title: Zscan10 suppresses osteoclastgenesis by regulating expression of osteoclast differentiation inhibitory factors

status: Public on Mar 25 2019

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: Zinc finger and SCAN domain containing 10 (Zscan10) was identified as a novel transcription factor in osteoclast differentiation by our previous study. However, the biological functions of Zscan10 have not been fully understood except its role in maintenance of genome stability and pluripotency in embryonic stem cells. Therefore, the purpose of this study is clarification of Zscan10 function in somatic cells, especially during osteoclast differentiation. First, Zscan10 KO RAW264 (KO) cells were established using CRISPR/Cas9 system and single cell sorting. Then, Control (Ctrl) and KO cells were differentiated into osteoclast by RANKL stimulation. As a result, TRAP activity and expression levels of differentiation marker genes, such as Nfatc1, were significantly increased and the expression of inhibitory factors, such as Irf8, was decreased in KO cells as compared to Ctrl cells. These results suggested that Zscan10 might regulate transcription of the genes which negatively control osteoclastogenesis. To understand the transcriptomes controlled by Zscan10, RNA-seq was performed and the stringent analyses identified significantly down-regulated Haptoglobin (Hp) in KO cells. Additionally, Zscan10 binding sequence was located near the genomic region of Hp gene locus. ChIP against Zscan10 followed by qPCR for the region revealed that Zscan10 binds to the region located near Hp gene locus and transcript start site, suggesting that Zscan10 may regulate transcription of Hp. Next, to examine the effect of Hp under Zscan10 mediated osteoclastogenesis, KO cells were treated with recombinant Hp (rHp). As a result, Hp treatment could suppress the elevated TRAP activity of KO cells without affecting cell viability. Furthermore, Hp KO mice exhibit decreased bone mass and increased osteoclast number, and Hp has been reported to be involved in suppression of osteoclastogenesis. Also, In hemolytic disease, Hp had been decreased and also bone density. These facts suggested that Zscan10 negatively regulates osteoclast differentiation through transcription of Hp.

overall_design: mRNA profiles of Control and Zscan10 KO cells established by CRISPR/Cas9 system with RAW264 cells were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Yuta

last: Yanagihara


title: Acinetobacter baumannii gene expression in the presence of calprotectin

status: Public on Mar 26 2019

city: Nashville

first: Eric

last: Skaar

state: TN

department: Pathology, Microbiology, and Immunology

country: USA

institute: Vanderbilt University Medical Center

type: Expression profiling by high throughput sequencing

summary: Calprotectin (CP) inhibits bacterial viability through extracellular chelation of transition metals. However, how CP influences general metabolism remains largely unexplored. We show here that CP restricts bioavailable Zn and Fe to the pathogen Acinetobacter baumannii, inducing an extensive multi-metal perturbation of cellular physiology. Detailed here are the RNA sequencing files of WT A. baumannii ATCC 17978 grown plus or minus recombinant human calprotectin.

overall_design: Growth of three biological replicates of A. baumannii ATCC 17978 plus or minus 250 microgams/ml CP in lysogeny broth (LB) supplemented with CP buffer.

middle: P

first: Zachery

middle: R

last: Lonergan


title: Does high fibre diet or acetate supplementation cause changes to DNA methylation in the heart or spleen?

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

type: Methylation profiling by high throughput sequencing

summary: Mice were fed either a control diet, high fibre diet or a diet supplemented with acetate for 3 weeks. Heart (left ventricle) and spleen tissues were harvested for DNA methylation analysis.

overall_design: Three sample groups (1) control diet, (2) high fibre diet, and (3) diet with supplemented acetate. Heart (left ventricle) and spleen tissues are included . Three to four replicates were included.

first: Francine

middle: Z

last: Marques

first: David

middle: M

last: Kaye

first: Waled

last: Shihata

first: Hamdi

last: Jama

first: Kirril

last: Tsyganov

first: Helen

last: Kiriazis

first: Duncan

last: Horlock

first: Bererley

last: Giam

first: Antony

last: Vinh

first: Chad

last: Johnson

first: April

last: Fiedler

first: Daniel

last: Donner

first: Matthew

last: Snelson

first: Melinda

last: Coughlan

first: Sara

last: Phillips

first: Xiao-Jun

last: Du

first: Assam

last: El-Osta

first: Grant

last: Drummond

first: Gavin

last: Lambert

first: Charles

last: Mackay


title: Mode of action characterization of antibiotics using expression profile fingerprints generated by RNA-sequencing technology

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary:
RNA-seq based transcriptome profiling  allows a detailed molecular analysis of the E.coli transcriptome (~4200 genes) after perturbation with different antibiotics. Transcriptome fingerprints enable the identification of gene and pathway level responses to treatment to derive a mechanistic understanding of antibiotics mode of action and to differentiate antibiotics. For this goal, treatment has to be performed in a short time period and with sublethal concentrations of the antibiotics. Sublethal concentrations were chosen based on the EC90 concentration of the antibiotic necessary to change the cellular morphology compared to control conditions.
Conclusions: Our study represents the first detailed analysis of E.coli transcriptomes after treatment with different antibiotics, with biologic replicates, generated by RNA-seq technology. The experimental design and data analysis reported here should provide a framework for comparative investigations of expression profiles of known and novel antibiotics. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of E.coli treated with different antibiotics at sublethal concentration and measured by deep RNA-sequencing, in triplicate, using Illumina HiSeq2500

first: Tobias

last: Heckel

first: Inga

last: Clausen

first: Marco

last: Prunotto

first: Sannah

last: Jensen Zoffmann


title: Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioural and myelin alterations rescuable by a remyelinating drug

city: Tel Aviv

first: Boaz

last: Barak

address: 122 Sharett Bldg

country: Israel

institute: Tel Aviv University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of PTBA on acute kidney injury during AKI

city: Pittsburgh

first: Neil

middle: A

last: Hukriede

state: PA

address: 3501 Fifth Ave, 5061 BST3

department: Developmental Biology

institute: University of Pittsburgh

summary: PTBA has been published to increase renal tubular cell proliferation, increased survival, and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial-to-mesenchymal transition in the RTECs.  In order to elucidate pathways responsible for the increased repair response after compound treatment, larval zebrafish were given AKI and treated with PTBA analogue, UPHD25 or DMSO.  Results suggests that epithelial-related genes were downregulated while mesenchymal-related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post-AKI repair by increasing EMT in renal tubular cells.

overall_design: At 3dpf, larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 days post injury, larvae with AKI are selected and treated with 1uM of PTBA analogue, UPHD25 or vehicle control, 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then, pronephric kidneys were collected using DDT,  collagenase I, and manual collection. Total 100 larvae were collected per sample, per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.

first: Abha

middle: S

last: Bais


title: mRNA-seq of immortailized bone marrow derived macrophages (iBMDM) infected with type II Toxoplasma gondii

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

country: China

institute: Peking University

summary: Analysis of mRNA-seq reveals difference in gene expression profiles of wild type iBMDM, IRF3-/- iBMDM and  IRF7-/- iBMDM infected with ME49, a type II Toxoplasma gondii


title: Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioural and myelin alterations rescuable by a remyelinating drug [mouse P30]

summary: Williams syndrome (WS), caused by a heterozygous microdeletion in 7q11.23, is a neurodevelopmental disorder characterized by hypersociability and neurocognitive abnormalities. Of the deleted genes, general transcription factor II-i (Gtf2i) has been linked to hypersociability in WS, though the underlying mechanisms are poorly understood. We show that selective deletion of Gtf2i in forebrain excitatory neurons caused neuroanatomical defects, fine motor deficits, increased sociability and anxiety. Unexpectedly, 70% of the genes with significantly decreased mRNA levels in the mutant mouse cortex are involved in myelination, and mutant mice had reduced mature oligodendrocyte cell numbers, reduced myelin thickness and impaired axonal conductivity. Restoring myelination properties with clemastine or increasing axonal conductivity rescued the behavioural deficits. Frontal cortex from WS patients similarly showed reduced myelin thickness, mature oligodendrocyte cell numbers and mRNA levels of myelination-related genes. Our study provides molecular and cellular evidence for myelination deficits in WS linked to neuronal deletion of Gtf2i.

overall_design: Whole cortex RNAseq of 30-day-old mutant and control mice.

first: Guoping

last: Feng


title: Reprogramming of somatic cell fate in fetal mouse testis by FOXL2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
From fish to human, FOXL2 is considered one of the most conserved markers of ovarian granulosa cell identity. To determine if the sole expression of FOXL2 can determine ovarian differentiation, we created a mouse model that allows the conditional expression of FOXL2. Rosa26-CAG-LSL-Foxl2 mice were crossed to Sf1-Cre mice to induce the expression of FOXL2 in the SF1+ somatic cells of the fetal gonads.When FOXL2 was induced in the somatic cells of the undifferentiated testis, the Sertoli cells and consequently the other cell lineages composing the fetal gonads were feminized, resulting in a partial testis-to-ovary sex reversal
We created a mouse genetic model that conditionaly express FOXL2 in the somatic cells of the fetal gonads. All embryos used in this study resulted from the crossing between Rosa26-CAG-LSL-Foxl2+/f and Sf1-cre+/Tg mice. XX and XY fetal gonads were collected at embryonic day E14.5.  This microarray analysis led to the identification of the genes misregulated upon ectopic induction of FOXL2 in the fetal testis, and showed that FOXL2 expression resulted in feminization of both somatic and germ cells of the fetal gonad.

overall_design: Gene expression analysis was conducted using Affymetrix Mouse Transcriptome 1.0 arrays (Affymetrix, Santa Clara, CA) on 4 biological replicates (one single pair of 14.5 dpc gonads) for each genotype.

first: Barbara

last: Nicol

first: Humphrey

last: Yao


title: CD4+ resident memory T cells dominate immunosurveillance and orchestrate local recall responses

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

summary: This study examines the extent to which memory CD4+ T cells share immunosurveillance strategies with CD8+ resident memory T cells (TRM). After acute viral infection, memory CD4+ T cells predominantly utilized residence to survey nonlymphoid tissues, albeit not as stringently as observed for CD8+ T cells. In contrast, memory CD4+ T cells were more likely to be resident within lymphoid organs than CD8+ T cells. Migration properties of memory-phenotype CD4+ T cells in non-SPF parabionts were similar, generalizing these results to diverse infections and conditions. CD4+ and CD8+ TRM shared overlapping transcriptional signatures and location-specific features, such as granzyme B expression in the small intestine, revealing tissue-specific and migration property-specific, in addition to lineage-specific, differentiation programs. Functionally, mucosal CD4+ TRM reactivation locally triggered both chemokine expression and broad immune cell activation. Thus, residence provides a dominant mechanism for regionalizing CD4+ T cell immunity, and location enforces shared transcriptional, phenotypic, and functional properties with CD8+ T cells.

