic mouse models of mammary carcinoma were compared to identify differentially expressed genes.

overall_design: For evaluating differential gene expression of the tumors arose from the NDL(UCD),  Met1(UCD) and SSM2(UCD) cell lines grown in the FVB mouse we collected snap-frozen tumor samples, and three samples per model were processed in Mouse Gene 1.0 ST Array.

first: Zsófia

last: Pénzváltó

first: Jane

last: Chen

first: Clifford

last: Tepper

first: Ryan

last: Davis

first: Matthew

last: Silvestrini

first: Maxine

last: Umeh-Gacia

first: Colleen

last: Sweeney


title: Illumina microarray analysis of three subpopulations of murine aortic adventitial cells freshly sorted by MACS, based on expression of Sca-1 and CD45

city: Adelaide

first: Peter

middle: James

last: Psaltis

state: South Australia

address: North Terrace

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

summary:
Comparison of gene expression between aortic adventitial Sca-1+CD45+ progenitor cells and Sca-1-CD45+ or Sca-1+CD45- cells.
The hypothesis tested was that Sca-1+CD45+ cells would differentially express genes relating to angiogenesis and vasculogenesis when compared to Sca-1-CD45+ leukocytes.

overall_design: Total RNA obtained and purified from freshly MACS sorted cells obtained from enzymatic digests of aortic adventitia from pools of 12 week-old C57BL/6 mice

first: Robert

last: Simari


title: Transcriptome responses to the natural phytotoxin t-chalcone in Arabidopsis thaliana L.

status: Public on Mar 05 2019

city: University

first: Zhiqiang

last: Pan

state: MS

address: 1558 University Ave

institute: USDA-ARS-NPURU

summary:
BCKGROUND: New modes of action are needed for herbicides. The flavonoid synthesis intermediate t-chalcone causes apoptosis-like symptoms in roots and bleaching of shoots of Arabidospsis, suggesting a unique mode of action as a phytotoxin.
RESULTS: Using RNA-Seq, transcriptome changes were monitored in Arabidopsis seedlings during the first 24 h of exposure (at 1, 3, 6, 12 and 24 h) to 21 μM t-chalcone (I50 dose), examining effects on roots and shoots separately.  Expression of 892 and 1000 genes was affected in roots and shoots, respectively.  According to biological function, many of the affected genes were transcription factors and genes associated with oxidative stress, heat shock proteins, xenobiotic detoxification, ABA and auxin biosynthesis, and primary metabolic processess. These are secondary effects found with most phytotoxins. Potent phytotoxins usually act by inhibiting enzymes of primary metabolism. KEGG pathway analysis of transcriptome results from the first 3 h of t-chalcone expsoure indicated several potential primary metabolism target sites for t-chalcone. Of these, p-hydroxyphenylpyruvate dioxygenase (HPPD) and tyrosine amino transferase were consistent with the bleaching effect of the phytotoxin. Supplementation studies with Lemna paucicostata and Arabidiopsis supported HPPD as the target, although in vitro enzyme inhibition was not found.
CONCLUSIONS: t-Chalcone is possibly a protoxin that is converted to a HPPD inhibitor in vivo.

overall_design: Arabidopsis seedlings (14 days-old) were treated with t-chalcone at IC50 concentration (21 µM). After treatment, plants were incubated for 0, 1, 3, 6, 12 and 24 h. Three replicate samples were collected from control plants (0.1% EtOH) and treated plants for each time point.

first: Carla

last: Díaz-Tielas

first: Elisa

last: Graña

first: Adela

middle: M

last: Sánchez-Moreiras

first: Manuel

last: Reigosa

first: Justin

last: Vaughn

first: Joanna

last: Bajsa-Hirshel

first: Mary

middle: V

last: Duke

first: Stephen

middle: O


title: Evolution of Replication Origins in Vertebrate Genomes: Rapid Turnover Despite Selective Constraints [SNS-seq]

city: Berlin

first: Florian

last: Massip

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicin

summary:
Background: The replication program of vertebrate genomes is driven by the chromosomal distribution and timing of activation of ten of thousands replication origins. Genome-wide studies have shown the frequent association of origins with promoters and CpG islands, and their enrichment in G-quadruplexes sequence motifs (G4). However the genetic determinants driving their activity remain poorly understood. To gain insight on functional constraints operating on replication origins and on their spatial distribution, we conduct the first evolutionary comparison of genome-wide origins maps across vertebrates.
Results: We generated a high resolution genome-wide map of chicken replication origins (the first of a bird genome), and performed an extensive comparison with human and mouse maps. The analysis of intra-species polymorphism revealed a strong depletion of genetic diversity on a ∼ 40bp region centered on the replication initiation loci. Surprisingly, this depletion in genetic diversity is not linked to the presence of G4 motifs, nor to the association with promoters or CpG islands. In contrast, we also show that origins have experienced a rapid turnover during vertebrates evolution, since pairwise comparisons of origin maps revealed that only 4 to 24% of them are conserved between any two species.
Conclusions: This study unravels the existence of a novel genetic determinant of replication origins, whose precise functional role remains to be determined. Despite the importance of replication initiation activity for the fitness of organisms, the distribution of replication origins along vertebrate chromosomes is highly flexible.

overall_design: Short Nascent Strand sequencing of the DT40 chicken cell line

first: Marc

last: Laurent

first: Caroline

last: Brossas

first: José

last: Fernández-Justel

first: María

last: Gómez

first: Marie-Noelle

last: Prioleau

first: Laurent

last: Duret

first: Franck

last: Picard


title: Comprehensive transcriptional profiling of porcine liver aging

city: Ya'an

first: Jianning

last: Chen

state: Sichuan

address: 46, Xinkang Road

country: China

institute: Sichuan Agricultural University

summary: Aging is a major risk factor for the development of many diseases, and liver as the most important metabolic organ is significantly affected by aging. Earlier studies have shown that liver weight tends to increase and decrease with age in rodents and human, respectively. Intriguingly, the pig has a genomic structure, physiological and biochemical features similar to those of humans, and has been found to be a valuable model for studying human diseases. Moreover, the molecular mechanisms of large mammal’s liver aging in a comprehensive transcriptional level has been poorly understood. Therefore, the pig can be an ideal model animal to clearly and fully understand the molecular mechanism of human liver aging. We have identified many age-related genes in the porcine liver, GO annotation showed that up-regulated genes were mainly related to immune response, and the down-regulated genes were mainly involved in metabolism. Moreover, some lncRNAs and their target genes were also found differentially expressed during liver aging. In addition, we assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during liver aging.

overall_design: Four healthy female Yana pigs (indigenous Chinese breed) were investigated, including two young sows (180-days-old) and two old sows (8-years-old). Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during porcine liver aging process.

first: Qin

last: Zou

first: Daojun

last: Lv

first: Xuewei

last: Li

first: Yanzhi

last: Jiang


title: The trophic effect of nerve growth factor in primary cultures of rat hippocampal neurons is associated to an anti-inflammatory and immunosuppressive transcriptional program

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

institute: IRIB-CNR

summary: Nerve growth factor, the prototype of a family of neurotrophins, elicits differentiation and survival of peripheral and central neuronal cells. Although its neural mechanisms have been studied extensively, relatively little is known about the transcriptional regulation governing its effects. We have previously observed that in primary cultures of rat hippocampal neurons treatment with nerve growth factor for 72 hours increases neurite outgrowth and cell survival. To obtain a comprehensive view of the underlying transcriptional program, we performed whole-genome expression analysis by microarray technology. We identified 541 differentially expressed genes and characterized dysregulated pathways related to innate immunity: the complement system and neuro-inflammatory signaling. The exploitation of such genes and pathways may help interfering with the intracellular mechanisms involved in neuronal survival and guide novel therapeutic strategies for neurodegenerative diseases.

overall_design: Whole genome expression profiling by microarray technology was performed in HNs following treatment with vehicle (Control) or Ngf (100 ng/ml) for 72h. Total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates (derived from the same litter) for each of the two experimental conditions examined: vehicle and Ngf treated HNs. RNA integrity was confirmed by using a RNA chip and a 2100 Bioanalyzer (Agilent Technologies), with the protocol outlined by the manufacturer. Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies), following the manufacturer's protocol. Aliquots (750 ng) of Cy3-labeled cRNA targets were hybridized on 8 ×64K Whole Rat Genome Oligo expression microarrays (Agilent Technologies). Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as previously indicated (Cavallaro, 2015b). Significant changes in gene expression levels were evaluated by a Moderated T-Test followed by the Westfall-Young procedure  as a multiple testing correction. Genes with a corrected P value < 0.05 were considered as differentially expressed.