overall_design: 17 samples were analyzed by RNA-Sequencing: 3 replicates of resident memory SMARTA CD4 cells (CD62L- CD69+)  from the female reproductive tract (FRT) , 2 replicates of resident memory SMARTA CD4 cells (CD62L- CD69+)  from the small intestine epithelium (IEL), 3 replicates of resident memory SMARTA CD4 cells (CD62L- CD69+) small intestine lamina propria (LP), 3 replicates of resident memory SMARTA CD4 cells (CD62L- CD69+) from the spleen (SLO), 3 replicates of SMARTA CD4 cells (CD62L+ CD69- or TCM) from the spleen of mice, and 3 replicates of SMARTA CD4 cells (CD62L- CD69- or TEM)  from the spleen of mice infected with LCMV-Armstrong 54 days prior.

first: Lalit

middle: K

last: Beura

first: Nancy

middle: J

last: Fares-Frederickson

first: Elisabeth

last: Steinert

middle: C

first: Emily

last: Thompson

first: Kathryn

last: Frazser

first: Jason

last: Schenkel

first: Vaiva

last: Vezys

first: David

last: Masopust


title: Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA

status: Public on Mar 23 2019

city: Santander

first: Miguel

middle: Angel

last: Lafarga

address: Avd,. Cardenal Herrera Oria sn

department: Department of Anatomy and Cell Biology

country: Spain

institute: Faculty of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated the nuclear topography, organization and genome-wide gH2AX distribution of unrepaired DNA in rat cortical neurons 15 dyas upon X-Ray ionizing adiation (4Gy). Unrepaired DNA is confined in persistent DNA damage foci which would help preserving genome integrity. ChIp-seq analysis revealed a number of genomic regions enriched in gH2AX. Some of these regions are in close proximity to genes encoding essential proteins for neuronal function and human neurodegenerative disorders.

overall_design: ChIP-seq analysis of genome-wide gH2AX distribution in persistent DNA damage foci of unrepaired DNA in both irradiated and non-irradiated cortical neurons

first: Jorge

last: Mata-Garrido

first: Olga

last: Tapia

first: Iñigo

last: Casafont

first: Maria

middle: T

last: Berciano

first: Ana

last: Cuadrado


title: In situ 10-cell RNA sequencing in tissue and tumor biopsy samples

status: Public on Mar 24 2019

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells.  This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients.   By using small pools of microdissected cells, 10cRNA-seq thus results in improved per-cell reliability and sensitivity beyond existing approaches for single-cell RNA sequencing (scRNA-seq).  Accordingly, in multiple tissue and tumor settings, we observe 1.5–2-fold increases in genes detected and overall alignment rates compared to scRNA-seq.  Combined with existing approaches to deconvolve small pools of cells, 10cRNA-seq offers a reliable, unbiased, and sensitive way to measure cell-state heterogeneity in tissues and tumors.

overall_design: 10-cell samples from various tissue sources captured by laser capture microdissection. mRNA was extracted and PCR amplified for RNA-sequencing

first: Shambhavi

last: Singh


title: Expression analysis of human DC differentiation and maturation

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

summary: We explored the expression profile during DC differentiation from peripheral monocytes and DC maturation induced by lipopolysaccharide (LPS).

overall_design: RNA samples of human peripheral blood monocytes, monocytes differentiated immature and mature DCs from the three donors with equal amount were mixed together to get monocyte sample, immature DC sample and mature DC sample.

first: Pin

last: Wang

first: Yiquan

last: Xue

first: Cong

last: Wu

first: Yanmei

last: Han

first: Li

last: Lin

first: Zhengping

last: Jiang

first: Yizhi

last: Yu

first: Xuetao

last: Cao


title: Identifying Tumor Progression by Genome-Wide Characterization of Immature Myeloid Cells In the Peripheral Blood

first: Yoel

last: Bogoch

address: 6 Weizmann

institute: Sourasky Tel Aiv Meical Center

summary: characterize the molecular signature of PB-IMC in different stages of tumor development, thus possibly leading to a novel, sensitive and elegant approach for early cancer detection and surveillance.

overall_design: Two types of cancer. For each type 4 groups (day 0, day 4, day 8, day 11), for each group 3 biological repeats

first: Niv

last: Pencovich


title: Serum dependent-gene expression patterns of S. pneumoniae D39 and its isogenic vncR mutant

city: Birmingham

first: Sang-Sang

last: Park

state: AL

address: 845 19th ST S

department: Medicine

institute: UAB

summary: mRNA pattern of 1,882 genes in Streptococcus pneumoniae D39 and its isogenic vncR (response regulator) mutant after supplementation of serum was analyed by microarray analysis.

overall_design: Streptococcus pneumoniae wild type and vncR mutant were incubated in the presence or absence of human serum, and mRNA pattern of the 1,882 genes was determined by micro-array.

first: Dong-Kwon

last: Rhee


title: The dual role of mast cells in sporadic colorectal tumorigenesis: clinical and experimental evidence

city: Ribeirao Preto

first: Vinicius

last: Kannen

state: SP

address: Av Café, s/ N°

department: DACTB

country: Brazil

institute: Universidade de São Paulo

summary: Mast cells (MCs) impact significantly on the development of colorectal cancer (CRC), although their precise activity remains controversial. To this end, we analyzed human samples and performed a comprehensive meta-analysis to show that MC numbers vary in CRC cases, a fact related not only to different cell proliferation rates but also to complex immunological reactions. In carcinogenically exposed mice, deficient MC numbers (KitW/sh mouse model) increased the development of colorectal tumors and showed a significant immunological reaction related to T cell activity. Shortly after the carcinogenic exposure, MC deficiency decreased DNA damage levels but promoted proliferation in colonocytes. Exposing interleukin 33 receptor knockout (KO) mice to the same carcinogenic protocol revealed that increased MC density was related to a decrease in cell proliferation and β-catenin expression levels. Further experimentation with different KO mouse strains demonstrated that the major histocompatibility complex I decreased MCs density while its type II increased their numbers. Interestingly, MCs deficient mice given half of the carcinogenic dosage showed reduced development of preneoplastic lesions. Bone marrow transplantation increased not only stromal MC density but also the expression of CRC biomarkers in KitW/sh mice. Whether pharmacologically inhibiting MCs activity throughout carcinogenic exposure promoted the development of preneoplastic lesions, applying the same treatment following carcinogen injections inhibited such events. Our data suggest that the pro- and anti-tumorigenic effects of MCs are not only related to the intensity of carcinogenic exposure but also other immunological reactions controlling the multi-stepped development of CRC.

overall_design: Colon tumor mRNA profiles of AOM-exposed Kit-B6 and Kit-W/sh mice were generated by RNA sequencing using QIAseq Targeted RNAseq Mouse Immuno-Oncology panel and QIAseq Targeted RNA 96-Index I (#333117) in a in MiSeq Sequencing System (Illumina; Illumina MiSeq Reagent Kit v3 - 150 cycles, #15043894).

first: Juliana

middle: Y

last: Sakita

first: Luciana

last: Almeida

first: Emerson

last: de Souza Santos

first: Tathiane

last: Malta

first: Mariângela

middle: O

last: Brunaldi

first: Sergio

last: Albuquerque

first: Cleide

middle: L

last: Araújo Silva

first: Daniela

last: Carlos

first: Marcus

middle: V

last: Andrade

middle: B

last: Garcia

first: Fernando

middle: Q

last: Cunha

first: Guilherme

last: Cebinelli

first: Madhuri

last: Koti

first: Jeremy

last: Squire

last: Uyemura


title: Comparison of Mature Megakaryocytes Differentiated by TPO or Small Molecule TPO Mimetics

city: San Diego

first: Wen

last: Luo

state: CA

address: 6331 Nancy Ridge Drive

institute: Denovo Biopharma

summary:
TPO mimetics have been shown to activate TPO receptor, the downstream JAK-STAT pathway, and induce differentiation of hematopoietic stem cells into megakaryocytes.  However, the action of these TPO mimetics is initiated by binding to the transmembrane domain of the TPO receptor, which is distinct from the binding site of the native ligand, TPO.  To determine whether TPO mimetics can differentiate hematopoietic stem cells into the same megakaryocytes as native TPO does, we performed a microarray experiment to compare the globe gene expression in purified CD61+ cells derived from TPO or TPO mimetic treated CD34+ bone marrow cells.

Keywords: Drug Treatment

overall_design: Purified human bone marrow hematopoietic CD34+ cells were cultured with rhSCF at 100 ng/mL, and either 100 ng/mL rhTPO, 3 µM eltrombopag, or 1 µM LGD-4665 for 10 days. The mature megakaryocytes were enriched using anti-CD61 Miltenyi beads, and RNA was purified from these CD61+ cells.  Each RNA sample was used to create a probe which was hybridized to a single microarray.  In sum, there were four biological replicates for TPO treatment group, and three replicates for LGD-4665 and eltrombopag (each group had a missing sample due to low quantity or quality of RNA), with no technical replicates.

first: Louise

last: de Grandpre

first: Jennifer

last: Sanders


title: Comparison of Human Bone Marrow CD34+ Cell Cultures Treated With TPO or Small Molecule TPO Mimetics

summary:
Small molecular TPO mimetics, LGD-4665 and eltrombopag, were efficacious in stimulating the formation of CD41+ cells from human bone marrow CD34+ cells.  To better understand the mechanism of action of TPO mimetics, a microarray study was performed to compare global gene expression in CD34+ cells induced by small molecular TPO mimetics eltrombopag and LGD4665, to changes in response to recombinant human thrombopoietin (TPO).