first: Barbara

last: Maino

first: Antonio

last: Spampinato

first: Cinzia

last: Severini

first: Carla

last: Petrella

first: Maria

last: Ciotti

first: Velia

last: D'Agata

first: Pietro

last: Calissano


title: Mushroom body-specific RNA sequencing to examine the role of Bap60, a core SWI/SNF subunit, in the regulation of neuronal genes.

city: London

first: Jamie

last: Kramer

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

institute: University of Western Ontario

summary: RNA sequencing was used to identify genome wide transcriptional changes occurring in the Drosophila mushroom body in juvenile and mature adult flies expressing a mushroom body-specific RNAi knockdown of Bap60. The results of this analysis suggested a role for Bap60 in the regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development.

overall_design: RNA from mushroom body nuclei was sequenced from Drosophila melanogaster expressing a mushroom body-specific RNAi knockdown of Bap60 or mCherry (control) in both juvenile (2 and 3 replicates, respectively) and mature (5 replicates each) adult flies.

first: Kevin

middle: C

last: Nixon


title: An essential mycolate remodeling program for mycobacterial adaptation in host cells

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

type: Genome binding/occupancy profiling by high throughput sequencing


title: Infection drives long-term meningeal engraftment by inflammatory monocytes that impair central nervous system immunity [II]

city: Bethesda

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Tissue-resident macrophages have an embryonic origin, but are replenished under steady state conditions in some tissues by blood monocytes that can adopt genotypic and phenotypic features of the residents. However, little is known about the residency and functional properties of infiltrating macrophages after an inflammatory challenge. The meninges of the central nervous system (CNS) are populated by a dense network of specialized macrophages that act as resident immune sentinels. Here we show that following lymphocytic choriomeningitis virus infection resident meningeal macrophages become activated by innate inflammatory cytokines, acquire viral antigen, and interact directly with infiltrating cytotoxic T lymphocytes (CTL), which leads to their depletion.  Concurrently, the meninges are heavily infiltrated by peripherally-derived inflammatory monocytes that engraft the meningeal niche and remain in situ for months after viral clearance. This engraftment leads to phenotypic and functional changes in the pool of resident meningeal macrophages that depends in part on IFNγ signaling. These changes include loss of bacterial and immunoregulatory sensors that impede subsequent CNS immune reactions.  Collectively, these data indicate that peripheral monocytes can engraft the meninges after an inflammatory challenge, imprinting the compartment with long-term defects in immune function.

overall_design: Transcript profiles for 8x20-25 separate mice representing CD206+ MHC-II+ or CD206+ MHC-II- macrophages of the meninges at Day 30 post PBS-treatment (n=4 pools of 20-25 mice) or LCMV infection (n=4 pools of 20-25 mice).

first: Rejane

last: Rua

first: Jane

middle: Y

last: Lee

first: Alexander

middle: B

last: Silva

first: Dragan

last: Maric

first: Dorian

last: McGavern


title: Human Cellular Model of Hypoxic Brain Injury of Prematurity

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane

department: Institute for Neurodegenerative Diseases

institute: UCSF

summary: Extremely premature birth is associated with an increased risk for hypoxic brain injury due to lung immaturity and this results in severe long-term neurodevelopmental impairments. The susceptible cell types in the cerebral cortex at this critical developmental time point and the molecular mechanisms underlying associated gray matter defects in premature infants are not known. Here, we used a human three-dimensional (3D) cellular system to study the effect of changes in oxygen tension on the mid-gestation human cerebral cortex. We identified specific defects in intermediate progenitors, a cortical cell type associated with the expansion of the human cerebral cortex, and show that these are related to the unfolded protein response (UPR) and cell cycle changes. Moreover, we verify these findings in human primary cortical tissue and demonstrate that a modulator of the UPR pathway can prevent the reduction in intermediate progenitors following hypoxia. We anticipate that this human cellular platform will be useful in studying other environmental and genetic factors underlying brain injury in premature infants. We investigated the transcriptional changes associated with exposure to <1% O2 by performing RNA sequencing.

overall_design: RNA-seq, 101 bp singlepaired-end reads; minimum of 40 million high quality reads per sample) at 24 and 48 hours (middle and end of <1% O2 for hypoxic condition), as well as after 72 hours of re-oxygenation at 21% O2.

first: Anca

last: Pașca

first: Qihao

last: Qi

first: Jeffrey

last: Mandell

first: A

middle: J

first: Sergiu

middle: P


title: FMR1 reactivating treatments in Fragile X iPSC-derived neural progenitors in-vitro and in-vivo

city: Jerusalem

first: Nissim

last: Benvenisty

state: Outside the United States or Canada

address: Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Fragile X syndrome (FXS) is caused primarily by a CGG repeat expansion mutation in the FMR1 gene that triggers its epigenetic silencing. In order to investigate the role of different epigenetic regulatory layers in the silencing of FMR1 expression, we tested a collection of epigenetic modulators for the ability to reactivate the FMR1 locus. While inhibitors of DNA methylatransferase induced the highest levels of FMR1 mRNA expression, a combination of a DNMT inhibitor and a novel epigenetic agent was able to potentiate the effect of reactivating treatment. To better assess the rescue effect observed following direct demethylation, we characterized the long-term and genome-wide effects of FMR1 reactivation, and established an in vivo system for FMR1 reactivating therapy analysis. Systemic treatment with a DNMT inhibitor in mice carrying transplants of differentiated FXS-iPSCs was able to robustly induce FMR1 expression in the affected tissue, which was maintained for a prolonged period of time. Finally, we show a proof-of-principle for FMR1 reactivating therapy in the context of the central nervous system.

overall_design: Gene expression analysis was performed on a total of 3 human cell lines, including Fragile X syndrome neural progenitor cells, genome edited Fragile X neural progenitor cells, and 5-aza-deoxycytidine treated Fragile X neural progenitor cells

first: Dan

last: Vershkov


title: Transcriptome analysis of ΔLMP1-MAVS transfected MARC-145 cells

city: nanjing

first: zhao

last: yongxiang

address: NO.1,Weigang, Xuanwu District of Nanjing

institute: Nanjing Agricultural University

summary: We found that fuse ΔLMP1 to MAVS could strengthen MAVS mediated inhibition of PRRSV replication in MARC-145 cells. To better understand the biological function of the fusion protein ΔLMP1-MAVS, overall gene expression of MARC-145 cells transfected with ΔLMP1-MAVS or MAVS was evaluated by mRNA-seq. The result showed that ΔLMP1-MAVS upregulated a number of genes associated with innate immune responses to viral infection, including plenty of interferon-stimulated genes. This study provides reference date to research the working mechanism of ΔLMP1-MAVS.

overall_design: MARC-145 cells were transfected with ΔLMP1-MAVS or MAVS plasmid or empty vector respectively, mRNA profiles of  the transfected cells were generated by deep sequencing at 24, 36 and 48 hours post transfection(hpt).

first: Yongxiang

last: Zhao


title: Infection drives long-term meningeal engraftment by inflammatory monocytes that impair central nervous system immunity

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

overall_design: Refer to individual Series


title: Active Mycobacterium tuberculosis regulatory networks from alveolar macrophages of in vivo mouse infection uncovered by Path-seq

status: Public on Mar 04 2019

first: Eliza

summary: Transcriptional profiling of Mycobacterium tuberculosis mRNA enriched from host-pathogen samples from in vivo alveolar macrophages (Mus musculus).