Keywords: Drug Treatment

overall_design: CD34+ human bone marrow cells were obtained from five independent healthy donors.  Cells from each donor population were seeded at 500,000 cells/well in six-well culture dishes, and treated with vehicle control,100 ng/ml rhTPO, 1 uM eltrombopag, or 1 uM GD-4665.  A timepoint of five days was chosen to capture early events since CD41 mRNA expression peaks at this time.  Following five days of treatment, each culture well was harvested for RNA isolation.  Two wells of vehicle-treated cells from each donor were pooled to yield sufficient RNA.  This resulted in a total of 20 RNA samples representing five independent donors (or biological replicates) and four independent treatments.  Each RNA sample was used to create a probe which was hybridized to a single microarray. In sum, there were five biological replicates, each subjected to three parallel treatments, with no technical replicates.

first: Sharon

last: Dana

first: Jennife

first: Li

last: Sun


title: TPO mimetics study


title: Energy metabolism and cell motility defect in NK-cells from patients with Hepatocellular Carcinoma

city: Parma

first: Alessandra

last: Zecca

state: Parma

address: via Gramsci 14

country: Italy

institute: Azienda Ospedaliero-Universitaria di Parma

summary:
Natural Killer (NK) cells play a central role in cell-mediated immune response to cancer. In previous studies number and function of NK-cells have been shown to be positively correlated with HCC outcome. In this study, we have performed a genetic expression analysis comparing mRNA expression by NK cells from HCC patients to patients with the pre-neoplastic condition of liver cirrhosis and to healthy donors. The bioinformatic analysis has been completed by an immunophenotypic study and functional analysis of the main NK cell functions. It is known that NK cells may present functional defects in HCC patients however previous studies have not systematically address the molecular mechanisms associated with these defects by an unbiased genetic expression study. We could identify altered cellular pathways and hypothesize possible mechanisms that could be targeted for restoring an immune-protective NK cell response.
NK cells were isolated and sorted from Hepatitis C virus (HCV)-related liver cirrhosis (10 patients), early stage HCC and HCV-related liver cirrhosis (14 patients) and seven healthy donors. RNA from sorted NK cells was processed, labeled and hybridized to Agilent microarrays.

overall_design: Alessandra, Zecca

first: Valeria

last: Barili

first: Elisabetta

last: Cariani

first: Gabriele

last: Missale


title: Transcriptome analysis of a chlorosis mutant of Pakchoi

city: Shenyang

first: Zhiyong

last: Liu

institute: Shenyang Agriculture University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of a chlorosis mutant of Pakchoi. The goals of this study are to transcriptome analysis of a chlorosis.
Methods: mRNA profiles of the aboveground parts of WT and a chlorosis mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://brassicadb.org/brad/index.php, v1.5）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays.
Results: Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2958 DEGs was identified. Among 2958 DEGs, 9 DEGs related to chlorophyll synthesis and chlorophyll metabolism were identified. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular mechanisms of leaf color mutant.
Conclusions: The results presented here reveal changes in the transcriptome profile of a chlorosis mutant. DEGs related to chlorophyll biosynthesis were detected.. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.

overall_design: mRNA profiles of chlorosis mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq platform.

first: Xueling

last: Ye


title: Persistent effects on bovine granulosa cell transcriptome after resolution of uterine disease

status: Public on Mar 22 2019

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Metritis is associated with reduced fertility in dairy cows, but the mechanisms are unclear because the disease resolves several weeks before insemination. One hypothesis is that metritis causes persistent changes in granulosa cells during follicle development, which might be evident in the transcriptome of granulosa cells from dominant follicles weeks after parturition. To test this hypothesis we collected follicular fluid and granulosa cells from dominant follicles 63 days post partum from cows previously diagnosed with metritis, at least 6 weeks after resolution of the disease, and from cows not diagnosed with metritis (control cows). Bacterial lipopolysaccharide was detected in follicular fluid, and concentrations were associated with follicular fluid IL-8 and glucose concentrations. Transcriptome analysis using RNAseq revealed 177 differentially expressed genes in granulosa cells collected from cows that had metritis compared with control cows. The most upregulated genes were ITLN1, NCF2, CLRN3, FSIP2 and ANKRD17, and the most downregulated genes were ACSM1, NR4A2, GHITM, CBARP and NR1I3. Pathway analysis indicated that the differentially expressed genes were involved with immune function, cell-cell communication, cell cycle and cellular metabolism. Predicted upstream regulators of the differentially expressed genes included NFκB, IL-21 and lipopolysaccharide, which are associated with infection and immunity. Our data provide evidence for a persistent effect of metritis on the transcriptome of granulosa cells in ovarian follicles after the resolution of disease

overall_design: It was a prospective cohort study conducted from June 2016 to February 2017 at the University of Florida Dairy Unit using a group of 45 lactating Holstein Bos taurus dairy cows fed a total mixed ration. Milk yield (AfiFlo milk meters, S.A.E. Afikim, Israel) and concentrations of fat, true protein, and lactose (AfiLab online real-time milk analyzer, S.A.E. Afikim) were recorded at each milking, and cows were weighed on a walk through scale (AfiWeigh, S.A.E. Afikim) immediately after each milking as they left the milking parlor. Data were collected for the first 280 days postpartum or until the cow died or was culled, whichever occurred first. Cows were evaluated every 48 h for the first 21 days after parturition for signs of metritis as defined by a fetid, red-brown watery vaginal discharge and rectal temperature > 39.5°C. Cows with metritis received antimicrobial treatment with 2.2 mg/kg body weight ceftiofur hydrochloride (Excenel, Zoetis, Parsippany, NJ, USA) for 5 consecutive days. The veterinarians and farm staff recorded other diseases diagnosed within 21 d post partum, including mastitis, ketosis, displaced abomasum and lameness. Cows were examined for endometritis, as determined by a purulent vaginal discharge after d 21 post partum, and for subclinical endometritis, as determined by > 5% neutrophils in endometrial cytology samples collected on the day of follicle aspiration, at 63 days postpartum. Cows started a an ovulation synchronization protocol with the double Ovsynch program (Souza et al. 2008) using 100 mg GnRH (gonadorelin diacetate tetrahydrate; Ovacyst, Bayer Animal Health, Whippany, NJ, USA) i.m. 53 ± 3 d post partum followed by 25 mg prostaglandin (PG) F2α (dinoprost tromethamine; Prostamate, Bayer) i.m. 60 ± 3 d post partum. The contents of the pre-ovulatory follicle were aspirated by transvaginal ultrasounography on d 63 ± 3 postpartum (see below for details), immediately before cows received a second GnRH injection 72 h after PGF2α. A second Ovsynch protocol was then started 7 d later, and the final GnRH injection was administered approximately 16 h before timed AI performed at 80 d postpartum. Pregnancy was diagnosed by transrectal ultrasonography 32 d after timed AI. Blood was collected from the coccygeal vessels into evacuated tubes containing sodium heparin (Vacutainer, Becton Dickson, Franklin Lakes, NJ, USA) on d 7, 21, 35, and 50 post partum.

first: R

last: Piersanti

first: A

middle: D

last: Horlock

first: J

last: Block

middle: P

last: Santos

first: I

last: Sheldon

last: Bromfield


title: RNA-Seq on wild-type and Ezh2 knock-out invariant natural killer T cells and CD44hi CD4+ T cells

city: Adelaide

first: Damon

middle: John

last: Tumes

state: South Australia

address: North Terrace

department: Centre for Cancer Biology

institute: University of South Australia

summary: Several subsets of NKT cells have been identified, including IFNγ-producing NKT1 cells, IL-4-producing NKT2 cells and IL-17-producing NKT17 cells.  We sought to determine to the effect of loss of the polycomb repressive complex 2 protein Ezh2 on gene expression in NKT cells and CD44high CD4+ T cells from mice. Transcriptional profiles of iNKT cells from wild-type (WT) and Ezh2 KO iNKT mice were determined.

overall_design: Four samples were analysed. One sample of each of wild-type iNKT cells, Ezh2 KO iNKT cells, wild-type CD44-high CD4+ T cells and Ezh2 KO CD44-high CD4+ T cells.


title: Transcriptome of mature erythrocytes

city: Bengaluru

first: Sandeep

last: Eswarappa

state: Karnataka

address: C V Raman Avenue, Devasandra layout

department: Biochemistry

country: India

institute: Indian Institute of Science

summary:
Purpose: This study identifies the top transcripts expressed in mature erythrocytes and the top transcripts expressed in the polysome fractions of mature erythrocyte lysate
Methods: RNA from total erythrocyte lysate and polysome fractions was isolated and purified using GeneJet RNA purification column  (Thermo Fisher Scientific). The RNA library was prepared using NEBNext ULTRA II RNA library preparation kit for Illumina. The libraries were sequenced using Illumina Seq.
Results: The transcriptome analysis revealed the abundance of mRNAs encoding globins genes, long non-coding RNAs, and micro RNAs. Deciphering the role and functions of these non-coding RNAs in these specialised cells could enable us to understand their biology in greater detail

overall_design: RNA transcriptome profiling was done for total mature erythrocyte lysates and polysome fractions using Illumina Seq

middle: M

first: Sangeetha

last: Devi Kumar


title: A NIK-SIX signaling axis controls inflammation by targeted silencing of noncanonical NF-κB

city: Dallas

first: Neal

last: Alto

state: TX

address: 6000 Harry Hines Blvd, NL3.108

institute: UT Southwestern Medical Center

summary: The non-canonical NF-κB signaling cascade is essential for lymphoid organogenesis, B-cell maturation, osteoclast differentiation, and inflammation in mammals, whereas dysfunction of this system is associated with human diseases, including immunological disorders and cancer. While controlled expression of NF-κB Inducing Kinase (NIK) is the rate-limiting step in non-canonical NF-κB activation, mechanisms of inhibition remain largely unknown. Here, we report the identification of the sine oculis homeobox homolog family transcription factors SIX1 and SIX2 as essential inhibitory components of the non-canonical NF-κB signaling pathway. The developmentally silenced SIX-proteins are reactivated in differentiated macrophages by NIK-mediated suppression of the ubiquitin proteasome pathway. Consequently, SIX1 and SIX2 target a subset of inflammatory gene promoters and directly inhibit RelA and RelB trans-activation function in a negative feedback circuit. In support of a physiologically pivotal role for SIX-proteins in host immunity, human SIX1 transgene suppressed inflammation and promoted the recovery of mice from endotoxic shock. In addition, SIX1 and SIX2 protected RAS/p53-driven lung adenocarcinoma cells from inflammatory cell death induced by SMAC-mimetic chemotherapeutic agents, small-molecule activators of the non-canonical NF-κB pathway. Collectively, our study reveals a NIK-SIX signaling axis that fine-tunes inflammatory gene expression programs under both physiological and pathological conditions.