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: A mid log-phase stock of M. tuberculosis H37Rv was used to infect mice in an aerosol infection chamber. At 24 h after infection, bronchoalveolar lavage was performed on euthanized mice. Cells from BAL were filtered, spun down and resuspended in 96-well plate for antibody staining. Cell sorting was performed on a FACS Aria and the entire alveolar macrophage was resuspended in  TRIzol (Invitrogen) where total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media was also collected at 24 h as a control. Samples were processed by Path-seq, for enrichment of MTB transcripts. The sequence reads that passed quality filters were aligned to a combined M. tuberculosis and M. musuclus genome with Bowtie2 and processed using the R package DuffyNGS.

first: Nitin

middle: S

last: Baliga


title: RNA-seq for PA4595

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas aeruginosa is an important human pathogen which uses the type III secretion system 21 (T3SS) as a primary virulence factor to establish infections in humans. The results presented in this 22 report revealed that the ATP-binding protein PA4595 (named ArtR, a Regulator that is an ATP-activated 23 Repressor of T3SS) represses T3SS expression in P. aeruginosa. The expression of T3SS genes, 24 including exoS, exoY, exoT, exsCEBA and exsD-pscB-L, increased significantly when artR was 25 knockout. The effect of ArtR on ExsA is at the transcriptional level, not at the translational level. The 26 regulatory role and cytoplasm localization of ArtR suggest it belongs to the REG sub-family of 27 ATP-binding cassette (ABC) family. Purified GST-tagged ArtR showed ATPase activity in vitro. The 28 conserved aspartate residues in the dual Walker B motifs prove to be essential for the regulatory 29 function of ArtR. The regulation of T3SS by ArtR is unique, which does not involve the known 30 GacS/A-RsmY/Z-RsmA-ExsA pathway or Vfr. This is the first REG subfamily of ATP-binding 31 cassette that is reported to regulate T3SS genes in bacteria. The results specify a novel player in the 32 regulatory networks of T3SS in P. aeruginosa.

overall_design: RNA-seq for PA4595

last: Deng


title: Path-seq identifies an essential mycolate remodeling program for mycobacterial adaptation in host cells [ChIP-seq]

last: Peterson

summary: Study of the DNA binding sites of the transcriptional regulator MSMEG_0916 through chromatin immunoprecipitation couple with deep sequenicng (ChIP-seq) and induced or uninduced overexpression of MSMEG_0916 in Mycobacterium smegmatis

overall_design: Cultures of Mycobacterium smegmatis with pDTCF-MSMEG_0916 were grown in the presence or absence of anhydrotetracycline (ATc) for 4 hour and DNA-protein interactions were characterized by cross-linking 50 ml of culture with 1% formaldehyde for 30 min. Immunoprecipitated DNA was sequenced aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Calcium Toolkit genes expression in the zebrafish brain

city: Warsaw

first: Iga

last: Wasilewska

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute of Molecular and Cell Biology

summary:
Zebrafish are well suited for in vivo calcium imaging because the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK).
Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling.

overall_design: qPCR gene expression profiling. 3 different samples of adult brain RNA and 3 different samples of larvae head RNA were used in the analysis. cDNA (25 ng) was used for each reaction. Actin beta 1 (actb1), glyceraldehyde-3-phosphate dehydrogenase (gapdh), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide (yhwaz), and ribosomal protein S18 (rps18) were used as reference genes. No-templete-control samples were included. All the PCR reactions were run in the duplicates.

first: Rishikesh

middle: K

last: Gupta

first: Oksana

last: Palchevska

first: Jacek

last: Kuźnicki


title: Fission yeasts CENPA and H3K9me Chip-seq

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

summary: Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes.  Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly.  Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication.  Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences such as human alpha satellite arrays.  Such analyses suggest that properties of centromeric DNA itself may favour assembly of CENP-A rather than H3 nucleosomes.  To investigate the innate properties of centromeric DNA we have examined histone dynamics on this DNA assembled in CENP-A chromatin at endogenous centromeres and when assembled only in H3 chromatin at an ectopic location. We demonstrate that H3 occupancy on centromeric DNA is innately low while H3 turnover is high.  Moreover, even at an ectopic location centromeric DNA programs H3 deposition in S phase and its eviction during G2 when CENP-A is otherwise deposited.  G2 accumulation of RNAPII on centromeric DNA during G2 is consistent with transcription-coupled destabilisation of H3 nucleosomes to favour CENP-A deposition.

sample_organism:
Schizosaccharomyces pombe
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Schizosaccharomyces cryophilus

overall_design: ChIP-seq samples were preprared for centromeric chromatin

first: Pin

last: Tong

first: Harald

last: Berger

first: Nick

last: Toda

first: Ryan

last: Ard

first: Jesus

last: Torres-Garcia

first: Alison

last: Pidoux


title: Infection drives long-term meningeal engraftment by inflammatory monocytes that impair central nervous system immunity [I]

first: Kory

last: Johnson

overall_design: Transcript profiles for 8x20-25 separate mice representing macrophages of the meninges at Day 4 post PBS-treatment (n=4 pools of 20-25 mice) or LCMV infection (n=4 pools of 20-25 mice).

first: Rejane

last: Rua

first: Jane

last: Lee

first: Alexander

last: Silva

first: Dragan

last: Maric

first: Dorian

last: McGavern


title: RNA-Seq analysis of human keratinocytes stimulated with synthetic PSMα3

city: La Jolla

first: Michael

middle: Rey

last: Williams

address: 9452 Medical Center Drive LL1W 420C

department: Dermatology

institute: UC San Diego

summary: To determine the genes that change mRNA transcript abundance in primary human keratinocytes treated by S. aureus phenol-soluble modulins (PSM), we stimulated keratinocytes for 24h with either DMSO(-) Ctl or synthetic PSMα3 (5μg/mL).

overall_design: keratinocytes treated with either DMSO(-) Ctl or synthetic PSMα3 (5μg/mL) for 24 h

first: James

middle: A

last: Sanford


title: SNAI1 knockdown under VEGF stimulus in HUVECs

city: Xi‘an’

first: Jiaxing

last: Sun

state: Shaanxi

address: Changlexi 169#

institute: Fourth Military Medical University

summary: The goal of this study was to reveal SNAI1 function in angiogenesis. SNAI1 is up-regulated by VEGF stimulus. Using RNASeq method (single-ended 150-bp sequencing on Illumina Hi-seq 3000 instrument), we measured the transcriptional difference between siSNAI1 or NC-transfected HUVECs.

overall_design: RNA-seq of HUVECs were transfected with siSNAI1 or NC.

first: Guorui

last: Dou


title: A Syngeneic ErbB2 Mammary Cancer Model for Preclinical Immunotherapy Trials

status: Public on Mar 03 2019

city: Davis

middle: D

last: Borowsky

address: 1 Shields Ave

institute: University of California at Davis


title: Active Mycobacterium tuberculosis regulatory networks from in vitro infection of mouse macrophages uncovered by Path-seq

first: Eliza

last: Peterson

summary: Transcriptional profiling of Mycobacterium tuberculosis mRNA enriched from host-pathogen samples from in vitro bone marrow derived macrophages (Mus musculus).

overall_design: Mouse bone marrow derived macrophages (BMDMs) were infected with MTB H37Rv strain (MOI 10), followed by washing 3x with RPMI at 2 h post infection. At 2 h, 8 h, and 24 h MTB infected BMDMs were lysed with TRIzol (Invitrogen) and total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media and uninfected BMDMs were also collected at the same time points. Samples were either processed by Path-seq, RNA-seq or and profiled by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned to a combined M. tuberculosis and M. musuclus genome with Bowtie2 and processed using the R package DuffyNGS.

first: Nitin

last: Baliga


title: Oncogenic drivers in 11q13 associated with prognosis in advanced oropharyngeal carcinomas

city: Sao Paulo

first: mateus

middle: camargo

last: barros filho

state: SP

address: Tagua Street 440

country: Brazil

institute: AC Camargo Cancer Center

type: Genome variation profiling by genome tiling array


title: Risk SNPs mediated promoter-enhancer switching promotes prostate cancer progression through lncRNA PCAT19 (RNA-seq data sets)

status: Public on Mar 11 2019

city: Toronto

first: Junjie

last: Hua

address: 101 College Street

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: To determine the functional mechanisms of PCAT19-long isoform and HNRNPAB, we conducted siRNA knockdown RNA-sequencing in prostate cancer cell line V16A.

overall_design: Profiling transcriptomic changes after knockdown of PCAT19-long isoform and HNRNPAB in V16A cells.

first: Housheng

middle: H

last: He


title: Path-seq identifies essential mycolate remodeling program for mycobacterial adaptation in host cells [RNA-seq]

summary: Comparison of  transcriptional differences (RNA-seq) between induced and uninduced overexpression of MSMEG_0916 in Mycobacterium smegmatis

overall_design: Cultures of Mycobacterium smegmatis with pDTCF-MSMEG_0916 were grown in the presence or absence of anhydrotetracycline (ATc) for 4 hour and harvested for mRNA expression profiling by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Oncogenic drivers in 11q13 associated with prognosis in advanced oropharyngeal carcinomas (aCGH data set)

summary: aCGH was used to evaluate 33 OSCC aiming to unveil potential prognostic markers.

overall_design: Copy number alterations were evaluated using Agilent Human CGH 180K Oligo Microarrays array-CGH (Agilent Technologies) in 33 OSCC aiming to unveil potential prognostic markers.

first: Mateus

last: Barros-Filho

first: Fabio

last: Marchi


title: High resolution  X chromosome copy number analysis in fertile and POI females

status: Public on Mar 01 2019

city: Pittsburgh

first: Svetlana

last: Yatsenko

state: PA

address: 300 Halket St

institute: University of Pittsburgh

summary: comparison of copy number profile between health fertile females and women affected by POI

overall_design: 100 affected and 269 unaffected  individuals were studied to identify landscape and integrity of the X chromosome

first: Aleksandar

last: Rajkovic


title: Oncogenic drivers in 11q13 associated with prognosis in advanced oropharyngeal carcinomas (Expression data set)

summary: Expression microarray analyses was used to analyze 33 OSCC to unveil potential prognostic markers. A quality control filter was applied based on Feature Extraction flags (NA replacing values). Cy3/Cy5 ratios were log2 transformed

overall_design: Experiment condition, 33 OSCC samples obtained from biopsy from previous untreated patietns were laleled with Cy3 and a reference sample (pool of cell lines) was labled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 4x40k platform.


title: RNA-seq data showing the effects of rpoD mutation t1682c in Pseudomonas fluorescens

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

institute: Max Planck Institute for Evolutionary Biology

summary: We report RNA-seq data for four Pseudomonas fluorescens SBW25 types: SBW25 (wild type) and dervied types 6A4, 6B4-Cap- and 6B4-Cap+. The aim of the study is to see the effect of a mutation in rpoD (carried by 6B4) on the transcriptome.

overall_design: Method: 3x single colonies of each of SBW25, 6A4 and 6B4 were grown on KB agar, precultured in shaken KB, grown to mid-exponential phase in shaken KB flasks. Total mRNA isolated with RiboPureTM Bacteria Kit (Ambion®). Note that 6B4 was separated into Cap- and Cap+ fractions by centrifugation before RNA extraction.  Normalized mRNA-seq library preparation, followed by 100 bp single end sequencing, was performed by the Australian Genome Research Facility (Brisbane, Australia).

first: Frederic

last: Bertels

first: Gayle

last: Ferguson

first: Paul

last: Rainey


title: Functional role of CPPED1 in trophoblasts.

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

summary: Analysis of the effect of CPPED1 siRNA experiment

overall_design: RNA-seq analysis of silenced CPPED1 (n = 3) and negative control (n=3) samples

first: Ravindra

last: Daddali


title: Gene expression data from differentiated myoblastic C2C12 cells expressing constitutively active estrogen receptor α

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of estrogen in muscle, differentiated myoblastic C2C12 cells were transduced with adenoviruses expressing constitutively active estrogen receptor α mutant (Ad-caERα) or DsRed (Ad-DsRed) as a control. Microarray analysis showed that the mRNA level of nuclear receptor subfamily 4 group A member 1 (NR4A1) was upregulated by the Ad-caERα compared with the control Ad-DsRed.

overall_design: Total RNA was extracted from differentiated myoblastic C2C12 cells transduced with Ad-caERα or Ad-DsRed and used for Affymetrix microarrays analysis.

first: Saki

last: Nagai

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Rigidity and inflammatory responses of interconnected endothelial cells are stimulated by rhodocetin-αβ via the neuropilin-1-MET-axis

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary:
Using the snake venom component rhodocetin-αβ (RCαβ), we elucidated how neuropilin-1 (NRP1)-dependent signaling of the hepatocyte growth factor/scatter factor (HGF/SF) receptor, MET, modulates endothelial cell-cell contacts, cell tension, and consequently nuclear factor kappa B (NFκB)-triggered proinflammatory response.
We show that RCαβ in confluent ECs, also if exposed to fluid shear forces, induces loss of force-transmitting focal adhesions and a change of vinculin localization from cell-matrix contacts to cell-cell contacts. Together with RhoA activation, this enhances force transmission via intercellular contacts and raises cell rigidity within the EC monolayer. Presumably due to the combined effects of redirecting forces and NRP1-MET-signaling, RCαβ, in contrast to HGF, activates NFκB and thus a distinct set of genes. Transcriptome analysis revealed an RCαβ-induced activation of the intercellular adhesion molecule-1 (ICAM1), of other markers of EC activation and of several inflammatory cytokines, resulting in increased pericellular permeability and enhanced leukocyte attachment and transmigration.

overall_design: HUVECs from passage 1 were seeded on collagen I-coated plates. Fluid shear stress experiments were performed in a cone plate-based BioTechFlow system. After treatment with or without 200 nM RCαβ, statically incubated and shear-subjected cells were collected and analyzed by MFTServices. To compare the genes up- and downregulated by HGF or RCαβ, we stimulated ECs with 200 nM RCαβ or 200 ng/ml HGF under static condition for 8 hour. Cells then were collected and analyzed by MFTServices.

first: Johannes

last: Eble

first: Maryam

last: Rezaei

last: Matthes


title: DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells [ChIP-seq]

status: Public on Feb 23 2019

city: Chexbres

first: Alexandre

last: Coudray

state: Vaud

address: 11, Chemin de Baulet

department: Life Science

country: Switzerland

institute: EPFL

summary: After fertilization of the transcriptionally silent oocyte, expression from both parental chromosomes is launched through so-called zygotic genome activation (ZGA), occurring in the mouse at the 2-cell (2C) stage. Amongst the first elements to be transcribed are the Dux gene, the product of which secondarily induces a wide array of ZGA genes, and a subset of evolutionary recent LINE-1 retrotransposons, which regulate chromatin accessibility in the early embryo. The maternally-inherited factors that activate Dux and LINE-1 transcription have so far remained unknown. Mouse embryonic stem cells (mESCs) recapitulate some aspects of ZGA in culture, owing to their ability to cycle through a 2C-like stage where Dux, its target genes and LINE-1 integrants are expressed. Here we identify the paralog proteins DPPA2 and DPPA4 as necessary for activation of Dux and LINE-1 expression in mESCs. Since their encoding RNAs are maternally transmitted to the zygote, it is likely that these factors are important upstream mediators of murine ZGA.

overall_design: ChIP-sequencing analyses of ectopically expressed DPPA2 and the two isoforms of DPPA4 in mESCs: Dppa4 FL (ENSMUST00000096045) and Dppa4 short (ENSMUST00000050705).

first: Alberto

last: De Iaco


title: Macrophage polarization controlled by fibroblast crosstalk and targeted by medications in rheumatoid arthritis

city: New York

first: David

last: Kuo

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: In this study, we performed RNAseq on human macropahges following a tumor necrosis factor response with and without human fibroblasts, the representative stromal cell type in the synovial lining of joints that become activated during inflammatory arthritis. Our RNAseq analysis reveals a crosstalk pathway between macrophages and fibroblasts that emerges as a result of co-culture that we call the MTF polarization phenotype. We test multiple drugs with RA indications and candidate therapies and report that the genes that shaped by the MTF phenotype are opposed in their expression by known therapies. Our RA joint inflammation model data provides insights into the cellular crosstalk mechanisms between macrophages and fibroblasts as well additional knowledge into RA drug mechanisms of action.

overall_design:
Human CD14+ MCSF-differentiated macrophages were cultured with or without synovial fibroblasts in transwell chambers. Samples include an unstimulated condition, TNF condition (added at Day 0 and harvested at Day 1), and drug treatments including Auronfin (Aur), Dexamethasone (Dex), Tofacatinib (Tofa), Hydroxychloroquine (Hydrox), Methotrexate (Meth), Diclofenac (Diclo), Sulfasalazine (Sulf), AG ( AG 1478), Naproxen (Naprox), TNF was added at Day 0, macrophages were harvested at Day 1. Macrophage RNA was purified using RNeasy mini kit (Qiagen). Tru-seq sample preparation kits (Illumina) were used to purify poly-A transcripts and generate libraries with multiplexed barcode adaptors. All samples passed quality control on a Bioanalyzer 2100 (Agilent). Single-end reads (50 x 2 cycles per sample) were obtained on an Illumina HiSeq 4000. The STAR program was used to align the reads to the UCSC Hg19 human reference genome and reads were counted by the HTSeq program.