overall_design: In this data set, we first analyzed NIK-stimulated genes by expressing NIK and Fluc (control experiment) in STAT1-deficient fibroblasts. Each group has 2 independent experiments. Second, we analyzed the SIX2-downregulated NIK-stimulated genes, FlucRFP/FlucBFP, NIKRFP/FlucBFP, NIKRFP/SIX2BFP, or FlucRFP/SIX2BFP lentivirus was transduced into WT fibroblasts. We then analyzed the whole genome transcription prfiles. Each group has 2 independent experiments. Third, WT and SIX1-/- SIX2-/- H1792 treated with mock or BV6/TNF for 24 hours. we analyzed the whole genome transcription profiles. Each group has 2 independent experiments.

first: Zixu


title: Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioural and myelin alterations rescuable by a remyelinating drug [mouse P1]

city: Tel Aviv

first: Boaz

last: Barak

address: 122 Sharett Bldg

institute: Tel Aviv University

summary: Williams syndrome (WS), caused by a heterozygous microdeletion in 7q11.23, is a neurodevelopmental disorder characterized by hypersociability and neurocognitive abnormalities. Of the deleted genes, general transcription factor II-i (Gtf2i) has been linked to hypersociability in WS, though the underlying mechanisms are poorly understood. We show that selective deletion of Gtf2i in forebrain excitatory neurons caused neuroanatomical defects, fine motor deficits, increased sociability and anxiety. Unexpectedly, 70% of the genes with significantly decreased mRNA levels in the mutant mouse cortex are involved in myelination, and mutant mice had reduced mature oligodendrocyte cell numbers, reduced myelin thickness and impaired axonal conductivity. Restoring myelination properties with clemastine or increasing axonal conductivity rescued the behavioural deficits. Frontal cortex from WS patients similarly showed reduced myelin thickness, mature oligodendrocyte cell numbers and mRNA levels of myelination-related genes. Our study provides molecular and cellular evidence for myelination deficits in WS linked to neuronal deletion of Gtf2i.

overall_design: Whole cortex RNAseq of 1-day-old mutant and control mice.

first: Guoping

last: Feng


title: RNA-seq profiling of basal and luminal mammary cells from Foxp1-deficient and control mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Long-lived quiescent mammary stem cells (MaSCs) are presumed to coordinate the dramatic expansion of ductal epithelium that occurs through the different phases of postnatal development, but little is known about the molecular regulators that underpin the activation of MaSCs. Here we show that ablation of the transcription factor Foxp1 in the mammary gland profoundly impairs ductal morphogenesis, resulting in a rudimentary tree throughout adult life. Foxp1-deficient glands were highly enriched for quiescent Tspan8hi MaSCs, which failed to become activated, even in competitive transplantation assays, and therefore harbor a cell-intrinsic defect. Luminal cells aberrantly expressed basal genes, suggesting that Foxp1 may also contribute to cell-fate decisions. Notably, Foxp1 was uncovered as a direct repressor of the Tspan8 gene in basal cells and deletion of Tspan8 could rescue the profound defects in ductal morphogenesis elicited by Foxp1 loss. Thus, a single transcriptional regulator, Foxp1, can control the exit of MaSCs from dormancy to orchestrate differentiation and development.

overall_design: Basal and luminal epithelial cells were extracted from the mammary glands of floxed Foxp1 control and Foxp1 mammary gland conditional knockout mice. mRNA from three biological replicates of each cell population was profiled by RNA sequencing. All mice were female.

first: Nai

last: Fu

first: Yunshun

last: Chen

first: Jane

last: Visvader


title: The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. chlororaphis and Bacillus subtilis growing in co-cultures in solid medium

sample_organism:
Bacillus subtilis
Pseudomonas chlororaphis

overall_design: P. chlororaphis and B. subtilis mRNA profiles comparing their growth in single-cultures and in interactions in solid LB medium after 72h of growth

last: Molina-Santiago

first: Diego

last: Romero


title: Genome-wide analysis of circRNA expression profile in non-small cell lung cancer (NSCLC) tissues and matched adjacent normal tissues

city: Changsha

first: Yeping

last: Dong

institute: Xiangya Hospital

summary: Non-small cell lung cancer (NSCLC) is a common lung disorder.Recent studies have shown that circRNA plays critical roles in a myriad of biological processes and human diseases,Since the roles of circRNA in NSCLC remain unknown,they were investigated in the study.Our findings indicate that the expression profiles of circRNAs have changed in NSCLC as compared with normal lung, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for NSCLC.

overall_design: Microarray expression profiling of circRNAs  were conducted using RNA extracted from three NSCLC lung samples and three matched adjacent normal samples.

first: Chaojun

last: Duan

first: Yang

last: Gao

first: Wei

last: Peng

first: jun

last: Wang

first: Zhenzi

first: Bin

last: Shan

first: Wenwen

last: Shi

first: Wenyuan

last: Zhao

first: Chunfang

last: Zhang


title: ChIP-seq profiling of Foxp1 binding in basal and luminal mouse mammary cells

middle: K

overall_design: Basal and luminal epithelial cells were extracted from the mammary glands of 10-12 week old FVB/N wild-type female mice. Foxp1 ChIP-seq and DNA input was sequenced for each sample.


title: Analysis of Changes in Gene Expression and Genomewide H3K27 trimethylation Triggered upon C2C12 Myotube Differentiation in Normoxia versus Hypoxia

city: Boston

first: William

middle: G

last: Kaelin

state: MA

address: M457, 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We report changes in gene expression and corresponding H3K27 trimethylation induced upon myotube differentiation in C2C12 cells that were cultured under Normoxia (21% oxygen) or Hypoxia (2% oxygen)

overall_design: Two biological replicates (A and B) for analysis of gene expression (RNA-Seq) and H3K27 trimethylation (ChIP-Seq) in C2C12 cells cultured under 2 different conditions: Growth Medium (GM) versus Differentiation Medium (DM) under 2 different oxygen concentrations: 21% oxygen (NOR) or 2% oxygen (HYP)

first: Abhishek

middle: A

last: Chakraborty

last: Kaelin Jr.


title: Transcriptome analysis to characterize DNA methylation changes associated with colorectal carcinogenesis

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

institute: University Hospital Bern

summary: Gene expression analysis of a CRC cell line showing wide-spread DNA hypermethylation (SW48) before and after 5-Aza-Cytidine/Trichostatin A induced DNA demethylation to identify targets of Cytosine methylation-dependent gene silencing.

overall_design: Gene expression of SW48 colorectal cancer cell line before and after DNA demethylating 5'-Azacytidine and/or Trichostatin A treatment was analyzed on two Illumina HumanWG-6_V3 microarrays and each 3 replicates were distributed over the two chips.

first: Patric

last: Urfer

first: Stefan

last: Weis

first: Kaspar

last: Truninger

first: Ulrich

last: Certa

first: Primo

last: Schär


title: Transcriptomics of Marchantia polymorpha that ectopically expresses MpGL3

city: Noda-shi

first: Kengo

last: Morohashi

state: Chiba

address: 2641 Yamazaki, Morohashi Lab 3rd Floor at 6-go-kan

department: Applied Biological Science

country: Japan

institute: Tokyo University of Science

summary: An understanding of the evolutionary aspects of gene regulatory network (GRN) is fundamental to elucidate mechanisms of environmental adaptations; nevertheless, how the GRNs leading to land adaptation evolved remains poorly understood. In this study, we isolated a single IIIf bHLH TF from M. polymorpha, MpGL3. Transgenic M. polymorph ectopically expressing MpGL3 (referred to MpGL3ox) decreased the size and numbers of gemma cups, suggesting that MpGL3 is involved in the regulation of morphological development. Transcriptomics analysis of MpGL3ox was performed.

overall_design: We made transgenic M. polymorpha that carries MpGL3 fused to citrione driven by constitutive expression promoter. We performed RNA-Seq of two independent lines and compared with wild type (Tak-1) with biologically triplicates.

first: Haruka

last: Arai

first: Kazuya

last: Yanagiura

first: Yuko

last: Toyama


title: The Anti-Arthritis Effect of Olive-Derived Maslinic Acid in Mice is Due to its Promotion of Tissue Formation and its Anti-Inflammatory Effects.

city: Atsugi

first: Kyoko

last: Shimazu

state: Kanagawa

address: 5-1-3 Midorigaoka

department: Innovation Center

institute: Nippon Flour Mills Co., Ltd.

summary:
SCOPE: A previous study demonstrated that intake of olive pomace extract containing maslinic acid (MA), a triterpene, effectively prevents and alleviates arthritis in animals and humans. Here, the molecular mechanisms involved in the anti-arthritis effect of MA have been elucidated by determining gene expression changes induced by olive-derived MA intake in collagen antibody-induced arthritis (CAIA) mice.
METHODS AND RESULTS: Mice are divided into the untreated (CT), CAIA (CA), and CAIA administered MA (CA + MA) groups. The CA + MA mice are fed MA at a daily dose of 200 mg kg-1 of body weight from day 1. CAIA is then induced on day 8 and evaluated on day 12. Arthritis symptoms are alleviated, and the gene expression of inflammatory cytokines is reduced in the CA + MA group compared with the CA group. A DNA microarray analysis of synovial membranes reveals that MA alters the expression levels of genes related to inflammation, including glucocorticoid responses, immune responses, and the extracellular matrix.
CONCLUSIONS: The preventive effect of MA on arthritis is attributable to the promotion of tissue formation as well as suppression of inflammation in the synovium via inactivation of Toll-like receptor signaling and downregulation of leukotrienes through the glucocorticoid receptor.

overall_design: 10 arrays are included. All animal protocols were approved by the Ethical Committee of Nippon Flour Mills Co., Ltd (permission number: 2015-2). Five-week-old male DBA/1J mice were obtained from Japan SLC Inc. (Shizuoka, Japan) and housed under conventional conditions (24°C ± 1°C, 50% ± 10% relative humidity with a 12 h light/dark cycle). The mice were fed the AIN-93G diet, where fat is provided by corn instead of soy, and were provided ad libitum access to the diet and water for 24 h. After a week of acclimatization, the mice were divided into three groups: untreated (CT), CAIA (CA), and CAIA plus MA treatment (CA + MA). MA was suspended in corn oil and orally administered to CA + MA mice daily at a dose of 200 mg/kg of body weight. The other two groups were administrated corn oil instead of MA. CAIA was induced by intraperitoneal injection with 1 mg of a type II collagen mAb (Chondrex, Inc., Redmond, WA, USA) on day 8 and 0.025 mg of LPS (Chondrex) on day 11. Mice were sacrificed on day 12. Five mice selected from the CA and CA + MA groups respectively were used for DNA microarray analysis.