Additional coculture samples [GSM2527917-GSM2527920] include replicates of the previous study [GSE57723] following the treatment protocols described in GSE57723 (PMID: 25057003). The major distinction of these samples and the drug samples is the TNF condition is over 2 days and the RNA-seq libraries were paired end.
The 'coculture_htseq_counts.txt' contains processed data for the additional samples.

first: Laura

last: Donlin


title: Differential gene expression in strital and cerebellar tissues from wildtype C57Bl/6 and Thap1 conditional knockout mice

city: Chicago

first: Natalie

last: Frederick

address: 303 East Chicago Ave, Ward 10-321

institute: Northwestern University

summary: RNA-seq study comparing gene expression in wildtype and nervous system specific Thap1  knock out mice at 6 months of age in striatal and cerebellar tissues.

overall_design: RNA-Seq was performed on RNA isolated from the striatum and cerebellum of Thap1 conditional knockout mice and wildtype littermate controls.

first: Puneet

last: Opal


title: Prunus avium transcriptome profiling

status: Public on Feb 26 2019

city: Santiago

first: Jonathan

last: Maldonado

address: Av. Santa Rosa 1131, La Pintana

country: Chile

institute: Universidad de Chile

summary: Profiling of fruit and leaves transcriptomes of cherry cultivars

overall_design: Sequencing of total RNA from different cultivars of Prunus avium and RNAseq against CDSs of public genome.

first: Silva

last: Herman


title: Effects of 1,25-dihydroxyvitamin D (1,25D) on global gene expression of human fibroblasts with (CO) or without (MUT) a functional VDR

status: Public on Feb 28 2019

first: Bruno

last: Ferraz-de-Souza

address: Av Dr Arnaldo, 455 sala 4344

department: Endocrinology

institute: Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo

summary:
Human skin fibroblasts from an individual with hereditary vitamin D-resistant rickets bearing a homozygous p.Arg30* VDR mutation [Damiani et al., Osteoporos Int 2015; 26(6):1819-23] and from an age/sex-matched control were obtained from 4-mm punch biopsies of the forearm skin, after institutional board approval and with informed consent. Skin explants were fragmented in 6-well tissue culture plates and covered in complete AmnioMAX™ C-100 medium until attachment to surface; after approximately 12 days fibroblasts grown out of explants covered well surfaces completely. Secondary fibroblast cultures were maintained in high glucose DMEM supplemented with 10% FBS and 1% P/S. Fibroblasts were used for experiments between passages five to fifteen.
Global gene expression of CO and MUT fibroblasts in response to 1,25D or ethanol vehicle (Veh) was analysed using microarrays. Six independent biological replicates were performed for each experimental condition: CO Veh, CO 1,25D, MUT Veh and MUT 1,25D. Cells were grown in 6-well plates and treated with 10 nM 1,25D or ethanol (1 ul/ml of medium) for 24 hours before RNA extraction. Based on quality control of extracted RNA performed with the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), four samples of each condition were chosen for microarray gene expression analysis, all with RNA integrity number above 8.00. Samples were processed according to manufacturer’s instructions, starting with 200 ng total RNA. Altogether, sixteen samples of labeled fragmented cDNA were hybridized to GeneChip Human Gene 2.0 ST Arrays (Affymetrix). Array data was analysed using Partek Genomics Suite, and based on quality control one array (MUT_Veh_4) was excluded. A Benjamini-Hochberg-corrected p-value cut-off of 0.05 was used for selecting significant differentially expressed genes.

overall_design: Four biological replicates of control fibroblasts treated with vehicle (arrays CO_Veh 1 to 4), four biological replicates of control fibroblasts treated with 1,25D (arrays CO_1,25D 1 to 4), three biological replicates of mutant p.Arg30* VDR fibroblasts treated with vehicle (arrays MUT_Veh 1 to 3) and four biological replicates of mutant p.Arg30* VDR fibroblasts treated with 1,25D (arrays MUT_1,25D 1 to 4)

first: Pedro

middle: L

last: Costa

first: Maria

last: Katayama

last: Folgueira


title: Genome-wide transcriptional response to random aneuploidy in human cells

city: Singapore

first: YANG

last: SHEN

address: Genome Institute of Singapore (A*STAR) 60 Biopolis Street, #02-01 Genome

country: Singapore

institute: Genome Institute of Singapore

summary: Previous studies on transcriptional response to aneuploidy have focused on comparing model cell lines harbouring defined aneuploidy (specific chromosomes) with their parental diploid cell lines. However, the majority of tumours are composed of cancer cells with complex karyotypes (diverse chromosome assortment). Despite this fact, proven functions of random aneuploidies in promoting tumourigenesis are lacking. This prompted us to investigate the transcriptional response to heterogenous cell populations with discernible random aneuploidies.

overall_design: mRNA expression analysis of mild and severe forms of aneuploid RPE-1 cells induced by microtubule poison nocodazole (Noc) treatment for 8h and 16h, respectively, compared to diploid RPE-1 cells. Two biological replicates were performed.

first: Karen

last: Crasta

first: Yang

last: Shen


title: DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells

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

overall_design: Refer to individual Series


title: Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

status: Public on Feb 22 2019

city: BOSTON

first: Henry

middle: Hung-Yi

last: Lee

state: Massachusetts

address: 77 AVENUE LOUIS PASTEUR, NRB 233

department: Genetics

institute: Harvard Medical School

summary: RNA-seq analysis to support CRISPRi functional genomics screening.

sample_organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

overall_design: Analysis of Vibrio natriegens ATCC 14048 growth at 37C in rich media (LB3) and minimal media with glucose (M9).


title: Genome-wide identification and analysis of A-to-I RNA editing events in the malignantly transformed cell lines from BEP2D induced by α-particles radiation

status: Public on Feb 20 2019

city: Beijing

first: Chenghui

last: Zhao

address: Haidian Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Adenosine (A) to inosine (I) RNA editing is the most prevalent RNA editing mechanism in humans and play critical roles in tumorigenesis. However, the effects of radiation on RNA editing and the mechanisms of radiation-induced cancer were poorly understood. Here, we analyzed human bronchial epithelial BEP2D cells and radiation-induced malignantly transformed cells with next generation sequencing. By performing an integrated analysis of A-to-I RNA editing, we found that genome-encoded single-nucleotide polymorphisms (SNPs) might induce the downregulation of ADAR2 enzymes, and further caused the abnormal occurrence of RNA editing in malignantly transformed cells. These editing events were significantly enriched in differentially expressed genes between normal cells and cancer cells. In addition, oncogenes CTNNB1 and FN1 were highly edited and significantly overexpressed in cancer cells, thus may be responsible for the lung cancer progression. Our work provides a systematic analysis of RNA editing from lung tumor specimens with high-throughput RNA sequencing and DNA sequencing. Moreover, these results demonstrate further evidence for RNA editing as an important tumorigenesis mechanism.

overall_design: we analyzed human bronchial epithelial BEP2D cells and radiation-induced malignantly transformed cells with next generation sequencing. Then we identified RNA editome by three identification method. We integrated these RNA editome to eight stages and record their position, reference, alter, strand, editing level.

first: Qiaowei

last: Liu

first: Hebing

last: Chen

first: Hao

last: Li


title: Inhibition of TAZ contributes radiation-induced senescence and growth arrest in glioma cells

status: Public on Feb 25 2019

city: Hershey

first: Wei

address: 500 University Drive, PO Box 850, MC H085

institute: Penn State Hershey College of Medicine

summary: Glioblastoma (GBM) is the most aggressive brain tumor and resistant to current available therapeutics, such as radiation. To improve the clinical efficacy, it is important to understand the cellular mechanisms underlying tumor responses to radiation. Here, we investigated long-term cellular responses of human GBM cells to ionizing radiation. Comparing to the initial response within 12 hours, gene expression modulation at 7 days after radiation is markedly different. While genes related to cell cycle arrest and DNA damage responses are mostly modulated at the initial stage; immune-related genes are specifically affected as the long-term effect. This later response is associated with increased cellular senescence and inhibition of transcriptional coactivator with PDZ-binding motif (TAZ). Mechanistically, TAZ inhibition does not depend on the canonical Hippo pathway, but relies on enhanced degradation mediated by the β-catenin destruction complex in the Wnt pathway. We further showed that depletion of TAZ by RNAi promotes radiation-induced senescence and growth arrest. Pharmacological activation of the β-catenin destruction complex is able to promote radiation-induced TAZ inhibition and growth arrest in these tumor cells. The correlation between senescence and reduced expression of YAP as well as β-catenin also occurs in human gliomas treated by radiation. Collectively, these findings suggested that inhibition of TAZ is involved in radiation-induced senescence and might benefit GBM radiotherapy.

overall_design: Examination of gene expression in a cell line with or without irradiation at two different time points. 4 samples are analyzed. Each sample has duplicates.

first: Lei

last: Zhang

first: Fang-Ling

last: Cheng

first: Yiju

last: Wei

first: Lijun

first: Dong-Sheng

last: Guo

first: Bao-Feng

last: Wang


title: Differential YAP expression in glioma cells induces cell competition and promotes tumorigenesis

summary: Intratumor heterogeneity associates with cancer progression and may account for a substantial portion of therapeutic resistance. Although extensive studies have focused on the origin of the heterogeneity, biological interactions between heterogeneous malignant cells within a tumor are largely unexplored. Glioblastoma (GBM) is the most aggressive primary brain tumor. Here, we found that the expression of Yes-associated protein (YAP) is intratumorally heterogeneous in GBM. In a xenograft mouse model, differential YAP expression in glioma cells promotes tumorigenesis and leads to clonal dominance by cells expressing more YAP. Such clonal dominance also occurs in vitro when cells reach confluence in the two-dimensional culture condition or grow into tumor spheroids. During this process, growth of the dominant cell population is enhanced. In tumor spheroid, such enhanced growth is accompanied by increased apoptosis in cells expressing less YAP. The cellular interaction during clonal dominance appears to be reminiscent of cell competition. RNA-seq analysis suggested that the interaction induces expression of tumorigenic genes, which may contribute to the enhanced tumor growth. These results suggested that tumorigenesis benefits from competitive interactions between heterogeneous tumor cells.

overall_design: Examination of gene expression in cell lines growing in different tumor spheroids containing two different groups of cells. 8 samples are analyzed without duplicates.

first: Zhijun

first: Patricia

last: Yee

first: Zhenqiu

first: Yuka

middle: I

last: Kawasawa


title: The ALK downregulated target gene HBP1 and repressor of MYCN activity as synergistic target for combined PI3K/HDAC inhibition [microarray]

status: Public on Feb 14 2019

city: Ghent

first: Shana

last: Claeys

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics Ghent

summary: ALK mutations occur in 10% of primary neuroblastoma and represent a major target for precision treatment. In combination with MYCN amplification, ALK mutations infer an ultra-high-risk phenotype with very poor prognosis. To anticipate to future precision drugging, a deeper understanding of the molecular consequences of constitutive ALK signaling and its relationship to MYCN activity in this aggressive pediatric tumor, will be essential to understand treatment responses and failure as well as to ensure improved design of drugging combinations. We show that mutant ALK downregulates the HMG-box transcription factor 1 (HBP1) through the PI3K-AKT-FOXO3a signaling axis. Interestingly, we also demonstrate that HBP1 is under control of MYCN, through negative regulation of the miR-17~92 cluster. Moreover, modulation of HBP1 in neuroblastoma negatively affect MYCN activity, including alleviating MYCN/PRC2 controlled gene repression. Combined targeting of PI3K and MYCN signaling induced strong synergistic blocking of tumor growth, thus offering potential for targeted therapeutic interventions.

overall_design: Gene expression was measured in NGP HBP1 neuroblastoma cells upon lentiviral transduction with an HBP1 overexpression construct. This was performed for 2 biological replicates.

first: Katleen

last: De Preter

first: Frank

last: Speleman


title: The ALK downregulated target gene HBP1 and repressor of MYCN activity as synergistic target for combined PI3K/HDAC inhibition [RNA-Seq]

overall_design: poly-A RNA sequencing was performed after treatment of NB-1 cells with DMSO, 0.5 μM BEZ-235, 0.5 μM SAHA or the combination for 48h . This was performed for 3 biological replicates.


title: Heterochromatin drives organization of conventional and inverted nuclei

city: Cambridge

first: Martin

middle: Jin-teng

last: Falk

state: MA

address: 77 Massachusetts Avenue

department: Physics

institute: MIT

summary: The mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer shell. This inverted architecture likely converts rod nuclei into microlenses to facilitate nocturnal vision, and may relate to the absence of particular proteins that tether heterochromatin to the lamina. However, both the mechanism of inversion and the role of interactions between different types of chromatin and the lamina in nuclear organization remain unknown. To elucidate this mechanism we performed Hi-C and microscopy on cells with inverted nuclei and their conventional counterparts. Strikingly, despite the inversion evident in microscopy, both types of nuclei display similar Hi-C maps. To resolve this paradox we developed a polymer model of chromosomes and found a universal mechanism that reconciles Hi-C and microscopy for both inverted and conventional nuclei. Based solely on attraction between heterochromatic regions, this mechanism is sufficient to drive phase separation of euchromatin and heterochromatin and faithfully reproduces the 3D organization of inverted nuclei. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. To further test our models, we eliminated lamina interactions in models of conventional nuclei and found that this triggers a spontaneous process of inversion that qualitatively reproduces the pathway of morphological changes during nuclear inversion in vivo. Together, our experiments and modeling suggest that interactions among heterochromatic regions are central to phase separation of the active and inactive genome in inverted and conventional nuclei, while interactions with the lamina are essential for building the conventional architecture from these segregated phases. Ultimately our data suggest that an inverted organization constitutes the default state of nuclear architecture.

overall_design: This submission contains experiments on wildtype thymocytes (WT_thym), Lbr-/- tymocytes (LBR_thym), rods (rod) and non-rod retinal neurons (neurons) mice - 2 biological replicates of Hi-C in all four cell types.

first: Yana

last: Feodorova

first: Natasha

last: Naumova

first: Maxim

last: Imakaev

first: Bryan

last: Lajoie

first: Heinrich

last: Leonhardt

first: Boris

last: Joffe

first: Job

last: Dekker

first: Fudenberg

last: Geoffrey

first: Irina

last: Solovei

first: Mirny

last: Leonid


title: Japanese quail embryonic skin samples

city: Los Angeles

first: Masafumi

last: Inaba

state: CA

address: 2011 Zonal Ave.

department: Pathology

institute: University of Southern California

summary: To understand molecular mechanism of stripe patterning in the embryonic skin of Japanese quail, we compared gene expression profile between black stripe and yelllow stripe by using RNA seq method. Most of differential expression genes were known pigmentation-related genes, but some are unknown role in pigment pattern formation.

overall_design: Black and yellow stripes areas were dissected form E7 Japanese quail. Each sample (Black1, 2, Yellow1, 2) were from 4 embryos. Total RNA were prepared by Trizol. RNA seq. was done by using Illumina NextSeq 500.

first: Ya-Chen

last: Liang


title: DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells [RNA-seq]

first: Alexandre

last: Coudray

overall_design: RNA sequencing analysis for mESC depleted of endogenous DPPA2 or DPPA4, and DPPA4 KO cells overexpressing ectopically full-length DPPA4 (ENSMUST00000096045) or a truncated version of the protein (ENSMUST00000050705).

first: Alberto

last: De Iaco


title: Whole-transcriptome profiling of murine steady state CD69+ and CD69- memory CD8+ T cells from the bone marrow [expression microarray]

status: Public on Feb 11 2019

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To understand the tissue-resident features of memory CD8+ T cell subpopulations isolated from the bone marrow according to the tissue retention marker CD69, we compared the global gene expression of ex vivo isolated CD69+ and CD69- bone marrow memory CD8+ T cells.

overall_design: Single cell suspensions were prepared from bone marrow of 8-week old untreated C57BL/L male mice. CD8+ T cells were enriched with anti-CD8a microbeads and the CD69+ and CD69- subpopulations of CD3+CD8+CD44+ memory cells were then FACS purified. Total RNA of  isolated cells was extracted using a NucleoSpin RNA XS Kit (Macherey-Nagel) according to the manufacturer’s recommendations. Gene expression was analyzed using MG_U430_2 GeneChips (Affymetrix), according to the manufacturer’s recommendations. The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The microarray analysis of gene expression was performed in house at the DRFZ as described before. Gene expression was quantified by RMA using the affy R algoroithm.

first: Francesco

last: Siracusa

first: Mairi

last: McGrath

first: Özen

last: Sercan-Alp

first: Anna

last: Rao

first: Weijie

last: Du

first: Carla

last: Cendón

first: Hyun-Dong

last: Chang

first: Gitta

last: Heinz

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Radbruch

first: Jun

last: Dong


title: Identification of cell cycle-related genes up-regulated during the G2-phase in Giardia lamblia

city: Seoul

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

country: South Korea

institute: Yonsei University

summary: To identify the component(s) involved in cell cycle control in the protozoan Giardia lamblia, cells arrested at the G1- or G2-phase by treatment with nocodazole and aphidicolin were prepared from the synchronized cell cultures. RNA-sequencing analysis of the two stages of Giardia cell cycle identified several cell cycle genes that were up-regulated at the G2-phase. This result indicates that the cell cycle machinery operates in this protozoan, one of the earliest diverging eukaryotic lineages.