first: Satoshi

last: Fukumitsu

first: Tomoko

last: Ishijima

first: Tsudoi

last: Toyoda

first: Yuji

last: Nakai

first: Keiko

last: Abe

first: Kazuhiko

last: Aida

first: Shinji

last: Okada

first: Akihiro

last: Hino


title: Exhausted-like CD8 resident memory T cells balance immunity and fibrotic sequelae

status: Public on Mar 21 2019

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: CD8 tissue-resident memory T cells (TRM) provide frontline immunity in mucosal tissues. The mechanisms regulating CD8 TRM maintenance, heterogeneity, protective and pathological functions are largely elusive. Here we identify an epitope-specific CD8 TRM population that is maintained by in situ MHC-I and B7 signaling following acute influenza infection. These TRM cells co-exhibit exhausted-like phenotypes and memory features, and provide heterologous immunity against secondary infection. PD-L1 blockade at the memory stage promotes exhausted-like TRM rejuvenation and secondary immunity at the cost of developing post-infection fibrotic sequelae. Increased numbers of CD8 TRM cells are observed in the lungs of pulmonary fibrosis patients compared to control patients. Thus, TRM exhaustion results from a tissue-specific cellular adaptation to balance fibrotic sequelae and secondary immunity.

overall_design: Examination of mRNA expression in NP and PA specific resident memory CD8 T cells in C57BL/6 mice.

first: Zheng

last: Wang

first: Shaohua

first: Robert

last: Vassallo

first: Jie

last: Sun


title: Epigenome analysis to identify DNA methylation changes associated with colorectal carcinogenesis

first: Fredy

last: Siegrist

summary: DNA methylation profiling of matched primary tumor (CRC), cancer-associated mucosa (CAM) and blood from two colorectal cancer patients to identify cancer-specific methylation targets.

overall_design: Sodium bisulfite converted DNA from 18 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2. (6 remaining positions were used for unrelated project)

first: Rachel

middle: W

last: Scott

first: Patric

last: Urfer

first: Kaspar

last: Truninger

first: Ulrich

last: Certa

first: Primo

last: Schär


title: Cervical lymph node metastasis high metastatic HNSCC lines vs non-metastatic HNSCC lines

city: YOKOHAMA

first: Hiroshi

last: Hyakusoku

state: KANAGAWA

department: ENT

institute: Yokohama City University

summary: This study is the orthotopic nude mouse model of Head and neck squamous cell carcinoma (HNSCC).

overall_design: FaDu/Detroit562' cell lines are high cervical lymph node metastases and 'YCU-OR891/YCU-MS861' cell lines are non-cervical lymph node metastases, and then the cervical lymph nodes were evaluated for the presence of metastases.


title: Genome wide identification of FOXL2 binding sites in mouse fetal ovaries

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary:
The identity of the gonads is determined by which fate, ovarian granulosa cell or testicular Sertoli cell, the bipotential somatic cell precursors choose to follow. In most vertebrates, the fate of granulosa cells is controlled by a conserved regulator FOXL2. To understand how FOXL2 elicits its fate-determining action, we performed genome-wide analysis of FOXL2 chromatin occupancy in fetal ovaries. Combining genome-wide analysis of FOXL2 binding in the fetal ovary with transcriptomic analyses of Foxl2 gain-of-function and Foxl2 loss-of-function models, we identified potential pathways responsible for the feminizing action of FOXL2. Finally, comparison of FOXL2 genome-wide occupancy in the fetal ovary with testis-determining factor SOX9 genome-wide occupancy in the fetal testis revealed extensive overlaps, implying that antagonistic signals between FOXL2 and SOX9 occur
at the chromatin level.

overall_design: ChIP-seq for FOXL2 and input on chromatin from pools of mouse CD1 fetal ovaries (E14.5)

first: Barbara

last: Nicol

first: Sara

last: Grimm

first: Artiom

last: Gruzdev

first: Greg

first: Manas

last: Ray

middle: H


title: DMSO-free chemically defined cryopreservation of human mesenchymal stem cells and chondrocytes

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Serum- and xeno-free cryopreservation is suitable for cells to be used in clinical applications. However, dimethyl sulfoxide (DMSO), which is often used in conventional cryoprotectant medium, has been shown to be toxic to many cell types and can induce morphological and gene expression changes that can lead to changes in cell function when they are cultured. In order to evaluate this issue in depth, we examined the efficiency of a DMSO-free/serum-free/xeno-free chemically defined cryoprotectant media, STEM-CELLBANKER DMSO-Free, when culturing human mesenchymal stem cells (MSCs) and chondrocytes. Interestingly, the cells cryopreserved in STEM-CELLBANKER DMSO-Free had a similar growth rate, morphology, and global gene expression profile compared to that observed for cells preserved in conventional freezing medium, which contains 10% DMSO and 20% fetal bovine serum. From these data, we therefore propose that STEM-CELLBANKER DMSO-Free may be an effective tool for maintaining the cellular characteristics of MSCs and chondrocytes during cryo-storage prior to clinical application.

overall_design: Gene expressions in human mesenchymal stem cells and chondrocytes were measured after freezing and thawing in several kinds of cryopreservation media.

first: Yasuko

last: Onuma


title: STAT5 activation enhances Paneth cell function by regulated ileal Wnt3a-Tcf4-Sox9 or Gfi1 to sustain niche differentiation.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
To determine the potential molecular mechanisms by which STAT5 signaling control ileal Paneth cell homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).
With an average of 22.3 million reads per sample, we observed 27540 transcripts when reads were aligned to the mm10 genome with annotations provided by Ensembl.  Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition, leaving 10197 transcripts for analysis.  To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

overall_design: Sincle-end RNA sequencing of total RNA extracted from ileal crypts obtained from Stat5 knockout, wildtype, and overexpressing mice.

first: R

first: X

last: Han


title: Single-cell RNA-seq of human cardiovascular progenitor cells generated with a chemically defined, xeno-free laminin based differentiation protocol

status: Public on Mar 20 2019

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates pluripotency and teratoma associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical quality cells for use in regenerative cardiology.

overall_design: We generated four independent single-cell RNA-sequencing datasets with day 9 and 11 cardiovascular progenitor cells derived from HS1001 and H1 hES cells respectively. H1 and HS1001 cells were cultured for 9 and 11 days in wells coated with LN-521+221 from day 0. We used nutristem to maintain the cells. Differentiation commenced when cells reached confluency. Small molecule inhibitor CHIR99021 (inhibitor of GSK3) was added at day 4 followed by IWP2 (inhibitor of Wnt production) at day 7.

first: Lynn

last: Yap

first: Enrico

last: Petretto

first: Karl

last: Tryggvason


title: Rdh1 supresses adiposity by promoting brown adipose adaptation to fasting and re-feeding

city: Berkeley

first: Joseph

last: Napoli

address: 119 Morgan Hall

department: NST

institute: UC Berkeley

summary: Rdh1 is one of the several enzymes that catalyze the first of the two reactions to convert retinol into all-trans-retinoic acid (atRA). Here we show that Rdh1-null mice fed low-fat diet gain more weight as adiposity thann wild-type mice by 20 weeks old, despite neither consuming more calories nor decreasing activity. RNAseq revealed dysregulation of 424 BAT genes in null mice, with segregated predominantly into differences after fasting vs after re-feeding. Rdh1-generated atRA in BAT regulates multiple genes that promote BAT adaptation to whole-body energy status, such as fasting and re-feeding.

overall_design: Transcriptome analysis of brown adipose tissue from Rdh1KO and WT mice after 16h fasting and 16h fasting followed by 6h re-feeding.


title: Cas9/sgRNA selective targeting of the P23H Rhodopsin mutant allele for treating retinitis pigmentosa by intravitreal AAV9.PHP.B-based delivery

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: P23H is the most common mutation in the RHODOPSIN (RHO) gene leading to a dominant form of retinitis pigmentosa (RP), a rod photoreceptor degeneration that invariably causes vision loss. Specific disruption of the disease P23H RHO mutant while preserving the wild-type (WT) functional allele would be an invaluable therapy for this disease. However, various technologies tested in the past failed to achieve effective changes and consequently therapeutic benefits. We validated a CRISPR/Cas9 strategy to specifically inactivate the P23H RHO mutant, while preserving the WT allele in vitro. We, then, translated this approach in vivo by delivering the CRISPR/Cas9 components in murine Rho+/P23H mutant retinae. Targeted retinae presented a high rate of cleavage in the P23H but not WT Rho allele. This gene manipulation was sufficient to slow photoreceptor degeneration and improve retinal functions. To improve the translational potential of our approach, we tested intravitreal delivery of this system by means of adeno-associated viruses (AAVs). To this purpose, the employment of the AAV9-PHP.B resulted the most effective in disrupting the P23H Rho mutant. Finally, this approach was translated successfully in human cells engineered with the homozygous P23H RHO gene mutation. Overall, this is a significant proof-of-concept that gene allele specific targeting by CRISPR/Cas9 technology is specific and efficient and represents an unprecedented tool for treating RP and more broadly dominant genetic human disorders affecting the eye, as well as other tissues.

overall_design: 3x AAV-transduced, 2x electroporated, and 1x control retinae

first: Vania

last: Broccoli

first: Serena

last: Giannelli


title: The impact of Pax5 overexpression on gene expression profile in A549 cells

city: Tianjin

first: Zhe

last: Liu

address: Heping District Qixiangtai Road No. 22

institute: Tianjin Medical University

summary: Pax5, a transcription factor, is expressed exclusively in pro B cells. To understand the genes regulated by Pax5 in epithelial cells, we overexpressed Pax5 in lung cancer cell line A549 and examined the change of transcription profile using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Agilent Technologies).

overall_design: Two-condition experiment, A549-empty vs. A549-Pax5 cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested. One replicate per array.

first: Lin

last: Wang

first: Junrong


title: Global gene expression of SLC35F2 Knock-out (KO) H9 with control hESCs

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Analysis of SLC35F2 KO hESCs compared with control hESCs. In order to investigate whether SLC35F2 KO affect pluripotency in hESCs, we performed RNA-Seq with SLC35F2 KO and control H9 cells. After establishing SLC35F2 KO hESCs, total RNA was extracted from each cell lines and RNA-Seq was performed after Quality control.

overall_design: Total RNA obtained from hESCs of SLC35F2 KO and control H9 cells

first: Hyuk-Jin

last: Cha


title: Small Sample-Big Data: Integrative Indexed Systems Biology Reveals Dramatic Molecular Ontogeny over the First Week of Human Life in Papua New Guinea

first: Joann

middle: Diray

last: Arce

address: 300 Longwood Ave

department: Infectious Disease

institute: Boston Childrens Hospital- Harvard Medical School

summary: This study examines the global transcriptomic profiles in peripheral blood of Papua New Guinea newborns at birth (D0) comparing with follow up at day 1 (D1), day 3 (D3), or day 7 (D7) post birth.

overall_design: Systems biology provides a powerful approach to unravel complex biological processes yet it has not been applied systematically to samples from newborns, a group highly vulnerable to a wide range of diseases. Published methods rely on blood volumes that are not feasible to obtain from newborns. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1ml of blood, a volume readily obtained from newborns. Furthermore, indexing to baseline and applying innovative integrative computational methods that address the challenge of few data points with many features enabled identification of robust findings within a readily achievable sample size. This approach uncovered dramatic changes along a stable developmental trajectory over the first week of life. The ability to extract information from ‘big data’ and draw key insights from such small sample volumes will enable and accelerate characterization of the molecular ontogeny driving this crucial developmental period.

first: Ofer

last: Levy

first: Tobias

last: Kollmann

first: Bob

last: Hancock

first: EPIC

last: Consortium


title: Sphingosine-kinase-1 pathway offers positive therapeutic targets in triple-negative breast cancer for effective inhibition of metastasis

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: We identified sphingosine kinase 1 (SPHK1) as a top candidate. SPHK1-overexpression in human TNBC cell-line promotes spontaneous metastasis to lungs in nude mice. Moreover, genetic knockdown of SPHK1 in TNBC patient-derived xenograft (PDX) cells and TNBC cell-line decreases spontaneous metastasis to lungs in nude mice. SPHK1 regulates the FSCN1 gene expression in order to drive metastasis. Mechanistically, SPHK1 transcriptionally upregulates metastasis-promoting FSCN1 gene expression via NFκB activation to promote metastasis. SPHK1/NFκB/FSCN1 signaling pathway activation is associated with distance metastasis and poor clinical outcome in TNBC patients.

overall_design: MDA-MB-435 breast cancer cell lines (shRNA control and SPHK1 knockdown lines) were injected under mouse mammary fat pad (MFP). Spontaneous lung metastases were harvested and compared with MFP samples.

first: Sunil

last: Acharya

first: Jun

last: Yao

first: Ping

last: Li

first: Chenyu

last: Zhang

first: Frank

middle: J

last: Lowery

first: Qingling

first: Hua

last: Guo

first: Jingkun

last: Qu

first: Fei

last: Yang

first: Ignacio

middle: I

last: Wistuba

first: Helen

last: Piwnica-Worms

first: Aysegul

last: Sahin

first: Dihua

last: Yu


title: SRSF1 role in cellular gene expression and splicing

city: Boca Raton

first: Massimo

last: Caputi

state: Florida

address: 777 Glades Road

department: Biomedical Science

institute: Florida Atlantic University

summary: SRSF1 is an abundant RNA-binding protein with functions in mRNA splicing, stability, translation and transcription of cellular and viral genes. We analyzed the role that SRSF1 plays in cellular gene transcription and splicing by transfecting HEK293 cells with a SRSF1 expression plasmid and by analyzing the transcriptome of the transiently transfected cells 15 hrs and 48 hrs post transfection. We also explored the role of the SRSF1 domains by transfecting a deletion clone of SRSF1 carrying only the RNA Recognition Motifs 1 and 2 (RRM1,2) but not the Arg-Ser rich (SR) domain.

overall_design: Comparison of the transcriptome of HEK293 cells transfected with SRSF1,SRSF1  RRM12 and control expression vector at 15 and 48 hours post transfection

first: Evan

last: Clark

first: Sean

last: Paz


title: RNA sequencing of GlyH-101-treated MCF-7 cell line

city: Zhejiang

first: Anqi

state: Hangzhou

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: To interrogate the pathways downstream of CFTR-regulated hyperpolarization in quiescent cells, RNA sequencing of GlyH-101-treated MCF-7 cells was performed.

overall_design: The transcriptome profiles of three replicates of MCF-7 cells treated with GlyH-101 for 0, 1, and 24 h were compared.

first: An-Qi

first: Wei-Jun

first: Zhan-Peng

last: Sun

first: Xu

last: Liu

first: Jin-Shu

first: Feng

last: Jin

first: Lin

last: Zhu

first: Wen-Huan

last: Jia

first: Stephanie

last: De Vos

first: Gilbert

last: Van Stappen

first: Peter

last: Bossier


title: Gene-expression profiling of SLK-knockout NeuNDL-transformed cell lines

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Subconfluent cycling cells from immortalized SLK-expressing and knockout NeuNDL-derived cells were profiled across multiple passages to identify differentially regulated genes in the absence of SLK using an Affymetrix Mouse  Gene 2.0 ST array

overall_design: Three independent samples from SLK-expressing and knockout cell lines were from passages 9, 19 and 29 in culture were compared for differentially regulated genes amongst the conditions

first: Khalid

middle: N

last: Al-Zahrani

first: Luc

last: Sabourin


title: UVB drives different stages of epigenome alterations during progression of skin cancer

city: Piscataway

first: Renyi

last: Wu

state: NJ

address: 160 Frelinghuysen road

department: Pharmacy School

institute: Rutgers University

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

overall_design: Refer to individual Series


title: UVB drives different stages of epigenome alterations during progression of skin cancer [Bisulfite-seq]

summary: Exposure to UVB irradiation results in multitude of cellular responses including generation of reactive oxygen species (ROS) and DNA damage and is responsible for non-melanoma skin cancers (NMSCs). Although genetic mutation is well documented, the epi-mutation, the alteration in epigenetics, remains elusive. DNA methylation is a stable and heritable epigenetic change in the control of gene expression. Furthermore, it is unclear how the epigenomic DNA methylome would change during progression of UVB-induced carcinogenesis. In this study, we utilized CpG Methyl-seq to identify a genome-wide DNA CpG methylation, to profile the DNA methylation in ultraviolet B (UVB)-irradiated SKH-1 mouse skin epidermis and non-melanoma skin papillomas at various stages. Agilent mouse SureSelect Methyl-seq Kit was used for enrichment of about 3.3 million CpG sites in the mouse genome. Simultaneously, RNA-seq was performed to examine the corresponding transcriptome alterations. Bioinformatic analysis was utilized to identify differentially methylated and differentially expressed genes. The methylation profiles in mouse epidermis were altered by UVB-irradiation as time progresses.  Comparing all epidermis samples at week-15 versus week-25, UVB had great impact on DNA methylome alteration.  Examination of the differentially methylated regions (DMRs), most of the DMRs were located in the distal intragenic (>3 kb upstream of TSS or downstream of 3’ UTR) and the promoter regions.  Interestingly, at week-25 the methylation profiles between the whole skin versus the tumor samples were different. Ingenuity Pathways Analysis (IPA) identified many cancer related pathways including PTEN, p53, Nrf2 and inflammatory signaling in UVB-irradiation induced carcinogenesis. Cell cycle regulation and cell growth related pathways including State3 signaling and estrogen-mediated S-phase entry were also identified. Additionally, some novel genes involved in skin carcinogenesis that were not previously reported were differentially methylated, including Enf2, Mgst2, Vegfa, and Cdk4. The methylation and expression of these genes were validated by pyrosequencing and qPCR. Taken together, the current study provides novel profiles of methylation and transcriptomic changes at different stages of carcinogenesis in UVB-irradiation induced NMSC and offer potential targets for prevention and treatment of NMSC at different stages of human skin cancer.

overall_design: Skin samples (either epidermis, tumor, or whole skin) were used for extraction of DNA and RNA; DNA was enriched by Agilent SureSelect Kit then bisulfite converted methyl-seq was performed. RNA-seq was performed with routine. Strategies. This dataset contains data for the RNA-seq only; Check the other SubSeries under this SuperSeries for RNA-seq data

first: Yuqing

last: Yang

first: Davit

last: Sargsyan

first: Ran

last: Yin

first: Hsiao-Chen

last: Kuo

first: Lujing

last: Wang

last: Cheng

first: Chao

first: Shanyi

last: Li

first: Rasika

last: Hudliar

first: Yaoping

last: Lu

first: Ah-Ng

last: Kong


title: Gene expression analysis in U251 and U87 cells transduced with NANEP5 vector.

city: Geneva

first: Ariel

last: Ruiz i Altaba

address: 1 rue Michel Servet

department: GEDEV

institute: University of Geneva Medical School

summary: NANEP5 is a heterologus repressor of NANOG, which consist of NANOG homeodomain and HES1 repressor domain. In this study we explore transcriptomes of glioblastoma cells expressing NANEP5 in order to reveal putative mediators of pro-tumorigenic NANOG function.

overall_design: U251 and U87 cells were infected with control (CT) or NANEP5-expressing lentiviral vectors. Total RNA was extracted 10 days after infection using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepares using Illimina TruSeq protocols. The samples were sequenced on a Illumina HiSeq 4000 machine with 50bp reads followed by standard analyses.

first: Monika

last: Kuciak


title: UVB drives different stages of epigenome alterations during progression of skin cancer [RNA-Seq]

overall_design: Skin samples (either epidermis, tumor, or whole skin) were used for extraction of DNA and RNA; DNA was enriched by Agilent SureSelect Kit then bisulfite converted methyl-seq was performed. RNA-seq was performed with routine. Strategy. This dataset contains data for the RNA-seq only; Check the other SubSeries under this SuperSeries for Methyl-seq data


title: RNAseq analysis of Arabidopsis to test for gene expression in response to low CO2 concentration

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: Our research describe the influence of aeration conditions in petri dishes for A. thaliana growth. We analyze the difference between plants grown in standard Petri dish (Non-aerated) and modified Petri dish that include aeration (Aerated). To characterize the differences between those conditions the gene expression analysis was performed. We also wanted to analyze the effect of using a micropore filter, so we designed another experiment with Aerated, Non-aerated and Micropore filter conditions.