overall_design: mRNA expression profiles of the arrested Giardia trophozoites at G1- and G2-phase by treatment with nocodazole and aphidicolin, using Illumina Hi-seq 4000.

first: Soon-Jung

last: Park


title: The ion channels and transporters gene expression profile analysis indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma.

status: Public on Feb 08 2019

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

country: Italy

institute: University of Firenze

summary: Determination of the ion channel and transporters gene expression profile of Follicular Lymphoma (FL). We have compared it with that of the relapsed follicular pymphomas and with that of the more aggressive Diffuse Large B Cell Lymphoma (DLBCL).

overall_design: Gene expression of primary lymphoma samples. It has been compared with that of a pool of lymphnodes from healthy donors of both sex.

last: Magi

first: Marika

last: Masselli

first: Cesare

last: Sala

first: Angela

last: Guerriero

first: Pasquale

last: Laise

first: Benedetta

last: Puccini

first: Luigi

last: Rigacci

last: Breschi

first: Olivia

last: Crociani

first: Serena

last: Pillozzi


title: The transcriptional profile of 786O cells with PLEKHO1 knockdown

status: Public on Feb 09 2019

city: Shenyang

first: Zi

last: Yu

state: Liaoning

address: Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: China Medical University

summary: To explore the pathway through which PLEKHO1 functioned, we silenced PLEKHO1 and performed the micro-array analysis in 786-O cells.

overall_design: 786O cells were transfected with lentivirus with shRNAs (negative control or shRNA targeting PLEKHO1). All of these samples were prepared in three replicates.

first: Yu

last: Zeng


title: An interferon-like small chemical compound CDM-3008 suppresses hepatitis B virus through induction of interferon-stimulated genes

status: Public on Feb 06 2019

city: Wako-shi

first: Yutaka

last: Furutani

address: 2-1 Hirosawa

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Oral administration of nucleotide analogues and injection of interferon-alpha (IFNalpha) are used to achieve immediate suppression in replication of hepatitis B virus (HBV).  Nucleotide analogs and IFNalpha inhibit viral polymerase activity and cause long-term eradication of the virus at least in part through removing covalently closed circular DNA (cccDNA) via induction of the APOBEC3 deaminases family of molecules, respectively.  This study aimed to explore whether the orally administrable low molecular weight agent CDM-3008 (RO8191), which mimics IFNalpha through the binding to IFNalpha receptor 2 (IFNAR2) and the activation of the JAK/STAT pathway, can suppress HBV replication and reduce cccDNA levels.  In primary cultured human hepatocytes, HBV DNA levels as well as cccDNA levels were decreased after CDM-3008-treatment in a dose-dependent manner with a half-maximal inhibitory concentration (IC50) value of 0.1 micro M, and this was accompanied by significant reductions in both HBeAg and HBsAg levels in the cell culture medium.  Using a microarray we comprehensively analyzed and compared changes in gene (mRNA) expression in CDM-3008- and IFNalpha-treated primary cultured human hepatocytes.  As reported previously, CDM-3008 mimicked the induction of　molecules that participate in the interferon signaling pathway.  OAS1 and ISG20 mRNA expression was similarly enhanced by both CDM-3008 and IFNalpha.  Thus, CDM-3008 could suppress pgRNA expression to show anti-HBV activity.  APOBEC3F and 3G mRNA expression was induced by CDM-3008 and IFNalpha treatment suggesting that cccDNA could be degraded through induced APOBEC3 family proteins.  Finally, we identified the genes whose expression was specifically enhanced in CDM-3008-treated cells compared to IFNalpha-treated cells.  The expression of SOCS1, SOCS2, SOCS3, and CISH, which inhibit STAT activation, was enhanced in CDM-3008-treated cells suggesting that a feedback inhibition of the JAK/STAT pathway was enhanced in CDM-3008-treated cells compared to IFNalpha-treated cells.  In addition, CDM-3008 showed an additive effect with entecavir on inhibition of HBV replication.  In summary, CDM-3008 showed anti-HBV activity through activation of the JAK/STAT pathway, inducing the expression of interferon-stimulated genes (ISGs), with greater feedback inhibition than IFNalpha.

overall_design: Overall 24 samples were analyzed.  PXB cells were PXB cells cultured in 24-well plates were not infected or were infected with 3 genome equivalents per cell of HBV C_AT.  After 30 days of infection, the infected cells were treated with DMSO, 30 microM CDM-3008 and 10 ng/ml pegylated IFNalpha2a for 4 and 8 h (n=3).  The non-infected cells were treated with DMSO for 4 and 8 h (n=3).

first: Xian-Yang

last: Qin

first: Harukazu

last: Suzuki

first: Soichi

last: Kojima


title: quanTIseq: quantifying immune contexture of human tumors

city: Innsbruck

first: Francesca

last: Finotello

address: Innrain 80-82

department: Division of Bioinformatics

country: Austria

institute: Biocenter, Medical University of Innsbruck

summary: We introduce quanTIseq, a method to quantify the tumor immune contexture, determined by the type and density of tumor-infiltrating immune cells. quanTIseq is based on a novel deconvolution algorithm for RNA sequencing data that was validated with independent data sets. Complementing the deconvolution output with image data from tissue slides enables in silico multiplexed immunodetection and provides an efficient method for the immunophenotyping of a large number of tumor samples.

overall_design: Blood-derived immune-cell mixtures from 9 healthy donors

first: Zlatko

last: Trajanoski


title: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence [RNA-seq]

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

summary: Cellular senescence is a state of stable proliferative arrest induced by stress and is associated with a pro-inflammatory program. Senescent cells have anti-tumorigenic properties, however, their accumulation during aging contributes to chronic inflammation and age-related diseases. While senescence is associated with profound alterations of the epigenome, a systematic view of epigenetic factors in regulating senescence is lacking. Here, we curated a library of short hairpin RNAs for targeted silencing of all known epigenetic factors and performed a high-throughput loss-of-function screen to identify epigenetic proteins whose downregulation can delay replicative senescence of primary human cells. This screen identified multiple new players regulating senescence, including the histone acetyltransferase p300 that was found to be a primary driver of the senescent phenotype.  p300, but not the paralogous CBP, induces a dynamic hyper-acetylated chromatin state in senescence and promotes the formation of active enhancer elements in the non-coding genome, leading to a senescence-specific gene expression program.  Our work illustrates a causal role of histone acetyltransferases and acetylation in senescence, and suggests p300 as a potential therapeutic target for senescence and age-related diseases.

overall_design:
Includes two replicates each of proliferating and senescent IMR90 fibroblasts

RNA-seq was performed in IMR90 fibroblasts with either an shRNA knockdown of histone acetyltransferase CBP (two replicates) or with a control luciferase vector (one replicate)

first: Payel

last: Sen

first: Yemin

last: Lan

first: Catherine

last: Li

first: Simone

last: Sidoli

first: Greg

first: Adam

last: Field

first: Zhixun

last: Dou

first: Brian

last: Frederick

first: Qijun

last: Chen

first: Benjamin

last: Garcia

first: Weiwei

last: Dang

first: F

last: Johnson

first: Peter

last: Adams

first: David

middle: C

last: Schultz

first: Shelley

last: Berger


title: The ALK downregulated target gene HBP1 and repressor of MYCN activity as synergistic target for combined PI3K/HDAC inhibition

first: Shana

last: Claeys

overall_design: Refer to individual Series


title: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence

first: Gregory


title: Host transcriptome sequencing of FACS-sorted human induced pluripotent stem cell-derived brain endothelial cells infected with Neisseria meningitidis

status: Public on Feb 13 2019

city: Cologne

first: Till

middle: David

last: Sauerwein

address: Gleueler Str. 60

department: Data Science and Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: This study investigates host transcriptome changes of infected human iPS-derived brain endothelial cells in response to prolonged Nm infection (24h)

sample_organism:
Homo sapiens
Neisseria meningitidis MC58

overall_design: Infected cells were sorted and RNA was extracted. mRNA-Enriched Poly(A)-Tailed RNA was generated. Each cDNA library was then sequenced by Illumina to ~25-30 million reads.

first: Sara

middle: M

last: Gomes

first: Brandon

last: Kim

first: Antje

last: Menzel

first: Marco

last: Metzger

first: Alexandra

last: Unkmeir

first: Konrad

middle: U

last: Förstner

first: Alexander

last: Westermann


title: CD69+ memory T lymphocytes of the bone marrow and spleen express the signature transcripts of tissue-resident memory T lymphocytes

first: Pawel

last: Durek

summary: To understand tissue resident features of memory CD4+ and CD8+ T lymphocytes of the bone marrow and/or spleen according to expressing or not the tissue retention marker CD69, we performed whole transcriptome profiling of ex vivo antigen-specific CD69+ and CD69- memory CD4+ T cells isolated from bone marrow and spleen, and ex vivo CD69+ and CD69- memory CD8+ T cells isolated from bone marrow.

overall_design: For CD4 analysis, 8-week-old C57BL/6 mice were primed at day 0 with LCMV.GP61-80-NP-MSA + poly(I:C) and immunized again at day 14 with LCMV.GP61-80 + poly(I:C). Sixty days after the last immunization mice were sacrificed and LCMV.GP66–77-specific CD69+ and CD69- memory CD4+ T cells were isolated from BM and spleen by FACS. The whole transcriptome profiling of purified cells was performed by RNA-seq. For CD8 analysis, single cell suspensions were prepared from bone marrow of 8-week old untreated C57BL/6 male mice. CD8+ T cells were pre-enriched with anti-CD8a microbeads and the CD69+ and CD69- subpopulations of memory CD8+ T cells were then FACS purified. The whole transcriptome profiling of sorted cells was analyzed by microarray analysis.


title: Whole-transcriptome profiling of LCMV.GP66-77 specific CD4 T cells isolated from bone marrow (BM) and spleen, 60 days after last immunization [RNA-seq]

summary: To udnderstand the tissue-resident features of antigen-specific memory T cells of the bone marrow and spleen, we performed RNA-Seq and compared expression levels of genes of resting LCMV.GP66-77 specific CD4 T cells isolated from bone marrow (BM) and spleen of LCMV.GP61-80 primed C57BL/6 mice.

overall_design: C57BL/6 mice were primed at day 0 with LCMV.GP61-80-NP-MSA + poly(I:C) and immunized again at day 14 with LCMV.GP61-80 + poly(I:C). Sixty days after the last immunization mice were sacrificed and LCMV.GP66–77-specific CD69+ and CD69- memory CD4 T cells were isolated from BM and spleen.

first: Francesco

last: Siracusa

first: Mairi

last: McGrath

first: Özen

last: Sercan-Alp

first: Anna

last: Rao

first: Weijie

last: Du

first: Carla

last: Cendón

first: Hyun-Dong

last: Chang

first: Gitta

last: Heinz

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Radbruch

first: Jun

last: Dong


title: Defining genes in the Caulobacter crescentus SpdR regulon

status: Public on Jan 30 2019

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We measured steady-state transcript levels in 1) wild-type C. crescentus, 2) an spdR response regulator deletion strain (ΔspdR), and an spdR phosphomimic strain (SpdR(D64E))

overall_design: Caulobacter crescentus wild type strain CB15, ΔspdR and spdR(D64E) strains were grown to mid log phase (OD600 ~0.3) in M2 defined medium containing 0.15% xylose. Cells were rapidly pelleted and resuspended in Trizol for RNA purification and subsequent RNA sequencing.

first: Leila

last: Reyes-Ruiz

first: Aretha

last: Fiebig


title: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence [PRO-seq]

first: Gregory

last: Donahue

overall_design: Includes a single replicate each of precision run-on sequencing (PRO-seq) in proliferating (control) and replicative senescent IMR90 fibroblasts

first: Payel

last: Sen

first: Yemin

last: Lan

first: Catherine

last: Li

first: Simone

last: Sidoli

first: Greg

first: Adam

last: Field

first: Zhixun

last: Dou

first: Brian

last: Frederick

first: Qijun

last: Chen

first: Benjamin

last: Garcia

first: Weiwei

last: Dang

first: F

middle: B

last: Johnson

first: Peter

last: Adams

first: David

last: Schultz

first: Shelley

last: Berger


title: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence [DNA-seq]

overall_design: This is a short hairpin RNA screen designed to identify epigenetic regulator genes which limit lifespan and promote replicative senescence in fibroblasts. It operates on the principle that a cell infected with a lentiviral vector expressing an shRNA targeting such a gene should exhibit prolonged lifespan and delayed senescence, outcompeting other cells in a serially passaged culture. Individual plasmids for five short hairpin RNAs per target gene (3,455 hairpins representing 717 epigenetic regulator targets) were randomly assigned to five initial pools denoted A, B, C, D, or E. Each pool included additional control hairpins verified to accelerate (lamin B1) or delay (p53) senescence, as well as a non-targeting control hairpin (NTC). Lentiviral supernatants were generated from these pools and combined into all possible pairwise combinations (AB, AC, AD, etc) to form 10 paired pools that were used to infect 10 plates of IMR90 fibroblasts. Each plate was passaged out, and cells were removed and lysed at PD40 (proliferating control), PD45, PD50, PD55, and PD60 (senescence). Cell lysate from the five time-points was tested for the presence of shRNAs by high-throughput sequencing of genomic DNA to detect the expressing plasmid. Each initial pool (and each plasmid) is thus represented four times in the paired pool strategy. The data were sequenced paired-end over two lanes per sample, resulting in four FASTQ files per sample.


title: PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) analysis to detect RNA-RNA interaction at poly(A) site region

status: Public on Jan 22 2019

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

country: China

institute: sysu

summary: In an attempt to discover potential RNA-RNA interactions in mRNA 3’ processing regulation, we developed PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) method, which combines  reported CLASH and poly(A) site sequencing protocols. Briefly, HeLa cells were treated with AMT, or without AMT as control, and irradiated at 365 nm for crosslinking. Following nuclear RNA fragmentation and purification, the potential proximate RNAs/PASs were ligated on the oligo d(T)25 beads, hybrids were reverse crosslinked and amplified with the QuantSeq Rev 3' mRNA sequencing library prep kit (Lexogen, Cat. 016.24) and sequenced with Hiseq, producing 150 bp paired end reads.

overall_design: For each sample (AMT treatment or without treatment), we have 2 biological replicates, in total there are 4 samples. Potential RNA-RNA interactions is supposed to be enriched in AMT treated samples

first: Junjie

last: Shi

first: Yanhui

last: Deng

first: Shanshan

last: Huang

first: Chengguo

last: Yao


title: Identification of Biomarkers of Vaccine Reactogenicity

status: Public on Jan 31 2019

city: London

first: Deniz

last: Cizmeci

address: Imperial College London

institute: Imperial College London

summary: Systems vaccinology approaches have been used to successfully define early signatures of the vaccine-induced immune response. However, the possibility that transcriptomics can also predict vaccine reactogenicity has not been fully explored. We have compared four licensed vaccines that have a demonstrated safety profile, as well as three agonists of TLRs that have a known inflammatory potential, to elucidate the transcriptomic profile of an acceptable response to a vaccination versus those which push the inflammatory envelope. In mice, we looked at the transcriptomic changes in the injected muscle, the lymph node that drained the muscle and the PBMC isolated from the circulating blood from the very early timepoint of 4 hours to over the period of one week. A detailed examination and comparative analysis of the transcriptome from each of these tissues, at all the timepoints of 4, 8, 24, 48, 72 and 168 hr and with these eight different vaccines, TLR or saline control injections, revealed a set of novel biomarkers that are reflective of inflammation after vaccination. These biomarkers are easily sampled and readily measurable in the peripheral blood, providing a useful tool to predict levels of reactogenicity, as a way to select candidates with acceptable immunogenicity and safety profiles.

overall_design: High-quality RNA samples isolated from muscle tissue excised around the injection site, the draining medial iliac lymph nodes (MLN) and total PBMCs of mice at 4, 8, 24, 48, 72, 168 hours after the vaccination were subjected to genome-wide transcriptome analysis.

first: Paul

middle: F

last: McKay


title: mRNA polyadenylation profile analysis in control and U1 AMO treated HeLa cells

summary: To globally assess the effect of polyadenylation site (PAS) usage upon functional knockdown of U1 snRNP, we carried out PAS-seq analysis with control and U1 AMO-treated HeLa cells using the QuantSeq Rev 3' mRNA sequencing library prep kit (Cat. 016-24).

overall_design: For each sample (U1 ASO or control ASO treatment), we have 2 biological replicates in total we have 4 samples. Significant PAS profile change is expected to be detected between U1 and control samples.