overall_design: In the first set there are a total of 8 biological samples. 4 biological replicates each of Aerated (control) and Non-aerated. Additionally in the second set, there are 4 biological replicates of  Aerated, Non-aerated and Micropore sealed conditions.

first: Oskar

last: Siemianowski

first: Souvik

last: Banerjee

first: Xinchun

last: Tian

first: Kara

middle: R

last: Lind

first: Pratyasha

last: Mohapatra

first: Jacek

last: Koziel

first: Ludovico

last: Cademartiri


title: microRNA profiling of ovarian cancer compared to normal ovary

city: hunan

first: Ding

last: qi

state: changsha

address: tong zi po

institute: huan cancer  hospital

summary: Comparison of ovarian cancer tissue and normal ovarian tissue to identify miRNA profiling.

overall_design: 6 ovarian cancer tissue samples and 3 normal ovarian tissue samples were used.

first: Zeng

last: Yong


title: Long noncoding RNA and mRNA expression profile in ovarian cancer

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

summary: Comparison of epithelial ovarian tissue and epithelial ovarian cancer.

overall_design: Human ovarian tissue samples including 3 normal tissue samples and 6 malignant ovarian tissue samples. lncRNA and mRNA integrated microarrays were used to quantitate gene expression from the collected ovarian tissue samples.


title: Global gene expression of histologically normal primary skin cells from BCNS subjects reveals “single-hit” effects that are influenced by rapamycin

city: Indianapolis

first: Brittney-Shea

last: Herbert

state: IN

address: 975 West Walnut St, IB 130

institute: IU School of Medicine

summary: The study of dominantly heritable cancers has provided significant insights about tumor development. Basal cell nevus syndrome (BCNS), or Gorlin syndrome (OMIM #109400), is an autosomal dominant inherited disorder that is characterized by developmental abnormalities and postnatal occurrence of various neoplasms, principally basal cell carcinomas (BCCs). We performed an exploratory gene expression profiling of primary cultures, including keratinocytes and fibroblasts derived from clinically unaffected skin biopsies of BCNS gene-carriers (PTCH1 +/-) and normal individuals.

overall_design:
Low pass Fibroblast and Keratinocyte cell lines from study participants were treated with 0 ng/ml, 10 ng/ml, and 50 ng/ml of Sirolimus for 48 hours. The RNA was extracted using our standard Guanidine Thiocyanate Procedure and cleaned using the Qiagen RNeasy Micro Kit (according to the manufacturer’s directions). We then analyzed the RNA on Affymetrix U133 Plus 2.0 expression arrays.

Description of Sample titles:
Example 1: 01F48S10 = participant 01, fibroblasts, 48-hour treatment with sirolimus, dose 10 ng/ml.
Example 2: 01K48S50 = participant 01, keratinocytes, 48-hour treatment with sirolimus, dose 50 ng/ml.
Example 3: 01Fib = participant 01, fibroblasts, no treatment with sirolimus.

first: Alan

last: Bale

first: Levy

last: Kopelovich


title: Transcriptomic and lipidomic analysis of an EPA-containing Nannochloropsis sp. PJ12 in response to nitrogen deprivation

city: Zhoushan

first: Jianhua

last: Liu

address: 1 Zheda Road, Lin-cheng street

institute: Ocean College, Zhejiang University

summary: Oleaginous microalgae Nannochloropsis spp. are considered to be promissing species   for production of biofuels and biomaterials. Nevertheless, its biofuel production remains to  be economically unviable. Hence, further improvement of cultivation conditions and genetic  traits for high-lipid contents without affecting growth is required. To understand genes  involved in neutral lipid accumulation upon nitrogen deprivation (ND) in a novel isolate of  Nannochloropsis sp. PJ12, we performed comparative transcriptomic and lipidomic analyses  of cells under ND and NR (nitrogen replete) conditions. Transcriptomic profiling indicated  that, while enzymes involved in TCA cycle in PJ12 under ND condition were upregulated  compared to that under NR condition, those involved in Calvin cycle and glycolysis under  ND condition were downregulated, consistent with the observation that quantum yield was  reduced under ND condition. Furthermore, we showed that enzymes involved in fatty acid  synthesis and glycerolipid synthesis were downregulated but not b-oxidation. Lipidomic  profiling indicated that, while the level of neutral lipids in ND cells was increased compared  to that of NR cells, level of photosynthetic membrane-lipids DGDG and MGDG was  decreased. Taken together, our analysis indicated that TAG accumulation is attributed to the  modification of membrane lipids derived primarily from “prokaryotic” pathway and  secondarily from “eukaryotic” pathway based on the 16:X or 18:X fatty acid at the sn2  position of the glycerol backbone. We propose that two-phase (NR-ND) growth is ideal for  biomass and biofuel production because ND reduces cell growth rate due to the loss of  photosynthetic membrane and decreased quantum yield.

overall_design: Examination of transcriptional profiling of PJ12 cells in response to nitrogen replete and nitrogen deprivation.

first: Jibei

last: Liang

first: Fang

last: Wen


title: Long noncoding RNA, microRNA, and mRNA expression profiles in ovarian cancer

platform_organism:
Homo sapiens
synthetic construct


title: Wnt/β-catenin signaling, which is activated in odontomas, reduces Sema3A expression to regulate odontogenic epithelial cell proliferation and tooth germ development

city: Fukuoka

first: Shinsuke

last: Fujii

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Faculty of Dental Science

institute: Kyushu University

summary: Odontomas are classified as odontogenic benign tumors, which show disorganized dental mineralized hard tissue formation in the jaw, but mechanisms in the induction of odontomas remain to be clarified. Odontomas are also thought to be developmental anomalies of tooth germ, which frequently occur in patients with familial adenomatous polyposis (FAP) involving activation of Wnt/b-catenin signaling. However, the roles of Wnt/b-catenin signaling in odontomas or odontogenic cells remain to be clarified. The current study was conducted to investigate the expression of b-catenin in odontomas and the function of Wnt/b-catenin signaling in odontogenic epithelial cells and tooth germ development. b-catenin frequently accumulated in the nucleus and/or cellular cytoplasm of remaining odontogenic epithelial cells in human odontoma specimens, immunohistochemically. Activation of Wnt/b-catenin signaling inhibited odontogenic epithelial cell proliferation and mouse tooth germ development, while inducing epithelial bud formation in the novel developed epithelial tooth bud culture system derived from mouse tooth germ. We identified Semaphorin 3A (Sema3A) as a downstream molecule of Wnt/b-catenin signaling using DNA microarray analysis and showed that Wnt/b-catenin signaling-dependent reduction of Sema3A expression resulted in suppression of odontogenic epithelial cell proliferation. Novel developed epithelial tooth bud culture system revealed that Sema3A expression is required in epithelial budding morphogenesis. These results suggest that Wnt/b-catenin signaling negatively regulates odontogenic epithelial cell proliferation and tooth germ development through decreased-Sema3A expression, and aberrant activation of Wnt/b-catenin signaling may be associated with the formation of odontomas.

overall_design: DNA microarray analysis of mDE6 cells with 6 h stimulation of CHIR99021 was performed. Candidate genes were selected based on the criterion that their expression levels were lower or higher in cells treated with CHIR99021 than in the control cells.

first: Kengo

last: Nagata

first: Shinji

last: Matsumoto

first: Ken-ichi

last: Kohashi

first: Akira

last: Kikuchi

first: Yoshinao

last: Oda

first: Tamotsu

last: Kiyoshima

first: Naohisa

last: Wada


title: Yeast mitochondrial protein Pet111p binds directly to two distinct targets in COX2 mRNA, suggesting a mechanism of translational activation.

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

summary: Genome-wide RNA binding profile of Pet111p by photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) confirmed that Pet111p preferentially associates with the 5'-end proximal portion of COX2 mRNA.

overall_design: Genome-wide RNA binding profile of Pet111p by PAR-CLIP.

first: Julia

middle: L

last: Jones

middle: B

first: Andrew

middle: T

last: Cowan

first: Dmitry

last: Temiakov

first: Patrick

last: Cramer

first: Michael

last: Anikin


title: PERK-dependent gene expression programs of the acute and chronic cellular response to ER stress

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

institute: Technion

summary: The UPR (Unfolded Protein Response) is a well-orchestrated response to ER protein folding and processing overload, integrating both transcriptional and translational outputs. Its three arms in mammalian cells, the PERK translational response arm, together with the ATF6 and IRE1-mediated transcriptional arms, have been thoroughly investigated.    Using ribosome footprint profiling, we performed a deep characterization of the gene expression programs involved in the acute and adaptive ER stress responses. We utilized MEFs (Mouse Embryonic Fibroblasts) treated with Thapsigargin for different durations, that were wither WT or PERK knockouts, to determine the role of PERK in the acute and chronic UPR. We characterized three major gene expression programs: acute induction, chronic induction, and repression, and found that they were all PERK dependent. All three programs were recapitulated in publicly available data and in NIH3T3 cells. While PERK -/- cells did not recapitulate these responses in the acute timepoints, late timepoints showed an extremely weak induction/repression, suggesting that the chronic responses in WT cells are largely PERK dependent as well. We found that most ER target proteins were significantly repressed; including transmembrane proteins, glycoproteins, and proteins with disulfide bonds. We further demonstrate the downregulation of cyclins, while the expression of the amino acid biosynthesis pathway was enhanced.

overall_design: We utilized MEFs (Mouse Embryonic Fibroblasts) treated with Thapsigargin for different durations (1h, 2h, 5h, 8h), that were wither WT or PERK knockouts, to determine the role of PERK in the acute and chronic UPR. Thapsigargin was applied also with NIH 3t3 cells within two differet time-points (2h 7h) as well.

first: Nir

last: Gonen


title: Pro-angiogenic Ginsenoside F1 and Rh1 Inhibit Vascular Leakage by Modulating NR4A1

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: Angiogenesis is an essential process in human physiology and disease pathology. Particularly, in ischemic disease condition, the proper induction of angiogenesis without vascular leakage will be crucial for its effective therapy. Ginsenosides, triterpenoid saponins from a well-known medicinal plant ginseng, have been considered as a strong candidate for modulating angiogenesis. However, the biologic activity of individual gensenoside compounds and their target pathway have not been elucidated systematically. To find the candidates of vascular-related therapeutic agents, we evaluated in vitro angiogenic efficacy of 10 ginsenosides using tube formation assay with human umbilical vein endothelial cells (HUVECs). Among them, F1 and Rh1 showed strong in vitro angiogenic properties including EC tube formation, proliferation, and migration similar to vascular endothelial growth factor (VEGF). However, RNA transcriptome analysis showed that F1 and Rh1 differentially regulate gene expressions in HUVECs compared to VEGF. Not only that, F1 and Rh1 significantly inhibited vascular endothelial growth factor (VEGF)-induced vascular leakage both in vitro and in vivo. From RNA transcriptome analysis, we identified that nuclear receptor subfamily 4 group A member 1 (NR4A1) is regulated by F1 and Rh1 for suppression of VEGF-induced vascular leakage. By suppressing the expression and transcriptional activity of NR4A1, F1 and Rh1 could stabilize the expression and localization of junctional vascular endothelial (VE)-cadherin. These findings demonstrate that F1 and Rh1 could be potential compounds in the development of vascular pharmaceuticals.

overall_design: mRNA profiles of VEGF- and ginsenoside F1/Rh1-treated HUVEC were generated by deep sequencing, in duplicate, using Hiseq-2500.

first: Ji

last: Kang

first: YoonJung

first: Chang-Hau

last: Cui

first: Daeyoup

last: Lee

first: Sun

middle: C

last: Kim

first: Ho

middle: M


title: Ga13 functions as a cytoskeletal and mitochondrial regulator to restrain osteoclast function

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

summary: We performed RNA-seq experiments, one with the WT control and Ga13ΔM/ΔM osteoclast precursors at baseline and after RANKL stimulation.

overall_design: Bone marrow macrophages mRNA profiles of WT and myeloid specific deletion of Ga13(Ga13ΔM/ΔM), control(LysMcre(+))  were generated by deep sequencing using Illumina Hiseq4000.

first: Baohong

last: Zhao


title: Microtubule regulators act in the nervous system to modulate fat metabolism and longevity through DAF-16 in C. elegans

city: San Antonio

first: Lizhen

last: Chen

address: 7703 Floyd Curl Dr

department: Barshop Institute

institute: Universality of Texas Health Science Center at San Antonio

summary: Purpose: We found that mutations in microtubule regulating factors lead to altered lifespan. In order to understand the mechnaisms, we carried out RNA-seq analyses to identify genes with differential expression in microtubule regulator mutants.

overall_design: Genetic mutants of efa-6, hdac-6, ptl-1 and ptrn-1 were compared to wildtype control. Synchronized Day 1 young adults were used for RNA extraction.

first: Xu

last: Aiping

first: Zhang

first: Chen

last: Lizhen


title: Identification of coordinately regulated microRNA-gene networks that differ in baboons discordant for LDL-Cholesterol

city: Winston-Salem

first: Genesio

last: Karere

address: 1 medical center blvd

department: Internal Medicne

institute: Wake Forest Baptist Health Sciences

summary:
Although the mechanisms underlying development of atherosclerosis are not well understood, LDL-C is known to influence expression of endothelial microRNAs (miRNAs) and gene-targets of miRNAs to promote cell senescence. However, the impact of LDL-C on expression of PBMC miRNAs and miRNA targeted genes in response to an atherogenic diet is not known. We hypothesized that miRNA expression profiles differ between baboons with low and high serum low-density lipoprotein cholesterol (LDL-C) concentrations in response to diet, and that microRNA-gene networks in baboons discordant for LDL-Cholesterol
We generated small RNA libraries from baboons differing in their LDL-C response to dietary fat and cholesterol (low LDL-C, n = 3; high LDL-C, n = 3) using liver biopsies collected before and after a high-cholesterol, high-fat (HCHF) challenge diet.  We sequenced the libraries using Next-Generation Illumina sequencing methods, analyzed the data using mirTools software and identified 517 baboon miRNAs: 490 homologous to human and 27 novel miRNAs.  HCHF diet elicited expression of more miRNAs compared to baseline (chow) diet for both low and high LDL-C baboons. Seventeen miRNAs exhibited significant differential expression in response to HCHF diet in high LDL-C baboons compared to nine miRNAs in low LDL-C baboons. Putative miRNA targets were identified with TargetScan/Base tools.  miRNAs significantly targeted more genes in high LDL-C baboons compared to low LDL-C responders.  Further, we identified miRNA isomers and other non-coding RNAs that were differentially expressed in response to the challenge diet.Our discovery of differentially expressed baboon miRNAs and their targets is a fundamental step in understanding the role of non-coding RNAs in the modulation of dsylipidemia.

overall_design:
Assess the differential miRNAs and genes response to a high-cholesterol, high-fat diet in blood of low and high LDL-C baboons, and identify potential miRNA targets and corodinated network.
---------------------------------------
This represents the mRNA component only

first: Jeremy

middle: P

last: Glenn

first: Shifra

last: Birnbaum

first: Roy

last: Garcia

first: John

last: VandeBerg

first: Laura

last: Cox


title: Histone mark profiling in renal cancer cells

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carcinoma (ccRCC), but the molecular mechanisms that lead to their activation has remained poorly understood. By chromatin and transcriptomic profiling and functional analysis we have identified Kruppel like factor 6 (KLF6), a transcription factor of the zinc-finger family, as a critical regulator of the PDGF-mTOR axis in ccRCC. KLF6 expression is supported by one of the strongest super enhancers in ccRCC cells. Inhibition of KLF6 in several ccRCC cell lines impaired cell proliferation in vitro and in vivo and reduced metastatic lung colonization. KLF6 depletion led to downregulation of lipid homeostasis pathways downstream of SREBF1 and SREBF2, suggesting a role for KLF6 as a regulator of mTOR. We find that KLF6 modulates mTORC1 activity in ccRCC via transcriptionally regulating the expression of PDGFB, an activator of the PIK3-AKT-mTOR signalling pathway. Targeting PDGFB in ccRCC inhibited mTORC1, and supplementing KLF6-depleted cells with recombinant PDGFB rescued mTORC1 activity. Our data suggest that a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway, supports an autocrine PDGFB-dependent signalling loop that promotes mTOR activity in ccRCC. These results suggest the possibility that combining low dose PDGFR and mTOR inhibition could be a viable therapeutic strategy for ccRCC.

overall_design: Examination of histone modifications in experimental model systems of renal cancer.

first: Saiful

middle: E

last: Syafruddin

first: Paulo

last: Rodrigues


title: KLF6-dependent transcription in renal cancer cells

overall_design: mRNA profiling in experimental models of metastasis. 113 kb SE deletion is chr10:3793002-3906184 in hg38


title: Transcriptional analysis of in vivo responses to acetaminophen induced hepatic injury in the murine liver

city: Edinburgh

first: Thomas

middle: Graham

last: Bird

state: Midlothian

address: Queens Medical Research Institute

country: United Kingdom

institute: University of Edinburgh

summary: Liver injury results in rapid regeneration through hepatocyte proliferation and hypertrophy. However, after acute severe injury, such as acetaminophen poisoning, effective regeneration may fail. We investigated how senescence underlies this regenerative failure. In human acute liver disease, and murine models, p21-dependent hepatocellular senescence was proportionate to disease severity and was associated with impaired regeneration. In an acetaminophen injury model a transcriptional signature associated with the induction of paracrine senescence is observed within twenty four hours, and is followed by one of impaired proliferation. In genetic models of hepatocyte injury and senescence we observed transmission of senescence to local uninjured hepatocytes. Spread of senescence depended upon macrophage derived TGFβ1 ligand. In acetaminophen poisoning inhibition of TGFβ receptor 1 (TGFβR1) improved survival. TGFβR1 inhibition reduced senescence and enhanced liver regeneration even when delivered after the current therapeutic window. This mechanism, in which injury induced senescence impairs regeneration, is an attractive therapeutic target for acute liver failure.

overall_design: RNA-seq analysis was performed on a total of 24 samples extracted from murine liver, post hepatic injury induced by acetaminophen administration.  Transcriptional profiles were from replicate samples generated at defined timepoints - 12, 24, 36, 48 and 72 hours post injury.  Replicate samples were generated from 4 individual animals sacrificed at each timepoint, and compared to a control cohort of 4 animals not subjected to acetaminophen treatment.

middle: G


title: Gene Expression Profiling of WT and KDM3A Knocked out Cell

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.  We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.

overall_design:
KDM3A was knocked out in HCT116 and the gene expression profile was studied by RNA sequencing
Please note that, in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours.

first: Huiyi

last: Wang

first: Qiao-yun

last: Long


title: Genome-wide maps of chromatin state in HCT116 cells.

summary:
We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.  We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.
We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.  We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.

overall_design:
KDM3A was knocked out in HCT116 and the gene expression profile was studied by RNA sequencing
Please note that
[1] in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours.
[2] each processed data file was generated from two replicate samples together and linked to the first replicate (REP1_*) of the corresponding samples.^SERIES = GSE108920
Examination of H3K4me3, H3K27me3, and pol II modifications in HCT116 wildtype cells,  and detection H3K9me2, H3K27ac and TEAD1 distribution in HCT116 wildtype and KDM3A knockout cells
Please note that
[1] in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours.
[2] each processed data file was generated from two replicate samples together and linked to the first replicate (REP1_*) of the corresponding samples.


title: Silencing of lnc-klhdc7b in the HCC1187 cell line

city: Ciudad de México

first: Alfredo

last: Hidalgo-Miranda

state: CDMX

address: Periferico Sur #4809

department: Cancer Genomic

country: Mexico

institute: INMEGEN

summary:
By using shRNAs the lnc-klhdc7b was silenced in the cell line HCC1187, the shRNA-1 carried a ~75% silencing compared to the negative control (NC).
We evaluated the role of LncKLHDC7B on oncogenic phenotypes in the IM breast cancer HCC1187 cell line model. The knockdown of LncKLHDC7B was achieved with ~75% of silencing efficiency. A complete genomic analysis of the transcriptomic state after silencing of LncKLHDC7B revealed an impact on the global expression of transcripts

overall_design: We analyzed expression profile from HCC1187 cell line silenced by shRNA-1 versus lnc-KLHDC7B using the Affymetrix Human Transcriptome Array 2.0 platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: Fredy

middle: O

last: Beltrán-Anaya